From c73c88ea86a3a97a245034eb3cda1cec952233d3 Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Thu, 16 Apr 2026 20:24:45 +0000 Subject: [PATCH 1/7] Add midplane z-slice to TestCase and thread through runner as optional kwarg MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Max-intensity projections collapse depth, so overlapping body segments fuse into one band — the key discriminative feature for fold stages is lost. This is the harness half of the z-slice subagent work: expose a single non-projected XY slice (z=Z//2) so a perception variant can count discrete body-segment profiles at one plane. - testset.py: new _create_slice_image() helper (same crop as the three-view projection); TestCase gains midplane_b64; iter_embryo populates it. Also collapses the duplicated load-volumes-or-not branch into one path. - run.py: introspect perceive_fn signature once and only pass midplane_b64 when the function declares it (or **kwargs), so all existing variants are called unchanged. - program.md: document the new optional kwarg. --- benchmark/testset.py | 56 +++++++++++++++++++++++++++++++++++------- experiments/program.md | 4 +++ program.md | 4 +++ run.py | 14 +++++++++++ 4 files changed, 69 insertions(+), 9 deletions(-) diff --git a/benchmark/testset.py b/benchmark/testset.py index 90e30a4..f5f5da1 100644 --- a/benchmark/testset.py +++ b/benchmark/testset.py @@ -41,6 +41,7 @@ class TestCase: image_b64: str # Combined view (for backward compatibility) top_image_b64: Optional[str] # TOP view only side_image_b64: Optional[str] # SIDE view only + midplane_b64: Optional[str] # Single XY slice at z=Z//2 (no projection) volume: Optional[np.ndarray] ground_truth_stage: Optional[str] @@ -215,6 +216,45 @@ def _create_three_view_image(volume: np.ndarray, max_dim: int = 1500) -> str: return base64.b64encode(buffer.getvalue()).decode("utf-8") +def _create_slice_image( + volume: np.ndarray, z: Optional[int] = None, max_dim: int = 800 +) -> str: + """Render a single XY z-slice as base64 JPEG. + + Unlike the projection helpers, this preserves depth information at one + plane: overlapping body segments stay separated rather than fusing. + Uses the same crop as the three-view projection so framing matches. + + Parameters + ---------- + volume : np.ndarray + 3D volume array (Z, Y, X) + z : int, optional + Slice index. Defaults to the midplane (Z // 2). + max_dim : int + Maximum output dimension in pixels. + """ + _ensure_dependencies() + + if z is None: + z = volume.shape[0] // 2 + z = max(0, min(z, volume.shape[0] - 1)) + + bounds = _compute_crop_bounds(volume) + slice_img = volume[z, bounds[0]:bounds[1], bounds[2]:bounds[3]] + slice_norm = _normalize_image(slice_img) + + pil_img = PIL_Image.fromarray(slice_norm) + if max(pil_img.size) > max_dim: + scale = max_dim / max(pil_img.size) + new_size = (int(pil_img.size[0] * scale), int(pil_img.size[1] * scale)) + pil_img = pil_img.resize(new_size, PIL_Image.Resampling.LANCZOS) + + buffer = io.BytesIO() + pil_img.save(buffer, format="JPEG", quality=90) + return base64.b64encode(buffer.getvalue()).decode("utf-8") + + def _create_separate_view_images(volume: np.ndarray, max_dim: int = 1000) -> Tuple[str, str]: """Create separate TOP and SIDE view images from volume, return base64 tuple. @@ -359,15 +399,12 @@ def iter_embryo( volume = _load_volume(vol_path) if self.load_volumes else None # Create images - if volume is not None: - image_b64 = _create_three_view_image(volume) - top_b64, side_b64 = _create_separate_view_images(volume) - else: - # Load just for image if not loading full volumes - temp_vol = _load_volume(vol_path) - image_b64 = _create_three_view_image(temp_vol) - top_b64, side_b64 = _create_separate_view_images(temp_vol) - del temp_vol + vol = volume if volume is not None else _load_volume(vol_path) + image_b64 = _create_three_view_image(vol) + top_b64, side_b64 = _create_separate_view_images(vol) + midplane_b64 = _create_slice_image(vol) + if volume is None: + del vol # Get ground truth gt_stage = self.ground_truth.get_stage_at(embryo_id, timepoint) @@ -378,6 +415,7 @@ def iter_embryo( image_b64=image_b64, top_image_b64=top_b64, side_image_b64=side_b64, + midplane_b64=midplane_b64, volume=volume, ground_truth_stage=gt_stage, ) diff --git a/experiments/program.md b/experiments/program.md index a727f96..cf09fbb 100644 --- a/experiments/program.md +++ b/experiments/program.md @@ -52,9 +52,13 @@ async def perceive_xxx( references: dict[str, list[str]], # stage -> [base64 reference images] history: list[dict], # previous timepoints: [{timepoint, stage}] timepoint: int, # current timepoint number + midplane_b64: str | None = None, # optional: single XY z-slice at z=Z//2 ) -> PerceptionOutput: # from perception._base ``` +`midplane_b64` is only passed if your function declares it (or `**kwargs`). +The runner inspects the signature, so existing variants don't need to change. + ## Available Utilities (from `perception._base`) - `call_claude(system, content)` — single API call, returns response text diff --git a/program.md b/program.md index a727f96..cf09fbb 100644 --- a/program.md +++ b/program.md @@ -52,9 +52,13 @@ async def perceive_xxx( references: dict[str, list[str]], # stage -> [base64 reference images] history: list[dict], # previous timepoints: [{timepoint, stage}] timepoint: int, # current timepoint number + midplane_b64: str | None = None, # optional: single XY z-slice at z=Z//2 ) -> PerceptionOutput: # from perception._base ``` +`midplane_b64` is only passed if your function declares it (or `**kwargs`). +The runner inspects the signature, so existing variants don't need to change. + ## Available Utilities (from `perception._base`) - `call_claude(system, content)` — single API call, returns response text diff --git a/run.py b/run.py index 86f6c5e..9b791f3 100644 --- a/run.py +++ b/run.py @@ -20,6 +20,7 @@ import argparse import asyncio +import inspect import json import logging import sys @@ -95,6 +96,17 @@ def make_prediction_dict(output, timepoint, ground_truth_stage) -> dict: } +_OPTIONAL_PERCEIVE_KWARGS = ("midplane_b64",) + + +def _accepted_optional_kwargs(perceive_fn) -> set[str]: + """Subset of _OPTIONAL_PERCEIVE_KWARGS that perceive_fn's signature accepts.""" + sig = inspect.signature(perceive_fn) + if any(p.kind is p.VAR_KEYWORD for p in sig.parameters.values()): + return set(_OPTIONAL_PERCEIVE_KWARGS) + return {k for k in _OPTIONAL_PERCEIVE_KWARGS if k in sig.parameters} + + async def run_variant(variant_name, perceive_fn, testset, references, max_timepoints, target_stages=None): """Run a single variant. Returns accuracy and full report dict. @@ -109,6 +121,7 @@ async def run_variant(variant_name, perceive_fn, testset, references, max_timepo started_at = datetime.now() all_predictions = [] embryo_results = [] + extra_kwargs = _accepted_optional_kwargs(perceive_fn) for embryo_id, tp_iter in testset.iter_all(): logger.info(f"[{variant_name}] Starting {embryo_id}") @@ -135,6 +148,7 @@ async def run_variant(variant_name, perceive_fn, testset, references, max_timepo references=references, history=history, timepoint=tc.timepoint, + **{k: getattr(tc, k) for k in extra_kwargs}, ) except Exception as e: logger.error(f"[{variant_name}/{embryo_id}] T{tc.timepoint} error: {e}") From 3d39a1959a9a06d7e72b47117f1544e0cd643418 Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Thu, 16 Apr 2026 21:24:04 +0000 Subject: [PATCH 2/7] Add zslice variant: scientific + midplane segment-count subagent on fold stages MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Max-intensity projections fuse overlapping body segments, which is the main reason 1.5fold/2fold/pretzel are hard to tell apart. This variant runs the scientific classifier, and when that lands on a fold stage it sends the midplane z-slice to a subagent that counts discrete body-segment cross-sections (≤1 → 1.5fold, 2 → 2fold, ≥3 → pretzel) and overrides. Trigger is deliberately the simplest baseline (primary ∈ fold stages) so the subagent only ever moves between fold stages, never into or out of them — count=1 is ambiguous between comma and 1.5fold, so triggering on comma would systematically push comma frames forward. Override is recorded in reasoning ("(overrode 2fold)") and in verification_triggered/phase_count for auditability. --- perception/__init__.py | 2 + perception/zslice.py | 118 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 120 insertions(+) create mode 100644 perception/zslice.py diff --git a/perception/__init__.py b/perception/__init__.py index ab3b94f..c180257 100644 --- a/perception/__init__.py +++ b/perception/__init__.py @@ -41,6 +41,7 @@ def get_functions() -> dict: from .compare import perceive_compare from .changegate import perceive_changegate from .duration_aware import perceive_duration_aware + from .zslice import perceive_zslice _FUNCTIONS = { "minimal": perceive_minimal, @@ -58,5 +59,6 @@ def get_functions() -> dict: "compare": perceive_compare, "changegate": perceive_changegate, "duration_aware": perceive_duration_aware, + "zslice": perceive_zslice, } return _FUNCTIONS diff --git a/perception/zslice.py b/perception/zslice.py new file mode 100644 index 0000000..7e72f93 --- /dev/null +++ b/perception/zslice.py @@ -0,0 +1,118 @@ +""" +Z-slice subagent perception. + +Max-intensity projections collapse depth: overlapping body segments fuse into +one bright band, destroying the discriminative feature for fold stages — how +many times the body folds back on itself. A biologist resolves this by +scrolling z-slices and counting body-segment cross-sections at the midplane. + +This variant runs the scientific classifier on the projection, then for +fold-region timepoints sends the midplane z-slice to a subagent that counts +discrete body-segment profiles. The count is mapped to a stage and overrides +the primary call. +""" + +import re + +from ._base import PerceptionOutput, call_claude, parse_stage_json +from .scientific import perceive_scientific + +FOLD_STAGES = {"1.5fold", "2fold", "pretzel"} + +SEGMENT_SYSTEM = """\ +You are analyzing a single optical z-slice through a folded C. elegans embryo \ +inside its eggshell. This is NOT a max-intensity projection — it is one plane, \ +so body segments that overlap in projections appear as separate cross-sections \ +here. + +Count the number of DISCRETE body-segment cross-sections visible inside the \ +eggshell. A segment cross-section is a bright, roughly elliptical or band-like \ +region of fluorescent nuclei. Segments separated by a clear dark gap are \ +distinct; segments touching or merged count as one. + +Typical counts by stage: +- 1 segment → comma or early 1.5fold (body not yet folded back at this plane) +- 2 segments → 2fold (one hairpin: two parallel passes) +- 3+ segments → pretzel (multiple coils crossing this plane) + +Respond with JSON: +{ + "segment_count": , + "reasoning": "Brief description of what you counted" +}""" + + +def _segment_count_to_stage(count: int) -> str: + if count >= 3: + return "pretzel" + if count == 2: + return "2fold" + return "1.5fold" + + +def _parse_segment_count(raw: str) -> int | None: + data = parse_stage_json(raw) + val = data.get("segment_count") + if isinstance(val, int): + return val + if isinstance(val, str): + m = re.search(r"\d+", val) + if m: + return int(m.group(0)) + return None + + +async def _count_segments(midplane_b64: str) -> tuple[int | None, str]: + """Ask the subagent to count body-segment cross-sections in the midplane slice.""" + content = [ + { + "type": "image", + "source": {"type": "base64", "media_type": "image/jpeg", "data": midplane_b64}, + }, + { + "type": "text", + "text": ( + "Count the discrete body-segment cross-sections visible in this " + "single z-slice. Respond with the JSON format above." + ), + }, + ] + raw = await call_claude(system=SEGMENT_SYSTEM, content=content, max_tokens=512) + return _parse_segment_count(raw), raw + + +async def perceive_zslice( + image_b64: str, + references: dict[str, list[str]], + history: list[dict], + timepoint: int, + midplane_b64: str | None = None, +) -> PerceptionOutput: + """Scientific classifier with a z-slice segment-counting subagent on fold stages.""" + primary = await perceive_scientific(image_b64, references, history, timepoint) + + if midplane_b64 is None or primary.stage not in FOLD_STAGES: + return primary + + count, sub_raw = await _count_segments(midplane_b64) + if count is None: + return PerceptionOutput( + stage=primary.stage, + reasoning=f"{primary.reasoning} | [zslice] parse failed; kept primary", + verification_triggered=True, + phase_count=2, + raw_response=primary.raw_response, + ) + + sub_stage = _segment_count_to_stage(count) + return PerceptionOutput( + stage=sub_stage, + reasoning=( + f"{primary.reasoning} | [zslice] {count} segment(s) at midplane → " + f"{sub_stage}" + + ("" if sub_stage == primary.stage else f" (overrode {primary.stage})") + ), + verification_triggered=True, + phase_count=2, + raw_response=sub_raw, + ) From 9608fc823b490a959487eb5b10462688bd30f417 Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Wed, 22 Apr 2026 16:51:32 +0000 Subject: [PATCH 3/7] zslice ablation (negative result): 27.9% vs scientific 77.3% on hard stages Midplane slice rarely shows >=3 separable cross-sections on pretzel embryos (body folds sit at different z-depths), so the segment-counting subagent systematically downgrades correct pretzel calls to 2fold/1.5fold. 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view shows a curved, bilobed body shape consistent with comma stage. Significant dark/empty space remains within the eggshell. No clear parallel body segments or hairpin fold visible yet. Matches comma reference images well. Previous 3 timepoints were all comma, and morphology has not clearly advanced to 1.5fold.", + "reasoning": "The XY view shows a bilobed/comma-shaped mass of nuclei with a clear constriction in the middle, similar to the comma reference images. The eggshell still has significant empty dark space around the embryo body. There is no clear evidence of a fold-back or parallel body segments that would indicate 1.5fold. The morphology is consistent with the comma stage references, and the previous three observations were all comma. While this is approaching the transition, I don't see a clear J-shape or hairpin fold yet, so I'll maintain the comma classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -28,10 +27,9 @@ "timepoint": 56, "predicted_stage": "comma", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo shows a curved body with significant empty space in the eggshell. While there's some elongation suggesting progression toward 1.5fold, a clear J-shape or partial hairpin fold is not yet definitively visible. The fill fraction remains sparse. Given previous observations of comma at T53-T55 and the rule to prefer earlier stages when uncertain, maintaining comma classification.", + "reasoning": "The XY view shows a curved/bilobed body shape consistent with comma stage. The eggshell still has significant empty space. No clear fold-back or J-shape is visible yet. The morphology closely matches comma reference images. Previous three timepoints were comma, and no definitive transition to 1.5fold is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -44,16 +42,15 @@ }, { "timepoint": 57, - "predicted_stage": "1.5fold", + "predicted_stage": "comma", "ground_truth_stage": "1.5fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo body has elongated beyond a simple comma shape and shows early folding back on itself. The XY view shows a J-shaped or partial hairpin morphology with the body curving and beginning to double back. The eggshell is still sparsely filled with significant dark space, consistent with 1.5fold. This represents a progression from the comma stage observed at T54-T56 with decreasing confidence.", + "reasoning": "The embryo shows a curved C-shaped body with significant empty space in the eggshell. While there may be early signs of folding, the morphology is still consistent with late comma stage. The eggshell fill is sparse, and no clear parallel body segments are visible yet. Previous three timepoints were comma, and the change is not definitive enough to advance the stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -64,10 +61,9 @@ "timepoint": 58, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo shows an elongated, partially folded body with sparse-to-moderate eggshell filling. The XY view shows a curved body with a partial fold but not yet two clearly parallel segments. The XZ view shows emerging fold structure but not a complete hairpin. Consistent with 1.5fold reference images and the previous timepoint classification. Not yet advanced enough for 2fold.", + "reasoning": "The embryo body has elongated beyond a simple comma shape, with the XY view showing a longer curved body and the XZ view showing hints of two parallel bright regions suggesting early fold-back. The eggshell remains sparsely filled with significant dark space. This matches the 1.5fold references better than comma, representing the transition from comma to 1.5fold at this timepoint.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -82,10 +78,9 @@ "timepoint": 59, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo shows increasing eggshell fill and early signs of a second parallel body segment forming, but the two-segment hairpin structure is not yet as clearly defined as in 2fold references. The fill fraction is still relatively sparse with dark spaces visible. Previous timepoints were 1.5fold, and the morphology hasn't clearly transitioned to show two distinct parallel segments, so defaulting to the earlier stage.", + "reasoning": "The embryo shows an elongated body beginning to fold within the eggshell, with sparse-to-moderate fill. The XZ view hints at early folding but no clear complete hairpin with two parallel segments yet. Matches 1.5fold references well. Consistent with previous T58 classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -98,16 +93,15 @@ }, { "timepoint": 60, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "XZ view shows two distinct parallel layers of signal suggesting a hairpin fold. Eggshell fill is moderate \u2014 more than 1.5fold references but less than pretzel. Morphology matches 2fold reference (T62). Transition from 1.5fold (T57-59) to 2fold at T60 is plausible, though borderline \u2014 could still be late 1.5fold.", + "reasoning": "The eggshell fill is still relatively sparse with visible dark spaces. While there are hints of two parallel body segments forming, the overall appearance is more consistent with late 1.5fold than clear 2fold. Previous timepoints were 1.5fold, and following the rule to prefer the earlier stage when uncertain.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -116,16 +110,15 @@ }, { "timepoint": 61, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with two visible parallel body segments in XY projection forming a hairpin/U-shape. XZ view shows two distinct signal layers. Matches 2fold reference images well. Consistent with previous T60 classification of 2fold. Not yet dense enough for pretzel stage.", + "reasoning": "The embryo shows increasing eggshell fill and hints of two parallel body segments forming, but significant dark space remains within the eggshell. The morphology is at the boundary between 1.5fold and 2fold. Given the previous three timepoints were 1.5fold and the rule to prefer the earlier stage when uncertain, this remains 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -136,10 +129,9 @@ "timepoint": 62, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with some dark space remaining. XY view shows two roughly parallel body segments consistent with a hairpin fold. Matches 2fold reference images well. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T60-T61.", + "reasoning": "The XY projection shows two roughly parallel body segments forming a hairpin/U-shape, with moderate eggshell filling. This matches the 2fold reference at T62. The fill fraction has increased beyond the sparse filling of 1.5fold, and two distinct body bands are visible, indicating the tail has folded back to approximately reach the head.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -154,10 +146,9 @@ "timepoint": 63, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "In the XY view, the embryo shows two main lobes of signal with a constriction between them, consistent with a hairpin/U-shaped fold characteristic of 2fold. The eggshell is moderately filled - there is still some dark space around the embryo body, not yet densely packed like pretzel. The XZ view shows bright signal with some layering but not the complex overlapping coils of pretzel. The morphology closely matches the 2fold reference images (T62-T68). The fill fraction is moderate rather than dense, supporting 2fold over pretzel. Consistent with previous observations at T60-T62.", + "reasoning": "In the XY view (top-left), I can see two roughly parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view (bottom-left) shows layered bright bands suggesting two overlapping body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel). Previous observation was 2fold at T62, and this appears consistent with continuing 2fold stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -172,10 +163,9 @@ "timepoint": 64, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with two parallel body segments visible in XY and XZ views. Matches 2fold reference images well. Not yet densely filled enough for pretzel. Consistent with previous three timepoints all classified as 2fold.", + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is some dark space remaining but less than in 1.5fold. In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments, consistent with a hairpin/U-shape fold. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous timepoints were classified as 2fold, so maintaining this classification is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -190,10 +180,9 @@ "timepoint": 65, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows a hairpin/U-shaped body with two parallel segments and moderate eggshell filling. YZ view shows ring-like pattern consistent with folded body. Fill fraction is moderate (some dark space remains), not yet dense enough for pretzel. Consistent with previous 2fold classifications at T62-T64.", + "reasoning": "The XY view shows a bean/kidney-shaped embryo with a clear fold - two parallel body segments visible forming a U or hairpin shape. The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but it's not densely packed like a pretzel. The YZ view shows a ring-like pattern consistent with a folded body. The XZ view shows bright signal that is moderately filling the space. This matches the 2fold reference images well. The fill fraction is moderate (not dense enough for pretzel), and the morphology shows two parallel segments rather than multiple overlapping coils. Consistent with previous observations at T62-T64.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -208,10 +197,9 @@ "timepoint": 66, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body is clearly folded. The body appears to have two parallel segments visible, consistent with a 2fold stage. The XZ view shows a pattern with two distinct bright regions separated by a darker zone, suggesting two parallel body layers. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well, and is consistent with the previous three timepoints all classified as 2fold. No clear evidence of a third fold or dense packing that would indicate pretzel.", + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body clearly shows two parallel segments forming a hairpin/U-shape. The XZ view shows layered signal consistent with two body folds. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel-level density or complexity yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -226,10 +214,9 @@ "timepoint": 67, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments forming a hairpin/U-shape. Matches 2fold reference images well. No evidence of the dense multi-coil pattern characteristic of pretzel. Consistent with previous three timepoints classified as 2fold.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible but less than in 1.5fold. In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous timepoints (T64-T66 all classified as 2fold). No clear transition to pretzel stage is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -244,10 +231,9 @@ "timepoint": 68, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin/U-shape. XZ view shows characteristic butterfly pattern of two folded segments. Matches 2fold references well. No dense multi-coil pattern of pretzel yet. Consistent with previous 2fold classifications.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo occupies a substantial portion of the eggshell. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments forming a hairpin/U-shape, consistent with 2fold morphology. The XZ view (bottom-left) shows a pattern with distinct bright regions separated by darker gaps, suggesting two body layers. The fill fraction is moderate (not densely packed like pretzel), and the morphology closely matches the 2fold reference images. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -262,10 +248,9 @@ "timepoint": 69, "predicted_stage": "2fold", "ground_truth_stage": "1.5fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows a complex pattern with bright regions suggesting two overlapping body layers. The YZ view (top-right) shows a ring-like pattern consistent with a folded body in cross-section. The fill fraction is moderate (not yet densely packed like pretzel), and I can distinguish approximately two parallel body segments rather than three or more coils. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear evidence of transition to pretzel yet.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is still some dark space visible, particularly around the edges, but less than in 1.5fold. The XZ view shows distinct layered bright bands consistent with two folded body segments. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would show denser filling and more complex coiling).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -280,10 +265,9 @@ "timepoint": 70, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view forming a folded shape. Consistent with 2fold reference images. No evidence of three or more overlapping coils that would indicate pretzel. Matches previous three timepoints classified as 2fold.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows layered bright bands indicating the folded body. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and there are two main parallel segments rather than multiple overlapping coils. Previous observations were all 2fold, and the morphology is consistent with continuing in this stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -298,10 +282,9 @@ "timepoint": 71, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments in XY and XZ views. Matches late 2fold reference images. Not yet showing the dense, multi-coil pattern of pretzel. Consistent with previous 2fold observations at T68-T70.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows layered signal bands consistent with two body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, so continuing at this stage is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -316,10 +299,9 @@ "timepoint": 72, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two distinct body lobes in a hairpin configuration. XZ view shows parallel bright bands consistent with two folded segments. Eggshell is moderately filled with some dark space remaining - not yet densely packed as in pretzel. Consistent with previous 2fold classifications at T69-T71.", + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly between the two lobes and around the edges, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows bright signal with some structure but not the complex overlapping coils characteristic of pretzel stage. This matches the 2fold reference images well, showing two parallel body segments. Previous observations were all 2fold, and while this is approaching the transition, the fill fraction is still moderate rather than dense, so I'll maintain the 2fold classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -334,10 +316,9 @@ "timepoint": 73, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with some dark space remaining, two parallel body segments visible in XY and XZ views forming a hairpin fold. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous T70-T72 classifications.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is still some dark space visible, particularly on the right side of the XY view, but less empty space than in 1.5fold. The XZ view shows two distinct layers of signal separated by a gap, consistent with 2fold. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -352,10 +333,9 @@ "timepoint": 74, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments in XY view. Matches late 2fold references. Not yet showing the dense multi-coil pattern characteristic of pretzel stage. Consistent with previous three timepoints classified as 2fold, though approaching the transition to pretzel.", + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows layered signal consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, so maintaining this classification is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -370,10 +350,9 @@ "timepoint": 75, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining, two visible body segments in XY view, layered structure in XZ view consistent with 2fold. Not yet densely filled enough for pretzel. Matches late 2fold references. Consistent with previous observations at T72-T74.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but less empty space than in 1.5fold. The XZ view (bottom-left) shows the characteristic layered pattern of a folded embryo. The fill fraction is moderate rather than dense - not yet at pretzel stage where the shell would be nearly completely filled with overlapping coils. This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -388,10 +367,9 @@ "timepoint": 76, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal, showing complex folding patterns. The body shows at least two parallel segments visible in XY view. Fill fraction is increasing compared to earlier 2fold timepoints but not yet densely packed like pretzel references. At the 2fold/pretzel boundary; defaulting to 2fold given previous observations and the rule to prefer earlier stage when uncertain.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space but the embryo body occupies a substantial portion. In the XY view (top-left), I can see what appears to be two parallel body segments with a folded/hairpin morphology, consistent with 2fold. The XZ view (bottom-left) shows a bilobed pattern with some internal structure suggesting two overlapping layers. Compared to the pretzel reference, the eggshell is not yet densely filled - there's still noticeable dark space, especially on the right side of the XY view. The pattern doesn't yet show the complex, tangled multi-coil appearance of pretzel. Previous three timepoints were all 2fold, and while this is approaching the transition, the fill fraction and morphology still best match 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -406,10 +384,9 @@ "timepoint": 77, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark space remaining. XZ view shows 2-3 bright bands suggesting body folding. Morphology is at the late 2fold/early pretzel boundary. Previous observations were 2fold with declining confidence. Following the rule to prefer earlier stage when uncertain, maintaining 2fold classification.", + "reasoning": "The XY view shows an elongated embryo with the body folded, showing two parallel segments visible. The eggshell is moderately filled - there is still some dark space remaining, particularly at the edges, but the signal occupies a good portion of the eggshell interior. The XZ view shows multiple bright bands consistent with two parallel body segments. Compared to the pretzel reference, the eggshell is not yet densely filled and the pattern is not as complex/tangled. This matches the 2fold reference images well. Previous observations were all 2fold, and the morphology is consistent with continuing at this stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -424,10 +401,9 @@ "timepoint": 78, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two main body lobes connected by a bend forming a hairpin/U-shape, consistent with 2fold. Eggshell is moderately filled but not densely packed with multiple overlapping coils as in pretzel. Matches 2fold reference images. Previous three timepoints were all 2fold, and no clear transition to pretzel is evident yet.", + "reasoning": "In the XY view (top-left), I can see two distinct lobes of fluorescent signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible between and around the body segments, but less than in 1.5fold. The XZ view (bottom-left) shows a similar pattern with distinct bright regions separated by darker gaps. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two parallel segments rather than three or more overlapping coils. Previous timepoints were all 2fold, and there's no clear transition to pretzel yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -442,10 +418,9 @@ "timepoint": 79, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is moderately filled with two main lobes visible in XY, consistent with late 2fold. The XZ view shows increasing complexity suggesting the body is beginning additional folding. However, the fill fraction is not yet as dense as pretzel references, and previous three timepoints were 2fold. Maintaining 2fold classification given slow stage progression, though transition to pretzel may be imminent.", + "reasoning": "The eggshell is moderately filled with signal - more complex than early 2fold but not yet densely packed like pretzel references. Two body segments visible in XY with a constriction between them. The YZ view shows a ring-like pattern suggesting increased folding, but overall fill fraction and complexity don't yet match pretzel references. Previous 3 timepoints were 2fold, and morphology is consistent with late 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -458,16 +433,15 @@ }, { "timepoint": 80, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark space remaining. The body shows folding complexity increasing beyond a simple hairpin but not yet the dense multi-coil pattern of pretzel. XZ view shows multiple bright bands but gaps persist. Previous timepoints were 2fold, and while this is approaching the transition to pretzel, the fill fraction and complexity don't yet clearly match pretzel references. Defaulting to earlier stage.", + "reasoning": "In the XY view, the embryo shows a complex, irregular shape with multiple lobes and overlapping structures rather than a clean two-parallel-segment hairpin. The body appears to have folded more than twice, creating overlapping coils. The XZ (bottom-left) view shows a complex internal pattern with multiple bright bands suggesting several body layers. The eggshell is becoming more densely filled compared to the 2fold references. The morphology closely matches the early pretzel reference images (e.g., T82). While the previous timepoints were classified as 2fold, the transition to pretzel is evident here with the increased complexity of folding and denser fill of the eggshell.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -476,16 +450,15 @@ }, { "timepoint": 81, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.4, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows a complex folded structure that is becoming more elaborate than a simple hairpin. XZ view shows multiple bright bands suggesting overlapping body segments. Eggshell fill is moderate. Morphology is transitional between late 2fold and early pretzel. Following the rule to prefer earlier stage when uncertain and given previous 2fold classification, maintaining 2fold, though pretzel transition appears imminent.", + "reasoning": "The eggshell is moderately to densely filled with signal showing complex folding patterns beyond a simple hairpin. The XZ view shows multiple bright bands suggesting 3+ body layers. Previous timepoint was pretzel, and the morphology is consistent with early pretzel stage, with increasing complexity of body folds compared to the 2fold stage seen at T78-79.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -494,16 +467,15 @@ }, { "timepoint": 82, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two main lobes of signal with a constriction between them, consistent with a hairpin/U-shaped fold (two parallel body segments). Eggshell fill is moderate - more than 1.5fold but not yet the dense packing of pretzel. XZ view shows layered structure but not the complex multi-coil pattern of pretzel. Matches 2fold references well. Previous observations were 2fold, and morphology hasn't clearly advanced to pretzel yet.", + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments creating a figure-8 or pretzel-like pattern. The XZ view shows multiple bright layers/bands indicating 3+ body folds. The eggshell is densely filled with signal. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -512,16 +484,15 @@ }, { "timepoint": 83, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell fill is moderate with some dark space remaining. XZ view shows 2-3 bright bands suggesting folded body segments. Morphology is consistent with late 2fold, possibly transitioning to pretzel, but not yet densely filled enough for clear pretzel classification. Previous observations were 2fold, and following the rule to prefer earlier stage when uncertain.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible. In the XY view (top-left), the signal fills most of the eggshell with complex, tangled patterns and multiple parallel body segments visible. The XZ view (bottom-left) shows bright, densely packed signal with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -532,10 +503,9 @@ "timepoint": 84, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with signal compared to 2fold references. The XZ view shows multiple overlapping body layers, and the XY view shows complex, tangled morphology rather than a clean two-segment hairpin. The pattern closely matches the pretzel reference at T82. While previous timepoints were classified as 2fold, the morphology here shows clear progression with increased fill fraction and multiple overlapping segments.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple overlapping segments creating a tangled pattern. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. The YZ view (top-right) shows a cross-pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -550,10 +520,9 @@ "timepoint": 85, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with signal, minimal dark space inside the shell boundary. XZ view shows complex curved/looping internal structures suggesting 3+ folds. Matches pretzel references better than 2fold. Consistent with previous T84 pretzel classification. Confidence moderate due to recent transition from 2fold.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal spans most of the eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows the eggshell nearly completely filled with bright signal and complex internal patterns suggesting multiple overlapping body coils. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -568,10 +537,9 @@ "timepoint": 86, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately to densely filled with signal. Complex internal structure visible in XY view with multiple overlapping body segments and internal dark gaps suggesting 3+ folds. XZ view shows layered bright regions. Matches pretzel reference images. Consistent with previous T85 classification of pretzel. Fill fraction is higher than 2fold references.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments and a complex, tangled pattern. The YZ view (top-right) shows multiple bright regions suggesting overlapping body layers. The XZ view (bottom-left) also shows dense, complex signal filling. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -586,10 +554,9 @@ "timepoint": 87, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is moderately to densely filled with signal. The XY view shows a complex, irregular elongated shape with multiple overlapping bright regions rather than a clean hairpin. The XZ projection shows multiple bright bands suggesting 3+ body folds. The YZ view shows a ring-like pattern consistent with coiled body. This matches pretzel references and is consistent with the previous three timepoints all classified as pretzel. Confidence remains moderate due to the somewhat ambiguous fill density.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating an irregular, tangled pattern with bright overlapping regions. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell interior. The YZ view (top-right) shows a ring-like pattern consistent with multiple body layers overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -604,10 +571,9 @@ "timepoint": 88, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds visible in both XY and XZ views. Complex tangled pattern with at least 3 body segments visible, consistent with pretzel stage. Matches pretzel reference images well. Embryo remains within eggshell (not hatching). Consistent with previous 3 timepoints classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex layered structure with multiple bright bands, indicating 3+ body folds. This matches the pretzel reference images well. The morphology is consistent with the previous three timepoints all classified as pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -622,10 +588,9 @@ "timepoint": 89, "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Complex, multi-lobed fluorescent signal in XY view with multiple overlapping body segments visible. The eggshell is densely filled with signal. The YZ view shows a ring-like pattern suggesting coiled body. Consistent with pretzel reference images and previous three observations all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled, complex pattern with several overlapping regions. The XZ view (bottom-left) shows dense, bright signal filling most of the eggshell with complex internal structure. The YZ view (top-right) shows a ring-like pattern consistent with multiple body layers overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -640,10 +605,9 @@ "timepoint": 90, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some complex folding visible in XY view. The body shows more than 2 parallel segments but the fill is not as dense as the clearest pretzel references. Previous 3 timepoints were pretzel, and stages change slowly. The morphology is consistent with early pretzel, though the fill fraction is on the lower end for this stage.", + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal - the XZ view shows bright, complex internal structure filling most of the shell. There appear to be multiple coils/folds visible, consistent with pretzel stage. This matches the pretzel reference images and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -658,10 +622,9 @@ "timepoint": 91, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "Previous three timepoints classified as pretzel. The eggshell shows moderate-to-dense filling with multiple body segments visible in XZ view. The XY view shows complex folding pattern. However, the fill fraction is not as dense as typical pretzel references, making this a borderline 2fold/pretzel case. Maintaining pretzel classification based on continuity with previous observations and the presence of what appears to be more than 2 parallel segments.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell. The XZ view shows complex layered signal with multiple bright bands. This matches the pretzel reference images well, with dense filling and multiple overlapping coils. No sign of hatching (no worm extending outside the eggshell). Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -676,10 +639,9 @@ "timepoint": 92, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing complex, overlapping body folds. Multiple coiled segments visible in XY view with layered structure in XZ view, consistent with pretzel stage. Matches pretzel reference images well. No sign of hatching. Consistent with previous pretzel classifications at T89-T91.", + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, multi-lobed structure with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a dense, complex pattern with coiled structures visible. The YZ view (top-right) shows the characteristic swirled/coiled pattern of a pretzel stage. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -694,10 +656,9 @@ "timepoint": 93, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible creating a complex tangled pattern. Matches pretzel reference images well. No signs of hatching. Consistent with previous pretzel classifications at T90-T92.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows layered bright structures consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -712,10 +673,9 @@ "timepoint": 94, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo body fills most of the eggshell with multiple overlapping coils/segments visible - more than just two parallel segments. The XZ view (bottom-left) shows complex layered structure with bright overlapping regions. The YZ view (top-right) shows several distinct bright spots suggesting multiple body layers overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments and a complex, tangled pattern. The XZ view (bottom-left) shows multiple layered body segments. The YZ view (top-right) shows bright spots from overlapping coils. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -730,10 +690,9 @@ "timepoint": 95, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated body shows multiple overlapping segments filling most of the eggshell, with some darker gaps characteristic of pretzel stage. The YZ view (top-right) shows a complex pattern with multiple bright regions suggesting overlapping body folds. The XZ view (bottom-left) shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated body shows multiple overlapping segments filling most of the eggshell interior. The YZ view (top-right) shows a complex pattern with multiple bright regions suggesting coiled body layers. The XZ view (bottom-left) also shows dense, complex signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -748,10 +707,9 @@ "timepoint": 96, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the signal fills most of the eggshell with multiple overlapping coils/body segments creating a complex pattern. The XZ view (bottom-left) shows multiple layered structures consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the shell). Consistent with previous observations at T93-T95.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the signal fills most of the eggshell with multiple overlapping body segments creating a tangled pattern. The XZ view (bottom-left) shows multiple layers of body segments with complex internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -766,10 +724,9 @@ "timepoint": 97, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, with multiple folded body segments overlapping. Consistent with previous observations at T94-T96.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -784,10 +741,9 @@ "timepoint": 98, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The YZ view shows internal structure with multiple overlapping layers. This is consistent with the previous three observations of pretzel stage, and no signs of hatching (no elongated worm outside the eggshell) are visible.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern with bright spots throughout. The YZ view (top-right) shows the characteristic complex internal structure of a pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three timepoints all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -802,10 +758,9 @@ "timepoint": 99, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 the XY view shows complex, overlapping coiled structures filling most of the eggshell interior with relatively little dark space. The XZ (bottom-left) view shows a bright, complex pattern with multiple overlapping layers. Multiple body segments are visible in the XY projection, consistent with 3+ folds. This matches the pretzel reference images well. The morphology is consistent with the previous three timepoints (T96-T98), all classified as pretzel. No signs of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows bright, densely packed signal filling most of the eggshell interior. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -820,10 +775,9 @@ "timepoint": 100, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a complex coiled pattern with multiple overlapping layers, consistent with 3+ folds. The YZ view (top-right) also shows a complex, densely packed pattern. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a complex coiled pattern with multiple overlapping layers, consistent with 3+ folds. The YZ view (top-right) also shows a complex, densely packed pattern. This matches the pretzel reference images well, and is consistent with the previous three timepoints all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -838,10 +792,9 @@ "timepoint": 101, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds. Complex tangled pattern visible in XY view with 3+ body segments. Matches pretzel reference images well. Consistent with previous observations at T98-T100. No signs of hatching.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments filling most of the eggshell interior. The XZ view (bottom-left) shows overlapping layers of signal. This is consistent with the pretzel reference images and the previous three observations at pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -856,10 +809,9 @@ "timepoint": 102, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments filling most of the eggshell interior. The YZ view (top-right) shows an irregular, complex pattern consistent with multiple overlapping body layers. The XZ view (bottom-left) also shows dense, complex signal. This matches the pretzel reference images well, with 3+ body folds creating the characteristic densely-packed appearance. Consistent with previous observations at T99-T101.", + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coils of the embryo body. Multiple body segments are visible with a tangled pattern in the XY view. The XZ view shows multiple layers of bright signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -874,10 +826,9 @@ "timepoint": 103, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "Previous three timepoints were pretzel. The XY view shows a complex folded structure within the eggshell with moderate-to-dense fill. The XZ view shows layered body segments suggesting multiple folds. While the fill fraction appears slightly less dense than ideal pretzel references, the overall morphology and continuity with previous observations support pretzel stage.", + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal - the XZ view (bottom-left) shows bright, complex overlapping patterns consistent with multiple body folds. The YZ view (top-right) shows a densely packed circular cross-section. This matches the pretzel reference images well, with multiple coils/folds creating a tangled appearance. No evidence of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -892,10 +843,9 @@ "timepoint": 104, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds. Complex tangled pattern visible in XY view with at least 3 body segments. Matches pretzel reference images. No sign of hatching. Consistent with previous observations at T101-T103.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments filling most of the eggshell interior. The YZ view (top-right) shows layered/banded signal consistent with multiple body folds. The XZ view (bottom-left) also shows multiple bright bands. This matches the pretzel reference images well, with 3+ body folds and dense eggshell filling. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -910,10 +860,9 @@ "timepoint": 105, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple bright segments crossing each other \u2014 more than two parallel segments are apparent. The YZ view (top-right) shows a circular/coiled pattern characteristic of pretzel stage. The XZ view (bottom-left) shows multiple bright horizontal bands indicating several body layers stacked in the projection. This matches the pretzel reference images well and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, tangled coils of the body. In the XY view (top-left), multiple overlapping body segments are visible with a complex pattern - more than two parallel segments can be discerned. The YZ view (top-right) shows a ring-like or coiled pattern characteristic of the pretzel stage. The XZ view (bottom-left) shows multiple bright bands/layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -928,10 +877,9 @@ "timepoint": 106, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, the embryo body shows a complex, tangled pattern with multiple parallel segments and bends, consistent with 3+ folds. The XZ view shows layered bright bands indicating overlapping body segments. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments folded within the eggshell. The XZ view (bottom-left) shows multiple layers of signal with complex internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -946,10 +894,9 @@ "timepoint": 107, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows an elongated, tangled pattern with multiple body segments overlapping. The XZ view shows a complex coiled pattern consistent with 3+ folds. This matches the pretzel reference images well. The signal extends across most of the eggshell interior with relatively little empty dark space. Consistent with previous observations at T104-T106.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern. The XZ view (bottom-left) shows multiple overlapping body layers with a complex internal structure. This matches the pretzel reference images well. The eggshell fill fraction is high (dense), consistent with pretzel stage. Previous three timepoints were all pretzel, and no clear morphological change toward hatching is evident (no elongated worm shape extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -964,10 +911,9 @@ "timepoint": 108, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple bright segments overlapping \u2014 more than two parallel segments are apparent. The XZ view (bottom-left) shows a complex pattern with multiple layers of signal filling the shell. The YZ view (top-right) shows bright spots distributed throughout, consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping layers. The XZ view (bottom-left) shows a densely packed, complex pattern consistent with 3+ folds. The YZ view (top-right) shows bright spots distributed throughout, indicating multiple body layers overlapping. This matches the pretzel reference images well, and is consistent with the previous three timepoints all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -982,10 +928,9 @@ "timepoint": 109, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible - I can see at least 3 parallel bands of signal forming a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows multiple layered body segments. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T106-T108.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments with multiple parallel tracks - at least 3 body segments are discernible, forming a pretzel-like pattern. The XZ view (bottom-left) also shows multiple layered body segments. The YZ view (top-right) shows the eggshell nearly completely filled. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1000,10 +945,9 @@ "timepoint": 110, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds. Complex tangled pattern visible in all three views. Matches pretzel reference images well. No sign of worm emerging from eggshell. Consistent with previous observations at T107-T109.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple body segments with a tangled/coiled pattern filling most of the eggshell. The XZ view (bottom-left) shows dense, complex signal with multiple overlapping layers. The YZ view (top-right) shows the characteristic ring-like pattern of a coiled pretzel-stage embryo. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1018,10 +962,9 @@ "timepoint": 111, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex, tangled coiling patterns visible in the XY view. Multiple overlapping body segments can be seen, consistent with 3+ folds. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well. The YZ view shows an irregular, multi-lobed bright pattern indicating overlapping coils. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled structures. In the XY view (top-left), the body shows multiple overlapping segments with a tangled appearance typical of pretzel stage. The YZ view (top-right) shows an irregular, complex pattern with multiple bright regions. The XZ view (bottom-left) shows dense signal filling most of the eggshell. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm shape outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1036,10 +979,9 @@ "timepoint": 112, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex folding with at least 3 overlapping segments - a bright region on the left and multiple curved structures on the right. The XZ view (bottom-left) shows bright, complex layered signal filling most of the eggshell. The YZ view (top-right) shows the characteristic tangled pattern of a pretzel stage. This is consistent with the previous three observations of pretzel stage, and no sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows complex, tangled body segments filling most of the eggshell interior, with multiple parallel body segments visible (more than 2). The XZ view (bottom-left) shows bright, complex overlapping structures. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1054,10 +996,9 @@ "timepoint": 113, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows an elongated, complex morphology with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a complex pattern with crossing/overlapping bright bands consistent with multiple body folds (3+). The YZ view (top-right) shows a densely filled, round cross-section. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows crossing/overlapping bright bands consistent with multiple coils of the body. The YZ view (top-right) shows a densely filled, round profile. This matches the pretzel reference images well, with multiple body folds creating a complex pattern. Previous three timepoints were all pretzel, and no clear morphological change toward hatching is evident (no worm extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1072,10 +1013,9 @@ "timepoint": 114, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows an elongated, complex pattern with multiple overlapping coils filling most of the eggshell. The XZ view (bottom-left) shows a complex, tangled pattern with multiple body layers. The YZ view (top-right) shows a densely filled cross-section with visible internal structure from overlapping folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows an elongated shape with multiple body segments and bright spots scattered throughout. The XZ view shows complex internal structure with multiple overlapping layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1090,10 +1030,9 @@ "timepoint": 115, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows complex, intertwined bright structures consistent with 3+ folds. The YZ view (top-right) shows diffuse, broadly distributed signal indicating dense packing. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in both the XY and XZ views. The XZ projection shows multiple intertwined body segments creating a tangled pattern. The YZ view shows diffuse, complex signal filling most of the oval. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1108,10 +1047,9 @@ "timepoint": 116, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows bright, complex overlapping structures consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T113-T115.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern. The XZ view (bottom-left) shows bright, complex overlapping structures consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1126,10 +1064,9 @@ "timepoint": 117, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments - more than two parallel segments are apparent. The XZ view (bottom-left) shows dense, bright signal filling most of the eggshell with complex internal structure. The YZ view (top-right) also shows dense filling. There is no sign of hatching (no elongated worm outside the shell). This is consistent with the pretzel stage and matches the previous observations at T114-T116. The slight protrusion visible on the left side of the XY view could suggest early movement but the embryo remains fully within the eggshell.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell interior. The XZ view shows multiple overlapping layers of signal. This matches the pretzel reference images well. There is no sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1144,10 +1081,9 @@ "timepoint": 118, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows complex, tangled body segments filling most of the eggshell interior with relatively little dark space remaining. The XZ view (bottom-left) shows multiple layered body segments. The YZ view (top-right) also shows a densely packed, complex pattern. This matches the pretzel reference images well, with 3+ body folds creating overlapping signal. No evidence of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T115-T117.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in the XY view. The complex, tangled pattern of nuclei with multiple parallel body segments is consistent with the pretzel stage. The XZ view shows bright, complex overlapping structures. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1162,10 +1098,9 @@ "timepoint": 119, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments filling most of the eggshell interior. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple overlapping body folds and minimal empty space within the eggshell. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments filling most of the eggshell interior. The XZ view (bottom-left) shows a complex, tangled pattern with multiple overlapping layers. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1180,10 +1115,9 @@ "timepoint": 120, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple body segments creating a tangled, complex pattern that fills most of the eggshell. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. The YZ view (top-right) shows a densely packed, irregular pattern consistent with multiple overlapping folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell interior. The XZ view shows multiple layers of signal. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three timepoints all classified as pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1198,10 +1132,9 @@ "timepoint": 121, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple folded segments - more than two parallel segments are apparent. The YZ view (top-right) shows a dense, complex signal pattern. The XZ view (bottom-left) shows bright overlapping layers. This matches the pretzel reference images well, with the dense fill and multiple body folds characteristic of this stage. Consistent with previous observations at T118-T120.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled, pretzel-like pattern that fills most of the eggshell. The XZ view (bottom-left) also shows dense, complex signal with multiple overlapping layers. The YZ view (top-right) shows a compact, bright mass with internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. There is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1216,10 +1149,9 @@ "timepoint": 122, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments and overlapping layers - more than two distinct body segments are visible. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows multiple bright bands indicating several body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments and overlapping layers filling most of the eggshell. The YZ view (top-right) shows a ring-like pattern characteristic of coiled body segments. The XZ view (bottom-left) shows multiple bright bands indicating several body folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1234,10 +1166,9 @@ "timepoint": 123, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a complex, tangled morphology with multiple overlapping coils visible within the eggshell. The eggshell is densely filled with signal, though the embryo appears to be moving/twitching (common in late pretzel). The XZ view shows complex internal structure with multiple body layers. The overall pattern matches pretzel reference images with multiple folded body segments. No evidence of hatching (no worm body extending outside the eggshell). Consistent with previous observations at T120-T122.", + "reasoning": "The XY view shows a complex, tangled morphology with multiple overlapping coils visible within the eggshell. The eggshell is densely filled with signal, though the embryo appears to be moving/twitching (characteristic of late pretzel stage). The XZ view shows complex layered structure. Multiple body segments are visible overlapping each other. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and while the embryo is getting close to hatching (it appears active), there's no clear sign of the worm extending outside the eggshell boundary yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1252,10 +1183,9 @@ "timepoint": 124, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body shows a complex, tangled pattern with multiple body segments overlapping - consistent with 3+ folds. The XZ view (bottom-left) shows bright, complex layered structure filling the shell. The YZ view (top-right) shows the characteristic dense, swirled pattern of a pretzel stage. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments filling most of the eggshell interior. The XZ view (bottom-left) shows bright, complex overlapping patterns consistent with multiple body folds. The YZ view (top-right) shows a densely packed structure. This matches the pretzel reference images well, with multiple coils and dense eggshell filling. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1270,10 +1200,9 @@ "timepoint": 125, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coiled body segments within the eggshell, with the body looping around itself in a complex pattern. The eggshell is densely filled with signal, though some dark spaces remain at the periphery. The XZ view shows a complex, multi-layered structure consistent with 3+ folds. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and no clear transition to hatching is evident (no elongated worm shape outside the eggshell).", + "reasoning": "The XY view shows multiple overlapping coils of the worm body within the eggshell, with a complex, tangled pattern visible. The eggshell is densely filled with fluorescent signal, though some dark spaces remain. The XZ view shows multiple body layers. This matches the pretzel reference images well, with multiple folded body segments creating an intricate pattern. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1288,10 +1217,9 @@ "timepoint": 126, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible creating a complex, tangled pattern. The XZ view (bottom-left) shows a dense, complex pattern with multiple overlapping layers. The YZ view (top-right) shows an elongated pattern with internal structure consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments filling most of the eggshell. The XZ view (bottom-left) shows bright, complex overlapping patterns consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1306,10 +1234,9 @@ "timepoint": 127, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows complex internal structure with multiple overlapping layers. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern within the eggshell. The XZ view shows complex layered structure. This is consistent with the pretzel stage reference images and the previous three observations. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1324,10 +1251,9 @@ "timepoint": 128, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, the body shows complex, tangled structure with multiple parallel segments - more than two distinct body layers can be discerned. The XZ view shows a dense, complex pattern consistent with multiple folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T125-T127.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple parallel body segments filling most of the eggshell interior. The XZ view (bottom-left) also shows dense, complex layered signal. This matches the pretzel reference images well, with 3+ folds creating overlapping coils. No sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1342,10 +1268,9 @@ "timepoint": 129, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments filling most of the eggshell interior with a tangled/complex pattern. The XZ view (bottom-left) shows bright, complex overlapping structures. This matches the pretzel reference images well, with multiple body folds creating a densely packed appearance. Consistent with previous three timepoints all classified as pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments filling most of the eggshell interior with a tangled/complex pattern. The XZ view (bottom-left) shows bright, complex overlapping structures. This matches the pretzel reference images well, with multiple body folds creating a densely packed appearance. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1360,10 +1285,9 @@ "timepoint": 130, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, the body shows complex, tangled morphology with multiple parallel segments - more than two distinct body segments can be traced, consistent with 3+ folds. The XZ view shows bright, complex overlapping structures filling most of the eggshell. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping structures filling most of the eggshell. The XZ view (bottom-left) shows dense, complex signal with multiple body layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1378,10 +1302,9 @@ "timepoint": 131, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex internal structure with multiple layers. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three observations of pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex, tangled body segments filling most of the eggshell interior. This is consistent with the pretzel stage reference images and the previous three observations. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1396,10 +1319,9 @@ "timepoint": 132, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments folded within the eggshell - consistent with 3+ folds. The XZ view (bottom-left) shows bright, complex overlapping structures filling most of the eggshell. This matches the pretzel reference images well. There is no sign of the worm emerging from the eggshell, so it has not progressed to hatching. Consistent with previous observations at T129-T131.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern within the eggshell. The XZ view (bottom-left) shows multiple bright layers of overlapping body segments. This is consistent with the pretzel stage reference images and the previous three observations. There is no sign of hatching (no elongated worm shape outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1414,10 +1336,9 @@ "timepoint": 133, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The YZ view (top-right) shows a ring-like pattern consistent with multiple body coils overlapping. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern that fills most of the eggshell. The YZ view (top-right) shows a ring-like pattern characteristic of coiled body segments in cross-section. The XZ view (bottom-left) shows dense, bright signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1432,10 +1353,9 @@ "timepoint": 134, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) shows bright, complex layered signal filling the shell. This matches the pretzel reference images well. The YZ view (top-right) also shows a ring-like pattern suggesting coiled body segments. No evidence of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern with bright spots throughout. The XZ view shows layered bright bands consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1450,10 +1370,9 @@ "timepoint": 135, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, elongated pattern with multiple body segments creating a tangled appearance that fills most of the eggshell. The XZ view (bottom-left) shows complex looping/coiling patterns consistent with 3+ folds. The YZ view (top-right) shows a densely packed, somewhat irregular shape. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in all three views. The XY view shows an elongated, complex pattern with multiple body segments packed tightly within the eggshell. The XZ view shows complex folding patterns consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1468,10 +1387,9 @@ "timepoint": 136, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments filling most of the eggshell interior, with complex tangled morphology. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows dense, layered signal. This matches the pretzel reference images well, with multiple folds visible and little empty space within the eggshell. Consistent with previous three observations all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping layers filling most of the eggshell interior. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1486,10 +1404,9 @@ "timepoint": 137, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple coiled body segments filling most of the eggshell, with complex overlapping patterns. The YZ view (top-right) shows distinct parallel bright bands indicating multiple body folds (at least 3 visible). The XZ view (bottom-left) also shows a densely packed, complex pattern. This matches the pretzel reference images well, with the characteristic dense fill and multiple overlapping coils. Consistent with previous observations at T134-T136.", + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple coiled body segments filling most of the eggshell interior, with complex overlapping patterns. The YZ view (top-right) shows distinct parallel bright bands indicating multiple body folds (at least 3 visible). The XZ view (bottom-left) also shows a complex, densely packed pattern. This matches the pretzel reference images well, with multiple overlapping coils and high eggshell fill fraction. Consistent with previous observations at T134-T136.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1504,10 +1421,9 @@ "timepoint": 138, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated shape shows multiple body segments with a tangled/coiled pattern filling most of the eggshell. The XZ view (bottom-left) shows dense, complex signal throughout. The YZ view (top-right) shows an asymmetric, densely filled pattern consistent with multiple overlapping folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no signal outside eggshell boundary).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex layered structure filling most of the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1519,9 +1435,9 @@ "candidate_stages": null } ], - "duration_seconds": 944.9823794364929, + "duration_seconds": 678.0339498519897, "error": null, - "accuracy": 0.7857142857142857, + "accuracy": 0.75, "adjacent_accuracy": 1.0 }, { @@ -1529,16 +1445,15 @@ "predictions": [ { "timepoint": 45, - "predicted_stage": "comma", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo body has elongated within the eggshell with significant dark space remaining (sparse fill). The shape is transitioning from comma toward 1.5fold, but clear parallel body segments are not yet visible. Compared to references, this is at the late comma / early 1.5fold boundary. Following the rule to prefer the earlier stage when uncertain, and given previous timepoints were all comma, maintaining comma classification.", + "reasoning": "The embryo body has elongated significantly compared to comma references, with the body beginning to show early folding. The eggshell is sparsely filled with significant dark space remaining. This matches early 1.5fold morphology (comparable to T47 reference), where the body has started folding back but hasn't formed a clear two-segment hairpin yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -1549,10 +1464,9 @@ "timepoint": 46, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo shows elongation with early folding visible in XY view - a J-shaped body beginning to fold back. Eggshell fill is sparse with significant dark space remaining. Matches the early 1.5fold reference (T47) well. The body has progressed beyond the comma C-shape into early folding. Previous timepoint was comma at 55% confidence, suggesting the transition was already underway.", + "reasoning": "The XY view shows an elongated embryo body that is beginning to fold, with a curved/J-shaped morphology. The eggshell is sparsely filled - there is still significant dark space within the eggshell boundary, particularly visible in the XY view where the body doesn't fill the entire shell. The XZ (bottom-left) view shows two somewhat distinct lobes of signal but not yet a clear parallel hairpin structure. This matches the 1.5fold reference images well, where the body has started folding back but hasn't completed a full 2fold. The previous timepoint was classified as 1.5fold, and stages change slowly, so maintaining 1.5fold is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1567,10 +1481,9 @@ "timepoint": 47, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "This image matches the T47 1.5fold reference exactly. The embryo body is elongated and beginning to fold (J-shape visible in XY), with sparse eggshell filling \u2014 significant dark space remains inside the shell boundary. No clear two parallel body segments yet. Consistent with previous observation of 1.5fold at T46.", + "reasoning": "The XY view shows an elongated embryo body that is beginning to fold, with the signal concentrated in a band that curves along the eggshell. There is still significant dark/empty space within the eggshell boundary, indicating sparse filling consistent with 1.5fold. The body appears as a single curved structure with a partial fold beginning (J-shape), not yet showing two clear parallel segments as in 2fold. This matches the 1.5fold reference image (T47) very closely. The previous stage was 1.5fold, and there's no clear morphological advancement to 2fold yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1585,10 +1498,9 @@ "timepoint": 48, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated embryo body with partial folding visible in XY view, consistent with J-shape/partial hairpin of 1.5fold. Eggshell is sparsely to moderately filled with significant dark space remaining. No clear two-parallel-segment hairpin pattern characteristic of 2fold. Matches 1.5fold reference images well. Consistent with previous T47 classification.", + "reasoning": "Eggshell is sparsely to moderately filled with signal, still showing dark space inside the shell boundary. The body appears elongated with partial folding but does not yet show two clearly parallel body segments characteristic of 2fold. Morphology matches 1.5fold references and is consistent with previous three timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1603,10 +1515,9 @@ "timepoint": 49, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is sparsely filled with significant dark space remaining. The body appears as one main elongated/curved structure without clear two-parallel-segment hairpin morphology. Matches 1.5fold references well. Consistent with previous three timepoints all classified as 1.5fold, and no clear advancement to 2fold is evident.", + "reasoning": "Eggshell is sparsely filled with significant dark space remaining. The body appears elongated with early folding (J-shape) but does not yet show two clear parallel segments characteristic of 2fold. Matches 1.5fold reference images well. Consistent with previous three timepoints all classified as 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1621,10 +1532,9 @@ "timepoint": 50, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo shows an elongated body with a partial fold (J-shape) in the XY view. Eggshell fill is sparse with significant dark space remaining. No clear two parallel body segments visible yet. Morphology matches 1.5fold references and is consistent with previous three timepoints.", + "reasoning": "The embryo shows an elongated body with a partial fold (J-shape) and sparse-to-moderate eggshell filling with significant dark space remaining. This matches the 1.5fold reference images. No clear complete hairpin/U-shape with two fully parallel segments is visible yet, which would indicate 2fold. Consistent with previous three timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1639,10 +1549,9 @@ "timepoint": 51, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated embryo body with partial folding visible in XY view, consistent with J-shape morphology. Eggshell is sparsely to moderately filled with significant dark space remaining. No clear two-parallel-segment hairpin pattern yet. Matches 1.5fold reference images well, particularly T52. Consistent with previous three timepoints all classified as 1.5fold.", + "reasoning": "The XY view shows an elongated embryo with the body curving/folding, but the eggshell is still sparsely filled - there is significant dark space, particularly at the lower-left portion of the eggshell. The signal doesn't yet show two clearly parallel body segments forming a complete hairpin/U-shape. The YZ view shows asymmetric bright clusters rather than the more filled pattern seen in 2fold references. This matches the 1.5fold reference images well, consistent with the previous three timepoints all being 1.5fold. No clear morphological change to warrant advancing to 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1657,10 +1566,9 @@ "timepoint": 52, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is sparsely to moderately filled with significant dark space remaining. The embryo shows an elongated body with early folding but not yet two clear parallel segments. Matches 1.5fold reference images well. Consistent with previous three timepoints classified as 1.5fold.", + "reasoning": "The XY view shows an elongated embryo with the body curving and beginning to fold, but the eggshell is still sparsely filled with significant dark space remaining, particularly on the right side. The signal distribution shows one main curved body segment without clear parallel segments characteristic of 2fold. The XZ view shows a bright mass that doesn't yet fill the eggshell densely. This matches the 1.5fold reference images well (compare to T52 reference). No clear evidence of two parallel body segments (hairpin) that would indicate 2fold. Consistent with previous observations at 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1675,10 +1583,9 @@ "timepoint": 53, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is sparsely to moderately filled with signal, consistent with 1.5fold. The embryo body shows elongation with partial folding but not yet a clear two-parallel-segment hairpin characteristic of 2fold. Matches 1.5fold reference images well. No clear morphological change from previous timepoints.", + "reasoning": "The XY view shows an elongated embryo with the body curving along the eggshell, consistent with 1.5fold. The eggshell is still sparsely filled - there's notable dark space, particularly at the edges. In the XZ (bottom-left) view, I can see some layering beginning but not yet the clear two parallel segments characteristic of 2fold. The YZ view (top-right) shows an irregular, not-yet-densely-packed shape. This matches the 1.5fold reference images well. The previous three timepoints were all 1.5fold, and there's no clear morphological change to indicate progression to 2fold yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1693,10 +1600,9 @@ "timepoint": 54, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated embryo body with curvature visible in XY view, but no clear two-parallel-segment hairpin pattern yet. Eggshell fill fraction remains sparse with significant dark space. Morphology is consistent with late 1.5fold, matching the T52-T57 reference images. Previous three timepoints were 1.5fold and no clear transition to 2fold is evident.", + "reasoning": "Eggshell is sparsely to moderately filled with significant dark space remaining. The embryo body is elongated and beginning to fold but does not yet show two clearly parallel body segments characteristic of 2fold. Morphology closely matches the 1.5fold T57 reference. Consistent with previous three observations of 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1711,10 +1617,9 @@ "timepoint": 55, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell fill is still relatively sparse with visible dark space. While there are hints of a second parallel body segment forming, the two-segment hairpin pattern is not yet clearly defined compared to 2fold references. The XZ view shows some layering but not the clear two-band pattern of 2fold. Maintaining 1.5fold classification consistent with previous observations, though transition to 2fold may be imminent.", + "reasoning": "The eggshell is still sparsely to moderately filled with signal, with dark space remaining. The body shows elongation with partial folding but not yet a clear two-parallel-segment hairpin pattern characteristic of 2fold. Matches late 1.5fold references. Previous three timepoints were 1.5fold, and no clear morphological transition to 2fold is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1729,10 +1634,9 @@ "timepoint": 56, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Two body segments are becoming visible in the XY and XZ views, suggesting transition toward 2fold. However, the eggshell fill is still relatively sparse with significant dark space, and the hairpin shape is not yet as clearly defined as in 2fold references. Previous observations were 1.5fold with declining confidence. Defaulting to earlier stage given uncertainty.", + "reasoning": "The XY view shows the embryo body beginning to fold with hints of two parallel segments, but the eggshell still has significant empty/dark space (sparse fill). The morphology is transitional between 1.5fold and 2fold but hasn't clearly reached the full hairpin/U-shape characteristic of 2fold. Consistent with previous 1.5fold observations; defaulting to earlier stage when uncertain.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1747,10 +1651,9 @@ "timepoint": 57, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Transitional morphology between 1.5fold and 2fold. Two body segments are becoming visible in XY and XZ views, but eggshell still has moderate dark space. Previous observations were 1.5fold with declining confidence. While approaching 2fold, the fill fraction is still somewhat sparse and the two parallel segments are not yet as clearly defined as in the 2fold reference. Defaulting to earlier stage given uncertainty.", + "reasoning": "The embryo shows moderate eggshell filling with some dark space remaining. The body shows early signs of a second fold forming but does not yet display the clear two parallel body segments characteristic of 2fold. The morphology is consistent with late 1.5fold, matching the T57 reference. Previous three timepoints were 1.5fold, and the change is not yet definitive enough to advance the stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1763,16 +1666,15 @@ }, { "timepoint": 58, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "XZ view shows two distinct bright lobes suggesting two parallel body segments forming a hairpin. Eggshell fill is moderate with some dark space remaining. Morphology matches early 2fold reference (T62) better than 1.5fold. Transitional between 1.5fold and 2fold, but two parallel segments are becoming apparent.", + "reasoning": "The eggshell is still sparsely to moderately filled with some dark space remaining. While the embryo is elongating and beginning to show folding, a clear two-parallel-segment hairpin pattern is not yet fully established. Compared to 2fold references, the fill fraction is lower and the fold is less defined. Previous three timepoints were 1.5fold, and the morphology hasn't clearly changed enough to advance the stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -1781,16 +1683,15 @@ }, { "timepoint": 59, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in both XY and XZ views, forming a hairpin/U-shape. Matches 2fold references better than 1.5fold (more filled) or pretzel (not densely packed). Consistent with T58 classification of 2fold.", + "reasoning": "Eggshell fill is moderate but still has significant dark space. While there are hints of a second parallel segment forming, the morphology is not yet clearly showing the definitive hairpin/U-shape of 2fold. Transitional between 1.5fold and 2fold; defaulting to earlier stage consistent with previous observations at T56-T58.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -1799,16 +1700,15 @@ }, { "timepoint": 60, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with visible dark space remaining. Two parallel body segments visible in XY view forming a U/hairpin shape. Matches 2fold reference images. Consistent with previous T59 classification of 2fold. Not yet dense enough for pretzel.", + "reasoning": "The embryo shows increasing elongation and a developing fold with hints of two parallel segments, approaching 2fold morphology. However, the eggshell still has notable dark space (sparse-to-moderate fill), and the previous three timepoints were 1.5fold. Following the rule to prefer the earlier stage when uncertain, this remains 1.5fold, though it's near the transition to 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -1819,10 +1719,9 @@ "timepoint": 61, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in both XY and XZ views, forming a hairpin/U-shape. Matches 2fold reference images well. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T58-T60.", + "reasoning": "The XY view shows two parallel body segments becoming clearly visible, and the XZ view shows two distinct horizontal bands of signal. The eggshell fill fraction is moderate - more filled than 1.5fold but still with some dark space. This matches the 2fold reference at T62 well. The transition from 1.5fold to 2fold appears to have occurred.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1837,10 +1736,9 @@ "timepoint": 62, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with some dark space remaining. XY view shows two main body regions consistent with a hairpin fold. XZ view shows 2 main signal bands. Matches 2fold reference well. Not yet densely filled enough for pretzel. Consistent with previous 3 observations of 2fold.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible, creating a hairpin/U-shape. The eggshell is moderately filled with signal - some dark space remains but less than in 1.5fold. The XZ view (bottom-left) shows distinct layered bands consistent with two parallel body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous timepoint was also 2fold, consistent with slow stage progression.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1855,10 +1753,9 @@ "timepoint": 63, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows bilobed structure with two parallel body segments connected by a bend, consistent with 2fold. Eggshell is moderately filled with some dark space remaining - not yet dense enough for pretzel. Matches 2fold reference images well. Consistent with previous observations at T60-T62.", + "reasoning": "In the XY view (top-left), the embryo shows a clear folded morphology with two parallel body segments visible - a broader upper region and a curved lower portion forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view (bottom-left) shows layered bright bands consistent with two body segments overlapping. The fill fraction is moderate, not yet dense enough for pretzel. This matches the 2fold reference images well and is consistent with the previous observations at T61-T62.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1873,10 +1770,9 @@ "timepoint": 64, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with visible dark spaces, two parallel body segments visible in XY and XZ views forming a hairpin/U-shape. Matches 2fold references well. No progression to the dense, multi-coiled pretzel pattern yet. Consistent with previous T61-T63 classifications.", + "reasoning": "In the XY view, I can see two main lobes of fluorescent signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. This matches the 2fold reference images well. The fill fraction is not yet dense enough for pretzel (no complex overlapping coils visible). Previous three timepoints were all 2fold, and the morphology is consistent with continuing at this stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1891,10 +1787,9 @@ "timepoint": 65, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments in XY view. Layered structure in XZ view consistent with 2fold. Not yet densely filled enough for pretzel - still some dark space within eggshell. Consistent with previous 2fold classifications at T62-T64.", + "reasoning": "The XY view shows an elongated embryo that moderately fills the eggshell, with some dark space remaining. The body appears to have two parallel segments visible, consistent with a 2fold stage. The XZ (bottom-left) view shows layered signal with some internal structure but not yet the dense, complex coiling pattern of a pretzel. The eggshell fill is moderate - more filled than 1.5fold but not densely packed like pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations at 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1909,10 +1804,9 @@ "timepoint": 66, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell filling with visible dark space remaining. Two parallel body segments visible in XY view forming a hairpin/U-shape. No evidence of three or more overlapping coils. Consistent with 2fold reference images and previous timepoint classifications.", + "reasoning": "In the XY view (top-left), I can see a clear folded embryo with two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is still some dark space visible within the eggshell boundary, but less than in 1.5fold. The XZ view (bottom-left) shows two distinct layers of signal consistent with a 2fold configuration. The fill fraction is moderate, not yet dense enough for pretzel stage. This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1927,10 +1821,9 @@ "timepoint": 67, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows layered signal with some complexity but not the dense, tangled pattern of pretzel. This matches well with the 2fold reference images (e.g., T68). The fill fraction is moderate rather than dense, supporting 2fold over pretzel. Consistent with previous observations at T64-T66.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - some dark spaces remain but the body occupies a substantial portion. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the pattern is consistent with the previous three observations of 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1945,10 +1838,9 @@ "timepoint": 68, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with some dark space remaining, two parallel body segments visible in XY view forming a hairpin/U-shape, consistent with 2fold reference images. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T65-T67.", + "reasoning": "In the XY view (top-left), the embryo shows an elongated curved body that fills moderately within the eggshell, with some dark space remaining below the body. The body appears as a curved band with two parallel segments visible, consistent with a 2fold stage. The eggshell is moderately filled - not densely packed like pretzel. The XZ view (bottom-left) shows layered bright signal with some internal structure but not the complex overlapping coils of pretzel. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would require denser filling and more complex coiling).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1963,10 +1855,9 @@ "timepoint": 69, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell filling with some dark space remaining, two parallel body segments visible in a hairpin/U-fold configuration. Matches 2fold reference images (T68 range). Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T66-T68.", + "reasoning": "In the XY view (top-left), I can see the embryo body forming a folded structure with two roughly parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The fill fraction is moderate, not yet densely packed as in pretzel. The XZ view (bottom-left) shows a similar pattern with moderate filling. This matches the 2fold reference images well. The previous three timepoints were all 2fold, and there's no clear morphological change to suggest progression to pretzel (which would show denser filling and more complex overlapping coils).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1981,10 +1872,9 @@ "timepoint": 70, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows a clear figure-8/dumbbell shape with two body segments connected by a fold, characteristic of 2fold. Eggshell fill is moderate with some dark space remaining. XZ view shows two distinct bright lobes consistent with two parallel body segments. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T67-T69.", + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear constriction/bend in the middle, forming two distinct lobes connected by a narrower region - this is consistent with a 2fold hairpin/U-shape with two parallel body segments. The eggshell is moderately filled - there is some dark space but the signal occupies a good portion of the eggshell interior. The XZ view (bottom-left) shows two bright masses consistent with two overlapping body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and there are clearly two parallel segments visible rather than three or more coils. Previous observations were all 2fold, and the morphology is consistent with continuing in this stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1999,10 +1889,9 @@ "timepoint": 71, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining, visible folded body with approximately two parallel segments in XY view. Layered bands in XZ view consistent with 2fold. Matches 2fold reference images (T62-T75 range). Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo is filling more of the shell than at 1.5fold. In the XY projection, I can see what appears to be two parallel body segments with a folded/hairpin structure. The XZ view (bottom-left) shows layered bright bands consistent with a 2fold configuration. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology closely matches the 2fold reference images. No clear evidence of three or more overlapping coils that would indicate pretzel stage. Consistent with previous observations at T68-T70.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2017,10 +1906,9 @@ "timepoint": 72, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two parallel body segments in a hairpin/U-shape configuration. Eggshell fill fraction is moderate - some dark space remains but body is elongated. Matches 2fold reference images well. Not yet showing the dense, multi-coil pattern of pretzel stage. Consistent with previous three observations of 2fold.", + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows layered bright bands suggesting two folded segments. The YZ view (top-right) shows a relatively compact cross-section with some internal structure. The fill fraction is moderate (not densely packed like pretzel), and I can distinguish approximately two parallel segments rather than the complex multiple overlapping coils of pretzel. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2035,10 +1923,9 @@ "timepoint": 73, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two main body lobes/segments in a folded configuration consistent with 2fold. Eggshell fill is moderate - more filled than 1.5fold but not yet densely packed like pretzel. No evidence of 3+ overlapping coils. Consistent with previous 2fold classifications at T70-T72.", + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows a moderately filled eggshell with some internal structure visible. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the two-lobed/hairpin morphology is consistent with 2fold. Previous observations at T70-72 were all 2fold, and there's no clear transition to pretzel yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2053,10 +1940,9 @@ "timepoint": 74, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows a clear hairpin/U-shaped body with two parallel segments connected by a bend, consistent with 2fold. Eggshell is moderately filled with some dark space remaining. The XZ projection shows layered bright bands but not the dense, complex coiling of pretzel. Morphology is consistent with previous 2fold classifications at T71-T73.", + "reasoning": "In the XY view (top-left), I can see a clear folded embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The embryo shows distinct lobes of signal with a bend connecting them. The eggshell is moderately filled - there is still some dark space visible, particularly around the edges, but the signal occupies a good portion of the eggshell interior. This is consistent with 2fold rather than pretzel, as the eggshell is not yet densely packed with multiple overlapping coils. The XZ view (bottom-left) shows layered bright bands consistent with two parallel body segments. This matches the 2fold reference images well. Previous observations were all 2fold, and while the embryo may be approaching the transition to pretzel, I don't see clear evidence of three or more overlapping folds yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2071,10 +1957,9 @@ "timepoint": 75, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Two parallel body segments visible in XY view forming a hairpin/U-shape. Moderate eggshell fill fraction with some dark space remaining. XZ view shows two distinct bright regions consistent with folded body. Matches 2fold references well. Not yet showing the dense, complex overlapping coils of pretzel stage. Consistent with previous 2fold classifications.", + "reasoning": "In the XY view (top-left), I can see what appears to be a folded embryo with two main body segments forming a U or hairpin shape - there are two distinct lobes of signal connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly around the edges, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows a complex pattern with what looks like two parallel segments. Comparing to references, this matches the 2fold stage well - the eggshell fill is moderate (not yet dense enough for pretzel), and the body shows two parallel segments rather than three or more overlapping coils. Previous observations were all 2fold, and while this could be approaching pretzel, the fill fraction is not yet dense enough to warrant advancing the stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2089,10 +1974,9 @@ "timepoint": 76, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo shows increasing complexity with body segments beginning to overlap more, but the eggshell fill fraction remains moderate with visible dark spaces. The morphology is transitional between 2fold and pretzel. The XZ view shows layered bands but not yet the dense, tangled pattern of pretzel. Following the rule to prefer the earlier stage when uncertain, and given consistent 2fold classification at previous timepoints.", + "reasoning": "In the XY view, the embryo shows an elongated body with what appears to be two parallel segments visible - a clear folded/hairpin structure. The eggshell is moderately filled with signal - there is still some dark space visible, particularly at the edges, but the body occupies a substantial portion of the eggshell. This is consistent with 2fold rather than pretzel, as the eggshell is not yet densely packed with multiple overlapping coils. The morphology matches the 2fold reference images (especially T75) well. Previous three timepoints were all 2fold, and while the embryo may be approaching the transition to pretzel, I don't see clear evidence of 3+ folds or the dense filling characteristic of pretzel stage yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2107,10 +1991,9 @@ "timepoint": 77, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal but not yet densely packed as in pretzel. The XY view shows an elongated body with some folding complexity but not the multiple overlapping coils characteristic of pretzel. The XZ view shows layering consistent with late 2fold. Previous observations were 2fold, and while this is approaching the transition, the fill fraction and coiling complexity don't yet clearly match pretzel references.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly in the XY view where the body doesn't completely fill the eggshell. The XZ (bottom-left) view shows what appears to be two parallel body segments with a layered structure. The fill fraction is moderate, not yet densely packed like the pretzel references. Comparing to references, this matches the 2fold stage (similar to T75 reference). The previous three timepoints were all 2fold, and there's no clear transition to the densely-filled pretzel morphology yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2123,16 +2006,15 @@ }, { "timepoint": 78, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark spaces remaining in center. XZ view shows multiple bright bands suggesting body is beginning to fold more than twice, but fill fraction is not yet as dense as pretzel references. Previous observations were 2fold; morphology is transitional but defaulting to earlier stage given uncertainty.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 there is very little dark/empty space inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex pattern with at least 3 parallel tracks of nuclei visible. The YZ view (top-right) shows a complex, multi-lobed structure consistent with multiple coils. The XZ view (bottom-left) shows dense, layered signal. This matches the pretzel reference images much better than the 2fold references, which show more empty space and only two parallel segments. The transition from 2fold at T77 to pretzel at T78 is plausible as the embryo continues to elongate and fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2141,16 +2023,15 @@ }, { "timepoint": 79, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two main body lobes with a dark gap between them, consistent with 2fold morphology. Eggshell fill is moderate - not yet densely packed as in pretzel. XZ view shows increasing complexity but not yet the multiple overlapping coils characteristic of pretzel. Previous observations were 2fold; while this is late 2fold approaching pretzel transition, defaulting to earlier stage given uncertainty.", + "reasoning": "The eggshell is densely filled with signal, showing complex overlapping body segments visible in both XY and XZ views. The XZ projection shows curved/looping patterns indicative of 3+ folds. Consistent with previous T78 pretzel classification and matches pretzel reference images.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2159,16 +2040,15 @@ }, { "timepoint": 80, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining, approximately two parallel body segments visible in XY view, layered signal in XZ view consistent with 2fold. Not yet densely filled enough for pretzel. Consistent with previous 2fold observations, though approaching transition.", + "reasoning": "The eggshell is densely filled with fluorescent signal - in the XY view (top-left), the signal extends across most of the eggshell with complex, overlapping structures visible. The YZ view (top-right) shows a complex pattern with multiple bright regions suggesting overlapping body coils. The XZ view (bottom-left) shows dense, layered signal filling most of the eggshell. Multiple body segments appear to overlap, creating the tangled appearance characteristic of pretzel stage. This is consistent with the previous two observations (T78, T79) both being pretzel stage, and the morphology matches the pretzel reference images well.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2179,10 +2059,9 @@ "timepoint": 81, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is becoming densely filled with signal, and the XZ view shows complex internal coiling/layering patterns suggesting more than two parallel body segments. The morphology closely matches the early pretzel reference (T82). However, confidence is moderate as the transition from 2fold is gradual and the previous timepoints were classified as 2fold.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping coils/segments visible. The XZ view (bottom-left) shows dense, complex signal filling the shell with what appears to be multiple folded body layers. The YZ view (top-right) shows bright spots distributed throughout, consistent with multiple overlapping body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2197,10 +2076,9 @@ "timepoint": 82, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal with little empty dark space. Multiple overlapping body coils visible in XY and XZ views creating complex tangled pattern. Matches pretzel reference images well. More densely filled than 2fold references. Consistent with previous T81 pretzel classification.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the elongated body shows multiple overlapping coils/segments creating a complex pattern. The XZ view (bottom-left) shows dense, layered signal with visible coiling patterns. This matches the pretzel reference images closely, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm body extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2215,10 +2093,9 @@ "timepoint": 83, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal with little empty dark space inside. Multiple overlapping body segments visible in XY view creating a complex coiled pattern. XZ view shows dense layered signal. Matches pretzel reference images well and is consistent with previous T82 pretzel classification.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows the shell nearly completely filled with signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2233,10 +2110,9 @@ "timepoint": 84, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible creating complex coiled pattern. YZ view shows ring-like structure consistent with multiple folds. Matches pretzel reference images well. Consistent with previous three observations all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, overlapping pattern of nuclei. The XZ view (bottom-left) shows multiple overlapping body layers with a complex coiled pattern. The YZ view (top-right) shows a ring-like or looped structure consistent with multiple folds. This matches the pretzel reference images well, with dense filling and multiple overlapping coils. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2251,10 +2127,9 @@ "timepoint": 85, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space, consistent with pretzel stage. Multiple overlapping body segments create a complex pattern in the XY and XZ views. Matches pretzel reference images well. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the signal fills most of the eggshell with complex, tangled patterns of nuclei - multiple body segments overlap creating a dense pattern. The XZ view (bottom-left) shows bright, complex layered signal filling the shell. The YZ view (top-right) shows scattered bright nuclei across the cross-section. This matches the pretzel reference images well, with dense fill and multiple folded body segments. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints all classified as pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2269,10 +2144,9 @@ "timepoint": 86, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo fills most of the eggshell with multiple overlapping body segments creating a complex pattern. The XZ view (bottom-left) shows multiple layered bands of signal consistent with 3+ folds. The YZ view (top-right) shows a complex internal structure with visible coiling patterns. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, tangled pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows multiple layered bands of signal consistent with 3+ folds. The YZ view (top-right) shows a complex internal structure with visible coiling. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2287,10 +2161,9 @@ "timepoint": 87, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.87, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell with visible layered structure. The YZ view (top-right) shows multiple bright spots indicating overlapping body segments. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern with little empty dark space inside the eggshell. The XZ view shows complex layered structure consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2305,10 +2178,9 @@ "timepoint": 88, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the elongated body shows complex, tangled morphology with multiple body segments overlapping \u2014 more than two parallel segments are discernible. The XZ view (bottom-left) shows a dense, complex pattern with multiple layers of signal filling most of the eggshell interior. The YZ view (top-right) shows an irregular, multi-lobed pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping layers. The XZ view (bottom-left) shows a densely packed pattern with internal structure consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2323,10 +2195,9 @@ "timepoint": 89, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping coils of the embryo body visible within the eggshell. The eggshell is densely filled with signal - the XZ view shows bright signal filling most of the eggshell interior with complex internal structure. Multiple body segments are visible in the XY projection, creating an overlapping/tangled appearance consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping coils of the embryo body visible within the eggshell. The eggshell is densely filled with fluorescent signal - the XZ view (bottom-left) shows the shell nearly completely filled with bright, complex signal patterns. Multiple body segments are visible overlapping each other, consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2341,10 +2212,9 @@ "timepoint": 90, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal, though there are some darker gaps between coils. The XZ (bottom-left) view shows multiple layers of bright signal with complex internal structure. The YZ view shows a rounded, moderately filled profile with bright spots. This matches the pretzel reference images well - multiple folded body segments creating a tangled appearance. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal, though some dark regions remain. The XZ (bottom-left) view shows multiple layers of bright signal consistent with overlapping body folds. This matches the pretzel reference images well, with multiple coils/folds visible. Previous three timepoints were all pretzel, and no clear morphological change toward hatching is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2359,10 +2229,9 @@ "timepoint": 91, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows multiple layered bright bands consistent with 3+ body folds. This matches the pretzel reference images well. The eggshell fill fraction is high with little empty dark space inside, consistent with pretzel stage. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in both the XY and XZ views. The XZ view shows complex layered structure with at least 3 parallel bands of signal, consistent with multiple body folds. The overall pattern matches the pretzel reference images well, with the tangled, complex appearance characteristic of 3+ folds. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2377,10 +2246,9 @@ "timepoint": 92, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The YZ view (top-right) shows a complex, non-uniform pattern with multiple bright regions suggesting overlapping body layers. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments - more than two parallel segments are apparent, consistent with 3+ folds. The YZ view (top-right) shows a complex, non-uniform pattern with multiple bright regions indicating overlapping body layers. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2395,10 +2263,9 @@ "timepoint": 93, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2413,10 +2280,9 @@ "timepoint": 94, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), multiple body segments can be seen creating a tangled pattern with at least 3 overlapping layers. The XZ view (bottom-left) shows complex internal structure with multiple bright bands. The YZ view (top-right) shows a non-circular, angular shape consistent with a folded body. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, particularly evident in the XZ (bottom-left) view where multiple layers of the body create a complex pattern. The YZ view (top-right) shows a compact, irregularly shaped cross-section consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2431,10 +2297,9 @@ "timepoint": 95, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple body segments overlapping \u2014 more than two parallel segments are apparent, consistent with 3+ folds. The XZ view (bottom-left) shows dense, complex internal structure filling most of the eggshell. The YZ view (top-right) shows multiple bright spots indicating overlapping body layers. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T92-T94.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple body segments overlapping \u2014 more than two parallel segments are apparent. The XZ view (bottom-left) shows dense, complex internal structure filling most of the eggshell. The YZ view (top-right) shows multiple bright spots indicating overlapping body layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2449,10 +2314,9 @@ "timepoint": 96, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows multiple coiled layers with a complex internal pattern characteristic of pretzel stage. The YZ view (top-right) shows a compact, densely packed structure. This matches the pretzel reference images well, with multiple folds creating overlapping signal throughout the eggshell. No sign of hatching (no worm body extending outside the eggshell). Consistent with previous observations at T93-T95.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping layers. The XZ view (bottom-left) shows the characteristic pretzel pattern with multiple body layers creating a complex bright pattern that fills most of the eggshell. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2467,10 +2331,9 @@ "timepoint": 97, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 multiple overlapping coils/body segments are visible in the XY view, with complex tangled pattern. The XZ (bottom-left) view shows bright, complex internal structure filling most of the eggshell. This matches the pretzel reference images well. The embryo remains contained within the eggshell with no sign of hatching. Consistent with previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, consistent with pretzel stage. The XZ view shows a densely packed interior with complex structure. This matches the pretzel reference images well, and the previous three timepoints were all pretzel with no clear morphological change toward hatching.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2485,10 +2348,9 @@ "timepoint": 98, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments forming a pretzel-like pattern. The eggshell is densely filled with signal, though there are some darker regions visible between coils. The XZ view shows multiple layered bands of signal consistent with several body folds. This matches the pretzel reference images well, with at least 3 body segments visible. Consistent with previous observations at T95-T97.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern characteristic of the pretzel stage. The eggshell is densely filled with signal, though some dark spaces remain at the periphery. Multiple body segments (3+) are visible overlapping each other. The XZ view shows dense, layered signal filling the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2503,10 +2365,9 @@ "timepoint": 99, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple overlapping segments filling most of the eggshell, with a complex tangled pattern. The XZ view (bottom-left) shows dense, bright signal filling the shell with visible internal structure from multiple body layers. The YZ view (top-right) shows a complex pattern with bright spots from overlapping coils. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the shell). Consistent with the previous three timepoints all classified as pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2521,10 +2382,9 @@ "timepoint": 100, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XY projection shows a complex, tangled pattern with at least 3 body segments overlapping, consistent with pretzel stage. The XZ (bottom-left) view shows dense, bright signal filling most of the eggshell with visible internal structure from multiple folds. This matches the pretzel reference images well and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The complex, tangled pattern of body segments with at least 3 folds is evident. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2539,10 +2399,9 @@ "timepoint": 101, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three timepoints classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, complex internal structure consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2557,10 +2416,9 @@ "timepoint": 102, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments forming a pretzel-like pattern. The eggshell is densely filled with fluorescent signal, with relatively little empty dark space inside the shell boundary. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern. The eggshell is densely filled with fluorescent signal - very little empty dark space remains inside the eggshell boundary. Multiple body segments (3+) are visible overlapping each other. The XZ view also shows dense, complex signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2575,10 +2433,9 @@ "timepoint": 103, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with complex tangled morphology characteristic of the pretzel stage. The eggshell is densely filled with signal, though there is some dark space at the right end. Multiple body segments (3+) are visible with overlapping loops. The XZ view shows dense, complex layered signal. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern visible. The eggshell is densely filled with signal, though some dark regions remain. Multiple body segments (3+) can be traced in the projection, consistent with pretzel stage. The YZ view shows an irregular, multi-lobed pattern also consistent with multiple folds. This matches the pretzel reference images well, and the previous three timepoints were all pretzel, consistent with the slow stage progression rule.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2593,10 +2450,9 @@ "timepoint": 104, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds. Complex tangled pattern visible in XY view with 3+ body segments. Matches pretzel reference images well. No sign of hatching (no worm extending outside eggshell). Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern with bright overlapping regions. The XZ view (bottom-left) shows complex internal structure with multiple layers. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2611,10 +2467,9 @@ "timepoint": 105, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view (bottom-left) shows bright, complex internal structure with multiple overlapping layers. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows the characteristic pretzel-stage complexity with multiple overlapping layers. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2629,10 +2484,9 @@ "timepoint": 106, "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a bilobed/figure-8 shape suggesting the worm body is beginning to extend beyond the eggshell boundary, unlike the compact elongated shape seen in pretzel references. The left lobe appears denser (eggshell region) while the right lobe shows the emerging body. However, confidence is moderate as this could still be a late pretzel with unusual morphology. The transition from pretzel to hatching is plausible at T106.", + "reasoning": "In the XY view (top-left), the embryo appears to have a bilobed or figure-8 shape, with signal extending beyond the original eggshell boundary. This is distinctly different from the pretzel stage references, where the signal remains contained within the eggshell. The appearance of two separated lobes suggests the worm is beginning to emerge from the eggshell - one lobe being the eggshell region and the other being the worm body extending outside. The previous three timepoints were pretzel, and this morphological change (signal extending beyond the eggshell boundary) is consistent with the transition to hatching.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2645,16 +2499,15 @@ }, { "timepoint": 107, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with multiple overlapping body coils visible in XY and XZ views. No clear evidence of worm emerging from or outside the eggshell. Complex tangled pattern matches pretzel references. Previous hatching call at T106 was low confidence (55%); morphology here still appears consistent with late pretzel stage.", + "reasoning": "The XY view shows the embryo densely packed within the eggshell with complex coiled morphology consistent with a late pretzel/hatching stage. The XZ (bottom-left) view shows signal extending below the main eggshell boundary, suggesting the worm is beginning to emerge. Compared to the pretzel reference, the signal appears to be spreading/extending beyond the compact eggshell shape. The previous observation was 'hatching' at T106, and the morphology here is consistent with continued hatching. The eggshell is densely filled with some signal extending beyond it.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2663,16 +2516,15 @@ }, { "timepoint": 108, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping coiled body segments (3+ folds). Complex tangled pattern in XY view with ring-like structure in XZ view matches pretzel references. No evidence of worm extending outside eggshell. Consistent with previous pretzel classification at T107.", + "reasoning": "The XY view shows the embryo body appearing to form a ring/loop shape with a dark center, suggesting the worm is beginning to emerge or has significantly rearranged within the eggshell. The YZ view shows a distinctive ring-like pattern with bright signal concentrated around the periphery and a dark center, which differs from the densely-filled pretzel pattern. This is consistent with the worm beginning to uncoil and emerge. The previous two timepoints were classified as hatching, and the morphology here continues to show this hatching pattern rather than a compact pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2681,16 +2533,15 @@ }, { "timepoint": 109, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing complex, overlapping coiled body segments visible in both XY and XZ views. Multiple body layers create a tangled pattern consistent with pretzel stage. No evidence of worm emerging from eggshell. Consistent with previous T108 pretzel classification.", + "reasoning": "The XY view shows the embryo appears to be partially emerging from the eggshell - there's a bright cluster on the left side that looks like it's extending/separating from the main body mass, consistent with the worm beginning to exit. The overall signal within the eggshell region appears less organized and less densely packed compared to the pretzel stage references, with some signal appearing to extend beyond the eggshell boundary. The previous three timepoints were all classified as hatching, and stages change slowly, so continuing as hatching is consistent.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2699,16 +2550,15 @@ }, { "timepoint": 110, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little dark/empty space inside the eggshell boundary. In the XY view (top-left), the embryo shows complex, overlapping coiled structures with multiple body segments visible - more than two parallel segments can be discerned, indicating multiple folds. The XZ view (bottom-left) shows dense, layered signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The embryo still appears to be within/emerging from the eggshell. The XY view shows a densely packed, elongated structure with complex folding patterns consistent with a late-stage embryo. The eggshell is densely filled with signal showing multiple overlapping coils. Previous three timepoints were all classified as hatching, and the morphology here is consistent with continued hatching - the embryo appears to be in the process of emerging, with the body still largely contained but showing signs of elongation/movement. No clear fully-hatched worm shape is visible outside the shell yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2717,16 +2567,15 @@ }, { "timepoint": 111, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated embryo body shows multiple folded segments creating a tangled pattern within the eggshell. The XZ view (bottom-left) shows multiple overlapping layers of signal. The YZ view (top-right) shows an irregular, multi-lobed pattern consistent with multiple body folds. This matches the pretzel reference images well, with dense eggshell filling and complex coiling. No sign of hatching (no signal outside eggshell boundary). Consistent with previous observations at T108-T110.", + "reasoning": "The embryo shows a densely filled eggshell with complex coiled body segments typical of a late pretzel/hatching stage. The YZ view (top-right) shows an irregular, non-circular shape suggesting the worm may be partially emerging or deforming the eggshell. The previous three timepoints were all classified as hatching, and stages change slowly. The morphology is consistent with continued hatching.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2735,16 +2584,15 @@ }, { "timepoint": 112, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a densely filled eggshell with complex, tangled body coils and multiple overlapping segments visible. Several bright spots (likely pharyngeal or neuronal nuclei) are scattered throughout. The XZ view shows multiple layered body segments. The eggshell is densely filled with signal, consistent with pretzel stage. This matches the pretzel reference images and is consistent with the previous three observations all being pretzel.", + "reasoning": "The embryo shows a complex, coiled morphology consistent with a late-stage worm still within or emerging from the eggshell. The XY view shows the worm body appears to be loosening/uncoiling compared to a tight pretzel, with the body appearing somewhat extended. The signal is dimmer and more spread out than a typical pretzel, suggesting the worm is in the process of hatching. Previous three timepoints were all classified as hatching, and stages change slowly, so maintaining the hatching classification is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2753,16 +2601,15 @@ }, { "timepoint": 113, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple folded segments - more than two parallel segments are apparent. The XZ view (bottom-left) shows dense, complex internal structure with multiple layers. The YZ view (top-right) shows a rounded, densely packed cross-section. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows the embryo body appearing to extend/deform beyond the typical eggshell boundary, with an irregular elongated shape that doesn't conform to the oval eggshell. The body appears to be partially emerging. The previous three timepoints were all classified as hatching, and the morphology is consistent with ongoing hatching - the worm is in the process of emerging from the eggshell. The shape is more irregular and extended compared to a pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2771,16 +2618,15 @@ }, { "timepoint": 114, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled morphology with multiple body segments folded within the eggshell - at least 3 layers of body are apparent, creating the characteristic pretzel pattern. The XZ view (bottom-left) also shows dense, complex internal structure filling most of the eggshell. This is consistent with the previous three timepoints classified as pretzel, and there is no sign of hatching (no elongated worm outside the shell).", + "reasoning": "The embryo shows a worm body that appears to be emerging/extending beyond the typical eggshell boundary. In the XY view (top-left), the body has an elongated, curved shape that extends asymmetrically, consistent with a worm beginning to emerge from the eggshell. The previous three timepoints were all classified as hatching, and the morphology here is consistent with continued hatching. The body appears to be partially outside the eggshell confines, with the overall shape no longer fitting neatly within the oval eggshell boundary.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2789,16 +2635,15 @@ }, { "timepoint": 115, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, elongated structure with multiple parallel body segments and overlapping layers filling most of the eggshell. The XZ view (bottom-left) shows a dense, complex pattern with multiple bright bands consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", + "reasoning": "The embryo shows a densely packed, elongated worm body within the eggshell with multiple coiled segments visible, consistent with a late pretzel/hatching stage. The XY view shows the worm body appearing to be organized along the length of the eggshell with visible body segments. The eggshell is densely filled. Given that the previous three timepoints were all classified as hatching, and the morphology still shows the worm contained within or emerging from the eggshell (no clear fully extended worm outside the shell), this remains consistent with the hatching stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2807,16 +2652,15 @@ }, { "timepoint": 116, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view (bottom-left) shows dense, bright signal filling the shell with complex internal structure. The YZ view (top-right) shows an irregular, multi-lobed pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The XY view shows an elongated worm shape that appears to be extending beyond the original eggshell boundary, with the body becoming more stretched out and less compact than a pretzel stage. The YZ view shows an irregular, non-oval shape suggesting the worm is partially emerging. Previous three timepoints were all classified as hatching, and the morphology is consistent with continued hatching - the worm is in the process of emerging from the eggshell.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2825,16 +2669,15 @@ }, { "timepoint": 117, - "predicted_stage": "pretzel", + "predicted_stage": "hatching", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows a complex, elongated pattern with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a complex, tangled pattern with bright overlapping coils consistent with 3+ folds. This matches the pretzel reference images well. The YZ view (top-right) also shows a densely packed, complex signal pattern. No evidence of hatching (no worm body extending outside the eggshell). Consistent with previous three observations of pretzel stage.", + "reasoning": "The embryo still appears to be within/emerging from the eggshell. The XY view shows a densely filled eggshell with complex coiled structure typical of a late pretzel/hatching stage. The eggshell is densely packed with signal showing multiple overlapping body segments. Previous three observations were all 'hatching', and the morphology is consistent with continued hatching - the worm appears to be in the process of emerging, with the body still largely contained within the eggshell boundary. No clear elongated worm shape fully outside the shell is visible yet, so it hasn't fully hatched.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2843,17 +2686,16 @@ }, { "timepoint": 118, - "predicted_stage": "pretzel", + "predicted_stage": "early", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body shows a complex, elongated pattern with multiple body segments creating overlapping layers. The YZ view (top-right) shows a ring-like or coiled pattern characteristic of pretzel stage. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell with visible internal structure from multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "Error: Error code: 429 - {'type': 'error', 'error': {'type': 'rate_limit_error', 'message': \"This request would exceed your organization's rate limit of 250,000,000 input tokens per minute (org: 88de94f7-8772-4d0b-8ac8-46ad57a86a44, model: claude-opus-4-6, model_group: claude_opus_4_5, qos: -5). For details, refer to: https://docs.claude.com/en/api/rate-limits. You can see the response headers for current usage. Please reduce the prompt length or the maximum tokens requested, or try again later. You may also contact sales at https://claude.com/contact-sales to discuss your options for a rate limit increase.\"}, 'request_id': 'req_011CaK4L8QTnb5FTeRzixvzH'}", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, + "is_correct": false, + "is_adjacent_correct": false, "verification_triggered": false, "phase_count": 1, "verification_result": null, @@ -2863,10 +2705,9 @@ "timepoint": 119, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, complex internal structure consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping body segments. Multiple folds are visible in both XY and XZ views. The fill fraction is high with little empty dark space inside the eggshell, matching pretzel reference images. The previous 'early' classification at T118 appears to have been an error - this is clearly a late-stage embryo with multiple body folds.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2881,10 +2722,9 @@ "timepoint": 120, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex internal structure with multiple body layers creating a tangled pattern. The YZ view shows a compact, filled cross-section. This matches the pretzel reference images well, with multiple folded body segments filling most of the eggshell. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo shows complex, overlapping coiled structures with multiple body segments visible, consistent with 3+ folds. The XZ view (bottom-left) shows a complex pattern with multiple overlapping layers creating a tangled appearance. This matches the pretzel reference images well, with the dense fill fraction and multiple coils being the key discriminators. The previous observation was also pretzel, and stages change slowly, supporting this classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2899,10 +2739,9 @@ "timepoint": 121, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments folded within the eggshell, consistent with pretzel stage. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel.", + "reasoning": "The XY view shows an elongated embryo with complex, overlapping coiled body segments filling most of the eggshell. Multiple parallel body segments are visible, consistent with 3+ folds. The eggshell is densely filled with signal. The XZ view shows a complex pattern with multiple overlapping layers. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2917,10 +2756,9 @@ "timepoint": 122, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows complex, overlapping coiled structures filling most of the elongated eggshell, with multiple body segments visible. The XZ view (bottom-left) shows a densely packed pattern with overlapping layers. This matches the pretzel reference images well, showing multiple folded body segments creating a complex tangled pattern. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments filling the elongated eggshell, with complex internal structure visible. The XZ view (bottom-left) also shows dense, layered signal consistent with multiple body folds. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no worm extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2932,10 +2770,10 @@ "candidate_stages": null } ], - "duration_seconds": 926.5043907165527, + "duration_seconds": 822.9110968112946, "error": null, - "accuracy": 0.9358974358974359, - "adjacent_accuracy": 1.0 + "accuracy": 0.7948717948717948, + "adjacent_accuracy": 0.9871794871794872 }, { "embryo_id": "embryo_3", @@ -2944,10 +2782,9 @@ "timepoint": 39, "predicted_stage": "comma", "ground_truth_stage": "1.5fold", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo shows elongated curved/comma shape in XY view without clear fold-back or parallel body segments. Eggshell has some empty space but body hasn't begun folding. Morphology matches comma references well. Previous 3 timepoints were comma, and no clear transition to 1.5fold is visible yet.", + "reasoning": "The XY view shows an elongated embryo with a curved body shape and some dark space within the eggshell, consistent with comma stage. The body shows one curved band of nuclei with a constriction/indentation visible, but no clear parallel folded segments yet. The eggshell is not sparsely filled enough for early 1.5fold - there's still substantial signal but with some empty regions. Comparing to references, this matches the comma examples (T40-T44) very well. The previous three timepoints were all comma, and there's no clear morphological change to 1.5fold yet (no J-shape or hairpin visible).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2962,10 +2799,9 @@ "timepoint": 40, "predicted_stage": "comma", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo is elongated with curvature but no clear fold-back or J-shape visible yet. Eggshell fill is sparse. Morphology is very similar to comma reference at T40. Previous three timepoints were comma, and while the embryo may be approaching 1.5fold transition, no definitive folding is visible. Defaulting to earlier stage.", + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but hasn't yet formed a clear fold-back. The eggshell still has significant empty/dark space, particularly at the edges. The body occupies a moderate fraction of the eggshell but doesn't show two parallel segments characteristic of 1.5fold. Comparing to references, this matches the comma stage examples well - the body is curved and elongating but not yet folding back on itself. The previous three timepoints were all comma, and there's no clear morphological change to indicate progression to 1.5fold yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2978,16 +2814,15 @@ }, { "timepoint": 41, - "predicted_stage": "1.5fold", + "predicted_stage": "comma", "ground_truth_stage": "1.5fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo body has elongated significantly compared to comma references and shows early J-shaped folding. The eggshell is sparsely filled with notable dark space remaining, consistent with 1.5fold. The decreasing confidence in comma classification over previous timepoints supports a transition. However, the fold is still subtle, placing this at the very beginning of 1.5fold.", + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but still occupies a relatively small fraction of the eggshell interior - there is significant dark space around the embryo, especially at the ends. The body shows one curved band of nuclei without clear parallel segments or folding back on itself. Compared to the 1.5fold reference, this image lacks the more elongated J-shape and the body hasn't started folding back yet. The morphology is consistent with the comma reference images, showing the characteristic C-shaped curvature. The eggshell fill fraction is still sparse but not yet showing the elongation pattern of 1.5fold. Given the previous three observations were all comma and stages change slowly, maintaining comma classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2998,10 +2833,9 @@ "timepoint": 42, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "The embryo body has elongated and begun folding within the eggshell. The XZ view shows two somewhat distinct bright regions suggesting early folding. The eggshell is sparsely to moderately filled, consistent with 1.5fold. Not yet showing the clear two parallel segments of 2fold. Consistent with progression from comma at T39-40 to 1.5fold at T41-42.", + "reasoning": "The embryo has clearly elongated beyond comma stage \u2014 the body now extends along the full length of the eggshell with an elongated oval shape. The eggshell is sparsely to moderately filled. The XZ view shows early folding organization. This matches 1.5fold references better than comma, which shows a more compact C-shaped body occupying less of the eggshell.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3016,10 +2850,9 @@ "timepoint": 43, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated embryo body with partial folding visible in XY view. Eggshell is sparsely filled with significant dark space remaining. Body shows J-shape/partial fold rather than clear two parallel segments. Matches 1.5fold reference images well. Consistent with previous 1.5fold classification at T42.", + "reasoning": "The XY view shows an elongated embryo body within the eggshell with the signal concentrated but not yet filling the entire shell - there is still notable dark space, especially at the edges. The body appears to be forming a J-shape or partial fold, consistent with 1.5fold. Compared to the 1.5fold reference images, the fill fraction is sparse (significant empty space within the eggshell), and I don't see two clear parallel body segments that would indicate 2fold. The morphology is very similar to the previous timepoint (T42), and since stages change slowly, maintaining 1.5fold is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3034,10 +2867,9 @@ "timepoint": 44, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated body with partial folding visible in XY view. Eggshell is sparsely to moderately filled with significant dark space remaining. XZ view shows early signs of body layering but not yet the clear two-parallel-segment hairpin of 2fold. Consistent with previous 1.5fold observations and matches 1.5fold reference images.", + "reasoning": "Eggshell is sparsely to moderately filled with signal, consistent with 1.5fold. The embryo body shows early folding but not yet two clearly parallel segments characteristic of 2fold. Matches 1.5fold reference images well. Previous timepoint was also 1.5fold, and no clear morphological advancement is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3052,10 +2884,9 @@ "timepoint": 45, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "Elongated body with J-shaped/partial fold morphology visible in XY view. Eggshell fill is sparse to moderate with dark space remaining. No clear two-parallel-segment hairpin pattern yet. Consistent with 1.5fold reference images and previous three timepoints classified as 1.5fold.", + "reasoning": "The XY view shows an elongated embryo with a clear constriction/narrowing creating a J-like or partial hairpin shape, with the body curving but not yet forming two fully parallel segments. The eggshell is still sparsely filled - there is significant dark space within the eggshell boundary, particularly at the bottom/ventral side. The fill fraction is not yet moderate enough for 2fold. Comparing to references, this matches the 1.5fold examples (T47-T57) well, with the body beginning to fold but not yet showing the clear two parallel segments characteristic of 2fold. Previous observations were all 1.5fold, and there's no clear morphological change to warrant advancing the stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3070,10 +2901,9 @@ "timepoint": 46, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo body shows elongation with beginning of fold-back (J-shape), but not yet a clear hairpin with two parallel segments. Eggshell is sparsely filled with significant dark space remaining. Matches 1.5fold references well. Consistent with previous three observations at 1.5fold, no clear morphological change to 2fold yet.", + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear fold/bend - there's a larger mass on the left connected to a smaller lobe on the right, forming a J-shape or partial hairpin. The eggshell is still sparsely filled - there's significant dark space around and below the embryo body, particularly visible in the XZ view (bottom-left) where the signal doesn't fill the full eggshell extent. I can see one main curved body with a partial fold back, but not yet two clearly parallel segments characteristic of 2fold. The morphology closely matches the 1.5fold reference images. Previous observations were all 1.5fold, and stages change slowly, so maintaining 1.5fold classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3088,10 +2918,9 @@ "timepoint": 47, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is sparsely filled with significant dark space remaining. The embryo body shows an elongated shape with partial folding (J-shape) but not yet a clear two-parallel-segment hairpin. Matches 1.5fold reference images well. Consistent with previous three observations at 1.5fold.", + "reasoning": "In the XY view, the embryo shows an elongated body that fills the eggshell but with a visible curved/folded structure - there's a clear arc of nuclei with the beginning of a fold-back, but not yet two distinct parallel segments. The eggshell is sparsely to moderately filled - there's still noticeable dark space, particularly at the edges. The XZ view shows the body concentrated but not yet forming the clear double-layered pattern seen in 2fold references. This matches the 1.5fold reference images well, and is consistent with the previous three observations at 1.5fold. No clear morphological change to 2fold is evident yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3106,10 +2935,9 @@ "timepoint": 48, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell fill fraction is moderate but still shows dark spaces, consistent with late 1.5fold. The body is elongated and beginning to show folding structure but clear parallel two-fold segments are not yet definitively visible. Matches late 1.5fold reference (T57). Previous three timepoints were 1.5fold; defaulting to earlier stage given uncertainty.", + "reasoning": "The XY view shows the embryo filling most of the eggshell length but with some dark space remaining, particularly on the right side where the signal is dimmer/sparser. The eggshell fill is moderate but not yet dense. In the XZ (bottom-left) view, I can see bright signal with some internal structure suggesting folding has begun, but the pattern is not yet showing clear two parallel segments as in the 2fold references. The overall appearance is consistent with the 1.5fold reference images - the embryo is elongating and beginning to fold but hasn't completed a full hairpin. Given the previous three observations were all 1.5fold and stages change slowly, and the morphology doesn't show a clear advancement to 2fold (no obvious two parallel body segments), this remains 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3124,10 +2952,9 @@ "timepoint": 49, "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "Two-lobed appearance in XY with constriction between them suggests partial folding. Eggshell is sparsely filled with significant dark space remaining. The fold appears incomplete - not yet showing two clearly parallel body segments characteristic of 2fold. Consistent with previous 1.5fold observations and reference images.", + "reasoning": "Eggshell is sparsely filled with significant dark space. XY view shows two lobes with a constriction suggesting a partial fold/J-shape, but not yet a complete U-shaped hairpin with two fully parallel segments. Consistent with 1.5fold reference images and previous three timepoints classified as 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3142,10 +2969,9 @@ "timepoint": 50, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo shows elongated curved body with partial fold in XY view, consistent with 1.5fold. Eggshell fill is sparse to moderate with significant dark space remaining. No clear two-parallel-segment hairpin visible yet. Matches 1.5fold references well and is consistent with previous three timepoints.", + "reasoning": "In the XY view (top-left), the embryo shows a curved, elongated shape with a J-like or partial fold morphology. The body curves from upper-left and bends back toward the lower-right, but I don't see two clearly parallel segments forming a complete hairpin/U-shape as in the 2fold references. The eggshell is still sparsely filled \u2014 there is significant dark space within the eggshell boundary, particularly at the bottom-right of the XY view. The XZ view (bottom-left) shows some structure but not the clear layered parallel bands seen in 2fold references. This matches the 1.5fold reference images well, and is consistent with the previous three observations of 1.5fold. No clear morphological change to 2fold is evident yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3160,10 +2986,9 @@ "timepoint": 51, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows J-shaped curved body with significant dark space remaining in eggshell (sparse fill). XZ view shows two separated bright lobes consistent with partial folding. No complete hairpin/U-shape visible yet. Matches 1.5fold references well. Consistent with previous three observations at 1.5fold.", + "reasoning": "The embryo shows a curved, partially folded body with a J-shape morphology in the XY view. The eggshell is sparsely to moderately filled with significant dark space remaining. No clear two-parallel-segment hairpin is visible yet. Consistent with 1.5fold references and previous three timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3178,10 +3003,9 @@ "timepoint": 52, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is sparsely to moderately filled with signal. The embryo body is elongated with hints of early folding (darker central region in XY, two-layer appearance in XZ), but two clearly distinct parallel body segments are not yet visible. Matches 1.5fold reference images well. Consistent with previous three timepoints classified as 1.5fold.", + "reasoning": "The eggshell is still sparsely filled - there is notable dark space within the eggshell boundary, particularly visible in the XY view where a dark region/gap is apparent in the center-right area. The embryo body shows elongation consistent with 1.5fold. I can see what appears to be one main curved body with a partial fold beginning, but not yet two clear parallel segments that would indicate 2fold. The fill fraction is sparse to moderate, more consistent with 1.5fold than 2fold. This matches well with the 1.5fold reference images (especially T52 in the reference series). Previous three timepoints were all 1.5fold, and no clear morphological advancement to 2fold is evident.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3196,10 +3020,9 @@ "timepoint": 53, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "Embryo shows moderate eggshell filling with some dark space remaining. XY view shows elongated body with a constriction suggesting early folding, but not yet a clear two-parallel-segment hairpin characteristic of 2fold. Transitional between 1.5fold and 2fold; defaulting to earlier stage given uncertainty and consistency with previous observations.", + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with a constriction/fold visible, consistent with a body that has begun folding back on itself. The eggshell is still sparsely filled - there is notable dark space within the eggshell boundary, particularly at the edges. I can see what appears to be one main curved body with a partial fold-back, but not yet two clearly parallel segments characteristic of 2fold. The XZ view (bottom-left) shows a moderately filled but not dense pattern. This matches the 1.5fold reference images well, and is consistent with the previous three observations all being 1.5fold. No clear morphological change to 2fold is evident yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3214,10 +3037,9 @@ "timepoint": 54, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two lobes forming a hairpin-like structure suggesting the embryo is folding, but eggshell still has significant dark space (sparse-to-moderate fill). The morphology is transitioning from 1.5fold toward 2fold - the fold is more pronounced than typical 1.5fold but the fill fraction and previous observations at 1.5fold suggest staying with the earlier classification. Close to 2fold boundary.", + "reasoning": "The XY view shows two body lobes beginning to form a hairpin, suggesting transition toward 2fold. However, significant dark space remains in the eggshell (sparse-to-moderate fill), and the previous 3 timepoints were all 1.5fold. The morphology is late 1.5fold, not yet clearly 2fold. Defaulting to earlier stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3232,10 +3054,9 @@ "timepoint": 55, "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell still sparsely to moderately filled with notable dark space remaining. Body shows folding but two distinct parallel segments are not yet clearly resolved. Morphology matches late 1.5fold references. Transitional toward 2fold but not clearly there yet - defaulting to earlier stage given uncertainty.", + "reasoning": "The XY view shows an elongated embryo body that is beginning to fold, with the signal occupying a moderate portion of the eggshell but still leaving significant dark space, particularly at the periphery. The eggshell fill is sparse to moderate - not yet densely filled. In the XZ (bottom-left) view, I can see what appears to be a partial fold beginning but not yet two clearly parallel segments connected by a hairpin bend. The morphology closely matches the 1.5fold reference images (e.g., T52/T57). There's no clear evidence of two fully parallel body segments (which would indicate 2fold), and the eggshell still has considerable empty space. Given the previous three observations were all 1.5fold and stages change slowly, this remains 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3248,16 +3069,15 @@ }, { "timepoint": 56, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two roughly parallel body segments with a bend, and moderate eggshell filling - more than 1.5fold references but less than pretzel. The embryo body appears to form a hairpin/U-shape. Transitioning from 1.5fold, the increased fill fraction and emerging parallel segments suggest early 2fold, though confidence is moderate as this is at the boundary.", + "reasoning": "Eggshell is still sparsely filled with significant dark space inside the shell boundary. The body shows an elongated curved shape with a partial fold (J-shape) but not yet a clear two-parallel-segment hairpin characteristic of 2fold. Matches late 1.5fold references. Consistent with previous three observations at 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3266,16 +3086,15 @@ }, { "timepoint": 57, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with some dark space remaining. XY view shows elongated body with evidence of two parallel segments from folding. XZ view shows layered signal consistent with hairpin/U-shape fold. Matches 2fold references better than 1.5fold (more filled) or pretzel (not yet densely packed). Consistent with previous T56 classification of 2fold.", + "reasoning": "The XZ view shows hints of two parallel body segments forming, and the eggshell fill is moderate. However, the fill fraction is still relatively sparse with significant dark space remaining, and previous three timepoints were all 1.5fold. The morphology is transitional between 1.5fold and 2fold, so following the rule to prefer the earlier stage when uncertain, I classify as late 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3284,16 +3103,15 @@ }, { "timepoint": 58, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.6, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two parallel body segments visible in XY and XZ views, consistent with 2fold hairpin morphology. Matches 2fold reference images. More filled than 1.5fold but lacks the dense overlapping coils of pretzel. Consistent with previous 2fold classifications at T56-T57.", + "reasoning": "Eggshell fill is still relatively sparse with dark space remaining. While there are hints of a second parallel body segment forming, the pattern is not yet as clearly defined as the 2fold references. Morphology is transitional between late 1.5fold and early 2fold. Following the rule to prefer the earlier stage when uncertain and given continuity with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3302,16 +3120,15 @@ }, { "timepoint": 59, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "2fold", - "confidence": 0.65, "is_transitional": false, "transition_between": null, - "reasoning": "Two distinct body segment lobes visible in XY view forming a hairpin/U-shape. Moderate eggshell fill fraction with visible dark spaces between segments. Matches 2fold references well. No evidence of third fold or dense filling that would indicate pretzel. Consistent with previous 2fold classifications at T56-T58.", + "reasoning": "The XY view shows two lobes forming with a constriction, suggesting the embryo is transitioning toward 2fold. However, the eggshell still has significant dark space (sparse-to-moderate fill), and the previous three timepoints were all 1.5fold. The two-segment appearance is emerging but not yet as clearly defined as the 2fold references. Following the rule to prefer the earlier stage when at a transition, I classify as late 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3322,10 +3139,9 @@ "timepoint": 60, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two parallel body segments with moderate eggshell fill. YZ view shows ring-like pattern consistent with folded body seen end-on. Matches 2fold reference images well. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T57-T59.", + "reasoning": "The YZ view shows a distinctive ring/donut pattern with a dark center, indicating two parallel body segments viewed end-on - characteristic of 2fold. The XY view shows moderate eggshell filling with two discernible parallel bands. This represents a clear morphological change from the previous 1.5fold observations, matching the 2fold reference images.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3340,10 +3156,9 @@ "timepoint": 61, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark space remaining, consistent with 2fold. Two parallel body segments visible in XY view with a folded structure. Not yet densely filled enough for pretzel. Consistent with previous three observations of 2fold.", + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear elongated shape with what appears to be two parallel body segments - a brighter band along the top/dorsal side and signal along the ventral side, with a darker region/gap in between, consistent with a hairpin/U-fold structure. The eggshell is moderately filled - there's some dark space remaining but less than in the 1.5fold references. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two parallel segments. Previous observation was 2fold at T60, and this is consistent with continuing at 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3358,10 +3173,9 @@ "timepoint": 62, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark spaces remain but the body is clearly folded. The XZ view shows what appears to be two parallel body segments with bright signal bands. The fill fraction is moderate (not densely packed like pretzel), consistent with 2fold. This matches the 2fold reference images well. The previous three timepoints were all 2fold, and there's no clear transition to the more densely filled pretzel stage yet.", + "reasoning": "The eggshell is moderately filled with signal - there's some dark space remaining but the embryo occupies a substantial portion. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a hairpin/U-fold pattern. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous observations were 2fold, so maintaining this classification is appropriate.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3376,10 +3190,9 @@ "timepoint": 63, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with visible dark space remaining, two parallel body segments visible in XY and XZ views forming a hairpin structure. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous observations at T60-T62.", + "reasoning": "The XY view shows an elongated embryo with the body folded into roughly two parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining (particularly at the edges/poles), but not densely packed like pretzel. The XZ view shows layered signal but not the complex overlapping coils characteristic of pretzel. The fill fraction is moderate, matching 2fold references. Previous three timepoints were all 2fold, and there's no clear transition to pretzel yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3394,10 +3207,9 @@ "timepoint": 64, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.78, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows elongated embryo with two parallel body segments forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, consistent with 2fold. Not yet showing the dense multi-coil pattern of pretzel. Consistent with previous three timepoints classified as 2fold.", + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, with a visible dark region/gap between them. The eggshell is moderately filled - there's still some dark space visible, particularly at the edges, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows a complex but not yet fully coiled pattern. Comparing to references, this matches the 2fold stage (T62-T75 range) rather than pretzel, which would show denser filling and more overlapping coils. The previous three observations were all 2fold, and while the embryo is progressing, there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3412,10 +3224,9 @@ "timepoint": 65, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments forming a hairpin/U-shape. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous observations at T62-T64.", + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows layered bright bands consistent with two folded segments. Compared to the 2fold reference images, this matches well. The fill fraction is not yet dense enough for pretzel (still visible dark regions within the eggshell boundary). Previous three timepoints were all 2fold, and there's no clear transition to pretzel-level complexity or density yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3430,10 +3241,9 @@ "timepoint": 66, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal showing increasing complexity and multiple layers visible in XZ projection. More filled than typical 2fold but not yet densely packed like pretzel references. Previous 3 timepoints were 2fold; following the rule to prefer earlier stage when uncertain. Transitional between 2fold and pretzel.", + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo is filling more of the shell than in 1.5fold. In the XY view, I can see what appears to be two parallel body segments with some internal structure/folding visible. The XZ (bottom-left) view shows layered bright bands consistent with a folded body. The fill fraction is moderate - not yet densely packed like pretzel references. This matches well with the 2fold reference images (e.g., T68). Previous observations were all 2fold, and the morphology is consistent with continuing in this stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3448,10 +3258,9 @@ "timepoint": 67, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "In the XY view, the embryo shows a clear folded morphology with two main body segments visible - a brighter dense region on the left and a more diffuse curved region on the right, forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows complex layered structure consistent with 2fold. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well, and is consistent with the previous observations at T64-T66 all being 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling) is evident yet.", + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear folded structure with two parallel segments visible - a bright curved band on the left side and another segment on the right, connected by a bend. The eggshell is moderately filled - there is some dark space remaining within the eggshell boundary but not densely packed like a pretzel. The XZ view (bottom-left) shows a moderately filled pattern with some layering but not the complex overlapping coils characteristic of pretzel stage. This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. No clear transition to pretzel is evident yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3466,10 +3275,9 @@ "timepoint": 68, "predicted_stage": "2fold", "ground_truth_stage": "2fold", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows a clear hairpin/U-shaped body with two parallel segments connected by a bend. Eggshell is moderately filled with some dark space remaining. Matches 2fold references well. Not yet densely filled enough or showing the multiple overlapping coils characteristic of pretzel. Consistent with previous 2fold observations at T65-T67.", + "reasoning": "XY view shows a clear hairpin/U-shaped fold with two parallel body segments connected by a bend. Eggshell is moderately filled with some dark space remaining, not yet densely packed like pretzel. Consistent with previous 2fold classifications at T65-T67. While complexity is increasing, the pattern doesn't yet show the multiple overlapping coils characteristic of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3484,10 +3292,9 @@ "timepoint": 69, "predicted_stage": "2fold", "ground_truth_stage": "pretzel", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Two parallel body segments visible in XY view with a clear midline constriction indicating a hairpin fold. Moderate eggshell fill fraction with some dark space remaining. Matches 2fold reference images well. Consistent with previous three observations of 2fold. Not yet showing the dense, multi-layered complexity of pretzel stage.", + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold rather than pretzel. The XZ view shows layered bright bands consistent with two parallel body segments. This matches the 2fold reference images well. No evidence of the dense, complex multi-coil pattern characteristic of pretzel stage. Previous three timepoints were all 2fold, and morphology hasn't changed significantly.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3502,10 +3309,9 @@ "timepoint": 70, "predicted_stage": "2fold", "ground_truth_stage": "pretzel", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "XY view shows two parallel body segments in a hairpin/U-shape configuration with moderate eggshell filling. Some dark space remains inside the shell. The XZ view shows complex layering but not yet the dense multi-coil pattern characteristic of pretzel. Consistent with late 2fold stage and matches previous observations at T67-T69. Approaching pretzel transition but not clearly there yet.", + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear folded structure with two parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows the body extending with visible folding/layering. Compared to the pretzel reference, the eggshell is not yet densely filled and the pattern is not as complex/tangled. The morphology is consistent with the 2fold reference images and matches the previous three observations of 2fold. No clear transition to pretzel is evident yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3520,10 +3326,9 @@ "timepoint": 71, "predicted_stage": "2fold", "ground_truth_stage": "pretzel", - "confidence": 0.8, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark space remaining, two parallel body segments visible in XY and XZ views forming a hairpin pattern. Matches 2fold references well. No evidence of three or more overlapping coils that would indicate pretzel. Consistent with previous three timepoints classified as 2fold.", + "reasoning": "Moderate eggshell fill fraction with some dark space remaining, two parallel body segments visible in XY view forming a hairpin pattern, consistent with 2fold references. Not yet densely packed enough for pretzel. Continuous with previous 2fold classifications at T68-T70.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3536,16 +3341,15 @@ }, { "timepoint": 72, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark spaces remaining. Multiple body segments visible suggesting complex folding, but not yet densely packed enough for pretzel. The pattern is more complex than clean 2fold references, suggesting late 2fold transitioning toward pretzel. Maintaining 2fold classification consistent with previous timepoints, as the change to pretzel is not yet definitive.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 there is very little dark/empty space inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex, tangled pattern with nuclei distributed throughout most of the eggshell interior. The YZ view (top-right) also shows signal spread across most of the cross-section. This is distinctly more filled than the 2fold reference images, which show moderate fill with clear dark spaces. The pattern shows more than two parallel body segments, indicating multiple folds. Compared to the pretzel reference images, this matches well \u2014 the body has folded 3+ times creating overlapping coils. While previous timepoints were classified as 2fold, the morphology here has clearly progressed to pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3554,16 +3358,15 @@ }, { "timepoint": 73, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell filling with two visible parallel body segments in XY and XZ views. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T70-T72.", + "reasoning": "The eggshell is moderately to densely filled with signal. The XZ view shows multiple layered bright bands suggesting more than two parallel body segments. Previous timepoint was pretzel, and the morphology is consistent with early pretzel stage - more complex folding than a simple 2fold hairpin, with increasing fill of the eggshell.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3572,16 +3375,15 @@ }, { "timepoint": 74, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with some dark spaces remaining. XY view shows folded body with approximately two parallel segments visible, though complexity is increasing. XZ view shows multiple bright bands. Compared to references, this matches late 2fold (T75). Approaching pretzel but fill fraction not yet dense enough. Maintaining 2fold consistent with previous observations.", + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows complex, overlapping coils of the body filling most of the eggshell interior with relatively little dark space. Multiple body segments are visible creating a tangled/complex pattern rather than a simple hairpin (2fold). The XZ view shows multiple bright bands/layers stacked vertically, consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous two observations at T72-T73 being pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3590,16 +3392,15 @@ }, { "timepoint": 75, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal but still has some dark space, consistent with 2fold. The body shows organized segments but not yet the dense multi-coiled pattern of pretzel. XZ view shows moderate complexity. Consistent with previous 2fold classifications at T72-T74, though approaching the transition to pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo fills most of the eggshell with a complex, overlapping pattern of nuclei. The XZ view (bottom-left) shows multiple overlapping body segments creating a complex, tangled pattern consistent with 3+ folds. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3608,16 +3409,15 @@ }, { "timepoint": 76, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.55, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal but not yet densely packed. Two parallel body segments visible in XY view forming a hairpin shape. No clear evidence of 3+ overlapping coils characteristic of pretzel. Matches late 2fold reference (T75) better than pretzel reference. Previous observations were 2fold, and morphology has not clearly transitioned to pretzel yet.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. The XZ (bottom-left) view shows multiple layered body segments with a tangled pattern. This matches the pretzel reference images well, with the body folded three or more times creating overlapping coils. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3626,16 +3426,15 @@ }, { "timepoint": 77, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.5, "is_transitional": false, "transition_between": null, - "reasoning": "Moderate eggshell fill with visible parallel body segments and some internal dark space remaining. The pattern shows approximately two parallel body segments consistent with 2fold. Not yet densely filled enough for pretzel - still some dark regions within the eggshell. Consistent with previous 2fold observations at T74-T76, though approaching the transition to pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body occupying most of the eggshell interior with multiple overlapping coils visible. The XZ (bottom-left) view shows complex layered structure with multiple bright bands, consistent with 3+ folds. The YZ view (top-right) shows bright, complex signal filling the cross-section. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3646,10 +3445,9 @@ "timepoint": 78, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.45, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is becoming densely filled with signal. In the XY view, the body shows a looping/wrapping pattern that is more complex than a simple two-segment hairpin - signal traces around the periphery with emerging multi-fold structure. The fill fraction has increased compared to typical 2fold references. The XZ view shows multiple bright bands suggesting overlapping body segments. While borderline, the increasing complexity and fill suggest early pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments filling most of the eggshell interior with at least 3 parallel/overlapping body segments visible. The XZ view (bottom-left) shows multiple bright layers stacked vertically, consistent with multiple folds. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3664,10 +3462,9 @@ "timepoint": 79, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.72, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a ring/loop pattern with the body wrapping around the eggshell periphery and a dark center, indicating multiple folds (3+). The eggshell is densely filled with signal. The YZ view shows a ring-like cross-section. This matches pretzel reference images better than 2fold, which would show a simpler U-shape with more empty space. Consistent with T78 pretzel classification.", + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments forming a complex looping pattern with a dark region in the center, consistent with a pretzel-stage embryo with 3+ folds. The YZ view (top-right) shows a ring-like pattern indicating coiled body segments. The XZ view (bottom-left) is also densely filled. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3682,10 +3479,9 @@ "timepoint": 80, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.7, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is moderately to densely filled with signal, showing multiple overlapping body segments visible in both XY and XZ views. The complex folding pattern with more than 2 parallel segments and the fill fraction match the early pretzel reference images (T82). Consistent with previous T79 pretzel classification.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex folding with more than two parallel segments, creating a tangled appearance. The XZ view shows multiple layers of signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No signs of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3700,10 +3496,9 @@ "timepoint": 81, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.75, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space inside. Multiple overlapping body segments visible in XY view creating a complex pattern. XZ view shows layered bright bands suggesting multiple folds. Consistent with pretzel reference images and with previous observations at T78-T80.", + "reasoning": "The eggshell is densely filled with fluorescent signal - the embryo body occupies most of the eggshell interior with relatively little dark space remaining. In the XY view (top-left), I can see multiple overlapping body segments creating a complex pattern with at least 3 parallel/overlapping bands of nuclei visible. The XZ view (bottom-left) also shows complex layered structure consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3718,10 +3513,9 @@ "timepoint": 82, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.85, "is_transitional": false, "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds. Complex tangled pattern visible in XY view with at least 3 body segments. Matches pretzel reference images well. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3736,10 +3530,9 @@ "timepoint": 83, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the embryo body shows multiple overlapping coils/segments filling most of the eggshell, with a complex tangled pattern of nuclei. The XZ view (bottom-left) shows bright, densely packed signal with multiple layers visible. This matches the pretzel reference images well, where 3+ folds create overlapping body segments. The fill fraction is high (dense), consistent with pretzel stage rather than 2fold (which would have more empty space). Previous observations at T80-T82 were all pretzel, and no morphological change toward hatching is evident.", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the embryo shows complex, overlapping coils of nuclei filling most of the eggshell, with multiple body segments visible. The XZ view (bottom-left) also shows dense, layered signal consistent with multiple folds. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3754,10 +3547,9 @@ "timepoint": 84, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.88, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows the embryo densely filling the eggshell with multiple overlapping body segments visible - I can see at least 3 folded layers creating a complex coiled pattern. The eggshell is densely filled with signal, with relatively little empty dark space inside the shell boundary. The XZ view shows multiple distinct bright layers/bands stacked, consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows the embryo densely filling the eggshell with multiple overlapping coils visible - I can see at least 3 body segments creating a complex folded pattern. The eggshell is densely filled with signal, with very little empty dark space inside the boundary. The XZ view shows multiple layered body segments. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3772,10 +3564,9 @@ "timepoint": 85, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible - at least 3 parallel tracks can be discerned. There is relatively little dark empty space within the eggshell boundary. The XZ view shows complex, layered signal consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, I can see complex, tangled body segments with at least 3 parallel tracks of nuclei, consistent with multiple folds. The XZ view shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3790,10 +3581,9 @@ "timepoint": 86, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all classified as pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3808,10 +3598,9 @@ "timepoint": 87, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.9, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view shows bright, complex layered structure. This matches the pretzel reference images well and is consistent with the previous three observations all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex layered structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3826,10 +3615,9 @@ "timepoint": 88, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with a complex, tangled pattern of multiple overlapping body segments. The XZ view (bottom-left) shows multiple bright layers/bands consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No signs of hatching (no signal outside the eggshell boundary).", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 the body occupies most of the eggshell interior with complex, overlapping coils visible. In the XY view (top-left), the signal fills the elongated eggshell shape with multiple overlapping body segments creating a tangled pattern. The XZ view (bottom-left) shows complex internal structure with multiple bright layers. This matches the pretzel reference images well, showing 3+ folds within the eggshell. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3844,10 +3632,9 @@ "timepoint": 89, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows a densely filled eggshell with multiple overlapping coils/body segments visible - at least 3 parallel segments can be discerned, creating a complex tangled pattern. The eggshell is densely filled with fluorescent signal with relatively little empty dark space inside. The XZ view shows complex folded structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The XY view shows an elongated embryo with multiple overlapping coils/body segments visible within the eggshell - at least 3 parallel segments can be discerned. The eggshell is densely filled with signal, though some dark gaps remain between the coiled body segments. The XZ view shows a complex, multi-layered pattern consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3862,10 +3649,9 @@ "timepoint": 90, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.92, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows multiple bright layers/bands indicating overlapping body folds. This matches the pretzel reference images well, with dense fill and complex coiling. No sign of hatching (no elongated worm outside the shell). Consistent with previous observations at T87-T89.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments folded within the eggshell. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. This matches the pretzel reference images well, with 3+ folds creating overlapping body segments. Consistent with previous observations at T87-T89.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3880,10 +3666,9 @@ "timepoint": 91, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the embryo body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The YZ view shows complex internal structure with multiple bright regions. The XZ view shows dense, layered signal filling the shell. This matches the pretzel reference images well, with multiple body folds creating the characteristic dense, complex pattern. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping patterns of nuclei visible throughout. In the XY view (top-left), the signal fills most of the elongated eggshell with multiple overlapping body segments creating a complex, tangled appearance. The YZ view (top-right) shows multiple bright clusters distributed throughout, and the XZ view (bottom-left) shows dense, layered signal filling the shell. This matches the pretzel reference images well, with multiple coils/folds visible. The previous three timepoints were all pretzel, and no morphological change toward hatching is evident (no worm extending outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3898,10 +3683,9 @@ "timepoint": 92, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), multiple body segments can be seen crossing and overlapping within the eggshell, creating a tangled pattern characteristic of pretzel stage. The XZ view (bottom-left) shows complex, multi-layered signal filling most of the eggshell. The YZ view (top-right) shows an irregular, complex pattern rather than simple parallel segments. This matches the pretzel reference images well and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments with multiple folds - more than two parallel segments are apparent. The XZ view (bottom-left) shows a complex pattern with multiple overlapping layers. The YZ view (top-right) shows a relatively filled, complex cross-section. This matches the pretzel reference images well, with the dense fill and multiple coils characteristic of 3+ folds. Consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3916,10 +3700,9 @@ "timepoint": 93, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "Multiple overlapping body coils visible in XY projection with dense eggshell filling. XZ view shows at least 3 parallel bright bands indicating multiple folds. Consistent with pretzel stage and matches previous observations at T90-T92. No signs of hatching.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with complex tangled morphology. The eggshell is densely filled with signal. The XZ view shows multiple parallel bright bands indicating 3+ body folds. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3934,10 +3717,9 @@ "timepoint": 94, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well and is consistent with the previous three observations all classified as pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in the XY view. The complex, tangled pattern of nuclei with at least 3 parallel body segments is consistent with the pretzel stage. The XZ view shows multiple layers of signal. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3952,10 +3734,9 @@ "timepoint": 95, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex folding with multiple parallel segments and a looping pattern characteristic of pretzel stage. The XZ view (bottom-left) shows multiple bright layers stacked, consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body shows complex folding patterns with multiple parallel segments and a looping/coiled structure characteristic of the pretzel stage. The XZ view (bottom-left) shows multiple bright layers of overlapping body segments. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3970,10 +3751,9 @@ "timepoint": 96, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view shows bright, complex layered signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations at pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view shows bright, complex layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3988,10 +3768,9 @@ "timepoint": 97, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible - consistent with pretzel stage. The body appears to have 3+ folds creating a complex, tangled pattern within the eggshell. The XZ view shows complex overlapping structures. Very little empty dark space remains inside the eggshell boundary. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments. In the XY view (top-left), I can see a complex, tangled pattern with multiple body folds visible - consistent with 3+ folds characteristic of pretzel stage. The XZ view (bottom-left) also shows complex overlapping structures. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4006,10 +3785,9 @@ "timepoint": 98, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, the body fills most of the eggshell with a complex, tangled pattern showing multiple parallel segments - more than two distinct body segments are visible, consistent with 3+ folds. The XZ view shows a complex internal structure with overlapping layers. This matches the pretzel reference images well and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with complex, tangled patterns of nuclei and some darker gaps between coils. The XZ view (bottom-left) shows multiple overlapping body segments creating a complex pattern. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4024,10 +3802,9 @@ "timepoint": 99, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) shows a dense, complex pattern with multiple layers of signal. This matches the pretzel reference images well and is consistent with the previous three observations at pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The complex, tangled pattern of body segments filling most of the eggshell interior is consistent with the pretzel stage. The XZ view shows multiple layered body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4042,10 +3819,9 @@ "timepoint": 100, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), multiple overlapping coils/body segments are visible forming a complex, tangled pattern characteristic of the pretzel stage. The body wraps around the interior of the eggshell with at least 3 parallel segments visible. The XZ view (bottom-left) shows dense, complex layered signal filling the eggshell. This matches the pretzel reference images well and is consistent with the previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, particularly clear in the XZ (bottom-left) view where multiple bright bands are stacked. The YZ view (top-right) shows a complex, roughly circular pattern consistent with multiple body folds overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4060,10 +3836,9 @@ "timepoint": 101, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern. The eggshell is densely filled with fluorescent signal, though there are some dark gaps between coils. The XZ view shows multiple bright layers/bands consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no signal outside eggshell boundary). Consistent with previous observations at T98-T100.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern. The eggshell is densely filled with fluorescent signal, though some dark spaces remain in the interior loops. Multiple (3+) body segments are visible, consistent with pretzel stage. The XZ view also shows dense, complex layering. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4078,10 +3853,9 @@ "timepoint": 102, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible - at least 3 parallel tracks of nuclei can be seen forming a complex looping pattern. The eggshell is well-filled with relatively little dark space inside, consistent with pretzel stage. The XZ view also shows dense, complex layered signal. This matches the pretzel reference images and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see multiple parallel body segments forming a complex, looped pattern that fills most of the eggshell - consistent with 3+ folds. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4096,10 +3870,9 @@ "timepoint": 103, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well and is consistent with the previous three observations at pretzel stage. No sign of hatching (no elongated worm outside the shell).", + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 multiple overlapping coils are visible in the XY view, with complex tangled patterns of nuclei filling most of the eggshell interior. The XZ view also shows dense, complex signal throughout. This matches the pretzel reference images well, with multiple body folds creating overlapping layers. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4114,10 +3887,9 @@ "timepoint": 104, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view, the embryo shows multiple coiled body segments filling most of the eggshell interior, with a tangled/complex pattern characteristic of pretzel stage. The XZ view shows layered bright signal with multiple body segments overlapping. This matches the pretzel reference images well and is consistent with the previous three observations at pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4132,10 +3904,9 @@ "timepoint": 105, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple body folds creating the characteristic dense, complex pattern. No sign of hatching (no signal outside the eggshell boundary). Consistent with previous three timepoints classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell interior. The XZ view shows dense, complex signal throughout. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4150,10 +3921,9 @@ "timepoint": 106, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.93, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with a complex, tangled pattern of nuclei showing multiple body segments. The XZ view (bottom-left) shows complex overlapping structures consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body fills most of the eggshell with a complex, tangled pattern of nuclei. The XZ view (bottom-left) shows multiple layered body segments with complex overlapping structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4168,10 +3938,9 @@ "timepoint": 107, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), multiple overlapping coils of the body are visible - I can see at least 3 parallel segments forming a complex, tangled pattern within the eggshell. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, with the characteristic dense packing and multiple body folds. Consistent with previous three timepoints all classified as pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, consistent with pretzel stage. The XZ view shows dense, bright signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4186,10 +3955,9 @@ "timepoint": 108, "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.94, "is_transitional": false, "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coiled body segments forming a complex, tangled pattern within the eggshell - characteristic of pretzel stage. The eggshell is densely filled with signal, though some dark spaces are visible in the interior (consistent with the coiled body leaving gaps between loops). The XZ view shows dense, complex signal filling the shell. Multiple (3+) body segments are visible in the coils. This matches the pretzel reference images well and is consistent with the previous three timepoints all being pretzel.", + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern characteristic of the pretzel stage. The eggshell is densely filled with signal. Multiple body segments are visible crossing over each other. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -4202,16 +3970,15 @@ }, { "timepoint": 109, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", - "confidence": 0.82, "is_transitional": false, "transition_between": null, - "reasoning": "In the XY view (top-left), the embryo appears to be emerging from the eggshell - there's a clear bilobed/dumbbell shape with what looks like part of the worm body extending outside the eggshell boundary. This is distinctly different from the pretzel stage references where the body remains contained within the eggshell. The shape shows the worm pushing out of one end of the shell, creating that characteristic hatching morphology. The previous timepoints were pretzel, and this transition to hatching is consistent with developmental progression at T109.", + "reasoning": "The XY view shows a complex, densely coiled structure with multiple overlapping body segments filling the eggshell. The eggshell appears densely filled with signal. The XZ view shows complex internal structure with multiple layers. The morphology is consistent with the pretzel reference images showing multiple folded coils. Previous three timepoints were all pretzel, and no clear transition to hatching is visible (no elongated worm outside the eggshell).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -4219,1625 +3986,39 @@ "candidate_stages": null } ], - "duration_seconds": 890.4531455039978, + "duration_seconds": 598.227730512619, "error": null, - "accuracy": 0.7464788732394366, + "accuracy": 0.7746478873239436, "adjacent_accuracy": 1.0 }, { "embryo_id": "embryo_4", - "predictions": [ - { - "timepoint": 69, - "predicted_stage": "1.5fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The embryo body has elongated significantly compared to comma references and shows early folding with a J-like shape in XY. The eggshell is sparsely filled with notable dark space remaining. The XZ view shows hints of two layers beginning to form. This matches early 1.5fold morphology better than comma, though the transition is just beginning.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 70, - "predicted_stage": "1.5fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.7, - "is_transitional": false, - "transition_between": null, - "reasoning": "Elongated embryo body with beginning of folding visible in XY and XZ views. Eggshell is sparsely to moderately filled with significant dark space remaining. Body layering is beginning in the side view but two clearly parallel segments are not yet established. Matches 1.5fold references better than 2fold. Consistent with previous T69 observation.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 71, - "predicted_stage": "1.5fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.72, - "is_transitional": false, - "transition_between": null, - "reasoning": "Embryo shows elongated body beginning to fold with sparse-to-moderate eggshell fill. XY view shows a J-shaped or early folding morphology without clear two parallel segments. Fill fraction is still relatively sparse with dark space remaining. Consistent with previous 1.5fold classification and matches 1.5fold reference images better than 2fold.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 72, - "predicted_stage": "2fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows elongated body with two parallel segments visible, and XZ view shows two distinct layers of signal consistent with a hairpin fold. Eggshell fill is moderate - more than 1.5fold references but less than pretzel. Morphology matches 2fold references (T62-T75). Transitioning from 1.5fold seen at T69-T71.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 73, - "predicted_stage": "2fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.65, - "is_transitional": false, - "transition_between": null, - "reasoning": "Moderate eggshell fill fraction with two apparent parallel body segments visible in XY view. Matches 2fold reference images. Consistent with previous T72 classification. Not yet dense enough for pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 74, - "predicted_stage": "2fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.7, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal - more than 1.5fold but not densely packed like pretzel. XY view shows elongated body with what appears to be two parallel segments (hairpin fold). Matches 2fold reference images well. Consistent with previous T72-T73 observations of 2fold. Not yet showing the dense, complex multi-coil pattern of pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 75, - "predicted_stage": "2fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is moderately filled with some dark spaces remaining. YZ view shows a ring-like pattern suggesting body folding, but the overall fill is not yet dense enough for pretzel. The morphology is advancing from previous 2fold observations but hasn't clearly transitioned to pretzel's densely packed, multi-coil appearance. Defaulting to 2fold given uncertainty and preference for earlier stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 76, - "predicted_stage": "2fold", - "ground_truth_stage": "1.5fold", - "confidence": 0.65, - "is_transitional": false, - "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible parallel body segments in XY view. Some dark space remains inside the eggshell. The XZ view shows layered structure consistent with 2fold. Not yet densely filled enough for pretzel - lacks the complex multi-coil pattern seen in pretzel references. Consistent with previous 2fold observations at T73-T75.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 77, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.5, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell fill is moderate to moderately dense, with some dark space remaining. The body shows elongation consistent with late 2fold. Compared to pretzel references, the eggshell is not yet densely filled with complex overlapping coils. Previous three timepoints were 2fold, and while this is approaching the transition, the morphology hasn't clearly shifted to pretzel-level complexity yet. Defaulting to earlier stage given uncertainty.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 78, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "Moderate eggshell fill with two visible body segments in XY view. XZ view shows layered signal suggesting folded body. Fill fraction is moderate (some dark space remains), not yet dense enough for pretzel. Consistent with late 2fold stage, matching previous observations at T75-T77. Morphology hasn't clearly transitioned to the densely-packed pretzel pattern yet.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 79, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.45, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell fill is moderate with some dark spaces remaining, suggesting late 2fold rather than pretzel. Body shows increasing complexity but not yet the dense, multi-coiled pattern of pretzel. Previous three timepoints were 2fold; morphology shows gradual progression but not a clear transition to pretzel yet. Preferring earlier stage given uncertainty.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 80, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two main body segments in a hairpin/U-shape with moderate eggshell filling and visible dark space between segments. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T77-T79. Approaching but not yet at pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 81, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with signal, with little dark space remaining. The YZ view shows a complex ring-like pattern suggesting multiple overlapping coils. The XZ view shows at least 3 distinct layers of signal. This matches the T82 pretzel reference more closely than the 2fold references. The transition from 2fold at T80 to pretzel at T81 is plausible given the low confidence of previous 2fold classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 82, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XZ projection shows at least 3 distinct bright lobes suggesting multiple body folds. The XY view shows a complex multi-lobed shape beyond a simple U/hairpin. Eggshell fill is moderate-to-dense. This matches early pretzel morphology and is consistent with the previous T81 pretzel classification. The complexity exceeds what would be expected for 2fold.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 83, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.65, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with signal, the XZ projection shows 3+ distinct bright bands indicating multiple body folds, and the YZ view shows a complex ring-like pattern. This matches pretzel references better than 2fold. Consistent with previous observations at T81-T82.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 84, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.65, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell shows moderate-to-dense filling with complex, multi-lobed body morphology visible in the XY view, suggesting multiple body folds. The XZ view shows overlapping internal structures. This matches pretzel reference images and is consistent with previous timepoints (T81-T83 all pretzel). The fill fraction and complexity exceed what would be expected for 2fold.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 85, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.45, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell fill fraction is moderate with visible dark spaces inside the shell boundary, more consistent with 2fold than pretzel. The XY view shows approximately two parallel body segments rather than the multiple overlapping coils expected for pretzel. While previous timepoints were classified as pretzel, the morphology here looks more like a late 2fold. Following the rule to prefer the earlier stage when uncertain.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 86, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.6, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is moderately-to-densely filled with signal. The XZ projection shows multiple (3+) horizontal bands of bright signal indicating multiple body folds/coils. This matches pretzel references better than 2fold. Previous T83-T84 were pretzel, and developmental regression is unlikely. The T85 2fold call was likely an error given low confidence.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 87, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is moderately-to-densely filled with signal. The XY view shows complex overlapping body structures suggesting multiple folds rather than a simple two-segment hairpin. The XZ view shows layered internal structure. Consistent with previous pretzel classification at T86, and the fill fraction and complexity match pretzel references better than 2fold, though confidence is moderate as this appears to be near the 2fold/pretzel boundary.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 88, - "predicted_stage": "pretzel", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XZ side view shows multiple layered/banded structures suggesting 3+ body folds. Eggshell fill fraction is moderate-to-dense. The morphology is more complex than typical 2fold references but not as densely packed as late pretzel. Consistent with previous pretzel classifications at T86-T87. This appears to be early pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 89, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.5, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows a bilobed/figure-8 shape with a clear constriction between two body segments, consistent with a hairpin fold (2fold). The eggshell fill is moderate with visible dark spaces, not the dense filling expected for pretzel. The pattern lacks the complex multiple overlapping coils characteristic of pretzel. Previous classifications at pretzel had low confidence; this morphology better matches 2fold references.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 90, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two distinct lobes of signal with a clear constriction between them, consistent with a hairpin/U-shaped fold (two parallel body segments). Eggshell fill is moderate with visible dark space between the lobes, not dense enough for pretzel. Matches 2fold reference images better than pretzel. Consistent with previous T89 classification.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 91, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows bilobed/figure-8 shape consistent with two parallel body segments (hairpin fold). Eggshell fill is moderate - not sparse enough for 1.5fold but not densely packed like pretzel references. Matches 2fold reference morphology. Consistent with T89-T90 classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 92, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.45, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is moderately filled with signal, showing increasing complexity in body folding. The XZ view hints at more than two parallel segments, suggesting transition toward pretzel. However, the fill fraction is not yet as dense as pretzel references, and previous observations were 2fold. Staying with 2fold given uncertainty and preference for earlier stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 93, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.5, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two main lobes of signal in a figure-8/dumbbell pattern consistent with two parallel body segments (hairpin fold). Moderate eggshell fill fraction with visible dark space between and around the lobes. Not yet showing the dense, complex multi-coil pattern of pretzel. Consistent with previous 2fold classifications at T90-T92, though may be approaching transition to pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 94, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.5, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two main body lobes with a clear constriction between them, consistent with a hairpin/U-shaped 2fold morphology. Eggshell fill is moderate with some dark space remaining, not yet densely packed like pretzel. Previous 3 timepoints were 2fold. While complexity may be increasing, clear evidence of 3+ folds is not yet present.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 95, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two distinct lobes of signal with a constriction between them, consistent with a hairpin/U-shaped fold (two parallel body segments). Eggshell fill is moderate - not yet densely packed as in pretzel. Pattern matches 2fold references better than pretzel. Previous three timepoints were 2fold, and no clear transition to pretzel-level complexity is evident.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 96, - "predicted_stage": "2fold", - "ground_truth_stage": "2fold", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "XY view shows two main body segments with a fold/bend, moderate eggshell filling with some dark space remaining. XZ view shows layered bands consistent with two parallel segments. Matches 2fold references well. Not yet showing the dense, complex multi-coil pattern of pretzel. Consistent with previous 2fold classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 97, - "predicted_stage": "2fold", - "ground_truth_stage": "pretzel", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "Moderate eggshell fill with visible dark spaces, two parallel body segments visible in XY and XZ views, consistent with 2fold reference images. Not yet showing the dense multi-coil filling pattern characteristic of pretzel stage. Consistent with previous three timepoints classified as 2fold.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 98, - "predicted_stage": "2fold", - "ground_truth_stage": "pretzel", - "confidence": 0.45, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is moderately to densely filled with signal, and internal structure shows increasing complexity. However, a clear three-fold pattern is not definitively visible yet. The morphology is denser than typical 2fold references but not as complex/tangled as pretzel references. Previous observations were 2fold, and following the rule to prefer earlier stage when uncertain.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 99, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.45, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is moderately-to-densely filled with signal showing complex internal folding patterns. The XY view shows multiple body segments with internal dark gaps suggesting 3+ folds rather than a simple U-shape. The XZ view shows layered structure. This exceeds typical 2fold morphology and matches early pretzel references (T82). Previous observations were low-confidence 2fold, consistent with a transition occurring around this timepoint.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 100, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is moderately to densely filled with signal. Multiple parallel body segments are visible in the XY view, and the XZ view shows layered structures suggesting 3+ folds. The YZ view shows scattered bright spots consistent with overlapping coils. This matches the pretzel reference better than 2fold, and is consistent with the T99 pretzel classification. Confidence is moderate due to the transition zone between 2fold and pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 101, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.6, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is densely filled with signal, complex internal structure visible in XY and XZ views suggesting multiple overlapping body folds. Pattern matches pretzel references better than 2fold. Consistent with previous T99-T100 pretzel classifications. Fill fraction is high though not maximal, and body organization appears more complex than a simple hairpin/U-shape.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 102, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.65, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments visible in XY view creating a complex, tangled pattern. YZ view shows ring-like structure consistent with coiled body. Matches pretzel reference images well. Consistent with previous three pretzel classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 103, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.75, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows an elongated embryo with multiple overlapping coils/body segments filling most of the eggshell. The YZ view (top-right) shows a ring-like pattern with a dark center, consistent with coiled body segments characteristic of pretzel stage. The XZ view (bottom-left) shows multiple bright bands with complex layering. The eggshell is densely filled with signal, though some dark spaces remain. Multiple (3+) body segments are visible, consistent with pretzel. This matches the pretzel reference images and is consistent with the previous three observations all being pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 104, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.82, - "is_transitional": false, - "transition_between": null, - "reasoning": "Multiple overlapping body coils visible in XY view with complex tangled pattern. Eggshell is densely filled with signal and little empty space remains. YZ view shows swirled/ring pattern consistent with multiple folds. Matches pretzel reference images well. No sign of emergence from eggshell. Consistent with previous pretzel classifications at T101-T103.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 105, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.85, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the oval eggshell with a complex, tangled pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows bright, broadly distributed signal filling the shell. The YZ view (top-right) shows complex internal structure with multiple bright spots suggesting overlapping coils. This matches the pretzel reference images well, with dense fill and complex folding patterns. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 106, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "Dense filling of eggshell with complex, multi-layered coiled body segments visible in all views. Multiple overlapping folds seen in XZ projection. Consistent with pretzel reference images and previous three timepoints. No signs of hatching (no elongated worm outside shell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 107, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows a complex, coiled pattern with multiple overlapping body segments forming a ring/loop-like structure - characteristic of pretzel stage. The eggshell is densely filled with signal, and the body has clearly folded 3+ times creating the tangled appearance. The XZ view shows multiple layers of bright signal stacked vertically. The YZ view shows a complex, non-uniform pattern consistent with multiple coils. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 108, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "Multiple overlapping body coils visible in all three views. XZ shows at least 3 parallel body segments. YZ shows swirling coiled pattern. Eggshell is densely filled with signal. Consistent with pretzel stage and previous observations at T105-T107.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 109, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.9, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping body segments visible. In the XY view (top-left), the embryo fills most of the eggshell with a complex, coiled pattern showing multiple parallel segments. The XZ view (bottom-left) shows bright, complex overlapping structures consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 110, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal spans most of the eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows multiple layered body segments with a complex coiled pattern. The YZ view (top-right) shows a ring-like pattern consistent with multiple overlapping coils. This matches the pretzel reference images well, with 3+ body folds creating the dense, tangled appearance. No sign of hatching (no elongated worm outside the shell). Consistent with previous observations at T107-T109.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 111, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 112, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple overlapping coils filling most of the eggshell. The YZ view (top-right) shows a complex lobed pattern consistent with multiple body folds. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with 3+ body folds creating overlapping layers. Consistent with previous three observations all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 113, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo shows multiple coiled body segments filling most of the eggshell, with bright spots distributed throughout. The XZ view (bottom-left) shows complex layered structure consistent with multiple folds. The overall pattern matches the pretzel reference images well, with dense filling and tangled appearance. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 114, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view, the body fills most of the eggshell with multiple coiled segments visible - more than two parallel segments can be discerned, indicating multiple folds. The XZ view shows a complex, layered pattern consistent with the pretzel reference images. The overall morphology is consistent with the previous three timepoints classified as pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 115, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view, multiple overlapping coils/body segments are visible creating a complex, tangled pattern. The XZ view shows multiple layers of signal with complex internal structure. This matches the pretzel reference images well. Consistent with previous observations at T112-T114.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 116, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, I can see a complex, tangled pattern with at least 3 body segments creating an S-shaped or pretzel-like arrangement. The XZ view shows multiple layers of signal stacked vertically. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 117, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments filling most of the eggshell interior with relatively little dark space. The YZ view (top-right) shows a characteristic ring/loop pattern consistent with multiple folds. The XZ view (bottom-left) also shows dense, complex signal filling the shell. At least 3 parallel body segments are discernible, consistent with pretzel stage. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 118, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple overlapping coils and several bright spots, consistent with multiple body folds. The XZ view (bottom-left) shows dense, complex signal filling the shell. The YZ view (top-right) shows bright spots indicating overlapping body layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 119, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments. In the XY view (top-left), I can see complex, tangled body segments with multiple folds - at least 3 parallel segments are visible, consistent with pretzel stage. The XZ view (bottom-left) shows multiple layered body segments. The overall pattern matches the pretzel reference images well, with the characteristic dense filling and complex coiling. Consistent with previous observations at T116-T118.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 120, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo body shows multiple overlapping coils/segments filling most of the eggshell, with complex tangled morphology. The XZ view (bottom-left) shows multiple bright bands indicating several body layers overlapping. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, with 3+ body folds creating the dense, complex pattern. No sign of hatching (no elongated worm outside the shell). Consistent with previous three timepoints all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 121, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 122, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple overlapping coils filling most of the eggshell. The XZ view (bottom-left) shows multiple bright layers/bands consistent with 3+ body folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 123, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments and loops characteristic of 3+ folds. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows multiple bright layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 124, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping body coils. XZ view shows complex multi-layered structure consistent with 3+ folds. Matches pretzel references well. Some signal extends slightly below the main body in XZ but no clear elongated worm outside the eggshell, so not yet hatching. Consistent with previous pretzel classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 125, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments visible in all three views. Complex tangled pattern in XY, swirling pattern in YZ, and layered structure in XZ all consistent with pretzel stage. No sign of hatching. Matches previous observations at T122-T124.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 126, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments filling most of the eggshell, with a complex tangled pattern. There appears to be a dark region in the center suggesting the body is looping around itself (visible as an oval/ring-like pattern). The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple folded body segments creating overlapping layers. Consistent with previous three timepoints all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 127, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo body shows multiple folded segments filling most of the eggshell, with some internal dark gaps characteristic of pretzel stage. The XZ view (bottom-left) shows a complex, tangled pattern with multiple overlapping body layers. The YZ view (top-right) shows a relatively filled cross-section with internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 128, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple folded segments - more than two parallel segments are apparent. The XZ view (bottom-left) shows overlapping bright bands consistent with multiple body folds. The YZ view (top-right) shows a complex internal structure with bright spots distributed throughout. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 129, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in both the XY and XZ views. The XZ (bottom-left) view shows multiple intertwined body segments creating a tangled pattern characteristic of the pretzel stage. The YZ view (top-right) shows a complex, non-uniform signal distribution consistent with multiple overlapping folds. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 130, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with a complex, tangled pattern of multiple overlapping body segments. The XZ view (bottom-left) shows bright, complex overlapping coils filling the shell. This matches the pretzel reference images well, with multiple folded body segments creating a dense, bright pattern. No sign of hatching (no worm body extending outside the eggshell). Consistent with previous three timepoints all classified as pretzel.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 131, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view (bottom-left) shows complex internal structure with multiple bright layers. This matches the pretzel reference images well, and is consistent with the previous three observations all classified as pretzel. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 132, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view shows multiple layers of body segments. The YZ view shows a complex, non-uniform pattern consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 133, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body fills most of the eggshell with multiple overlapping segments creating a tangled pattern. The XZ view shows complex internal structure with multiple layers. The YZ view shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 134, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex tangled pattern. The eggshell is densely filled with signal - very little empty dark space remains inside the shell boundary. The XZ view shows complex layered structure. This matches the pretzel reference images well, with multiple (3+) body folds visible. Consistent with previous observations at T131-T133.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 135, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled structure with more than two parallel segments, consistent with pretzel stage. The XZ view shows multiple layered bands of signal. This matches the pretzel reference images well and is consistent with the previous three observations at pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 136, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated pattern with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows curved/coiled structures consistent with multiple folds - there appear to be at least 3 body segments visible as overlapping layers. The YZ view (top-right) shows a compact, bright mass with some internal structure. This matches the pretzel reference images well, with dense filling and complex coiling. No evidence of hatching (no signal outside eggshell boundary). Consistent with previous observations at T133-T135.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 137, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern within the eggshell. The XZ view shows bright, complex layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 138, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments. The YZ view (top-right) shows a ring-like pattern characteristic of coiled body segments in cross-section. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple body folds creating a tangled appearance. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 139, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.93, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated body shows multiple overlapping segments filling most of the eggshell. The XZ view (bottom-left) shows the characteristic pretzel pattern with multiple folded body layers creating a complex internal structure. The YZ view (top-right) shows scattered bright nuclei consistent with multiple overlapping body segments. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel. No sign of hatching (no worm body extending outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 140, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.95, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with complex tangled structure and at least 3 parallel body segments visible. The eggshell is densely filled with fluorescent signal, though some dark gaps remain between coils. The XZ view shows a complex layered pattern consistent with multiple folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous observations at T137-T139.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 141, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping loops characteristic of the pretzel stage. The XZ view (bottom-left) shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 142, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.94, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the elongated shape shows complex, tangled body segments filling most of the eggshell interior. The YZ view (top-right) shows a ring-like pattern consistent with multiple coiled body segments. The XZ view (bottom-left) shows dense, complex signal with multiple overlapping layers. This matches the pretzel reference images well, with 3+ body folds creating the characteristic dense, complex pattern. No sign of hatching (no worm extending outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 143, - "predicted_stage": "hatching", - "ground_truth_stage": "pretzel", - "confidence": 0.55, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows the embryo body extending/curving beyond the eggshell boundary with a distinct loop extending downward, suggesting the worm is beginning to emerge. This differs from pretzel references where the body remains coiled within the shell. However, much of the body is still near/within the shell, making this early hatching rather than fully hatched.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 144, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.72, - "is_transitional": false, - "transition_between": null, - "reasoning": "Eggshell is densely filled with fluorescent signal showing multiple overlapping coiled body segments - characteristic of pretzel stage. No clear evidence of worm extending outside the eggshell boundary. The complex tangled pattern matches pretzel references well. Previous hatching call at T143 was low confidence (55%); reverting to pretzel as the morphology still shows a fully contained embryo.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 145, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "Multiple coiled body segments visible in XY view forming a loop/pretzel pattern within the eggshell. The XZ view shows multiple layered bright bands from overlapping folds. The body remains entirely within the eggshell (not hatching). Consistent with pretzel reference images and previous T144 classification.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 146, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.85, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view (bottom-left) shows multiple bright layers with complex internal structure. The YZ view (top-right) shows a compact, coiled pattern with bright spots distributed throughout. This matches the pretzel reference images well. The embryo remains contained within the eggshell with no evidence of emergence, so it has not progressed to hatching. Consistent with previous T144-T145 pretzel classifications.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 147, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in the XY view. The XY projection shows a complex, tangled pattern with at least 3 body segments visible, consistent with pretzel stage. The XZ (bottom-left) view shows multiple layers of signal filling the shell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 148, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo fills most of the eggshell with multiple body segments creating a complex, tangled pattern. The XZ view (bottom-left) shows multiple overlapping layers of signal with a complex internal structure consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 149, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.88, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments and a tangled appearance. Several bright punctate nuclei are visible scattered throughout. The YZ view (top-right) shows a complex, swirling pattern consistent with multiple body folds. The XZ view (bottom-left) shows dense, layered signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three timepoints all classified as pretzel. No evidence of hatching (no elongated worm outside the shell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 150, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.9, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows a complex, tangled pattern of multiple overlapping body segments within the eggshell, consistent with pretzel stage. The eggshell is densely filled with signal - multiple coiled body layers are visible creating a complex pattern. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, with multiple folds creating an intricate pattern. No sign of hatching (no elongated worm outside the shell). Consistent with previous observations at T147-T149.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 151, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.9, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments rather than a simple hairpin. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) also shows complex overlapping structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 152, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.9, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo body fills most of the eggshell with multiple overlapping segments and some dark gaps characteristic of pretzel stage. The XZ view (bottom-left) shows multiple curved/looping body segments consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 153, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled structures. In the XY view, the body fills most of the eggshell with multiple overlapping segments visible - more than two parallel segments can be discerned, indicating 3+ folds. The XZ view shows a complex tangled pattern with bright spots throughout. This matches the pretzel reference images well. Consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 154, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows a densely filled eggshell with multiple overlapping coils/body segments visible - complex tangled pattern with bright spots throughout. The XZ view shows multiple parallel layers of the body within the eggshell. The eggshell is densely filled with signal, consistent with pretzel stage. At least 3 body segments are visible in the side view. This matches the pretzel reference images well and is consistent with the previous observations at T151-T153.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 155, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.92, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows an elongated embryo with multiple overlapping coils/body segments densely filling the eggshell. The YZ view shows a complex, tangled pattern with multiple bright regions consistent with overlapping body folds. The XZ view shows multiple layers of signal with a complex internal structure. The eggshell is densely filled with signal, and the pattern matches the pretzel reference images. Consistent with previous observations at T152-T154.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - }, - { - "timepoint": 156, - "predicted_stage": "pretzel", - "ground_truth_stage": "pretzel", - "confidence": 0.82, - "is_transitional": false, - "transition_between": null, - "reasoning": "The XY view shows a curved, coiled worm body within the eggshell with multiple overlapping segments visible. Arc-like structures on the left suggest active movement but the body remains contained within the eggshell. The XZ projection shows dense, complex signal filling the shell. Consistent with late pretzel stage, though approaching hatching.", - "reasoning_trace": null, - "tool_calls": 0, - "tools_used": [], - "is_correct": true, - "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, - "verification_result": null, - "candidate_stages": null - } - ], - "duration_seconds": 1055.2100794315338, + "predictions": [], + "duration_seconds": 0.1755971908569336, "error": null, - "accuracy": 0.8295454545454546, - "adjacent_accuracy": 1.0 + "accuracy": 0.0, + "adjacent_accuracy": 0.0 } ], - "started_at": "2026-03-17T06:23:06.022468", - "completed_at": "2026-03-17T07:26:43.173463", - "total_predictions": 321, - "overall_accuracy": 0.8255451713395638, + "started_at": "2026-04-22T15:13:18.235955", + "completed_at": "2026-04-22T15:48:17.584886", + "total_predictions": 233, + "overall_accuracy": 0.7725321888412017, "metrics": { - "accuracy": 0.8255451713395638, - "adjacent_accuracy": 1.0, - "mean_confidence": 0.7775389408099694, + "accuracy": 0.7725321888412017, + "adjacent_accuracy": 0.9957081545064378, "per_stage": { "1.5fold": { - "accuracy": 0.5510204081632653, - "n": 49 + "accuracy": 0.6585365853658537, + "n": 41 }, "2fold": { - "accuracy": 0.759493670886076, - "n": 79 + "accuracy": 0.6101694915254238, + "n": 59 }, "pretzel": { - "accuracy": 0.9222797927461139, - "n": 193 + "accuracy": 0.8796992481203008, + "n": 133 } } } diff --git a/data/results/zslice_1.5fold+2fold+pretzel.json b/data/results/zslice_1.5fold+2fold+pretzel.json new file mode 100644 index 0000000..80a22bd --- /dev/null +++ b/data/results/zslice_1.5fold+2fold+pretzel.json @@ -0,0 +1,4025 @@ +{ + "config": { + "description": "Variant: zslice" + }, + "embryo_results": [ + { + "embryo_id": "embryo_1", + "predictions": [ + { + "timepoint": 55, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a curved, bilobed mass of nuclei with a clear C-shape/comma morphology. The eggshell is still mostly empty - the body occupies only a portion of the eggshell interior with significant dark space remaining. There is one curved band of nuclei visible, not yet showing the parallel segments characteristic of 1.5fold. The XZ view shows two bright lobes separated by a gap, consistent with the comma reference images. The morphology matches the comma reference well and hasn't clearly progressed to 1.5fold yet. Previous observations were all comma, and stages change slowly.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a curved, bilobed body shape with significant empty space in the eggshell, consistent with late comma stage. No clear J-shape or fold-back is visible yet. The morphology closely matches comma reference images. Previous three timepoints were comma, and the change to 1.5fold is not yet clearly evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows clear elongation and curvature beyond a simple comma shape. In the XY view, the body appears to be folding back on itself in a J-like shape, with the tail beginning to curl back. The eggshell is still sparsely filled with significant dark space remaining. The XZ view shows two distinct lobes suggesting the beginning of a fold. This morphology matches the early 1.5fold reference images better than the comma references, indicating the transition from comma to 1.5fold has occurred. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is only moderately filled with significant dark space remaining, especially on the edges. The XY view shows an elongated body with a curve/fold but the fill fraction looks sparse-to-moderate, more consistent with 1.5fold than full 2fold. Comparing to references, this resembles the 1.5fold examples more than the 2fold ones. Given the rule to prefer the earlier stage when uncertain, and that T55-56 were comma, 1.5fold at T58 is more plausible than jumping to 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two distinguishable parallel body segments with moderate eggshell filling. The XZ view shows layered signal structure consistent with a folded body. This matches the early 2fold reference (T62) better than 1.5fold. The embryo has progressed from the 1.5fold at T58, with clearer parallel segments now visible. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - not sparse like 1.5fold but not densely packed like pretzel. In the XY view (top-left), the embryo body shows an elongated shape with what appears to be two parallel body segments, consistent with a 2fold stage. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. Compared to reference images, this matches the 2fold references (T62-T68 range) well - moderate fill fraction with some dark space remaining. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments forming a hairpin/U-shape, with moderate eggshell filling. The morphology matches the 2fold reference (T62) well. The embryo has clearly folded back on itself with two discernible parallel bands of nuclei. The fill fraction is moderate - more than 1.5fold but not yet densely packed like pretzel. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY projection shows two roughly parallel body segments with moderate eggshell filling, matching the 2fold reference at T62. The signal distribution is more spread than typical 1.5fold, with less empty dark space inside the eggshell. The YZ view shows asymmetric signal consistent with a folded body. This represents a clear morphological advance from the previous 1.5fold observations. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a curved/folded shape, but I can see what appears to be a J-shape or partial hairpin rather than two clearly parallel segments. The eggshell is still sparsely to moderately filled - there is notable dark space remaining within the eggshell boundary, particularly around the edges. The XZ view (bottom-left) shows bright signal concentrated in distinct regions with some gaps. Comparing to references, this looks very similar to the 1.5fold reference images and not yet as filled or showing the clear two-parallel-segment pattern of the 2fold references. Given the previous observations were all 1.5fold and stages change slowly, and the morphology hasn't clearly transitioned to 2fold yet, I maintain 1.5fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is still sparsely to moderately filled with some dark space remaining. While there are hints of a second parallel segment forming, the clear hairpin/U-shape of 2fold is not yet definitive. Previous three timepoints were 1.5fold, and the morphological change is not dramatic enough to confidently advance the stage. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a clear curved/folded morphology with two parallel body segments visible - a brighter region on the left curving around to a second segment on the right, forming a U or hairpin shape. The eggshell is moderately filled - there's some dark space remaining but less than in 1.5fold. The YZ view (top-right) shows a ring-like pattern consistent with a folded body. This matches the 2fold reference images well. The previous timepoint was also classified as 2fold, and the morphology is consistent with continuing in this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body occupies a good portion of the shell. The body appears to have two parallel segments visible, consistent with a hairpin/U-shape fold. The XZ view shows layered signal suggesting two body segments stacked. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous observations were 2fold, and there's no clear evidence of progression to pretzel (no dense multi-coil filling). | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space but less than 1.5fold. In the XY view, I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology is consistent with the previous three timepoints classified as 2fold. No clear transition to pretzel stage is evident. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view with a clear fold. XZ view shows bifurcated signal pattern consistent with two folded segments. Matches 2fold references well. Previous T65-T66 were 2fold; morphology here is consistent with continued 2fold stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. YZ view shows ring-like pattern consistent with folded body. Morphology matches 2fold references (T62-T75). T66 was already classified as 2fold, and development doesn't regress, so 2fold is appropriate at T69. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear elongated shape with two parallel segments visible - a brighter upper portion and a lower portion connected by a bend, consistent with a 2fold hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view (bottom-left) shows layered bright signal consistent with two overlapping body segments. This matches the 2fold reference images well. The previous observation was 2fold at T69, and stages change slowly, so 2fold is consistent. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments forming a hairpin/U-shape with moderate eggshell filling. The XZ view shows layered signal consistent with two folded body segments. This matches the 2fold reference images well. While the previous timepoint was classified as 1.5fold, the morphology here clearly shows the transition to 2fold with two distinct parallel segments visible. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. Eggshell is moderately filled with some dark space remaining. This matches 2fold reference images. Clear morphological change from 1.5fold with two distinct parallel segments now visible. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear fold - two parallel segments of the body are visible, with a brighter dense region on the left and a dimmer folded portion extending to the right. The eggshell is moderately filled - there's some dark space remaining but less than in 1.5fold. The XZ view (bottom-left) shows two distinct layers of signal separated by a gap, consistent with a folded body. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two parallel body segments rather than three or more overlapping coils. Consistent with previous T72 classification of 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view shows layered signal consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology is consistent with the previous observations at T72-T73. No clear transition to pretzel stage is evident. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments with a fold/bend, and moderate eggshell filling with some dark space remaining. XZ view shows layered signal consistent with a folded body. Matches 2fold reference images well. Previous T72-T73 were 2fold; development doesn't reverse, so this is consistent with continued 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body folded back on itself, creating two parallel segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion of the eggshell interior. The XZ view shows a complex pattern with multiple bright regions consistent with two overlapping body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two clear parallel segments rather than three or more coils. Previous observation was 2fold, and this is consistent with that stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body folded back on itself, creating two parallel segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion. The XZ view shows multiple bright bands consistent with two parallel body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous observations at T75-T76 were 2fold, consistent with slow stage progression. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of fluorescent signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly around the constriction between the two lobes, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows a similar pattern with moderate fill. This matches the 2fold reference images well. The morphology hasn't changed significantly from the previous timepoints (T75-T77, all 2fold), and the fill fraction is not yet dense enough to indicate pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear bilobed/hairpin structure with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly around the edges and between the lobes, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows a complex but not yet fully coiled pattern. Comparing to references, this matches the 2fold stage well - the two parallel segments are clearly visible but there aren't yet three or more overlapping coils that would indicate pretzel. The fill fraction is moderate, not dense. Previous observations were all 2fold, and while this is approaching the transition, I don't see clear evidence of a third fold yet. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments forming a hairpin/U-shape with moderate eggshell filling. The XZ view shows layered signal consistent with a folded body. This matches 2fold references well. Previous T77-T78 were 2fold; the morphology is consistent with continued 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view forming a hairpin/U-shape with a clear constriction between them. Eggshell fill is moderate - some dark space remains but body occupies a significant portion. Consistent with 2fold reference images and previous classification. Not yet showing the dense, complex overlapping coils characteristic of pretzel stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct lobes of nuclei connected by a constriction, forming a clear hairpin/U-shape. XZ view shows two stacked layers of signal consistent with a folded body. Eggshell fill is moderate with some dark space remaining. The clear two-segment morphology matches 2fold references better than 1.5fold, representing progression from the borderline state seen in recent timepoints. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping body segments (more than 2 parallel segments visible). The XZ view shows multiple bright bands indicating multiple folds. This matches the pretzel reference images and is consistent with the previous T82 classification of pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - more than sparse but not yet densely packed like pretzel references. The XY view shows an elongated body with some complexity but not the clearly tangled, multi-coil pattern of pretzel. The XZ view shows layered signal suggesting folding but not yet the dense overlapping of 3+ folds. Previous observation was 2fold, and while there's some progression, the fill fraction and complexity don't yet clearly match pretzel references. Defaulting to earlier stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments visible in both XY and XZ views creating complex internal patterns. Matches pretzel references better than 2fold. T82 was pretzel, and since stages don't reverse, this should be pretzel as well. | [zslice] 3 segment(s) at midplane \u2192 pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal showing complex, overlapping body segments. Multiple coils visible rather than a simple two-segment hairpin. Matches pretzel reference images. Consistent with previous T85 classification of pretzel. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated body with at least two parallel segments visible, and moderate eggshell filling with some dark space remaining. The XZ view shows dense but structured signal suggesting folded body layers. This matches 2fold references better than 1.5fold (which would be sparser) or pretzel (which would be more densely packed). The previous observations have been inconsistent, but the morphology here clearly shows more than 1.5fold complexity. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows at least 3 distinct bright horizontal bands indicating multiple overlapping body folds. The XY view shows a complex folded structure beyond a simple U-shape. The eggshell is moderately-to-densely filled. This matches the pretzel reference images well, and is consistent with the T85 pretzel classification and expected forward progression at T88. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The YZ view shows a ring/arc pattern with a dark center, indicating two parallel body segments viewed end-on. The XY view shows a folded body structure with moderate eggshell filling. The fill fraction is moderate (not sparse like 1.5fold, not dense like pretzel). The morphology matches the 2fold reference images better than 1.5fold, with clear evidence of the body having folded back to create two parallel segments. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with visible dark spaces remaining. XY view shows two main body regions forming a hairpin/U-shape rather than the dense multi-coil pattern of pretzel. XZ view shows layered but not densely packed signal. Morphology matches 2fold references better than pretzel - not enough overlapping coils or dense filling for pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with visible dark spaces remaining. Two parallel body segments visible in XY view (bright left, dimmer right) and layered signal in XZ view consistent with a hairpin fold. Matches 2fold references well. Not dense enough for pretzel \u2014 still has significant empty space within the eggshell. Consistent with previous T90 classification of 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, with complex overlapping body structures visible in all three views. The XZ projection shows layered internal structure consistent with multiple body folds. This matches pretzel reference images. The previous classifications of 2fold and 1.5fold at T90-T91 were likely errors since embryos cannot regress; T89 was correctly classified as pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining, two parallel body segments visible in XY and XZ views, consistent with 2fold references. Not yet densely filled enough for pretzel. Matches previous 2fold classification at T92. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body with what appears to be two parallel segments visible - a brighter region on the left and a dimmer curved region on the right, consistent with a 2fold hairpin shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view shows layered structure with some complexity but not yet the dense, tangled pattern of pretzel. The fill fraction is moderate rather than dense. This matches the 2fold reference images well. Previous observations were 2fold, and there's no clear evidence of progression to pretzel (which would show denser filling and more complex overlapping coils). | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo body appears elongated and fills most of the eggshell with a complex, somewhat tangled pattern. The eggshell is densely filled compared to the 2fold references. In the YZ view (top-right), I can see multiple bright clusters suggesting overlapping body segments rather than just two parallel segments. The XZ view (bottom-left) shows dense, complex signal filling. Compared to the 2fold reference which shows two distinct parallel segments with moderate fill, this image shows more complexity and denser filling consistent with the pretzel stage. The morphology has progressed from the previous 2fold observations, with the body now showing multiple overlapping coils rather than a simple hairpin shape. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two body regions with moderate eggshell filling, and the XZ view shows two parallel bands of signal characteristic of 2fold. The fill fraction is moderate (not sparse like 1.5fold, not dense like pretzel). This is consistent with T93-T94 being 2fold; the embryo remains at 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments visible - a brighter region on the left and a dimmer curved region, consistent with a hairpin/U-shape fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows multiple bright bands suggesting layered body segments. Comparing to references, this matches the 2fold stage better than pretzel (not densely enough filled, not enough overlapping coils) and is more advanced than 1.5fold. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body is clearly folded with two parallel segments visible. The YZ view shows a structured pattern with what appears to be two body layers. The XZ view shows moderate fill with distinguishable body segments. The eggshell is moderately filled (not densely packed like pretzel), consistent with 2fold. This matches the previous observations at T96-T97 of 2fold, and there's no clear evidence of the dense, complex coiling pattern characteristic of pretzel stage. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex, tangled pattern with at least 3 visible parallel/overlapping bands of nuclei. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, where multiple coils fill the shell. The previous timepoint (T98) was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - more than 1.5fold but not as densely packed as pretzel references. The XZ view shows complex folding patterns suggesting at least two parallel body segments. The XY view shows an elongated body with curvature and some empty space remaining at the edges. This matches 2fold morphology better than 1.5fold (too much fill and complexity) or pretzel (not dense enough). Previous observations have been inconsistent (2fold/pretzel/1.5fold), suggesting this embryo is in the 2fold-to-pretzel transition zone. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two main body lobes forming a hairpin/U-shape with moderate eggshell filling. Two parallel body segments are visible connected by a bend. Dark space remains within the eggshell but less than 1.5fold. Matches 2fold reference images well. No evidence of the dense, multi-coil pattern characteristic of pretzel. Consistent with previous T100 classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear curved/folded body showing two parallel segments connected by a bend - consistent with 2fold morphology. The eggshell is moderately filled with signal - there is some dark space remaining but less than in 1.5fold. The YZ view (top-right) shows an irregular, non-circular pattern suggesting folded body segments. The XZ view (bottom-left) shows layered bright bands consistent with two parallel body segments. The fill fraction is moderate (not densely packed like pretzel), and I can distinguish approximately two parallel body segments rather than the multiple overlapping coils of pretzel. This matches the 2fold reference images well and is consistent with the previous observations at T100-T101. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is sparsely to moderately filled with significant dark space remaining. The XY view shows a two-lobed structure with a dark gap but no clear parallel hairpin/U-shape characteristic of 2fold. Morphology is consistent with 1.5fold, matching the previous observation. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal. The XY view shows a folded body structure with approximately two parallel segments. The XZ view shows multiple bright bands suggesting increasing complexity, but the overall fill fraction is not yet as dense as pretzel references. Previous stage was 2fold, and while approaching pretzel, the morphology is still consistent with late 2fold. Defaulting to earlier stage when uncertain. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 there is very little dark/empty space within the eggshell boundary. In the XY view (top-left), I can see multiple overlapping coils/body segments creating a complex, tangled pattern rather than a simple two-parallel-segment hairpin. The YZ view (top-right) shows a ring-like pattern suggesting coiled body segments. The XZ view (bottom-left) shows multiple bright bands stacked, indicating three or more body layers overlapping. This matches the pretzel reference images much better than the 2fold references, which show clearer two-segment hairpin patterns with more empty space. The transition from 2fold at T104 to pretzel at T105 is plausible as the embryo continues elongating and folding. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo body fills most of the eggshell with a complex, elongated shape showing multiple overlapping segments. The eggshell is densely filled with signal compared to the 2fold references, where more dark space was visible. In the XZ (bottom-left) view, I can see multiple layered bands of signal suggesting 3+ body folds overlapping. The YZ view also shows a complex, non-uniform pattern with bright spots indicating overlapping coils. This matches the pretzel reference images much better than 2fold. The transition from 2fold at T105 to pretzel at T106 is consistent with developmental progression. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with some dark space remaining. The XZ view shows increasing complexity with curved structures, but the fill fraction is not yet as dense as the pretzel references. Previous three timepoints were 2fold, and while there are hints of additional folding, the morphology is not clearly pretzel yet. Defaulting to earlier stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Looking at the XY view (top-left), the embryo body shows multiple overlapping coils/segments filling the eggshell more densely than a typical 2fold. The body appears to have more than two parallel segments visible, with a complex, tangled pattern. In the XZ view (bottom-left), there are multiple layers of signal visible with a complex internal structure suggesting 3+ folds. The YZ view (top-right) shows the eggshell is moderately to densely filled. Compared to the 2fold references (which show a clearer U-shape/hairpin with moderate fill), this image shows more complexity and denser filling, matching the pretzel references better. The transition from 2fold to pretzel is consistent with developmental progression from the previous timepoints. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see multiple overlapping body segments forming a complex coiled pattern within the eggshell - there appear to be at least 3 parallel/overlapping segments visible, creating a loop or pretzel-like arrangement. The eggshell is densely filled with signal compared to the 2fold reference images, with relatively little dark empty space inside the eggshell boundary. The XZ view (bottom-left) also shows multiple layered bands of signal consistent with multiple body folds. This morphology matches the pretzel reference images better than the 2fold references, which show only two parallel segments with more empty space. The transition from 2fold at T108 to pretzel at T109 is plausible as the embryo continues to elongate and fold. | [zslice] 3 segment(s) at midplane \u2192 pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - in the XY view (top-left), the body fills most of the eggshell with complex, overlapping structures. The XZ view (bottom-left) shows multiple overlapping layers of signal filling the shell densely. In the YZ view (top-right), the signal shows a complex pattern with multiple coils visible. There are more than two parallel body segments visible, consistent with 3+ folds. This matches the pretzel reference images well, with dense filling and complex coiled morphology. The previous timepoint (T109) was also classified as pretzel, and stages change slowly, so pretzel is consistent. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with approximately two parallel body segments visible in XY view. Some dark space remains inside the eggshell boundary. The pattern is not yet densely packed with multiple overlapping coils as in pretzel references. Previous observation was 2fold, and morphology is consistent with late 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark space remaining, consistent with late 2fold. The XY view shows two main body segments with a curved arrangement. While complexity is increasing (T109 was pretzel), the fill fraction still shows enough empty space to remain consistent with the 2fold classification from T110-111. Defaulting to earlier stage when uncertain. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two body segments visible in XY view with a folded pattern. XZ view shows crossing bands consistent with 2fold hairpin. Not yet densely filled enough for pretzel. Consistent with previous three observations of 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal, and the XY view shows two parallel body segments characteristic of 2fold. The XZ view shows layered internal structure consistent with a folded body. Fill fraction is moderate (not sparse like 1.5fold, not dense like pretzel). Matches 2fold reference images well. Previous T111-T112 were 2fold, and this morphology is consistent with that stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view. The XZ view shows folded structure but not the dense multi-coil pattern of pretzel. Consistent with previous 2fold classification and matches 2fold reference images. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear curved/folded morphology - two parallel body segments are visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is some dark space remaining but not densely packed like a pretzel. The XZ view (bottom-left) shows a curved structure consistent with 2fold. Comparing to references, this matches the 2fold examples well - the fill fraction is moderate (not yet dense enough for pretzel), and I can see approximately two parallel body segments rather than three or more overlapping coils. Previous observations were 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately to densely filled with signal showing multiple overlapping body segments visible in both XY and XZ views. The complex, layered pattern with multiple bright bands in the XZ projection indicates 3+ body folds, consistent with pretzel stage. This matches the pretzel references better than 2fold, and is consistent with the T116 pretzel classification. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal \u2014 not sparse (ruling out 1.5fold) but not densely packed with multiple overlapping coils (ruling out pretzel). The XY view shows two parallel body segments with a clear fold/bend, consistent with a hairpin U-shape. The XZ view shows layered bright regions suggesting two body layers. This matches the 2fold reference images best. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - in the XY view (top-left), the signal extends across most of the eggshell with complex, overlapping structures visible. The YZ view (top-right) shows a ring-like pattern suggesting multiple coiled body segments. The XZ view (bottom-left) also shows dense, complex signal filling most of the shell. This matches the pretzel reference images well, with multiple overlapping body folds creating a tangled appearance. The eggshell fill fraction is high (dense), consistent with pretzel stage. This is also consistent with the previous observation at T118 being pretzel. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible folding/layering in XZ view showing ~2 parallel body segments. More filled than 1.5fold references but not as densely packed as pretzel. The XY view shows an elongated body with clear curvature and folding. Previous observations oscillated between 1.5fold and pretzel; 2fold is the intermediate stage that best matches the current morphology. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, and the XY projection shows complex, multi-layered folding with more than two parallel body segments visible. The pattern matches the pretzel reference images better than 2fold. The body appears to have multiple overlapping coils rather than a simple hairpin shape. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape within the eggshell. The eggshell is moderately filled - there's some dark space remaining but the body occupies a good portion of the interior. The YZ view (top-right) shows a ring-like or donut pattern consistent with a folded body seen end-on. The XZ view (bottom-left) shows multiple bright bands suggesting two parallel segments. The fill fraction is moderate (not densely packed like pretzel), and the pattern matches the 2fold reference images well. This is consistent with the previous classification of 2fold at T121. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 123, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments and curves - more than just two parallel segments. The body appears to fold back on itself multiple times, creating a tangled/coiled appearance. The eggshell is densely filled with signal in the XZ view (bottom-left), with relatively little empty dark space inside the shell boundary. Compared to the 2fold references which show a clearer U-shape/hairpin with two parallel segments and moderate fill, this image shows more complex folding with greater eggshell fill. The morphology matches the pretzel reference images with multiple overlapping coils. While previous observations were 2fold, the clear increase in complexity and fill fraction indicates progression to pretzel stage. | [zslice] 3 segment(s) at midplane \u2192 pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 124, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body spanning most of the eggshell with complex, overlapping structures. The XZ (bottom-left) view shows multiple bright bands/layers indicating multiple body folds overlapping. The YZ view (top-right) shows a complex pattern with what appears to be multiple coiled segments. This is consistent with the pretzel stage reference images where 3+ folds create a densely packed, complex pattern. The previous timepoint (T123) was also classified as pretzel, and stages change slowly, supporting this classification. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 125, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body forming a looping/coiled pattern within the eggshell with at least 2-3 visible body segments curving around the eggshell periphery. The eggshell is moderately to densely filled with signal. The complex curved morphology with multiple overlapping segments matches pretzel references better than 1.5fold or 2fold. Despite the previous classification of 1.5fold, the morphology clearly shows advanced folding inconsistent with 1.5fold. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 126, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments/coils visible in XY and XZ views, creating a complex tangled pattern. Matches pretzel reference images. The previous classifications of 1.5fold and 2fold at T124-T125 were likely errors since T123 was already pretzel and stages don't regress. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 127, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell fill is moderate with some dark space remaining, and there are hints of two parallel body segments forming. However, given the previous observation was 1.5fold and the oscillation between 1.5fold/2fold in recent timepoints suggests a transitional stage, I default to the earlier stage (1.5fold) per the classification rules. The fill fraction is not yet clearly moderate enough to definitively call 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 128, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body with visible folding - I can see two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion of the eggshell. The XZ view shows layered bright bands consistent with two parallel body segments. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images. This is consistent with the previous observation of 2fold at T127. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 129, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows a complex but not yet densely packed pattern. Compared to the pretzel reference images, this embryo is not yet densely filling the eggshell and doesn't show the multiple overlapping coils characteristic of pretzel stage. The fill fraction is moderate (consistent with 2fold), not dense. The previous two observations were 2fold, and the morphology is consistent with continuing at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 130, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body that fills most of the eggshell with multiple overlapping segments visible - there appear to be more than two parallel body segments with a complex, coiled pattern. The eggshell is densely filled with signal compared to the 2fold references, which show more empty dark space. The XZ view (bottom-left) shows a complex pattern with overlapping bright regions consistent with multiple body folds. The YZ view (top-right) shows a ring-like or donut pattern suggesting the body is coiling around itself. This matches the pretzel reference images better than 2fold. While previous timepoints were classified as 2fold, the morphology here shows clear progression to pretzel with increased eggshell fill and multiple overlapping coils. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 131, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - there's still some dark space visible within the eggshell boundary, particularly on the right side. The signal shows what appears to be two parallel body segments with some complexity, but the eggshell is not yet densely packed as in pretzel stage. The XZ view shows a moderately filled pattern with some internal structure but not the dense, complex coiling pattern of pretzel. This matches the 2fold reference images well. Previous three observations were all 2fold, and while the fill fraction may be slightly increasing, it hasn't reached the dense pretzel level yet. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 132, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments forming a clear hairpin/U-shape with moderate eggshell filling \u2014 some dark space remains but less than 1.5fold. This matches the 2fold reference images well. Previous T129-T130 were 2fold; the T131 1.5fold classification was likely an error since development doesn't reverse. The morphology clearly shows two folded segments. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 133, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with elongated body visible in XY view. YZ view shows a loop/ring pattern suggesting body folding, but overall fill density is not yet at pretzel level. Two parallel body segments are most consistent with 2fold. Previous observation was 2fold, and morphology does not clearly show the dense, multi-coil pattern of pretzel. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 134, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments forming a clear hairpin/U-shape fold. The eggshell is moderately filled - more than 1.5fold but not densely packed like pretzel. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well, with moderate fill fraction and clear two-segment morphology. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 135, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape that moderately fills the eggshell, with visible parallel body segments suggesting a folded morphology. The XZ view (bottom-left) shows complex internal structure with what appears to be two parallel body segments connected by a bend. The eggshell fill is moderate - not sparse (ruling out 1.5fold) but not densely packed with multiple overlapping coils (ruling out pretzel). The morphology is consistent with the 2fold reference images, showing two parallel body segments. This is also consistent with the previous observation of 2fold at T134. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 136, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments with a dark gap between them forming a hairpin/U-shape. The YZ view shows a ring-like pattern with a dark center, characteristic of 2fold where two body layers create a ring in cross-section. Eggshell fill is moderate. This matches 2fold references better than 1.5fold, which would show sparser filling and less distinct parallel segments. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 137, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a looping body structure tracing the eggshell periphery with moderate fill fraction. The YZ view shows multiple bright bands suggesting body folding. While there are hints of additional complexity beyond a simple 2fold, the eggshell is not yet densely filled as in pretzel references. Previous stage was 2fold, and following the rule to prefer the earlier stage when uncertain, this remains 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 138, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. This is consistent with 2fold stage. The fill fraction is moderate (not densely packed like pretzel), and the morphology matches the 2fold reference images. The previous two timepoints were also classified as 2fold, and there's no clear evidence of a third fold or dense packing that would indicate pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1326.0906598567963, + "error": null, + "accuracy": 0.2619047619047619, + "adjacent_accuracy": 0.8571428571428571 + }, + { + "embryo_id": "embryo_2", + "predictions": [ + { + "timepoint": 45, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body with sparse eggshell filling and some curvature, but no clear J-shape or partial hairpin fold is visible yet. The morphology is very similar to the comma reference images and hasn't clearly transitioned to 1.5fold. Following the rule to prefer the earlier stage when uncertain and given three consecutive comma classifications.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Compared to the comma reference images, this embryo shows more elongation and the body appears to be starting to fold back on itself. In the XY view (top-left), the embryo has an elongated shape with what appears to be the beginning of a fold - the body is more stretched out than a comma shape. The eggshell is still sparsely filled with significant dark space remaining, consistent with 1.5fold rather than 2fold. Comparing to the 1.5fold reference (T47), the morphology matches well - an elongated body beginning to curve back with sparse eggshell filling. The transition from comma to 1.5fold is appropriate at T46 given the reference series shows 1.5fold beginning around T47. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that fills the eggshell sparsely - there is still significant dark space within the eggshell boundary, particularly at the lower-left region. The body appears to have one main curved band with a partial fold beginning (J-shape), but not yet two clear parallel segments characteristic of 2fold. This matches the 1.5fold reference image at T47 almost exactly. The eggshell fill fraction is sparse, consistent with 1.5fold. The previous observation was also 1.5fold at T46, and stages change slowly, so maintaining 1.5fold is appropriate. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Elongated body within eggshell with sparse-to-moderate fill fraction. Body shows early folding (J-shape) but not yet two clearly parallel segments characteristic of 2fold. Matches 1.5fold reference images well. Consistent with previous timepoint classification. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. The embryo body shows elongation with evidence of two parallel segments forming a fold. Consistent with the previous T48 classification of 2fold. The fill fraction is moderate (not sparse like 1.5fold, not dense like pretzel), supporting 2fold stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body with partial folding but not yet a clear complete hairpin/U-shape with two parallel segments. Eggshell fill is sparse-to-moderate with significant dark space remaining. Morphology closely matches 1.5fold references. At the boundary between 1.5fold and 2fold, defaulting to earlier stage consistent with T49 classification. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is sparsely filled with significant dark space remaining. The embryo body is elongated but does not show two clearly parallel segments forming a complete hairpin. Matches 1.5fold reference images well. Consistent with previous T50 classification of 1.5fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is still sparsely filled with significant dark space remaining. The body shows an elongated shape with partial folding (J-shape) but not yet two clearly parallel segments characteristic of 2fold. Matches 1.5fold reference images well. Consistent with previous observations at T49-T51. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body curving along the eggshell, but there is still significant dark/empty space within the eggshell boundary, indicating sparse filling. The body appears as a single curved band without clear parallel segments that would indicate 2fold. The YZ view shows an irregular, non-uniform shape consistent with early folding. This matches the 1.5fold reference images well, and is consistent with the previous three observations at 1.5fold. No clear transition to 2fold (two parallel segments) is evident yet. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Elongated embryo body with moderate eggshell filling. Some hint of folding visible in XZ view but not yet a clear two-parallel-segment hairpin pattern. Consistent with late 1.5fold stage, matching T57 reference. Previous three timepoints were 1.5fold and no definitive morphological change to 2fold is evident. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body that is beginning to fold, with the signal concentrated in a band that doesn't yet form two clear parallel segments. There is still significant dark/empty space within the eggshell boundary, indicating sparse filling. The XZ view (bottom-left) shows some structure but not the clear two-parallel-segment pattern characteristic of 2fold. Comparing to references, this matches the 1.5fold stage (similar to T52-T57 references) rather than 2fold. The eggshell fill fraction remains sparse to moderate. Given the previous three observations were all 1.5fold and no clear morphological advancement to 2fold is evident, this remains 1.5fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows two bright regions suggesting early folding, but the eggshell still has significant dark/empty space (sparse-to-moderate fill). The morphology is consistent with late 1.5fold, similar to the T57 reference. Not yet clearly showing the moderate fill and distinct parallel segments characteristic of 2fold. Previous three timepoints were 1.5fold, and the change is not definitive enough to advance. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. XY view shows two main body segments in a hairpin/U-shape configuration. XZ view shows layered bands consistent with two parallel folds. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous T56 classification of 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but less than 1.5fold. The body appears to have two parallel segments visible, consistent with a hairpin/U-shape fold. The XZ view shows a pattern with two distinct bright regions suggesting two parallel body segments. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. This is consistent with the previous observations at T56-T57 being 2fold, and no clear advancement to pretzel is evident. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there is some dark space remaining but the embryo body occupies a substantial portion. In the XY view (top-left), the elongated body shows what appears to be two parallel segments with some internal structure, consistent with a 2fold stage. The fill fraction is moderate (not densely packed like pretzel), and the morphology closely matches the 2fold reference images. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. Previous three timepoints were all 2fold, and there's no clear evidence of additional folding that would indicate pretzel stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two roughly parallel body segments with a curved connection, and moderate eggshell fill fraction with some dark space remaining. This matches the 2fold reference images. The previous T59 classification as 1.5fold was likely an error since T57 and T58 were both 2fold and development cannot regress. The morphology clearly shows 2fold characteristics. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a clear elongated shape with two parallel body segments visible - a brighter region on the left and a dimmer folded portion on the right, forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view shows two distinct layers of signal separated by a darker gap, consistent with a 2fold configuration. This matches the 2fold reference images well. The fill fraction is moderate (not densely packed like pretzel), and the morphology is consistent with the previous T60 classification of 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal \u2014 some dark space remains but not densely packed like pretzel. In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments forming a hairpin/U-shape. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not sparse like 1.5fold, not dense like pretzel). Previous observations were 2fold, and the morphology is consistent with continuing at this stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows bilobed structure with two parallel body segments and a clear fold/bend connecting them. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference images well. Previous T60 and T61 were 2fold, and morphology here is consistent with 2fold rather than 1.5fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct body segments forming a hairpin/U-shape fold, with moderate dark space remaining inside the eggshell. The fill fraction is moderate, not dense enough for pretzel. Morphology matches 2fold reference images well. Consistent with previous observation of 2fold at T63. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo that moderately fills the eggshell, with visible folding structure - two parallel body segments can be discerned. The XZ (bottom-left) view shows layered signal consistent with a folded body. The eggshell is moderately filled - more than 1.5fold but not yet densely packed like pretzel. The YZ view shows some internal structure with distinct bright spots. This matches the 2fold reference images well, and is consistent with the previous observations at T63-T64. No clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments in a hairpin/U-shape configuration with moderate eggshell filling. Dark space remains but less than 1.5fold. Matches 2fold reference images well. Previous T63-T64 were 2fold; development should not regress to 1.5fold at T65-T66. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments visible - a clear folded/hairpin structure. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well, with moderate eggshell fill and two parallel segments. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated curved body that occupies a moderate portion of the eggshell, with some dark space remaining below the body. The body appears to have two parallel segments visible - a curved band along the top/dorsal side with the body folding back. The XZ view (bottom-left) shows layered bright bands consistent with two parallel body segments. The eggshell fill is moderate - not sparse (ruling out 1.5fold) but not densely packed (ruling out pretzel). This matches the 2fold reference images well, and is consistent with the previous observations at T66-T67. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. The XZ view shows layered signal consistent with folded body segments. Compared to the reference images, this matches the 2fold stage (T62-T75 range). The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous 2fold observations at T66-T68. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear constriction/bend in the middle, forming two distinct lobes connected by a narrower region - this is consistent with a 2fold hairpin/U-shape with two parallel body segments. The eggshell is moderately filled - there is some dark space but the signal occupies a good portion of the eggshell interior. The XZ view (bottom-left) shows two bright masses consistent with two overlapping body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, consistent with slow stage progression. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with dark space on one side but substantial signal coverage. Two parallel body segments visible in XY view forming a hairpin/U-shape. Matches 2fold reference images well. T68-T69 were 2fold; the T70 1.5fold call was likely a misclassification as development doesn't regress. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments - a clear folded/hairpin structure with a bend visible. The eggshell is moderately filled - there's some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. The YZ view (top-right) shows a compact structure with some internal differentiation. This matches the 2fold reference images well, with moderate eggshell filling and two visible parallel segments. Consistent with previous observation at T71 (2fold). | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct body lobes forming a hairpin/U-shape consistent with 2fold. Eggshell is moderately filled with some dark space remaining. The pattern does not yet show the dense, complex overlapping coils of pretzel stage. Consistent with previous 2fold classification at T71-T72 and matches 2fold reference images. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see a clear folded embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The body shows two distinct lobes connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly around the edges, but the embryo occupies a good portion of the shell. This is consistent with 2fold morphology. The XZ view (bottom-left) shows multiple bright bands consistent with two parallel body segments. Comparing to references, this matches the 2fold examples (T62-T75) well - the fill fraction is moderate (not yet densely packed like pretzel). The previous three timepoints were all 2fold, and there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct parallel body segments forming a hairpin/U-shape, consistent with 2fold morphology. Eggshell fill is moderate - significant signal but still some dark space remaining. Matches 2fold reference images well. Previous T72-T73 were 2fold, and morphology here is consistent with continued 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body with clear folding - I can see two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled with signal - there's some dark space remaining but the body occupies a substantial portion of the eggshell. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two parallel segments rather than three or more overlapping coils. Previous observation was 2fold, and this is consistent with that stage. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately-to-densely filled with signal. Multiple body layers visible in XZ view. Previous timepoint was classified as pretzel, and the morphology is consistent with early pretzel stage - complex overlapping structure within the eggshell, though fill fraction is not as dense as later pretzel references. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal showing two parallel body segments visible in the XY projection, with a darker central region between them. The XZ view shows layered bright bands consistent with a folded body. The fill fraction is moderate (not sparse like 1.5fold, not densely packed like pretzel). This matches the 2fold reference images well. The previous observations were inconsistent (oscillating between stages), but the morphology here clearly shows a 2fold pattern. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal. The XZ view shows complex, multi-layered internal structure with overlapping coils rather than a simple two-segment hairpin. The fill fraction and complexity match pretzel references. At T79, this aligns with the pretzel timepoint range, and T76 was already classified as pretzel - development cannot regress. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The YZ view (top-right) shows a somewhat complex pattern with distinct bright regions suggesting folded body segments. The XZ view (bottom-left) shows layered bright bands consistent with two parallel body segments. Comparing to references, this matches the 2fold stage well - the fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two clear body segments. Previous observations at T78-T79 were 2fold, and stages change slowly, so maintaining 2fold is appropriate. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Looking at the eggshell fill fraction: the signal is densely filling the eggshell with relatively little dark space remaining inside the shell boundary, especially visible in the XZ (bottom-left) view where the signal appears complex and fills most of the interior. In the XY view (top-left), the body appears elongated and fills much of the eggshell, with what appears to be multiple overlapping segments creating a complex pattern rather than a simple two-parallel-segment hairpin. The YZ view (top-right) shows bright spots distributed throughout, suggesting multiple overlapping body layers. Comparing to references, this looks more like the T82 pretzel reference than the T75 2fold reference - the fill fraction is denser and the pattern more complex. The transition from 2fold at T80 to pretzel at T81 is plausible as the embryo has been at 2fold for several timepoints. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little dark space remaining. The XY projection shows complex, overlapping body structures rather than simple parallel segments, and the XZ view shows a swirling/coiled pattern. This matches the pretzel reference images closely. The fill fraction is too dense for 2fold, and the complexity of overlapping structures indicates 3+ folds. Previous 2fold classifications at T79-80 suggest natural progression to pretzel by T82. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with two roughly parallel body segments visible in a hairpin/U-shape configuration. The filling is not yet dense enough for pretzel stage. Consistent with previous 2fold classification and matches 2fold reference images. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view with a gap between them. YZ view shows ring-like pattern consistent with hairpin fold seen end-on. Matches 2fold references well. Not yet dense enough for pretzel. Consistent with previous 2fold classifications at T82-T83. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with some dark space remaining, particularly visible in XY view. Two parallel body segments visible but not the dense multi-coil pattern of pretzel. Consistent with previous 2fold observations at T82-T84. Not yet showing the densely packed, complex overlapping pattern seen in pretzel references. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with two parallel body segments visible in the XY projection, forming a hairpin/U-shape. Matches 2fold reference images well. Previous T83-T84 were 2fold; T85 regression to 1.5fold was likely misclassification. Morphology is consistent with 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - there are some dark regions but the body clearly shows folded structure with two parallel segments visible. The XZ (bottom-left) view shows a complex pattern with multiple bright bands suggesting at least two body layers. The fill fraction is moderate (not densely packed like pretzel, but more filled than 1.5fold). This matches the 2fold reference images well. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY projection shows two parallel body segments forming a hairpin/U-shape with moderate eggshell filling. Some dark space remains within the eggshell boundary. The pattern does not yet show the dense, multi-coiled complexity of pretzel stage. Consistent with previous 2fold classification at T87. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments forming a clear hairpin/U-shape fold. Eggshell is moderately filled with some dark space remaining. YZ view shows ring-like pattern consistent with folded body. Matches 2fold references well. Previous T86-T87 were 2fold; development cannot regress to 1.5fold, and morphology clearly shows two parallel segments. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY projection shows two parallel body segments forming a clear hairpin/U-shape fold. The eggshell is moderately filled with signal but still has dark spaces, consistent with 2fold. Not yet densely filled enough for pretzel. Matches 2fold reference images and is consistent with the previous T89 classification. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows two distinct parallel layers of signal separated by a darker gap, indicating a hairpin/U-fold. The eggshell is moderately filled with some dark space remaining. This matches the 2fold reference images. The embryo has progressed from the 1.5fold seen at T90, with clearer two-segment morphology now visible. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see the embryo body forming a clear elongated shape with what appears to be two parallel body segments visible - a hairpin/U-shape fold pattern. The eggshell is moderately filled with signal - there is some dark space remaining but less than what you'd see in 1.5fold. The YZ view shows a somewhat complex but not yet densely packed pattern. Comparing to references, this matches the 2fold stage well - the body has folded back on itself creating two parallel segments, but hasn't yet reached the dense, multi-coiled pretzel stage. The fill fraction is moderate rather than dense. Previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with signal - more than 1.5fold but not as densely packed as pretzel references. Two parallel body segments are visible in the XY projection. The XZ view shows layered structure consistent with 2fold. Dark spaces remain within the eggshell, distinguishing this from the densely filled pretzel stage. Consistent with previous 2fold classifications at T91-T92. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two roughly parallel body segments with a fold/bend, and moderate eggshell filling with some dark space remaining. The morphology matches 2fold references well - more filled than 1.5fold but not densely packed like pretzel. T91 and T92 were both 2fold, and this image is consistent with that stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with some dark space remaining, two parallel body segments visible in XY view, consistent with 2fold reference images. Not yet densely filled enough for pretzel. Matches previous observation of 2fold. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping body segments visible. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple coils/folds filling most of the eggshell. The XZ view (bottom-left) shows multiple layered bands of signal consistent with 3+ folds. The YZ view (top-right) shows a complex pattern with multiple bright regions. This matches the pretzel reference images well, with dense eggshell filling and multiple overlapping body segments. Consistent with the previous T95 classification of pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is becoming densely filled with fluorescent signal, and the XY and XZ views show complex, overlapping body segments suggesting 3+ folds. Compared to the 2fold reference, there is more signal coverage and structural complexity. The pattern matches the pretzel reference images more closely, with multiple coiled body segments visible. At T97, the transition from 2fold to pretzel appears to be occurring. | [zslice] 3 segment(s) at midplane \u2192 pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows multiple overlapping coils/body segments within the eggshell, with a complex looping pattern visible. The eggshell is densely filled with signal - there's relatively little empty dark space inside the eggshell boundary. The XZ view (bottom-left) shows multiple bright layers stacked, consistent with overlapping body folds. The YZ view (top-right) shows a compact, bright mass. This matches the pretzel reference images well, with 3+ body segments creating a tangled appearance. The previous observation was pretzel, and the morphology is consistent with continuing in this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping body segments visible in both XY and XZ views. Multiple coiled layers are apparent in the XZ projection, consistent with 3+ folds. The fill fraction and complexity match the pretzel references better than 2fold. While previous timepoints oscillated, the morphology here shows dense filling characteristic of pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space. Multiple overlapping body segments/coils are visible in the XY projection, creating a complex tangled pattern. This matches pretzel reference images. The fill fraction and complexity exceed what is expected for 2fold, which should show two parallel segments with moderate empty space. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell fill fraction is moderate with some dark space remaining. While the body shows increasing complexity suggesting progression toward pretzel, the fill is not yet dense enough to clearly classify as pretzel. Previous three timepoints were 2fold, and following the rule to prefer the earlier stage when uncertain, maintaining 2fold classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a folded embryo with two visible parallel segments and increasing complexity, but the eggshell is not yet densely filled as in pretzel references. Moderate fill fraction with some dark space remaining. The morphology is advancing but still consistent with late 2fold. Previous three timepoints were 2fold, and the change is not yet definitive enough to advance to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see multiple overlapping body segments with a complex, coiled pattern - there appear to be at least 3 parallel/overlapping body segments visible, creating a tangled appearance. The eggshell is densely filled with signal compared to the 2fold reference images, with less empty dark space inside the shell boundary. The YZ view shows a complex, non-uniform pattern with multiple bright regions suggesting overlapping coils. This morphology matches the pretzel reference images much better than the 2fold references, which show simpler U-shaped/hairpin patterns with more empty space. The transition from 2fold at T100-102 to pretzel at T103 is consistent with developmental progression. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY projection shows two main body segments in a hairpin/U-shape configuration with moderate eggshell filling. Dark space remains visible within the eggshell boundary, particularly in the constriction between the two lobes. This matches the 2fold references rather than pretzel, which would show denser filling with multiple overlapping coils. Consistent with previous three timepoints all classified as 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal showing complex internal structure with multiple body segments visible in both XY and XZ views. The fill fraction is moderate with some dark spaces remaining, consistent with 2fold. Previous T102-T103 were 2fold; the T104 1.5fold classification was likely erroneous as development doesn't regress. The morphology matches late 2fold references. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a figure-8/dumbbell shape with two lobes connected by a constriction, consistent with the body beginning to fold back. The eggshell is sparsely filled with significant dark space remaining. No clear parallel body segments characteristic of 2fold are visible. Morphology is consistent with 1.5fold and matches previous observations at T104-T105. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body with moderate eggshell filling and a dark gap suggesting early folding. Two parallel segments are beginning to emerge but are not yet as clearly defined as in the 2fold references. The XZ view shows hints of two layers. Previous three observations were 1.5fold, and while this is late 1.5fold approaching 2fold, the morphology hasn't clearly transitioned yet. Defaulting to earlier stage. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows a clear U-shaped/ring-like body with two parallel segments and a dark center, consistent with 2fold. Eggshell is moderately filled but not densely packed as in pretzel. The XZ view shows a looping pattern with two body layers. Matches 2fold references well and is consistent with previous T107 classification. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with complex, overlapping body segments filling most of the eggshell. There appear to be multiple coiled segments visible, with the signal densely packed within the eggshell boundary. The XZ view shows a densely filled pattern with complex internal structure consistent with multiple folds. The eggshell fill fraction is high (densely filled), matching the pretzel stage. This is consistent with the previous T108 classification of pretzel, and stages change slowly. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal (70-80%), more than expected for 1.5fold. The XY view shows an elongated body with two parallel segments visible, consistent with a hairpin/U-fold. The XZ view shows layered bright bands indicating folded body segments. The fill fraction is moderate (not dense enough for pretzel) and matches 2fold references. Previous observations were inconsistent, but the morphology here clearly exceeds 1.5fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Looking at the XY view (top-left), the eggshell is densely filled with fluorescent signal - there is very little dark/empty space within the eggshell boundary. The signal shows complex, overlapping structures with multiple body segments visible, creating a tangled pattern. In the XZ view (bottom-left), I can see multiple overlapping layers of the body creating a complex pattern with bright regions throughout. The YZ view (top-right) shows an irregular, multi-lobed structure consistent with multiple coils. This dense filling pattern with complex overlapping structures matches the pretzel reference images much better than 2fold (which would show moderate filling with a clear hairpin/U-shape). The T108 classification of pretzel was likely correct, and the T109-T110 classifications may have been underestimates. At T111, the morphology clearly shows pretzel-stage characteristics. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with visible folding structure - I can see what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows multiple bright bands suggesting two parallel segments. The fill fraction is moderate (not densely packed like pretzel), consistent with 2fold. This matches the previous observations of 2fold at T110-T111, and there's no clear evidence of three or more overlapping coils that would indicate pretzel stage. | [zslice] 3 segment(s) at midplane \u2192 pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, elongated shape with multiple overlapping body segments and coils visible within the eggshell. The eggshell is densely filled with signal - there's relatively little dark empty space inside the eggshell boundary. The XZ (bottom-left) view shows multiple layered bright bands consistent with overlapping body folds. The YZ view shows a complex pattern with multiple bright spots. This matches the pretzel reference images well, with 3+ body folds creating overlapping coils. The previous timepoint was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex folded body with what appears to be 3+ overlapping segments, including a tight curl on the left side. The eggshell is moderately-to-densely filled. The XZ view shows complex layered internal structure. This matches pretzel references better than the simpler U-shape of 2fold, despite oscillation in recent observations. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments are visible in the XY projection, creating a complex pattern. The XZ view shows coiled/overlapping structures. This matches pretzel references. Additionally, T112 was pretzel, so development cannot regress to 2fold - the T113-T114 classifications were likely errors. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body that fills the eggshell moderately but not densely - there is still some dark space visible within the eggshell boundary. The body appears to have two parallel segments visible, consistent with a 2fold stage. The XZ view (bottom-left) shows a moderately filled eggshell with some internal structure/layering but not the dense, complex coiling pattern characteristic of pretzel stage. The YZ view (top-right) shows a somewhat triangular/irregular shape with distinct bright clusters, suggesting folded body segments. Compared to the pretzel reference images which show much denser filling and more complex overlapping coils, this image still has moderate empty space. The fill fraction is moderate rather than dense, consistent with 2fold. Previous three timepoints were all 2fold, and there's no clear transition to pretzel-level complexity yet. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with some remaining dark space, particularly visible in the XY view. While there's increasing complexity suggesting the embryo is approaching pretzel stage, the fill fraction is not yet dense enough to clearly indicate pretzel. Previous three timepoints were 2fold, and without a definitive morphological change to multiple overlapping coils densely filling the shell, I maintain the 2fold classification. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments forming a hairpin/U-shape. YZ view shows a ring-like cross-section consistent with two overlapping body segments. Eggshell is moderately filled with some dark space remaining. Morphology matches 2fold references and is consistent with T115-T116 classifications of 2fold. More advanced than 1.5fold based on clear parallel segments. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body that moderately fills the eggshell, with some dark space remaining but not as much as in 1.5fold. There appear to be two parallel body segments visible, consistent with a 2fold stage. The XZ view shows a complex but not yet densely packed pattern - the eggshell is moderately filled rather than densely filled as in pretzel. This matches the 2fold reference images well. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments running along the eggshell length, and the XZ view shows two distinct layers separated by a dark gap - characteristic of a 2fold hairpin. Eggshell is moderately filled with some dark space remaining. Morphology matches 2fold references better than 1.5fold, with clear parallel organization rather than a J-shape. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there's some dark space remaining but the body occupies a good portion of the eggshell interior. The XZ view (bottom-left) shows a complex but not yet densely packed pattern. Comparing to references, this matches the 2fold stage well - two parallel segments visible, moderate fill fraction. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body that moderately fills the eggshell, with visible parallel body segments suggesting a folded morphology. The eggshell is moderately filled - not densely packed like pretzel stage, but more filled than 1.5fold. The XZ view (bottom-left) shows a pattern consistent with two parallel body segments. Comparing to references, this matches the 2fold stage well - the body has folded into a hairpin with two parallel segments visible, but hasn't yet reached the dense, multi-coiled pretzel configuration. Previous observations at T120-T121 were 2fold, and stages change slowly, so maintaining 2fold classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1194.3732302188873, + "error": null, + "accuracy": 0.358974358974359, + "adjacent_accuracy": 0.8589743589743589 + }, + { + "embryo_id": "embryo_3", + "predictions": [ + { + "timepoint": 39, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a curved body shape and some dark space within the eggshell, consistent with comma stage. The body shows one curved band of nuclei with a constriction/indentation visible, but no clear parallel folded segments yet. The eggshell is not sparsely filled enough for early 1.5fold - there's still substantial signal but with some empty regions. Comparing to references, this matches the comma reference images (T40-T44) very well. The previous three timepoints were all comma, and there's no clear morphological change to 1.5fold yet (no J-shape or hairpin visible).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 40, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but hasn't yet formed a clear fold-back. The eggshell still has some empty space, particularly visible in the XY projection where the body doesn't fully fill the oval boundary. Compared to the 1.5fold reference, this image lacks the clear J-shape or partial hairpin structure - the body appears as a single curved band rather than showing a fold. The morphology is consistent with the comma reference images, showing the characteristic C-shaped curvature. Previous three timepoints were all comma, and stages change slowly, so maintaining comma classification.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 41, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve, with the body occupying a moderate portion of the eggshell but still leaving significant dark space, particularly at the ends. The shape shows a curved band of nuclei consistent with comma stage. Compared to the 1.5fold reference, the embryo here hasn't yet developed a clear J-shape or partial hairpin fold - it's still more of a curved/comma morphology. The eggshell fill is sparse-to-moderate, consistent with comma/early 1.5fold. Given the previous three observations were all comma and stages change slowly, and I don't see a definitive fold-back of the tail, I maintain the comma classification.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 42, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body with some curvature but no clear parallel body segments yet. The eggshell is sparsely filled with significant dark space. While there's some progression from earlier comma stages, the morphology doesn't yet show a definitive J-shape or partial hairpin characteristic of 1.5fold. Previous three timepoints were comma, and the change is not clearly sufficient to advance the stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 43, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows elongation within the eggshell with sparse fill, similar to late comma/early 1.5fold transition. The XY view shows the body curving but not yet forming a clear J-shape or partial hairpin fold. Previous three timepoints were comma, and without a definitive fold-back visible, I default to the earlier stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 44, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo has elongated beyond the comma shape and shows early folding (J-shape) in the XY view. The eggshell is sparsely filled with significant dark space remaining. The XZ view shows bright regions suggesting the tail beginning to fold back. This matches the 1.5fold reference images better than comma, representing a clear morphological advancement from the previous comma observations. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 45, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated shape with a clear constriction/narrowing creating a J-like or partial hairpin shape. The body is beginning to fold back on itself but hasn't formed two fully parallel segments yet. The eggshell is sparsely filled - there's significant dark space within the eggshell boundary, particularly at the bottom-left of the XY view. This matches the 1.5fold reference images well. The previous timepoint was also classified as 1.5fold, and only one timepoint has passed, so maintaining this classification is appropriate. It's not yet 2fold because there aren't two clearly parallel body segments visible. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear curved/folded shape - there's a larger mass on the left and a narrower extension curving to the right, consistent with a J-shape or partial fold. The eggshell is still sparsely filled - there's significant dark space around and below the embryo body, particularly visible in the bottom portion of the XY view. The XZ view (bottom-left) shows the body splitting into what appears to be the beginning of a fold but not yet two clearly parallel segments. Compared to the 1.5fold reference images, this matches well - the body is elongating and beginning to fold but hasn't formed the clear two-parallel-segment hairpin characteristic of 2fold. The fill fraction remains sparse, consistent with 1.5fold rather than 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body that fills the eggshell but with a visible curved/folded structure - there's a clear arc of nuclei with the beginning of a fold-back, but not yet two distinct parallel segments. The eggshell is sparsely to moderately filled - there's still noticeable dark space, particularly at the edges. The overall morphology closely matches the 1.5fold reference images (T47 in the reference set). The previous three timepoints were all 1.5fold, and there's no clear transition to 2fold yet (no obvious two parallel body segments or hairpin shape). | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with some dark gaps remaining. Two parallel body segments visible in XY and XZ views, consistent with a hairpin fold. Matches 2fold reference images well. Previous timepoint was also 2fold, and morphology is consistent. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two lobes with a constriction and significant dark/empty space within the eggshell (sparse fill). The body is folding but does not yet show clear parallel segments characteristic of 2fold. Consistent with 1.5fold reference images and previous observation. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear curved/folded morphology - there appear to be two parallel body segments visible, consistent with a 2fold stage. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows a complex pattern with multiple bright regions suggesting overlapping body segments. Comparing to references, this matches the 2fold examples better than 1.5fold (which would show more empty space and a simpler J-shape) or pretzel (which would show denser filling). The previous observation was 2fold, and the morphology is consistent with maintaining this classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view forming a hairpin/U-shape. XZ view shows two distinct lobes consistent with 2fold. Eggshell is moderately filled with some dark space remaining - not densely packed enough for pretzel. Consistent with previous 2fold classification at T49-T50. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is some dark space visible but the embryo occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see what appears to be two parallel body segments with a darker region/gap between them, consistent with a hairpin/U-shaped fold. The XZ view (bottom-left) also shows two distinct layers of signal. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear morphological change to suggest progression to pretzel - the shell still has noticeable empty space. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY projection shows two distinct body lobes/segments with a constriction between them, indicating a hairpin fold. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference images well. Previous T50-T51 were 2fold, and morphology here is consistent with that stage rather than reverting to 1.5fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view forming a U/hairpin shape. Moderate eggshell fill fraction with some dark space remaining. Matches 2fold reference images. Consistent with previous observation of 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows emerging parallel body segments suggesting approaching 2fold, but the eggshell fill fraction is still relatively sparse with significant dark space. Comparing to references, this is at the 1.5fold/2fold boundary. Given the previous observation was 1.5fold and the rule to prefer the earlier stage when uncertain, maintaining 1.5fold classification. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a clear elongated body with two parallel segments visible - a brighter region on the left side and a folded body curving back along the right side, forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining (particularly at the bottom-right of the eggshell in XY), but it's not densely packed like a pretzel. The XZ view shows layered signal consistent with two body segments overlapping. This matches the 2fold reference images well, and is consistent with the previous observation of 2fold at T55. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there is still some dark space visible, particularly at the edges, but the embryo occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see what appears to be two parallel body segments with a folded/hairpin morphology. The XZ view (bottom-left) shows layered bright regions consistent with two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not densely packed like pretzel), and the morphology shows two parallel segments rather than three or more coils. Previous observations at T55 and T56 were 2fold, and stages change slowly, so 2fold remains appropriate. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments within the eggshell with moderate fill fraction. The XZ view confirms layered body structure. This matches the 2fold reference images well. Previous timepoints T55-T56 were also 2fold, and development doesn't regress, so 2fold is appropriate here. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two lobes of signal with a constriction between them and significant dark space within the eggshell boundary, indicating sparse filling. The body appears to be in an early fold. This matches 1.5fold references well - too much empty space for 2fold, and more folded than comma. Consistent with previous observations at T57-T58. | [zslice] 1 segment(s) at midplane \u2192 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two roughly parallel body segments with moderate eggshell filling. The YZ view shows a ring/C-shaped pattern with a dark center, consistent with two parallel body segments in cross-section. The fill fraction has increased compared to 1.5fold references. This matches the 2fold reference images (T62). Previous stage was 1.5fold, and the morphological change to two visible parallel segments supports progression to 2fold. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view with a dark gap between them forming a hairpin/U-shape. XZ view confirms two distinct layers. Eggshell is moderately filled \u2014 more than 1.5fold references but not as dense as pretzel. Morphology closely matches 2fold reference (T62). Clear progression from previous 1.5fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body folded back on itself, creating two parallel segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view shows layered signal consistent with two body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous timepoint was also 2fold, consistent with slow stage progression. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated body with a visible fold creating two roughly parallel segments, with moderate dark space remaining in the eggshell. The fill fraction is moderate rather than sparse, distinguishing it from 1.5fold. The XZ view shows layered signal consistent with a folded body. This matches the 2fold reference images (T62) well, with the body having folded enough to show two parallel segments connected by a bend. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear folded structure - there appear to be two parallel body segments forming a hairpin/U-shape, with a bright band along the top and another along the bottom connected by a curve. The eggshell is moderately filled - there's some dark space remaining but the body occupies a good portion of the shell interior. The XZ view (bottom-left) shows a complex but not yet densely packed structure with some dark gaps. Compared to the pretzel references, this is less densely filled and doesn't show the multiple overlapping coils characteristic of pretzel stage. The morphology matches the 2fold reference images well, showing two parallel segments. This is consistent with the previous observation of 2fold at T63. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "1.5fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY and XZ views forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. Matches 2fold references well. No evidence of the multiple overlapping coils or dense filling characteristic of pretzel. Consistent with previous 2fold classification at T63-T64. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal, with two parallel body segments visible in the XY view separated by a darker gap. The XZ view shows layered bright bands consistent with a folded body. This matches the 2fold reference images well. T63 and T64 were also 2fold, and the morphology here is consistent with that stage rather than 1.5fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear folded structure with two parallel segments visible - a bright dense region on the left and a curved extension on the right, creating a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows a complex layered structure consistent with 2fold. This matches the 2fold reference images well, and is consistent with the previous observation of 2fold at T66. The fill fraction is moderate (not yet densely packed like pretzel), supporting 2fold classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see two parallel body segments forming a clear hairpin/U-shape, with a bend connecting them. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The morphology shows two distinct parallel tracks of nuclei, consistent with 2fold. Compared to the pretzel reference, the shell is not yet densely filled with multiple overlapping coils. This matches the 2fold reference images well, and is consistent with the previous observations at T66-T67. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible but the embryo occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold morphology. The XZ view (bottom-left) shows layered bright bands suggesting two folded body segments. The fill fraction is moderate (not yet densely packed like pretzel), and the pattern closely matches the 2fold reference images. Previous three timepoints were all 2fold, and there's no clear transition to the more densely packed pretzel stage yet. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear folded structure with two parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. In the XZ view (bottom-left), the signal shows a complex but not yet densely packed pattern - there are still gaps/dark regions within the eggshell boundary. Comparing to references, this matches the 2fold examples (T62-T75 range) rather than pretzel, which would show denser filling with multiple overlapping coils. The previous three timepoints were all 2fold, and while the embryo is progressing, it hasn't yet reached the dense, tangled appearance of pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining, two parallel body segments visible in XY and XZ views forming a hairpin structure, consistent with 2fold reference images. No evidence of three or more overlapping coils that would indicate pretzel. Matches previous observations at T68-T70. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 the XY view shows complex, overlapping coiled structures filling most of the eggshell interior with relatively little dark space remaining. Multiple body segments are visible with a tangled/complex pattern rather than a simple two-parallel-segment hairpin. The YZ view also shows dense, complex signal. Compared to the 2fold references (which show moderate fill with a clear U-shape/hairpin), this image shows significantly more filling and complexity, matching the pretzel references. The transition from 2fold at T71 to pretzel at T72 is plausible given the progressive nature of development. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo filling moderately within the eggshell, with some dark space remaining. The body shows two parallel segments consistent with a 2fold hairpin pattern. The XZ view shows layered bright bands suggesting two folded body segments. The eggshell is moderately filled but not yet densely packed as in pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations at 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo filling a moderate portion of the eggshell with some dark space remaining, consistent with 2fold. There appear to be two parallel body segments visible with a curved/folded morphology. The eggshell is not yet densely packed as in pretzel - there's still noticeable empty space within the shell boundary. The XZ view shows multiple bright bands but not the dense, complex overlapping pattern of pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - more than 1.5fold but not yet densely packed like pretzel. In the XY view (top-left), I can see the embryo body forming roughly two parallel segments within the eggshell, consistent with a 2fold stage. The XZ view (bottom-left) shows a complex but not yet fully coiled pattern - there's a bright curved band suggesting the folded body but not the dense, multi-layered overlapping coils characteristic of pretzel. Comparing to references, this matches the 2fold reference (T75) well. The eggshell still has some dark space, particularly at the periphery, which is consistent with 2fold rather than pretzel. Previous observations were all 2fold, and there's no clear transition to pretzel yet. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo occupies a substantial portion of the eggshell. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments forming a hairpin/U-shape, consistent with 2fold morphology. The fill fraction is moderate rather than dense - comparing to the pretzel references where the shell is much more densely packed with overlapping coils, this image still has noticeable empty regions. The XZ view (bottom-left) shows a pattern consistent with two body layers but not the complex multi-layered pattern of pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo filling the eggshell moderately, with visible folding structure - I can see what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled but not yet densely packed as in pretzel stage - there are still some dark regions within the shell boundary. The XZ view shows layered bright bands consistent with 2fold morphology. This matches the 2fold reference images well. The fill fraction is moderate (not yet dense/pretzel), and the previous three timepoints were all 2fold, consistent with slow stage progression. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with some dark spaces remaining. The XY view shows a body that is folding with visible curvature, but the pattern is not yet as densely packed or complex as pretzel references. Previous three timepoints were 2fold, and while complexity is increasing, the fill fraction and body pattern are still more consistent with late 2fold than pretzel. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows a loop/ring-like body pattern with a darker center, indicating the body has folded back on itself forming two parallel segments. Eggshell is moderately filled. This matches the 2fold reference images and is consistent with T76-T77 classifications. The morphology is clearly more advanced than 1.5fold, which would show sparse filling and a J-shape. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not yet densely packed like pretzel. Consistent with 2fold reference images and previous T79 classification. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments - a brighter region on the left and a dimmer region on the right, consistent with a hairpin/U-fold morphology. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows layered signal consistent with two folded body segments. Compared to the reference images, this matches the 2fold stage well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't progressed to show the multiple overlapping coils characteristic of pretzel. Previous observations at T79-T80 were 2fold, and stages change slowly, so 2fold remains appropriate. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is now densely filled with fluorescent signal with little empty space, and the XY view shows complex overlapping coils rather than a simple two-segment hairpin. Multiple body layers are visible, creating a tangled pattern. This matches the pretzel reference images and represents a clear morphological change from the 2fold stage seen at T79-T81. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with signal - more than sparse but not yet densely packed. The XY view shows folded body segments consistent with 2fold, but the multi-coil pretzel pattern is not yet clearly established. Previous three timepoints were 2fold, and while the embryo is progressing, the morphology hasn't clearly transitioned to pretzel. Defaulting to earlier stage when uncertain. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows a clear hairpin/U-shaped fold with two parallel body segments and a bend on the left side. Eggshell fill is moderate with some dark space remaining. Not yet showing the dense, multi-coil overlapping pattern of pretzel stage. Consistent with previous 2fold observations at T81-T83. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see the embryo body forming a clear hairpin/U-shape with two parallel body segments visible. The eggshell is moderately filled - there is still some dark space visible, particularly in the lower-left portion of the eggshell in the XY view. The fill fraction is moderate, not yet densely packed like the pretzel reference images. The XZ view shows body segments but not the complex overlapping coils characteristic of pretzel stage. This matches the 2fold reference images well. Previous observations were all 2fold, and while the embryo may be approaching pretzel, the eggshell is not yet densely filled enough to classify as pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a complex, coiled morphology with multiple overlapping body segments visible - more than just two parallel segments. The eggshell is densely filled with signal, with relatively little dark/empty space inside the eggshell boundary. The pattern appears tangled with at least 3 body segments visible, consistent with pretzel stage. Compared to the 2fold reference (which shows a clearer U-shape with two parallel segments and more empty space), this image shows more complexity and denser filling. The XZ view also shows a complex, multi-layered pattern. This represents a clear transition from the previous 2fold stage to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the eggshell is densely filled with fluorescent signal \u2014 there is very little dark/empty space inside the eggshell boundary. The signal appears complex and tangled with multiple overlapping body segments visible, rather than the clear two-parallel-segment pattern of 2fold. The XZ view also shows a densely packed, complex pattern with multiple layers. Comparing to references, this matches the pretzel stage (e.g., T82-T88 reference) much better than the 2fold reference, which shows more empty space and clearer two-segment organization. The eggshell fill fraction has increased from moderate to dense, indicating the transition from 2fold to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark spaces remaining. The body shows complex structure but the fill fraction hasn't reached the dense level seen in pretzel references. Previous three timepoints were 2fold, and while the embryo is progressing, the morphology doesn't yet clearly show the dense multi-coil pattern characteristic of pretzel. Defaulting to earlier stage when uncertain. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with approximately two parallel body segments and a clear fold/loop. The eggshell fill is moderate \u2014 some dark space remains inside the shell boundary. While the folding is becoming more complex, it does not yet show the dense, multi-coil pattern characteristic of pretzel stage. Consistent with previous 2fold classifications at T86-T88. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a complex, elongated shape that fills most of the eggshell. The signal is densely packed with multiple overlapping body segments visible - more than just two parallel segments. In the XZ view (bottom-left), I can see multiple layers/bands of signal suggesting 3+ folds. The eggshell is densely filled compared to the 2fold references, with less dark space inside the shell boundary. This matches the pretzel reference images well, where the body has folded three or more times creating overlapping coils. The transition from 2fold to pretzel is consistent with developmental progression from T87-89 being 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with signal but not yet densely packed as in pretzel. The body shows folding consistent with 2fold stage. No clear evidence of 3+ overlapping coils. Consistent with previous observations at T88-T90 (all 2fold). Morphology matches late 2fold references better than pretzel references. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a complex, elongated pattern with multiple overlapping body segments - more than just two parallel segments. The eggshell is densely filled with signal compared to the 2fold references. In the XZ view (bottom-left), the signal fills most of the eggshell with a complex, coiled pattern showing multiple layers. The YZ view (top-right) also shows a more complex, irregular pattern consistent with multiple folds. Compared to the 2fold references which show a clearer hairpin with moderate fill, this image shows denser filling and more complex coiling consistent with the pretzel stage references. While previous observations were 2fold, the morphology here has clearly progressed to show 3+ folds and dense eggshell filling characteristic of pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows multiple bright bands suggesting increasing body folding, and the XY view shows a complex looping pattern. However, the eggshell is not yet densely filled as in pretzel references, and the previous 3 timepoints were 2fold. The morphology is at the late 2fold/early pretzel boundary; defaulting to 2fold per the conservative rule. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with some dark space remaining. While the body pattern is becoming more complex and approaching pretzel-like morphology, the fill fraction is not yet dense enough to clearly indicate pretzel stage. Following the rule to prefer the earlier stage when uncertain and given three consecutive 2fold classifications, I maintain 2fold. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little dark space remaining. The XY view shows multiple overlapping body segments with complex internal structure rather than a clean two-segment hairpin. The XZ view shows multiple bright layers. This matches pretzel reference images better than 2fold. The transition from 2fold at T94 to pretzel at T95 is consistent with developmental progression. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear constriction/fold visible, creating what appears to be two parallel body segments. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. The XZ view shows distinct bright regions with some internal structure suggesting folded body segments. Compared to the pretzel reference, the eggshell is not yet densely filled and the pattern is not as complex/tangled. The morphology is consistent with the 2fold reference images, showing two parallel segments. Previous observations were all 2fold, and there's no clear evidence of progression to pretzel stage yet. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a complex, looping pattern with what appears to be multiple overlapping body segments forming a ring/oval loop shape - this is characteristic of pretzel stage where the body has folded 3+ times. The eggshell is densely filled with signal compared to the 2fold references, with less empty dark space inside the eggshell boundary. The XZ view also shows a complex, multi-layered pattern consistent with multiple coils. Compared to the 2fold references (which show a simpler U-shaped hairpin with moderate fill), this image shows more complexity and denser filling. The morphology matches the pretzel reference images well, with the characteristic looping/coiled appearance. While previous observations were 2fold, the clear transition to multiple overlapping segments indicates progression to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty dark space inside the shell boundary. The XY view shows a complex pattern with multiple overlapping body segments rather than a simple two-segment hairpin. The YZ view shows a ring-like complex pattern. This matches pretzel references better than 2fold, indicating the embryo has progressed from the previous 2fold stage. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little dark space remaining. The XY view shows complex, overlapping body segments rather than a simple two-segment hairpin pattern. The XZ view shows looping/coiling internal structure. This dense fill and complex morphology matches pretzel references better than 2fold, which should show clearer two-parallel-segment patterns with more empty space. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows multiple overlapping coils/body segments forming a complex looping pattern within the eggshell - I can see at least 3 parallel body segments creating an oval/ring-like pattern. The eggshell is densely filled with signal compared to the 2fold reference images, with relatively little empty dark space inside the eggshell boundary. The XZ view (bottom-left) also shows a densely packed, complex pattern with multiple bright layers. This matches the pretzel reference images much better than the 2fold references, which show simpler U-shaped/hairpin patterns with more empty space. The transition from 2fold at T97-99 to pretzel at T100 is a reasonable progression. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see multiple overlapping coils/body segments forming a complex looping pattern within the eggshell - there appear to be 3+ body segments visible, not just 2 parallel ones. The eggshell is densely filled with signal compared to the 2fold references, with relatively little empty dark space inside the shell boundary. The XZ view also shows a complex, densely packed pattern. This matches the pretzel reference images much better than the 2fold references. Although previous timepoints were classified as 2fold, the morphology here clearly shows progression to pretzel with multiple overlapping folds. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a complex pattern with multiple overlapping body segments forming a loop/ring-like structure around the periphery of the eggshell, with a darker center. This is characteristic of pretzel stage where the body has folded 3+ times. The eggshell is densely filled with signal - much more so than the 2fold references which show only two parallel segments. The XZ view also shows dense, complex layering. Compared to the 2fold references, this image shows more body segments and greater eggshell fill. The ring-like appearance in XY with bright signal around the perimeter and multiple overlapping coils matches the pretzel reference images. This represents a clear morphological change from the previous 2fold classification. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little dark space remaining, and the XY view shows multiple overlapping body segments in a complex coiled pattern rather than a simple U-shaped hairpin. This matches pretzel references better than 2fold. The transition from 2fold at T102 is consistent with developmental progression. | [zslice] 2 segment(s) at midplane \u2192 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark spaces remaining. The body shows folded segments consistent with 2fold morphology. While complexity is increasing, it hasn't reached the dense, multi-coiled pretzel pattern yet. Previous three timepoints were 2fold, and the morphology hasn't clearly transitioned to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately to substantially filled but not yet densely packed like pretzel references. The XZ view shows layered structure consistent with folding, but the overall fill fraction and complexity are still closer to late 2fold than pretzel. Previous three timepoints were 2fold, and the morphological change is not yet definitive enough to advance to pretzel. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "1.5fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell fill fraction is moderate with some dark space remaining, particularly visible in the XY view. While internal structure is becoming more complex, it hasn't reached the dense, multi-coil filling characteristic of pretzel stage. Consistent with previous three observations of 2fold, and following the rule to prefer the earlier stage when uncertain. | [zslice] 1 segment(s) at midplane \u2192 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments forming a clear hairpin/U-shape with a bend visible at one end. The eggshell is moderately filled with some dark space remaining, consistent with 2fold. This represents a slight progression from the previous 1.5fold classification at T106. The fill fraction is not yet dense enough for pretzel stage. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a looping/curved body structure with moderate eggshell filling. More complex than a simple hairpin but not yet the densely packed multiple coils of pretzel. Some dark space remains within the eggshell. Previous stage was 2fold, and while morphology is advancing, it hasn't clearly transitioned to pretzel yet. Defaulting to earlier stage when uncertain. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct body segments forming a hairpin/U-shape with a clear constriction between them. Eggshell fill is moderate with some dark space remaining. The pattern matches 2fold references and does not yet show the dense, multi-coiled complexity of pretzel. Consistent with previous 2fold classification at T107-T108. | [zslice] 2 segment(s) at midplane \u2192 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1001.3303804397583, + "error": null, + "accuracy": 0.2112676056338028, + "adjacent_accuracy": 0.971830985915493 + }, + { + "embryo_id": "embryo_4", + "predictions": [], + "duration_seconds": 0.17670345306396484, + "error": null, + "accuracy": 0.0, + "adjacent_accuracy": 0.0 + } + ], + "started_at": "2026-04-22T15:48:17.598609", + "completed_at": "2026-04-22T16:46:59.570164", + "total_predictions": 233, + "overall_accuracy": 0.27896995708154504, + "metrics": { + "accuracy": 0.27896995708154504, + "adjacent_accuracy": 0.8927038626609443, + "per_stage": { + "1.5fold": { + "accuracy": 0.5121951219512195, + "n": 41 + }, + "2fold": { + "accuracy": 0.5932203389830508, + "n": 59 + }, + "pretzel": { + "accuracy": 0.06766917293233082, + "n": 133 + } + } + } +} \ No newline at end of file From c6f514b8def5e5695c65edd7a7d6e8e295573a77 Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Wed, 22 Apr 2026 17:00:42 +0000 Subject: [PATCH 4/7] Add zslice_asym variant: upgrade-only override to cap pretzel regression Same segment-counting subagent as zslice, but only applies the override when the count maps to a *later* stage than the primary (1.5fold->2fold->pretzel). Trigger excludes pretzel since there is nothing to upgrade to, so the worst case on pretzel is parity with scientific. Targets the 1.5fold/2fold gap without the catastrophic pretzel downgrade observed in the symmetric variant. --- perception/__init__.py | 2 ++ perception/zslice_asym.py | 59 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 perception/zslice_asym.py diff --git a/perception/__init__.py b/perception/__init__.py index c180257..e4d04db 100644 --- a/perception/__init__.py +++ b/perception/__init__.py @@ -42,6 +42,7 @@ def get_functions() -> dict: from .changegate import perceive_changegate from .duration_aware import perceive_duration_aware from .zslice import perceive_zslice + from .zslice_asym import perceive_zslice_asym _FUNCTIONS = { "minimal": perceive_minimal, @@ -60,5 +61,6 @@ def get_functions() -> dict: "changegate": perceive_changegate, "duration_aware": perceive_duration_aware, "zslice": perceive_zslice, + "zslice_asym": perceive_zslice_asym, } return _FUNCTIONS diff --git a/perception/zslice_asym.py b/perception/zslice_asym.py new file mode 100644 index 0000000..7a18dec --- /dev/null +++ b/perception/zslice_asym.py @@ -0,0 +1,59 @@ +""" +Z-slice subagent with asymmetric (upgrade-only) override. + +The original zslice variant regressed pretzel 88% -> 7% because a single +midplane slice rarely shows >=3 separable cross-sections on a pretzel embryo +(body folds sit at different z-depths). This variant keeps the segment-counting +subagent but only lets it move the prediction *forward* in the fold ordering +(1.5fold -> 2fold -> pretzel), never back. + +Trigger excludes pretzel since there is nothing to upgrade to, so the worst +case on that stage is parity with `scientific`. +""" + +from ._base import PerceptionOutput +from .scientific import perceive_scientific +from .zslice import _count_segments, _segment_count_to_stage + +_FOLD_ORDER = {"1.5fold": 0, "2fold": 1, "pretzel": 2} +_TRIGGER_STAGES = {"1.5fold", "2fold"} + + +async def perceive_zslice_asym( + image_b64: str, + references: dict[str, list[str]], + history: list[dict], + timepoint: int, + midplane_b64: str | None = None, +) -> PerceptionOutput: + """Scientific classifier + upgrade-only z-slice override on 1.5fold/2fold.""" + primary = await perceive_scientific(image_b64, references, history, timepoint) + + if midplane_b64 is None or primary.stage not in _TRIGGER_STAGES: + return primary + + count, sub_raw = await _count_segments(midplane_b64) + if count is None: + return PerceptionOutput( + stage=primary.stage, + reasoning=f"{primary.reasoning} | [zslice-asym] parse failed; kept primary", + verification_triggered=True, + phase_count=2, + raw_response=primary.raw_response, + ) + + sub_stage = _segment_count_to_stage(count) + if _FOLD_ORDER[sub_stage] > _FOLD_ORDER[primary.stage]: + final = sub_stage + note = f"{count} segment(s) -> {sub_stage} (upgraded from {primary.stage})" + else: + final = primary.stage + note = f"{count} segment(s) -> {sub_stage}; not above primary, kept {primary.stage}" + + return PerceptionOutput( + stage=final, + reasoning=f"{primary.reasoning} | [zslice-asym] {note}", + verification_triggered=True, + phase_count=2, + raw_response=sub_raw, + ) From eea097e09da415365e8e096fab38e4dd99a6835a Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Wed, 22 Apr 2026 18:31:54 +0000 Subject: [PATCH 5/7] zslice_asym ablation (negative): override fires 7x, wrong all 7; subagent has no signal Overall 72.1% vs scientific 77.3% (n=233). Asymmetric design successfully caps the pretzel catastrophe (85% vs 7% for symmetric zslice), but attribution shows the override itself only fired 7 times and was wrong every time (5x 1.5fold->2fold on GT=1.5fold, 2x 2fold->pretzel on GT=2fold). Segment-count distribution across 88 triggers: {1:40, 2:46, 3:2} -- the subagent returns <=2 in 98% of cases regardless of true stage, because a single midplane slice genuinely doesn't show >2 separable cross-sections. The large per-stage swings (1.5fold -46, 2fold +19) are run-to-run variance in the primary classifier, not the override. 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z?lL8|(h1qqa%x3max#O`Omme}_x+rXg@xb}^3inmq#e$fcFm(T#7@wo>Nh1Uisxhz z@>-#ITza|(_~2fad4AaRt=HI{BFjkbkK@Dq0|Pdy!FhHXeIQj{G_}Xjc@>w7>C)HP z#5*WH9|HSdr(65vbq55hy*k!gfmY6c!YG(S;wtGcDU?A3g|zyn`KEFfqxx9*Y#fn} zI%AaV?__*SGBR{8W>~#;SA_DLXF0!RDkd7arjxm{fTs z`5+5$F+~KW`jTQ+`T|8eX9m%sln 2fold (upgraded from 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is still sparsely filled with significant dark space visible, especially in the XY view. The body shows a curved/folded shape but the fill fraction is more consistent with 1.5fold than 2fold. Comparing to references, this matches 1.5fold better \u2014 the 2fold references show more complete filling. Given the rule to prefer the earlier stage when uncertain, and that T55-56 were comma, 1.5fold is the more appropriate classification for this transitional morphology. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell filling with emerging parallel body segments visible, but not yet clearly two distinct parallel segments as in the 2fold reference. The XZ view shows some layering but still has significant dark space. Previous stage was 1.5fold, and while this is transitioning toward 2fold, defaulting to the earlier stage given uncertainty. | [zslice-asym] 2 segment(s) -> 2fold (upgraded from 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - not sparse like 1.5fold but not densely packed like pretzel. In the XY view (top-left), the embryo body shows an elongated shape with what appears to be two parallel body segments, consistent with a 2fold stage. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. Compared to reference images, this matches the 2fold references (T62-T68 range) well - moderate fill fraction with some dark space remaining. The previous observation was 2fold, and the morphology is consistent with remaining at this stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible, forming a hairpin/U-shape. The eggshell is moderately filled with signal; there is some dark space remaining but less than in 1.5fold. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology is consistent with the previous T60 classification of 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is some dark space remaining but the embryo body occupies a substantial portion of the eggshell. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a 2fold stage. The fill fraction is moderate rather than dense - there are still visible dark regions within the eggshell boundary, which argues against pretzel stage. The morphology closely matches the 2fold reference images. Previous three timepoints were all 2fold, and there's no clear evidence of the additional folding/coiling that would indicate pretzel stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion. The XZ view shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous three timepoints classified as 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo body occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a 2fold stage. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear morphological change to suggest progression to pretzel yet. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a bean/kidney-shaped mass with a clear fold creating two parallel body segments visible as a U or hairpin shape. The eggshell is moderately filled - there's some dark space remaining but the embryo body occupies a substantial portion. The YZ view shows a ring-like pattern consistent with the folded body. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and there are two visible parallel segments rather than three or more overlapping coils. Previous observations were all 2fold, and the morphology is consistent with continuing in this stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body occupies a good portion of the shell. The body shows two parallel segments consistent with a hairpin/U-fold pattern. The XZ view shows layered signal with some gaps. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would show denser filling with multiple overlapping coils). | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible but less than in 1.5fold. In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The XZ view (bottom-left) shows layered bright bands consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous 2fold observations at T64-T66. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo occupies a substantial portion of the eggshell. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments forming a hairpin/U-shape, consistent with 2fold morphology. The XZ view (bottom-left) shows a pattern with distinct bright regions separated by darker gaps, suggesting two body layers rather than the dense, complex overlapping pattern of pretzel. This matches the 2fold reference images well. The fill fraction is moderate (not dense enough for pretzel), and the previous three timepoints were all 2fold, consistent with slow stage progression. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is still some dark space visible, particularly at the edges, but less than in 1.5fold. The XZ view shows distinct layered bright bands consistent with two folded body segments. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows layered bright bands indicating the folded body. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and there are two main parallel segments rather than multiple overlapping coils. Previous three timepoints were all 2fold, and the morphology hasn't changed significantly enough to advance to pretzel. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows layered signal bands consistent with two body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, so continuing at this stage is appropriate. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows two bright parallel bands consistent with 2fold morphology. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. There's no evidence yet of the three or more overlapping coils that would indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is still some dark space visible, particularly in the lower right of the XY view, but less empty space than in 1.5fold. The XZ view shows two distinct layers of signal separated by a gap, consistent with 2fold. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well, and is consistent with the previous three observations of 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows layered signal consistent with two folded body segments. Comparing to references, this matches the 2fold examples (T62-T75 range). The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous three timepoints which were all classified as 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments visible - a brighter region on the left and a dimmer region extending to the right, consistent with a hairpin/U-shaped fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows two distinct layers of signal separated by a darker gap, consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and I don't see evidence of three or more overlapping coils. Previous three timepoints were all 2fold, and the morphology hasn't changed dramatically enough to indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space but the embryo body occupies a substantial portion. In the XY view (top-left), I can see what appears to be two parallel body segments with a folded/hairpin morphology, consistent with 2fold. The XZ view (bottom-left) shows a bilobed pattern with some internal structure suggesting two overlapping body layers. Compared to the pretzel reference, the eggshell is not yet densely filled - there's still noticeable dark space, especially on the right side of the XY view. The pattern doesn't yet show the complex, tangled multi-coil appearance of pretzel. Previous three timepoints were all 2fold, and while this is approaching the transition, the fill fraction and morphology are still more consistent with late 2fold than pretzel. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body folded, showing two parallel segments visible. The eggshell is moderately filled - there is still some dark space visible, particularly at the edges, but the signal fills a good portion of the eggshell. The XZ view shows multiple bright bands consistent with folded body segments. Compared to the pretzel reference, the eggshell is not yet densely filled - there's still noticeable empty space. The morphology matches the 2fold reference images well, with two parallel body segments connected by a bend. Previous observations were all 2fold, and there's no clear transition to pretzel yet. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of fluorescent signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly around the constriction between the two lobes, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows a similar pattern with moderate fill. This matches the 2fold reference images well. The morphology hasn't changed significantly from the previous timepoints (T75-T77, all 2fold), and the fill fraction is not yet dense enough to indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal showing two main body lobes in XY view with some dark space remaining. The YZ view shows a ring-like pattern suggesting increasing folding complexity. While approaching pretzel stage, the fill fraction is not yet dense enough and the pattern is not as tangled/complex as pretzel references. Previous 3 timepoints were 2fold, and the morphology hasn't clearly transitioned yet. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated, irregular shape with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows complex layering with bright signal bands suggesting two folded body segments. Compared to the pretzel reference, the eggshell is not yet densely filled and the pattern is not as complex/tangled. The morphology is consistent with the previous three timepoints classified as 2fold, and while it may be approaching the transition to pretzel, there is no clear evidence of three or more overlapping coils yet. Following the rule to prefer the earlier stage when uncertain. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see two main lobes of signal connected by a bend, consistent with a hairpin/U-shape of 2fold. The eggshell is moderately filled - there's still some dark space visible, particularly between the two body segments, but it's not densely packed like pretzel. The XZ view shows multiple bright bands but they appear as two main parallel segments rather than the complex overlapping coils of pretzel. Comparing to references, this matches the 2fold examples better than pretzel. Previous observations were all 2fold, and while this is approaching the transition, the fill fraction is still moderate rather than dense, so I'll maintain 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see what appears to be a figure-8 or hourglass shape with two main lobes of signal connected by a constriction in the middle, consistent with two parallel body segments folded back on each other. The eggshell fill is moderate - there is still some dark space visible around the embryo body, particularly at the edges. The XZ view (bottom-left) shows a moderately filled pattern with some layering but not the dense, complex coiling pattern seen in pretzel references. Comparing to references, this matches the 2fold stage (similar to T62-T75 reference) rather than pretzel, which would show denser filling and more complex overlapping coils. Previous observations were all 2fold, and while the morphology is progressing, it hasn't yet reached the densely-packed pretzel appearance. | [zslice-asym] 3 segment(s) -> pretzel (upgraded from 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, overlapping pattern showing multiple body segments. The XZ view (bottom-left) shows multiple bright bands/layers indicating three or more folded body segments. This matches the pretzel reference images well, with the dense fill and complex coiling pattern. The previous timepoint (T82) was also classified as pretzel, and stages change slowly, so pretzel is consistent.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the body shows multiple overlapping coils/segments filling most of the eggshell interior. The XZ view (bottom-left) shows a complex, tangled pattern with multiple bright layers. The YZ view (top-right) shows an intricate cross-sectional pattern consistent with multiple body folds. This matches the pretzel reference images well, with 3+ body segments creating overlapping signal. The previous two timepoints were also classified as pretzel, consistent with the slow stage progression rule.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal spans most of the eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows the eggshell nearly completely filled with bright signal and complex internal patterns suggesting multiple overlapping body coils. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments and a complex, tangled pattern. The YZ view (top-right) shows multiple bright regions suggesting overlapping body layers. The XZ view (bottom-left) also shows dense, complex signal filling. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No signs of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled morphology with multiple body segments creating an irregular, elongated shape. The XZ view (bottom-left) shows dense, bright signal filling most of the eggshell with complex internal structure suggesting multiple folded layers. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex layered structure with multiple bright bands, indicating 3+ body folds. This matches the pretzel reference images well. The morphology is consistent with the previous three timepoints all classified as pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled, complex pattern with several overlapping regions. The XZ view (bottom-left) shows dense, bright signal filling most of the eggshell with complex internal structure. The YZ view (top-right) shows a ring-like pattern consistent with multiple body layers overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal - the XZ view shows bright, complex internal structure filling most of the shell. There appear to be multiple coils/folds visible, consistent with pretzel stage. This matches the pretzel reference images and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell. The XZ view shows complex layered signal with multiple bright bands. This matches the pretzel reference images well, with dense filling and multiple overlapping coils. No sign of hatching (no worm extending outside the eggshell). Consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments overlapping - characteristic of 3+ folds. The XZ view (bottom-left) shows dense, complex internal structure with overlapping layers. The YZ view (top-right) shows the swirling pattern of multiple coils. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows layered bright structures consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping segments and a complex, tangled pattern. The XZ view (bottom-left) shows multiple layered body segments. The YZ view (top-right) shows bright spots from overlapping coils. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the elongated body shows multiple overlapping segments filling most of the eggshell interior. The YZ view (top-right) shows a complex pattern with multiple bright regions suggesting coiled body layers. The XZ view (bottom-left) also shows dense, complex signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the signal fills most of the eggshell with multiple overlapping body segments creating a tangled pattern. The XZ view (bottom-left) shows multiple layers of body segments with complex internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex, layered signal with multiple body segments stacked. The overall pattern shows a tangled, complex morphology consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell. The YZ view shows internal structure with multiple overlapping layers. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three timepoints all classified as pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, consistent with the pretzel stage. The XZ view shows bright, densely packed signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a complex coiled pattern with multiple overlapping layers, consistent with 3+ folds. The YZ view (top-right) also shows a complex, densely packed pattern. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex folding with multiple overlapping segments creating a tangled pattern. The XZ view (bottom-left) shows dense, complex signal filling most of the eggshell. This is consistent with the pretzel reference images and the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled body segments. In the XY view, multiple body layers are visible with a tangled/coiled pattern filling most of the eggshell. The XZ view shows dense, layered signal. This matches the pretzel reference images well, with multiple folds creating overlapping structures. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal - the XZ view (bottom-left) shows bright, complex overlapping patterns filling most of the eggshell interior. The YZ view (top-right) also shows a densely filled oval. There are multiple body segments visible, consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments filling most of the eggshell interior. The XZ view (bottom-left) shows multiple parallel bright bands indicating 3+ body folds. The YZ view (top-right) shows a swirled pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled structures. In the XY view (top-left), multiple body segments are visible with a tangled/coiled appearance. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows multiple bright layers/bands. This matches the pretzel reference images well, with 3+ body folds creating the complex pattern. Previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments folded within the eggshell. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern. The XZ view (bottom-left) shows the characteristic pretzel pattern with multiple overlapping body layers filling the eggshell. This is consistent with the previous three observations of pretzel stage. There is no sign of hatching (no elongated worm shape outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments - more than two parallel segments are apparent. The XZ view (bottom-left) shows dense, complex internal structure consistent with multiple body folds. The YZ view (top-right) shows bright spots distributed throughout, indicating overlapping body layers. This matches the pretzel reference images well, and is consistent with the previous three timepoints all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments with multiple folds - at least 3 parallel segments are discernible, consistent with pretzel stage. The XZ view (bottom-left) shows dense, layered signal filling most of the eggshell. The YZ view (top-right) also shows the shell nearly completely filled. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple body segments with a complex, tangled pattern filling most of the eggshell. The XZ view (bottom-left) shows dense, overlapping structures with multiple layers. The YZ view (top-right) also shows a densely packed, complex pattern. This matches the pretzel reference images well, with multiple folded body segments creating overlapping signal. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled structures. In the XY view (top-left), the body shows multiple overlapping segments with a tangled appearance typical of pretzel stage. The YZ view (top-right) shows an irregular, complex pattern with multiple bright regions. The XZ view (bottom-left) shows dense signal filling most of the eggshell. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows complex, tangled body segments filling most of the eggshell interior, with multiple parallel body segments visible. The XZ view (bottom-left) shows bright, complex overlapping structures. This matches the pretzel reference images well, with dense filling and multiple folds. Consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, elongated shape with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows crossing/overlapping bright bands consistent with multiple coils of the body. This matches the pretzel reference images well, with dense fill and complex folding patterns. No sign of hatching (no worm extending outside the eggshell). Consistent with the previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows an elongated shape with multiple body segments and bright spots throughout. The XZ view shows a complex, tangled pattern consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in both the XY and XZ views. The XZ projection shows multiple intertwined body segments creating a tangled pattern. The YZ view shows diffuse, complex signal filling most of the oval. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows bright, complex overlapping structures consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell interior. The XZ view shows multiple overlapping layers of signal. This matches the pretzel reference images well. There is no sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in the XY view. The complex, tangled pattern of nuclei with multiple parallel body segments is consistent with the pretzel stage. The XZ view shows bright, complex overlapping structures. This matches the pretzel reference images well, and the previous three timepoints were all pretzel with no clear morphological change toward hatching.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments filling most of the eggshell interior. The XZ view (bottom-left) shows a complex, tangled pattern with multiple overlapping layers. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments overlapping - characteristic of pretzel stage. The XZ view (bottom-left) shows multiple layers of bright signal stacked vertically, indicating 3+ folds. The YZ view (top-right) also shows complex internal structure. This is consistent with the previous three timepoints all classified as pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled, pretzel-like pattern that fills most of the eggshell. The XZ view (bottom-left) also shows dense, complex signal with multiple overlapping layers. The YZ view (top-right) shows a compact, bright mass with internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. There is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments and overlapping layers filling most of the eggshell. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows multiple bright bands indicating several body folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 123, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments within the eggshell. The eggshell is densely filled with signal, though the embryo appears to be moving/twitching (characteristic of late pretzel stage). The XZ view shows complex internal structure with multiple layers. The pattern matches pretzel reference images with multiple folded body segments. Previous three timepoints were all pretzel, and while the embryo appears active, it is still contained within the eggshell boundary - no elongated worm shape is visible outside, so it hasn't reached hatching yet.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 124, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments filling most of the eggshell interior. The XZ view (bottom-left) shows bright, complex overlapping structures consistent with 3+ folds. The YZ view (top-right) shows a densely packed, complex pattern. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 125, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the worm body within the eggshell, with a complex, tangled pattern visible. The eggshell is densely filled with fluorescent signal, though some dark spaces remain. The XZ view shows multiple body layers. This matches the pretzel reference images well, with 3+ body folds visible. Consistent with previous observations at T122-T124.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 126, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments filling most of the eggshell. The XZ view (bottom-left) shows bright, complex overlapping patterns consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 127, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern within the eggshell. The XZ view shows complex layered structure consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 128, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple parallel body segments filling most of the eggshell interior. The XZ view (bottom-left) also shows dense, complex layered signal. This matches the pretzel reference images well, with 3+ folds creating overlapping coils. No sign of hatching (no worm extending outside the eggshell). Consistent with previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 129, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view (bottom-left) shows bright, complex overlapping structures. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 130, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping structures filling most of the eggshell. The XZ view (bottom-left) shows dense, complex signal with multiple body layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 131, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo occupying most of the eggshell interior with complex, overlapping coiled structures. The XZ view (bottom-left) shows bright, densely packed signal filling the shell with multiple overlapping layers visible. This is consistent with the pretzel stage reference images showing multiple body folds. No sign of hatching (no elongated worm outside the shell). Previous three timepoints were all pretzel, and the morphology is unchanged.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 132, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern within the eggshell. The XZ view (bottom-left) shows multiple bright layers of overlapping body segments. This is consistent with the pretzel stage reference images and the previous three observations. There is no sign of hatching (no elongated worm shape outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 133, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple folded body segments creating a tangled pattern that fills most of the eggshell. The YZ view (top-right) shows a ring-like pattern characteristic of coiled body segments in cross-section. The XZ view (bottom-left) shows dense, bright signal filling the eggshell with complex internal structure. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 134, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The XZ (bottom-left) view shows complex, layered body segments with bright overlapping structures. The YZ view shows a complex pattern consistent with multiple folds. This matches the pretzel reference images well, with 3+ body folds creating a tangled appearance. No sign of hatching (no elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 135, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in all three views. The XY view shows an elongated, complex pattern with multiple body segments overlapping. The XZ view shows a complex, tangled pattern consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no worm body outside the eggshell). Consistent with previous observations at T132-T134.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 136, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with complex, tangled patterns showing multiple parallel segments. The YZ view (top-right) shows a ring-like pattern consistent with coiled body layers. The XZ view (bottom-left) shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 137, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments within the eggshell, with complex tangled morphology. The YZ view (top-right) shows multiple parallel bright bands (at least 3 visible), indicating multiple body folds. The eggshell boundary is clearly visible as a bright oval outline in the XY view with the body coiled inside. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no worm body extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 138, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex layered structure filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 741.108738899231, + "error": null, + "accuracy": 0.7380952380952381, + "adjacent_accuracy": 1.0 + }, + { + "embryo_id": "embryo_2", + "predictions": [ + { + "timepoint": 45, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo body has elongated significantly compared to comma references, with the signal becoming more stretched along the eggshell long axis. The eggshell is sparsely filled with considerable dark space remaining. The body shape suggests the beginning of a fold-back, transitioning from comma to 1.5fold. This matches the early 1.5fold reference (T47) well. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to fold, with the body occupying more of the eggshell than comma stage but still with significant dark/empty space remaining inside the eggshell boundary (sparse fill). The shape shows one main curved body with a partial fold beginning - consistent with 1.5fold. There aren't two clearly parallel body segments yet (which would indicate 2fold). The morphology closely matches the 1.5fold reference images (T47). The previous timepoint was classified as 1.5fold, and stages change slowly, so maintaining this classification is appropriate. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that fills the eggshell sparsely - there is still significant dark space within the eggshell boundary, particularly at the edges. The body appears to have one main curved segment with a partial fold beginning, consistent with 1.5fold. There are not yet two clearly parallel body segments (which would indicate 2fold). The eggshell fill fraction is sparse, matching the 1.5fold reference images. This is also consistent with the previous observation of 1.5fold at T46, and this image actually matches the T47 reference for 1.5fold exactly. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body within the eggshell with the signal concentrated but still leaving some dark space within the eggshell boundary - consistent with sparse filling. The body appears as a single curved/elongated band without clear parallel segments that would indicate 2fold. Comparing to references, this matches the 1.5fold examples (T47-T57) well - the embryo is elongating and beginning to fold but hasn't yet formed two distinct parallel segments. The eggshell fill fraction is sparse to moderate, and there's no clear hairpin/U-shape with two parallel body segments visible. Previous three timepoints were all 1.5fold, and stages change slowly, so maintaining 1.5fold classification. | [zslice-asym] 2 segment(s) -> 2fold (upgraded from 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. The XY projection shows an elongated body with evidence of two parallel segments from folding. Consistent with early 2fold stage. Previous timepoint (T48) was 2fold, and morphology supports continuation of this stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY view forming a hairpin/U-shape fold. YZ view shows two distinct signal bands separated by a dark gap, confirming two body layers. Eggshell is moderately filled - more than 1.5fold but not densely packed like pretzel. Consistent with previous 2fold classifications at T48-T49. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo body occupies a substantial portion of the eggshell. In the XY view (top-left), the elongated body shows what appears to be two parallel segments consistent with a 2fold stage. The fill fraction is moderate (not densely packed like pretzel references), matching the 2fold reference images well. The XZ view (bottom-left) also shows a pattern consistent with 2fold - layered signal but not the complex overlapping coils of pretzel. Previous three timepoints were all 2fold, and there's no clear morphological change to suggest advancement to pretzel. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's some dark space remaining but the embryo occupies a substantial portion. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a hairpin/U-fold morphology. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous three timepoints which were all classified as 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space but less than in 1.5fold. In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments, consistent with 2fold. The XZ view (bottom-left) shows layered signal suggesting two body segments overlapping. The fill fraction is moderate, not yet densely packed as in pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations all being 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body clearly shows two parallel segments consistent with a 2fold stage. The XZ (bottom-left) view shows layered bright bands indicating two body segments. The eggshell is moderately filled but not densely packed like a pretzel. This matches the 2fold reference images well, and is consistent with the previous three observations at 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling). | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments visible, consistent with a 2fold stage. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. The fill fraction is moderate (not densely packed like pretzel), and the morphology matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel-level complexity or density yet. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows two distinct bright bands separated by a darker region, indicating two parallel body layers. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel). Previous three timepoints were all 2fold, and there's no clear transition to pretzel-level complexity or density. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see two main body segments forming a hairpin/U-shape, with the embryo body folded back on itself. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion of the eggshell interior. The XZ view shows layered signal consistent with two parallel body segments. This matches the 2fold reference images well. There is no evidence of three or more overlapping coils that would indicate pretzel stage. The fill fraction is moderate (not dense), and the previous three timepoints were all 2fold, consistent with slow stage progression. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo body occupies a substantial portion. In the XY view, I can see an elongated body with what appears to be two parallel segments forming a hairpin/U-shape. The XZ (bottom-left) view shows a complex but not yet densely packed pattern with some layering. This matches the 2fold reference images well - moderate fill fraction, two visible body segments. The eggshell is not yet densely filled enough for pretzel stage. Consistent with previous three observations of 2fold. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there is some dark space remaining but the embryo body occupies a substantial portion. In the XY view (top-left), the elongated body shows what appears to be two parallel segments with a complex but not yet densely tangled pattern. The fill fraction is moderate rather than dense, consistent with 2fold rather than pretzel. The XZ view (bottom-left) shows layered bright bands suggesting two body segments. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear morphological change to pretzel (which would show denser filling and more complex coiling). | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a curved/bean-like shape that has clear folding - I can see two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled with signal - there's still some dark space visible, particularly in the upper right of the eggshell in the XY view, but it's not densely packed like a pretzel. The XZ view shows layered signal consistent with two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not yet dense enough for pretzel), and I don't see evidence of three or more overlapping coils. Consistent with previous observations at T57-T59. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with two parallel body segments visible, consistent with a 2fold stage. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows two distinct bright bands/layers. Compared to the reference images, this matches the 2fold references (T62-T68) well. The fill fraction is not yet dense enough for pretzel, and the previous three timepoints were all 2fold, so continuing at 2fold is appropriate. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal \u2014 some dark space remains but not densely packed like pretzel. In the XY view (top-left), the embryo shows an elongated shape with what appears to be two parallel body segments visible, consistent with a 2fold stage. The XZ view (bottom-left) shows layered bright bands suggesting two folded segments. This matches the 2fold reference image very closely (in fact, this appears to be the same as the T62 2fold reference). The fill fraction is moderate, not yet dense enough for pretzel. Previous observations were all 2fold, and no clear transition to pretzel is evident. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible forming a hairpin/U-shape. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows layered bright bands consistent with two folded segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology is consistent with the previous three timepoints classified as 2fold. No clear transition to pretzel stage is evident. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see two main lobes of fluorescent signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. This matches the 2fold reference images well. The fill fraction is not yet dense enough for pretzel (no complex overlapping coils visible). Previous three timepoints were all 2fold, and the morphology is consistent with continuing in this stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo that moderately fills the eggshell, with some dark space remaining. The body appears to have two parallel segments visible, consistent with a 2fold stage. The XZ view shows layered signal with some internal structure but not yet the dense, complex coiling pattern of pretzel. The eggshell fill is moderate - more filled than 1.5fold but not densely packed like pretzel. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear morphological change to suggest progression to pretzel yet. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see a folded embryo with what appears to be two parallel body segments forming a U/hairpin shape. The eggshell is moderately filled - there is still some dark space visible within the eggshell boundary, but the body occupies a substantial portion. This is consistent with 2fold stage. The XZ view (bottom-left) shows two distinct bands of signal separated by a darker region, consistent with two parallel body segments. The fill fraction is moderate (not yet densely packed like pretzel). This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold or dense packing that would indicate pretzel. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark spaces, consistent with 2fold stage. The XZ view shows layered bright bands indicating the folded body. This matches the 2fold reference images well (comparable to T62-T68 references). The fill fraction is moderate - not yet dense enough for pretzel. Previous three timepoints were all 2fold, and no clear transition to pretzel (densely filled, multiple overlapping coils) is evident. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated curved body with what appears to be two parallel segments visible - consistent with a 2fold stage. The eggshell is moderately filled with signal - there is still some dark space visible (especially at the bottom of the XY view), but the body occupies a good portion of the eggshell. The XZ view shows layered bright bands consistent with two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, so maintaining this classification is appropriate. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see the embryo body forming a folded structure with two roughly parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The signal pattern shows a clear hairpin/U-shape morphology. Comparing to references, this matches the 2fold examples (T62-T75) well. The eggshell is not yet densely packed with multiple overlapping coils as in pretzel. Previous timepoints were all 2fold, and there's no clear transition to pretzel yet. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear constriction/bend in the middle, forming two distinct lobes connected by a narrower region - this is consistent with a 2fold hairpin/U-shape with two parallel body segments. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. The XZ view (bottom-left) shows two bright lobes, consistent with two folded body segments. Compared to the pretzel reference images, the eggshell is not yet densely filled and the pattern is not yet complex/tangled with multiple overlapping coils. The morphology matches the 2fold reference images well. Previous observations were all 2fold, and there's no clear evidence of progression to pretzel stage yet. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo is filling more of the shell than in 1.5fold. In the XY projection, I can see two parallel body segments forming a hairpin/U-shape pattern, consistent with 2fold. The XZ view shows layered bright bands suggesting two overlapping body segments. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology closely matches the 2fold reference images (e.g., T68-T75). No clear transition to pretzel (which would show 3+ overlapping coils and dense filling) is evident yet. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The XZ view (bottom-left) shows layered bright bands suggesting two folded segments. The YZ view (top-right) shows a relatively compact cross-section with some internal structure. The fill fraction is moderate (not densely packed like pretzel), and I can distinguish approximately two parallel segments rather than the complex overlapping coils of pretzel. This matches the 2fold reference images well, and is consistent with the previous three timepoints all being 2fold. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion. The XZ view (bottom-left) shows a moderately filled eggshell with visible internal structure but not the dense, complex overlapping pattern of pretzel stage. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology shows two parallel segments rather than three or more overlapping coils. Previous observations were all 2fold, and no clear transition to pretzel is evident. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see a clear folded embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The embryo shows distinct lobes of signal with a bend connecting them. The eggshell fill is moderate - there is still some dark space visible within the eggshell boundary, but the embryo is filling more of the shell than at 1.5fold. The XZ view (bottom-left) shows multiple bright bands consistent with two parallel body segments. Comparing to references, this matches the 2fold stage well - the body has folded back on itself creating two parallel segments, but hasn't yet reached the dense, complex coiling pattern of pretzel. The previous three timepoints were all 2fold, and the morphology is consistent with continuing in this stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see what appears to be two main body segments forming a U or hairpin shape - there are two distinct lobes of fluorescent signal connected by a bend. The eggshell is moderately filled - there is still some dark space visible between and around the body segments, but not as sparse as 1.5fold. The XZ view (bottom-left) shows a similar pattern with two distinct regions of signal separated by a darker gap in the middle, consistent with two parallel body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and I can count approximately two parallel segments rather than three or more overlapping coils. Previous observations were all 2fold, and the morphology is consistent with continuing at this stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body with what appears to be two parallel segments visible - a clear folded/hairpin structure. The eggshell is moderately filled with signal - there is still some dark space visible, particularly at the edges, but the body occupies a substantial portion of the eggshell. This is consistent with 2fold rather than pretzel, as the eggshell is not yet densely packed with multiple overlapping coils. The morphology matches the 2fold reference images (especially T75) well. Previous three timepoints were all 2fold, and while the body is becoming more complex, it hasn't yet reached the dense, multi-coiled pretzel appearance. Following the rule to prefer the earlier stage when uncertain. | [zslice-asym] 3 segment(s) -> pretzel (upgraded from 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with a complex, somewhat tangled pattern of nuclei. The XZ view (bottom-left) shows multiple overlapping layers of signal with complex internal structure. This matches the pretzel reference images where multiple body folds create dense, overlapping coils. The previous observation at T76 was pretzel, and stages change slowly, so continuing as pretzel is consistent.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex, tangled pattern with at least 3 parallel tracks of nuclei visible. The YZ view (top-right) shows a complex, multi-lobed structure consistent with multiple coils. The XZ view (bottom-left) shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous two observations being pretzel. The fill fraction is clearly dense (pretzel) rather than moderate (2fold).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, multi-lobed pattern with overlapping body segments filling most of the eggshell space. The XZ view (bottom-left) shows a complex internal pattern with multiple overlapping coils visible. The YZ view (top-right) shows the eggshell nearly completely filled. This is consistent with the pretzel stage reference images showing multiple body folds and dense filling. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the body shows multiple coiled segments filling most of the eggshell interior. The XZ view (bottom-left) shows dense, layered signal with multiple body segments overlapping. The YZ view (top-right) shows a complex pattern with bright spots distributed throughout, consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the body fills most of the eggshell with multiple overlapping coils/segments visible. The XZ view (bottom-left) shows dense, complex internal structure with multiple layers. The YZ view (top-right) shows bright signal with multiple distinct bright spots suggesting overlapping body segments. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the elongated body shows multiple overlapping coils/segments creating a complex pattern. The XZ view (bottom-left) shows dense, layered signal with visible coiling patterns. This matches the pretzel reference images closely, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm body extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows the shell nearly completely filled with signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, overlapping pattern of nuclei. The YZ view (top-right) shows a ring-like or coiled pattern consistent with multiple body folds. The XZ view (bottom-left) also shows dense, complex signal filling. Multiple overlapping body segments are visible, consistent with 3+ folds. This matches the pretzel reference images well, and the previous three timepoints were all pretzel, consistent with slow stage progression.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the signal fills most of the eggshell with complex, tangled patterns of nuclei. The XZ view (bottom-left) shows multiple layers of body segments overlapping. The YZ view (top-right) shows a complex pattern with bright spots distributed throughout, consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three timepoints all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, somewhat tangled pattern. The XZ view (bottom-left) shows multiple overlapping layers/coils of the body. The YZ view (top-right) shows a complex internal structure with visible folding patterns. This matches the pretzel reference images well, with multiple body folds creating overlapping coils. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern with relatively little empty dark space inside the eggshell. The XZ view shows complex layered structure consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple parallel segments and overlapping layers. The XZ view (bottom-left) shows a densely packed pattern with internal structure consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping coils of the embryo body visible within the eggshell. The eggshell is densely filled with fluorescent signal - the XZ view (bottom-left) shows the shell nearly completely filled with bright, complex signal patterns. Multiple body segments are visible overlapping each other, consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, coiled morphology with multiple overlapping body segments visible within the eggshell. The eggshell is densely filled with signal, though some dark regions remain. The XZ view shows multiple layers of bright signal consistent with overlapping body folds. This matches the pretzel reference images well, with multiple coils/folds visible. Previous three timepoints were all pretzel, and no clear morphological change toward hatching is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible in both the XY and XZ views. The XZ view shows complex layered structure with at least 3 parallel bands of signal, consistent with multiple body folds. The overall pattern matches the pretzel reference images well, with the tangled, complex appearance characteristic of 3+ folds. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments - more than two parallel segments are apparent, consistent with 3+ folds. The YZ view (top-right) shows a complex, non-uniform pattern with multiple bright regions indicating overlapping body layers. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well and is consistent with the previous three observations (T90-T92) all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, particularly evident in the XZ (bottom-left) view where multiple layers of the body create a complex pattern. The YZ view (top-right) shows a compact, irregularly shaped cross-section consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows a complex, tangled pattern with multiple body segments overlapping \u2014 more than two parallel segments are apparent. The XZ view (bottom-left) shows dense, complex internal structure filling most of the eggshell. The YZ view (top-right) shows multiple bright spots indicating overlapping body layers. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments rather than a simple hairpin. The XZ view (bottom-left) shows the characteristic pretzel pattern with multiple overlapping body layers creating a complex bright pattern. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, consistent with pretzel stage. The XZ view shows a densely packed interior with multiple body layers. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern characteristic of the pretzel stage. The eggshell is densely filled with signal, though some dark spaces remain at the periphery. Multiple body segments (3+) are visible overlapping each other. The XZ view shows dense, layered signal filling the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no elongated worm outside the shell). Consistent with the previous three timepoints all classified as pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The complex, tangled pattern of body segments with at least 3 folds is evident. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern. The eggshell is densely filled with fluorescent signal. Multiple body segments are visible with overlapping layers. The XZ view also shows dense, complex signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern visible. The eggshell is densely filled with fluorescent signal, though there are some darker regions. Multiple body segments (3+) can be seen overlapping. The YZ view shows an irregular, complex pattern consistent with multiple folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern with bright overlapping regions. The XZ view (bottom-left) shows complex internal structure with multiple layers. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows the characteristic pretzel-stage pattern with multiple overlapping layers. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo appears to have a bilobed or figure-8 shape, with signal extending beyond the original eggshell boundary. This is distinctly different from the pretzel stage references where the signal is contained within a single oval eggshell. The appearance of two connected lobes suggests the worm is beginning to emerge from the eggshell - one lobe being the eggshell region and the other being the worm body pushing out. The previous three timepoints were pretzel, and this morphological change (signal extending outside the eggshell boundary) is consistent with the transition to hatching.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo densely packed within the eggshell with complex coiled morphology consistent with a late pretzel/hatching stage. The XZ (bottom-left) view shows signal extending below the main eggshell boundary, suggesting the worm is beginning to emerge. Compared to the pretzel reference, the signal appears to be spreading/extending beyond the eggshell confines. The previous observation was 'hatching' at T106, and the morphology here is consistent with continued hatching. The eggshell is densely filled but there are signs of the worm extending outside the shell boundary.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body appearing to form a ring/loop shape with a dark center, suggesting the worm is beginning to emerge or reorganize within/outside the eggshell. The YZ view shows a fragmented, non-uniform bright cluster rather than a densely packed pretzel. The XZ view shows a ring-like pattern with a hollow center. This morphology is consistent with hatching - the worm is actively emerging from the eggshell. Previous observations at T106 and T107 were both hatching, and this continues that trend.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo appears to be partially emerging from the eggshell - there's a bright cluster on the left side that appears separated or extending from the main body mass, suggesting the worm is in the process of hatching. The signal distribution looks asymmetric and loosened compared to the pretzel stage references. The previous three timepoints were all classified as hatching, and stages change slowly, so continuing with hatching is consistent. The overall signal appears less densely packed than pretzel, with the body appearing to unfold/extend rather than being tightly coiled within the shell.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo still appears to be within/emerging from the eggshell. The XY view shows a densely packed, elongated structure with complex coiling patterns consistent with a late pretzel/hatching stage. The eggshell is densely filled with signal. Previous three timepoints were all classified as hatching, and the morphology is consistent with continued hatching. The worm body appears to be shifting/elongating compared to a typical pretzel, suggesting active hatching process.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows a densely filled eggshell with complex coiled body segments typical of a late pretzel/hatching stage. The YZ view (top-right) shows an irregular, non-circular shape suggesting the worm may be partially emerging or the eggshell is deforming. The previous three timepoints were all classified as hatching, and stages change slowly. The morphology is consistent with continued hatching.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows a complex, coiled morphology consistent with a late-stage worm still within or emerging from the eggshell. The XY view shows the worm body appears to be loosening/uncoiling compared to a tight pretzel, with some regions appearing dimmer and the overall shape becoming more elongated and less compact. The previous three timepoints were all classified as hatching, and stages change slowly. The morphology is consistent with an ongoing hatching process where the worm is in the process of emerging from the eggshell.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body appearing to extend/deform beyond the typical eggshell boundary, with an irregular elongated shape that doesn't conform to the oval eggshell. The body appears to be partially emerging. The previous three timepoints were all classified as hatching, and the morphology is consistent with ongoing hatching - the worm is in the process of emerging from the eggshell. The shape is more irregular and extended compared to a pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo appears to be emerging from the eggshell. In the XY view (top-left), the worm body shows an elongated, curved shape that extends beyond the typical eggshell boundary, with the body appearing to unfurl. The shape is no longer a compact pretzel confined within the eggshell - it looks like the worm is partially out, with a curved/extended morphology. Previous three timepoints were all hatching, and the morphology is consistent with continued hatching. The body appears less densely packed than a pretzel stage and shows signs of extension outside the shell boundary.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows a densely packed, elongated worm body within the eggshell with multiple coiled segments visible, consistent with a late pretzel/hatching stage. The eggshell is densely filled with signal. The XZ view (bottom-left) shows complex overlapping coils. Previous three timepoints were all classified as hatching, and the morphology remains consistent with that stage - the worm appears to be in the process of emerging, with the body still largely contained but showing the characteristic dense packing of a hatching-stage embryo.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated worm shape that appears to be extending beyond the original eggshell boundary, with the body stretching out to the left. The YZ view (top-right) shows a fragmented/irregular signal pattern rather than a compact oval, consistent with the worm emerging from the shell. The previous three timepoints were all classified as hatching, and the morphology here is consistent with continued hatching - the worm body is visibly elongated and partially outside the eggshell confines.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo still appears to be within/emerging from the eggshell. The XY view shows a densely filled eggshell with complex coiled body segments typical of a late pretzel/hatching stage. The eggshell is densely packed with signal showing multiple overlapping body segments. Previous three timepoints were all classified as hatching, and the morphology is consistent with continued hatching. The worm body appears to be in the process of emerging but hasn't fully left the eggshell yet.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated worm body that appears to be extending/emerging from the eggshell region. The YZ view (top-right) shows a ring-like or crescent pattern suggesting the worm is partially outside the compact eggshell volume. The XZ view shows complex coiled structure. Previous three timepoints were all hatching, and the morphology is consistent with an ongoing hatching process where the worm is emerging from the eggshell.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows a densely filled eggshell with complex coiled structure typical of a late pretzel/hatching stage. The previous three observations were all 'hatching'. The XY view shows the worm body appearing to extend/shift within or emerging from the eggshell, with the body appearing somewhat asymmetrically positioned and potentially beginning to emerge. Consistent with ongoing hatching process.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo still appears to be within/emerging from the eggshell. The XY view shows a densely packed pretzel-like morphology with multiple coiled body segments visible, but the signal appears to be shifting/elongating suggesting active hatching. The eggshell is densely filled with complex folded structures. Previous three timepoints were all hatching, and the morphology is consistent with continued hatching process - the worm hasn't fully emerged yet (no clear thin elongated worm outside the shell), so this remains hatching rather than hatched.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated worm shape that appears to be emerging from the eggshell - the body is stretched out and not tightly coiled like a pretzel. The YZ view (top-right) shows a smaller, asymmetric signal consistent with the worm partially exiting. The previous three timepoints were all classified as hatching, and the morphology here is consistent with continued hatching - the worm body is extended and loosening from the eggshell confinement.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "hatching", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The image shows the embryo still within/emerging from the eggshell. The XY view shows an elongated shape with the signal appearing to shift toward one end, consistent with the worm beginning to emerge. The eggshell is densely filled but the signal distribution is asymmetric, with brighter signal concentrated on the left side and dimmer/less organized signal on the right, suggesting the worm is in the process of exiting. Previous three timepoints were all classified as hatching, and stages change slowly, so maintaining the hatching classification is appropriate.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 726.1992108821869, + "error": null, + "accuracy": 0.5769230769230769, + "adjacent_accuracy": 1.0 + }, + { + "embryo_id": "embryo_3", + "predictions": [ + { + "timepoint": 39, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a curved body shape and some dark space within the eggshell, consistent with comma stage. The body shows one curved band of nuclei with a constriction/indentation visible, but no clear parallel folded segments yet. The eggshell is not sparsely filled enough for early 1.5fold - there's still substantial signal but with some empty regions. Comparing to references, this matches the comma reference images (T40-T44) very well. The previous three timepoints were all comma, and there's no clear morphological change to 1.5fold yet (no J-shape or hairpin visible).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 40, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but hasn't yet formed a clear fold-back. The eggshell still has some empty space, particularly visible in the XY projection where the body doesn't fill the entire shell. Compared to the 1.5fold reference, this image lacks the clear J-shape or partial hairpin structure - the body appears as a single curved band rather than showing a fold. The morphology is consistent with the comma reference images, showing the characteristic C-shaped curvature. Previous three timepoints were all comma, and stages change slowly, so maintaining comma classification.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 41, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but still occupies a relatively small fraction of the eggshell interior - there is significant dark space around the embryo, particularly at the ends. The body shows a single curved band of nuclei without clear parallel segments or folding back on itself. Compared to the 1.5fold reference, the embryo here hasn't yet developed the J-shape or partial hairpin characteristic of that stage. The morphology closely matches the comma reference images, with a curved body and mostly sparse eggshell filling. Previous three timepoints were all comma, and stages change slowly, so maintaining comma classification.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 42, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo body has elongated significantly within the eggshell compared to comma references. The XY view shows an elongated body beginning to fold, with sparse-to-moderate fill of the eggshell. Dark space remains visible within the shell boundary. No clear two parallel segments yet, consistent with early 1.5fold rather than 2fold. The morphology has clearly progressed beyond comma stage. | [zslice-asym] 2 segment(s) -> 2fold (upgraded from 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 43, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is sparsely to moderately filled with signal, with notable dark space remaining. The body appears elongated but does not show two clearly parallel segments characteristic of 2fold. Morphology closely matches 1.5fold reference images. The previous T42 classification of 2fold may have been premature; this image is more consistent with 1.5fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 44, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Elongated embryo body with early folding visible. Eggshell is sparsely to moderately filled with significant dark space remaining. XZ view shows two lobes suggesting partial fold but not a clear hairpin. Matches 1.5fold references well. Consistent with previous observation of 1.5fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 45, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body with partial folding visible in the XY view, consistent with 1.5fold. The eggshell is sparsely to moderately filled with significant dark space remaining. No clear two-parallel-segment hairpin pattern is visible that would indicate 2fold. Consistent with previous 1.5fold observations at T43-T44. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with a clear fold/bend - there's a larger mass on the left connected to a smaller lobe on the right, forming a J-shape or partial hairpin. The eggshell is still sparsely filled - there's significant dark space around and below the embryo body. In the XZ view (bottom-left), I can see the body extending with some folding but not yet forming two clear parallel segments. The fill fraction is sparse, consistent with 1.5fold rather than 2fold. This matches the 1.5fold reference images well, and the previous three observations were all 1.5fold. No clear evidence of two fully parallel body segments (which would indicate 2fold). | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 1.5fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated body that fills the eggshell but with a visible curved/folded structure - there's a clear arc of nuclei with the beginning of a fold-back, but not yet two distinct parallel segments. The eggshell is sparsely to moderately filled - there's still noticeable dark space, particularly at the edges. The overall morphology closely matches the 1.5fold reference images (T47 in the reference set). The previous three timepoints were all 1.5fold, and there's no clear transition to 2fold yet (no obvious two parallel body segments or hairpin shape). | [zslice-asym] 2 segment(s) -> 2fold (upgraded from 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with two parallel body segments visible in XY and XZ views. Dark gaps remain but less than 1.5fold. Matches 2fold references well. Consistent with previous T47 classification of 2fold - no clear advancement to pretzel stage yet. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two distinct lobes of signal with a constriction between them, indicating two parallel body segments in a hairpin fold. Moderate eggshell fill fraction with some dark space remaining. Matches 2fold reference images. Consistent with previous 2fold classification at T47-T48. Not yet densely filled enough for pretzel. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a clear elongated shape with a bend/fold visible - there appear to be two parallel body segments forming a U or hairpin shape. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. This is consistent with 2fold stage. The XZ view (bottom-left) shows multiple bright regions suggesting the folded body layers. Compared to the reference images, this matches the 2fold examples well - the fill fraction is moderate (not yet densely packed like pretzel). Previous observations were all 2fold, and there's no clear evidence of a third fold or dense packing that would indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows a U-shaped/hairpin body with two parallel segments connected by a bend. XZ view confirms two distinct lobes. Eggshell is moderately filled with some dark space remaining, consistent with 2fold. No evidence of multiple overlapping coils (pretzel). Matches previous 2fold classifications and 2fold reference images. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's some dark space visible but the embryo occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see what appears to be two parallel body segments with a darker region/gap between them, consistent with a hairpin/U-shaped fold. The XZ view (bottom-left) also shows a pattern with two distinct layers of signal. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear morphological change to suggest progression to pretzel - the shell still has noticeable empty space and the pattern isn't yet showing the complex, densely-packed coils characteristic of pretzel stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear bilobed/hairpin shape indicating two parallel body segments connected by a bend. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The XZ view shows layered signal consistent with two folded body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and there are two visible parallel segments rather than three or more overlapping coils. Previous observations were all 2fold, and no clear transition to pretzel is evident. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see two main lobes of fluorescent signal forming a figure-8 or U-shape pattern, consistent with two parallel body segments connected by a bend - characteristic of 2fold. The eggshell is moderately filled with signal - there is some dark space remaining but the body occupies a substantial portion. The XZ view shows complex but not yet densely packed signal. Compared to the pretzel reference where the eggshell is densely filled with overlapping coils, this image still has noticeable empty space. The morphology is consistent with the previous 2fold classifications and does not yet show the three or more overlapping folds characteristic of pretzel stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there is some dark space remaining but the embryo body occupies a substantial portion. In the XY view (top-left), I can see what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The fill fraction is moderate (not yet densely packed like pretzel). The XZ view (bottom-left) shows two distinct bright bands with some separation, matching the 2fold reference. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body with a clear elongated shape that has folded back on itself, creating two parallel body segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion of the eggshell interior. The fill fraction is moderate (not densely packed like pretzel), consistent with 2fold. The morphology matches the 2fold reference images well, and the previous three timepoints were all 2fold, so no stage change is indicated. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there is still some dark space visible, particularly on the right side of the XY view, but the embryo body occupies a substantial portion of the eggshell. In the XY view, I can see what appears to be two parallel body segments with a bend, consistent with a 2fold stage. The XZ (bottom-left) view shows a pattern with distinct bright regions suggesting two folded layers. The fill fraction is moderate - not sparse enough for 1.5fold but not densely packed enough for pretzel. This matches the 2fold reference images well. Previous three observations were all 2fold, and there's no clear morphological change to suggest advancement to pretzel. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but the embryo body occupies a substantial portion of the eggshell. In the XY view (top-left), I can see what appears to be two parallel body segments consistent with a 2fold stage. The XZ view (bottom-left) shows layered signal with some complexity but not the dense, tangled pattern of a pretzel. The fill fraction is moderate rather than dense, matching 2fold rather than pretzel. This is consistent with the previous three observations at 2fold, and there's no clear morphological change to indicate progression to pretzel stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two distinct lobes of fluorescent signal with a constriction between them, consistent with a hairpin/U-shaped fold with two parallel body segments. The eggshell is moderately filled - there is still some dark space visible, particularly around the edges and between the two lobes, but it's not densely packed like a pretzel. The XZ view shows a similar two-lobed pattern. This matches the 2fold reference images well. The fill fraction is moderate (not dense enough for pretzel), and the morphology shows two clear parallel segments. Previous observations were all 2fold, and there's no clear evidence of progression to pretzel (which would show denser filling and more complex overlapping coils). | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin. YZ view shows ring-like cross-section consistent with folded body. Matches 2fold references well. Not yet densely filled enough for pretzel. Consistent with previous 2fold classifications at T57-T59. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo within the eggshell with what appears to be two parallel body segments visible - a brighter region along the top/left and a darker groove/gap running through the middle, consistent with a 2fold hairpin structure. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. This matches the 2fold reference images well. The fill fraction is not yet dense enough for pretzel (still visible dark regions within the shell). The XZ view also shows layered structure consistent with two body segments. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold that would indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo body is taking up a substantial portion of the eggshell. In the XZ (bottom-left) view, I can see what appears to be two parallel body segments with bright signal bands, consistent with a 2fold stage. The fill fraction is moderate (not yet densely packed like pretzel). This matches well with the 2fold reference images. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows an elongated shape with the body folded back on itself, creating two parallel segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining (particularly at the edges/poles), but not densely packed like a pretzel. The XZ view shows layered signal consistent with two body segments overlapping. This matches the 2fold reference images well. The fill fraction is moderate (not dense enough for pretzel), and I can see approximately two parallel body segments. Previous observations were all 2fold, and there's no clear evidence of a third fold or dense packing that would indicate pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, with a visible dark gap/fold between them. The eggshell is moderately filled - there's some dark space remaining but the body occupies a good portion of the shell. The XZ view (bottom-left) shows a complex but not yet densely packed pattern. Compared to the reference images, this matches the 2fold stage (similar to T62-T68 references) rather than pretzel, which would show denser filling with multiple overlapping coils. The fill fraction is moderate, not dense enough for pretzel. Consistent with previous observations at T61-T63 being 2fold. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a good portion of the eggshell interior. The XZ view shows layered bright bands consistent with two folded body segments. Compared to the reference images, this matches the 2fold stage (T62-T75 range). The fill fraction is moderate (not yet densely packed like pretzel), and the morphology hasn't changed significantly from the previous three timepoints classified as 2fold. | [zslice-asym] 1 segment(s) -> 1.5fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo is filling more of the shell than in 1.5fold. In the XY view, I can see what appears to be two parallel body segments with some internal structure/folding visible. The XZ (bottom-left) view shows layered bright bands consistent with a folded body. The fill fraction is moderate - not yet densely packed like pretzel references. This matches well with the 2fold reference images (e.g., T68). Previous observations were all 2fold, and the morphology hasn't changed dramatically enough to indicate pretzel stage yet. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two parallel body segments forming a clear hairpin/U-shape, with a bend connecting them. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The fill fraction is moderate, not yet densely packed like pretzel stage. This matches the 2fold reference images well. The previous three observations were all 2fold, and there's no clear morphological change to suggest progression to pretzel (which would show 3+ overlapping coils and dense filling). | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex folding pattern with what appears to be more than a simple hairpin, but the eggshell fill fraction is still moderate with visible dark spaces. The XZ view shows multiple bright bands but not yet the dense filling characteristic of pretzel. Previous three timepoints were 2fold, and while this is approaching the transition, it's consistent with late 2fold. Defaulting to earlier stage when uncertain. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments are visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold rather than pretzel. The XZ view shows layered bright bands consistent with two parallel body segments. This matches the 2fold reference images well. No evidence of the dense, complex multi-coil pattern characteristic of pretzel stage. Previous three timepoints were all 2fold, and morphology appears consistent. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see the embryo body forming a clear folded structure with two parallel segments visible, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. In the XZ view (bottom-left), the signal shows a complex but not yet densely packed pattern - there are still gaps/dark regions within the eggshell boundary. Comparing to references, this matches the 2fold examples (T62-T75 range) rather than pretzel, which would show denser filling with multiple overlapping coils. The previous three timepoints were all 2fold, and while the embryo is progressing, it hasn't yet reached the dense, tangled appearance of pretzel stage. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining, two parallel body segments visible in XY and XZ views forming a hairpin structure, consistent with 2fold reference images. No evidence of three or more overlapping coils that would indicate pretzel. Matches previous observations at T68-T70. | [zslice-asym] 2 segment(s) -> 2fold; not above primary, kept 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 there is very little dark/empty space inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex, tangled pattern with nuclei distributed throughout most of the eggshell interior. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This is a clear transition from 2fold: rather than two parallel segments with moderate empty space, there are now multiple overlapping coils. The fill fraction is high and the pattern matches the pretzel reference images. While previous timepoints were 2fold, the morphology here clearly shows progression to pretzel stage with 3+ body folds.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately to densely filled with signal. The XZ view shows multiple layered bright bands suggesting 3+ body folds. Previous timepoint T72 was pretzel, and the morphology is consistent with early pretzel stage - more complex folding than 2fold with increasing eggshell fill. Maintaining pretzel classification from T72.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple overlapping body segments visible, consistent with 3+ folds. The XZ view (bottom-left) shows multiple bright bands/layers stacked vertically, indicating overlapping coils. The YZ view (top-right) also shows a complex pattern with internal structure. This matches the pretzel reference images well, with dense filling and multiple overlapping segments. Consistent with previous observations at T72 and T73 being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo fills most of the eggshell with a complex, overlapping pattern of nuclei. The XZ view (bottom-left) shows multiple overlapping body layers with a complex, tangled appearance. Multiple parallel body segments are visible, consistent with 3+ folds. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. The XZ (bottom-left) view shows multiple layered body segments with a tangled pattern. This matches the pretzel reference images well, with the body folded three or more times creating overlapping coils. Consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body occupying most of the eggshell interior with multiple overlapping coils visible. The XZ (bottom-left) view shows complex layered structure with multiple bright bands, consistent with 3+ folds. The YZ view (top-right) shows bright, complex signal filling the cross-section. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see a complex, tangled pattern with multiple body segments creating an elongated shape that fills most of the eggshell. The XZ view (bottom-left) shows multiple bright layers/bands stacked vertically, indicating three or more folds. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no signal outside the eggshell boundary).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows multiple overlapping coils/body segments forming a complex looping pattern with a dark region in the center, consistent with a pretzel-stage embryo with 3+ folds. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex folding with more than two parallel segments, creating a tangled appearance. The XZ view shows multiple layers of signal. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the embryo body occupies most of the eggshell interior with relatively little dark space remaining. In the XY view (top-left), I can see multiple overlapping body segments creating a complex pattern with several parallel bands of nuclei visible. The XZ view (bottom-left) also shows multiple layered structures consistent with 3+ folds. This matches the pretzel reference images well, with the dense fill fraction and complex coiled morphology. Consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo fills most of the eggshell with complex, overlapping structures showing multiple body segments coiled within. The XZ view (bottom-left) shows bright, complex layered signal filling the shell. This matches the pretzel reference images well, with multiple overlapping folds visible. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo densely filling the eggshell with multiple overlapping coils visible - I can see at least 3 body segments creating a complex folded pattern. The eggshell is densely filled with signal, with very little empty dark space inside the boundary. The XZ view shows multiple layered body segments. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view, I can see complex, tangled body segments with at least 3 parallel tracks of nuclei, consistent with multiple folds. The XZ view shows a dense, complex pattern. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex layered structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 the body occupies most of the eggshell interior with complex, overlapping coils visible. In the XY view (top-left), the signal fills the elongated eggshell shape with multiple overlapping body segments creating a tangled pattern. The XZ view (bottom-left) shows complex internal structure with multiple layers. This matches the pretzel reference images well, showing 3+ folds. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident (no worm extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with multiple overlapping coils/body segments visible within the eggshell - at least 3 parallel segments can be discerned. The eggshell is densely filled with signal, though some dark gaps remain between the coiled body segments. The XZ view shows complex, tangled body structure with multiple layers. This matches the pretzel reference images well, with the characteristic multiple-fold pattern. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident (no worm extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils/body segments visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body layers filling most of the eggshell interior. The XZ view (bottom-left) shows multiple bright bands indicating several folded body segments. This matches the pretzel reference images well, with dense filling and complex overlapping structures. Consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping patterns of nuclei visible throughout. In the XY view (top-left), the signal fills most of the elongated eggshell with multiple overlapping body segments creating a complex, tangled appearance. The YZ view (top-right) shows multiple bright clusters distributed across the cross-section, consistent with multiple coiled body layers. The XZ view (bottom-left) is also densely filled with bright signal showing complex internal structure. This matches the pretzel reference images well, with dense eggshell filling and multiple overlapping folds. Previous three timepoints were all pretzel, and no sign of hatching (no worm extending outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments with multiple folds - more than two parallel segments are apparent. The XZ view (bottom-left) shows a complex pattern with multiple overlapping layers. The YZ view (top-right) also shows a dense, complex pattern. This matches the pretzel reference images well, with the dense fill fraction and multiple coils characteristic of the pretzel stage. Previous three timepoints were all pretzel, and no clear morphological change toward hatching is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with complex tangled morphology. The eggshell is densely filled with signal. The XZ view shows multiple parallel bright bands indicating 3+ body folds. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments, consistent with the pretzel stage. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body shows complex, tangled folding patterns with multiple parallel segments - more than two body segments are visible, consistent with 3+ folds. The XZ view (bottom-left) shows multiple bright layers with complex internal structure. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view shows bright, complex layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments. In the XY view (top-left), I can see a complex, tangled pattern with multiple body folds visible - consistent with 3+ folds characteristic of pretzel stage. The XZ view (bottom-left) also shows complex overlapping structures. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body fills most of the eggshell with complex, tangled patterns of nuclei and some darker gaps between coils. The XZ view (bottom-left) shows multiple overlapping body segments creating a complex pattern. This matches the pretzel reference images well. The previous three timepoints were all pretzel, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments overlapping \u2014 characteristic of 3+ folds. The XZ view (bottom-left) shows a dense, complex pattern with multiple layers. This matches the pretzel reference images well. No sign of hatching (no elongated worm outside the eggshell). Consistent with previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, particularly clear in the XZ (bottom-left) view where multiple bright bands are stacked. The YZ view (top-right) also shows a complex, multi-lobed pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern. The eggshell is densely filled with fluorescent signal, though some dark spaces remain in the interior loops. Multiple (3+) body segments are visible, consistent with pretzel stage. The XZ view also shows dense, complex layering. This matches the pretzel reference images well and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see multiple parallel body segments forming a complex, looped pattern that fills most of the eggshell \u2014 consistent with 3+ folds. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 multiple overlapping coils are visible in the XY view, with complex tangled patterns of nuclei filling most of the eggshell interior. The XZ view also shows dense, complex signal throughout. This matches the pretzel reference images well, with multiple body folds creating overlapping layers. No sign of hatching (no elongated worm outside the shell). Consistent with previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view, multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows layered bright signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the shell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern that fills most of the eggshell interior. The XZ view shows dense, complex signal throughout. This matches the pretzel reference images well, with multiple folded body segments overlapping. No sign of hatching (no signal outside the eggshell boundary). Consistent with previous three observations of pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo body fills most of the eggshell with a complex, tangled pattern of nuclei. The XZ view (bottom-left) shows multiple overlapping body segments creating a dense, bright pattern. This matches the pretzel reference images well, with 3+ body folds creating the characteristic densely-packed appearance. No sign of hatching (no elongated worm outside the shell). Consistent with the previous three timepoints all classified as pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see complex, tangled body segments with multiple parallel tracks of nuclei wrapping around inside the eggshell - at least 3 body segments are discernible. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex, tangled pattern characteristic of the pretzel stage. The eggshell is densely filled with signal. Multiple body segments are visible crossing over each other. This matches the pretzel reference images well and is consistent with the previous three observations all being pretzel.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, densely coiled structure with multiple overlapping body segments filling the eggshell. The eggshell appears densely filled with signal, and the pattern shows multiple folded/tangled coils characteristic of the pretzel stage. The XZ view also shows complex internal structure with multiple layers. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 744.9375743865967, + "error": null, + "accuracy": 0.8591549295774648, + "adjacent_accuracy": 1.0 + }, + { + "embryo_id": "embryo_4", + "predictions": [], + "duration_seconds": 0.17711687088012695, + "error": null, + "accuracy": 0.0, + "adjacent_accuracy": 0.0 + } + ], + "started_at": "2026-04-22T17:00:30.746433", + "completed_at": "2026-04-22T17:37:23.169634", + "total_predictions": 233, + "overall_accuracy": 0.721030042918455, + "metrics": { + "accuracy": 0.721030042918455, + "adjacent_accuracy": 1.0, + "per_stage": { + "1.5fold": { + "accuracy": 0.1951219512195122, + "n": 41 + }, + "2fold": { + "accuracy": 0.7966101694915254, + "n": 59 + }, + "pretzel": { + "accuracy": 0.849624060150376, + "n": 133 + } + } + } +} \ No newline at end of file From 9e4695db1d63e9af64297be486ca83d94e1eafaa Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Wed, 22 Apr 2026 19:06:12 +0000 Subject: [PATCH 6/7] Add zslice_multi variant: max segment-count across 5 z-planes Single-midplane segment-counting (zslice, zslice_asym) returns <=2 in 98% of cases because body folds sit at different depths and one plane rarely intersects 3+ at separable locations. This variant samples slices at z = {0.25, 0.40, 0.50, 0.60, 0.75} of stack depth, runs the count subagent on each concurrently, and overrides with the *maximum*. Symmetric override on the full FOLD_STAGES trigger so the hypothesis is tested cleanly. Harness: TestCase gains zslices_b64 (list of 5 base64 JPEGs via _create_zslice_stack), and run.py whitelists it as an optional kwarg. Existing variants unaffected (kwarg routing is per-signature). --- benchmark/testset.py | 15 +++++++++ perception/__init__.py | 2 ++ perception/zslice_multi.py | 67 ++++++++++++++++++++++++++++++++++++++ run.py | 2 +- 4 files changed, 85 insertions(+), 1 deletion(-) create mode 100644 perception/zslice_multi.py diff --git a/benchmark/testset.py b/benchmark/testset.py index f5f5da1..b13306e 100644 --- a/benchmark/testset.py +++ b/benchmark/testset.py @@ -42,6 +42,7 @@ class TestCase: top_image_b64: Optional[str] # TOP view only side_image_b64: Optional[str] # SIDE view only midplane_b64: Optional[str] # Single XY slice at z=Z//2 (no projection) + zslices_b64: Optional[list[str]] # XY slices at _ZSLICE_FRACTIONS of Z volume: Optional[np.ndarray] ground_truth_stage: Optional[str] @@ -255,6 +256,18 @@ def _create_slice_image( return base64.b64encode(buffer.getvalue()).decode("utf-8") +_ZSLICE_FRACTIONS = (0.25, 0.40, 0.50, 0.60, 0.75) + + +def _create_zslice_stack(volume: np.ndarray, max_dim: int = 800) -> list[str]: + """Render XY slices at fixed Z fractions as a list of base64 JPEGs.""" + z_max = volume.shape[0] + return [ + _create_slice_image(volume, z=int(round(f * (z_max - 1))), max_dim=max_dim) + for f in _ZSLICE_FRACTIONS + ] + + def _create_separate_view_images(volume: np.ndarray, max_dim: int = 1000) -> Tuple[str, str]: """Create separate TOP and SIDE view images from volume, return base64 tuple. @@ -403,6 +416,7 @@ def iter_embryo( image_b64 = _create_three_view_image(vol) top_b64, side_b64 = _create_separate_view_images(vol) midplane_b64 = _create_slice_image(vol) + zslices_b64 = _create_zslice_stack(vol) if volume is None: del vol @@ -416,6 +430,7 @@ def iter_embryo( top_image_b64=top_b64, side_image_b64=side_b64, midplane_b64=midplane_b64, + zslices_b64=zslices_b64, volume=volume, ground_truth_stage=gt_stage, ) diff --git a/perception/__init__.py b/perception/__init__.py index e4d04db..fdf206a 100644 --- a/perception/__init__.py +++ b/perception/__init__.py @@ -43,6 +43,7 @@ def get_functions() -> dict: from .duration_aware import perceive_duration_aware from .zslice import perceive_zslice from .zslice_asym import perceive_zslice_asym + from .zslice_multi import perceive_zslice_multi _FUNCTIONS = { "minimal": perceive_minimal, @@ -62,5 +63,6 @@ def get_functions() -> dict: "duration_aware": perceive_duration_aware, "zslice": perceive_zslice, "zslice_asym": perceive_zslice_asym, + "zslice_multi": perceive_zslice_multi, } return _FUNCTIONS diff --git a/perception/zslice_multi.py b/perception/zslice_multi.py new file mode 100644 index 0000000..2a0b009 --- /dev/null +++ b/perception/zslice_multi.py @@ -0,0 +1,67 @@ +""" +Multi-plane z-slice subagent: max segment-count across several depths. + +The single-midplane variants (zslice, zslice_asym) failed because one z-plane +rarely intersects >=3 body segments at separable locations -- folds sit at +different depths. This variant counts segments at five z-fractions +(0.25/0.40/0.50/0.60/0.75 of Z) and takes the *maximum*. The hypothesis is +that a pretzel embryo will show >=3 segments on at least one plane even if no +single plane does. + +Override is symmetric (full FOLD_STAGES trigger) so the hypothesis is tested +cleanly; if max-count is still <=2 on pretzel, asymmetric damage control can +be layered on afterward. +""" + +import asyncio + +from ._base import PerceptionOutput +from .scientific import perceive_scientific +from .zslice import FOLD_STAGES, _count_segments, _segment_count_to_stage + + +async def _max_segment_count(zslices_b64: list[str]) -> tuple[int | None, list[int | None]]: + """Count segments on each slice concurrently; return (max, per-slice list).""" + results = await asyncio.gather(*(_count_segments(b64) for b64 in zslices_b64)) + counts: list[int | None] = [c for c, _ in results] + valid = [c for c in counts if c is not None] + return (max(valid) if valid else None), counts + + +async def perceive_zslice_multi( + image_b64: str, + references: dict[str, list[str]], + history: list[dict], + timepoint: int, + zslices_b64: list[str] | None = None, +) -> PerceptionOutput: + """Scientific classifier + max-count override across multiple z-slices.""" + primary = await perceive_scientific(image_b64, references, history, timepoint) + + if not zslices_b64 or primary.stage not in FOLD_STAGES: + return primary + + max_count, per_slice = await _max_segment_count(zslices_b64) + counts_str = "/".join("-" if c is None else str(c) for c in per_slice) + + if max_count is None: + return PerceptionOutput( + stage=primary.stage, + reasoning=f"{primary.reasoning} | [zslice-multi] all parses failed; kept primary", + verification_triggered=True, + phase_count=2, + raw_response=primary.raw_response, + ) + + sub_stage = _segment_count_to_stage(max_count) + return PerceptionOutput( + stage=sub_stage, + reasoning=( + f"{primary.reasoning} | [zslice-multi] counts {counts_str} max={max_count} -> " + f"{sub_stage}" + + ("" if sub_stage == primary.stage else f" (overrode {primary.stage})") + ), + verification_triggered=True, + phase_count=2, + raw_response=primary.raw_response, + ) diff --git a/run.py b/run.py index 9b791f3..40bb2ed 100644 --- a/run.py +++ b/run.py @@ -96,7 +96,7 @@ def make_prediction_dict(output, timepoint, ground_truth_stage) -> dict: } -_OPTIONAL_PERCEIVE_KWARGS = ("midplane_b64",) +_OPTIONAL_PERCEIVE_KWARGS = ("midplane_b64", "zslices_b64") def _accepted_optional_kwargs(perceive_fn) -> set[str]: From 9bfdba6dee1ad04bed885a8942a82a72baa1d589 Mon Sep 17 00:00:00 2001 From: Trisha Bansal Date: Wed, 22 Apr 2026 20:43:17 +0000 Subject: [PATCH 7/7] zslice_multi ablation (negative): max-count has no 2fold/pretzel separation Overall 42.5% vs scientific 77.3% (n=233). Max-count >=3 fires at 56% on GT=2fold and 55% on GT=pretzel -- zero discriminative power between the two stages we need to separate. The max over 5 planes amplifies per-slice noise (~20% false-3 rate -> ~67% any-slice-says-3). Override attribution: 111 fired, 26 helpful / 85 harmful (net -25.3%). Per-depth mean count on pretzel: z=0.25:2.19, 0.40:1.99, 0.50:1.83, 0.60:1.87, 0.75:2.12 -- quarter-planes show marginally more structure than midplane but no depth reliably hits 3. 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zH(fZyg|f{qxU##IiPttMv@^ey8Kg(nbw)`{?`MGR7nf7V88ARAFR&GG;CReIS?4gh zO)uR2{fi&8F^T5XcwD6_0UwE9ZBM;vX*t-;TqMM^mYjv@XkQ+gl#Wtkuk>C3w(NoM zii$x^R)G4&by-3|bfN$rp(6B?mr2<%4}36VDfrB~e0_ zfi%CZ0s{jD$Eo9oH4qD}fISbN>EAL4JeW6?d*s#ksbtPY2G=cvQRlM<2QSD>4Girv zK~R53yI*PAt`H2n?ERe(+*ef!@Zd!%Sb)dNL+rP!fvYG>s&J%F)X0d;QR&wPGU2pi z#Fm1LZIlKwzqg)$`(47^V9t;Wx)h|5Uj)?q4O7xC>75j;xu`-BHGzWqmdQtWDmn&@ zp%$pKYck+T;54p(=4QokcL5yq&8Zl?x83@s6G?8Tn zw9rxfdY>JB{EWCiPv@(4N%onE#N|StvOQvQ>zYva%RGauA;y?kY@r@`zFjShejSe2 z`INtMRnRS+&osIY%{Ab*$yR5e_59CdAgAeKx-(Wr33dKQ-v2+y!PSTU&+>QwFaO<_ aeNzsP+xTtsHI*!6)91rJi~e-txBmfq45eHE diff --git a/data/results/zslice_multi_1.5fold+2fold+pretzel.json b/data/results/zslice_multi_1.5fold+2fold+pretzel.json new file mode 100644 index 0000000..f3758c0 --- /dev/null +++ b/data/results/zslice_multi_1.5fold+2fold+pretzel.json @@ -0,0 +1,4025 @@ +{ + "config": { + "description": "Variant: zslice_multi" + }, + "embryo_results": [ + { + "embryo_id": "embryo_1", + "predictions": [ + { + "timepoint": 55, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a bilobed/C-shaped body with significant dark space in the eggshell, consistent with comma stage. No clear fold-back or parallel body segments visible. Matches comma reference images well. Previous three timepoints were comma, and no clear morphological advancement is evident.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a curved body with a constriction between two lobes, consistent with comma morphology. The eggshell has moderate empty space. No clear J-shape or fold-back is visible yet. The morphology is very similar to the comma reference images. Previous 3 timepoints were comma, and while this may be approaching 1.5fold transition, the fold-back is not yet definitive, so I default to comma.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows clear elongation beyond comma stage with the body beginning to fold back on itself. The eggshell is sparsely filled with significant dark space remaining. The XY view shows a J-like shape consistent with early 1.5fold. This matches the 1.5fold references better than comma, indicating the transition has occurred. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark spaces remaining. The XY view shows an elongated body with a fold, and the XZ view shows approximately two parallel bright bands consistent with a hairpin/U-shape. Matches 2fold references well. Consistent with previous T57 classification of 2fold. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin/U-shape. Matches 2fold reference images well. No dense multi-coil pattern characteristic of pretzel. Consistent with previous 2fold classifications at T57-T58. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible but the embryo occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a 2fold stage. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. The fill fraction is moderate (not yet densely packed like pretzel), and the morphology matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear evidence of a third fold or the dense packing characteristic of pretzel stage. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold rather than pretzel. The YZ view shows some internal structure but not the dense, complex overlapping pattern of pretzel. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would require denser filling and more complex coiling). | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is still some dark space visible, particularly at the edges, but the embryo body occupies a substantial portion of the eggshell. In the XY view (top-left), I can see what appears to be two parallel body segments with the body folded back on itself, consistent with a 2fold stage. The fill fraction is moderate (not yet densely packed like pretzel). The XZ view (bottom-left) shows a fairly filled but not completely packed pattern. This matches the 2fold reference images well. Previous observations were all 2fold, and there's no clear evidence of the dense, multi-coiled pattern characteristic of pretzel stage yet. | [zslice-multi] counts 1/1/2/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the signal occupies a substantial portion. The XZ view shows layered bright bands consistent with two folded body segments. Compared to the 2fold reference images, this matches well. The fill fraction is not yet dense enough for pretzel (still visible dark regions within the eggshell). Previous three timepoints were all 2fold, and no clear transition to pretzel morphology (dense, complex coiling) is evident. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is some dark space remaining but the embryo body occupies a substantial portion of the eggshell. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a hairpin/U-fold morphology. The XZ view (bottom-left) shows layered bright bands suggesting two body segments stacked. This matches the 2fold reference images well. The fill fraction is moderate (not densely packed like pretzel), and the morphology hasn't changed significantly from the previous three timepoints (T61-T63, all 2fold). No clear transition to pretzel stage is evident. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a bean/kidney-shaped embryo with a clear fold - two parallel body segments visible forming a U or hairpin shape. The eggshell is moderately filled with signal - there's still some dark space visible, particularly at the edges, but it's not densely packed like a pretzel. The YZ view shows a ring-like pattern consistent with a folded body. The XZ view shows bright signal that is moderately filling the space. This matches the 2fold reference images well. The fill fraction is moderate (not dense enough for pretzel), and I can see approximately two parallel segments rather than multiple overlapping coils. Previous observations were all 2fold, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body occupies a good portion of the shell. The body shows two parallel segments consistent with a hairpin/U-fold pattern. The XZ view shows layered signal with some gaps. The fill fraction is moderate (not densely packed like pretzel), matching the 2fold reference images well. Previous three timepoints were all 2fold, and there's no clear transition to pretzel (which would show denser filling with multiple overlapping coils). | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately to densely filled with signal. XZ view shows multiple (2-3) body layers with complex internal structure. Morphology is consistent with previous pretzel classification at T66. Fill fraction and body complexity exceed typical 2fold pattern, supporting pretzel stage. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY and XZ views forming a hairpin/U-shape. No evidence of three or more overlapping coils that would indicate pretzel. Matches 2fold reference images and is consistent with previous T67 classification. | [zslice-multi] counts 3/1/2/1/1 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark spaces inside the shell boundary. Two roughly parallel body segments visible in XY view. The YZ view shows a curved/ring pattern consistent with a U-fold. Fill fraction is not dense enough for pretzel - still has appreciable empty space. Matches 2fold reference images better than pretzel references. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two parallel body segments in a hairpin/U-shape fold with moderate eggshell filling. Dark space still visible within the eggshell boundary. No evidence of the dense, multi-coiled pattern of pretzel stage. Consistent with previous 2fold classification at T69. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with two visible parallel body segments forming a hairpin/U-shape. Consistent with 2fold reference images. Not yet densely filled enough for pretzel. Matches previous T70 classification of 2fold with no clear morphological change. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two distinct lobes of signal forming a clear hairpin/U-shape with two parallel body segments connected by a bend. The eggshell is moderately filled - there is still some dark space visible, particularly between the two lobes, but it's not densely packed like a pretzel. The XZ view (bottom-left) shows bright signal with some structure but not the complex overlapping coils characteristic of pretzel stage. This matches the 2fold reference images well. Previous observations were all 2fold, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/2/1/2/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated shape with two distinct lobes/segments visible, consistent with a 2fold hairpin morphology. The eggshell is moderately filled - there is some dark space remaining but less than in 1.5fold. The XZ view (bottom-left) shows two parallel bright bands separated by a darker region, indicating two body segments. Comparing to references, this matches the 2fold examples (e.g., T62-T75) well. The fill fraction is moderate, not yet dense enough for pretzel. The previous three timepoints were all 2fold, and the morphology is consistent with continuing at this stage. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape, consistent with 2fold. The eggshell is moderately filled - there is some dark space remaining but the embryo occupies a substantial portion of the eggshell interior. The fill fraction is moderate, not yet densely packed as in pretzel. The XZ view shows layered signal consistent with two body segments. This matches the 2fold reference images well, and is consistent with the previous three timepoints all being classified as 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling) is evident yet. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately-to-densely filled with signal. The XZ view shows complex internal structure with multiple layers/folds visible. The XY view shows an elongated body with emerging multi-fold complexity. Consistent with the T74 pretzel classification, and the morphology supports continued pretzel stage. | [zslice-multi] counts 3/2/1/1/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, tangled pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous two observations being pretzel. The fill fraction is clearly dense (pretzel) rather than moderate (2fold). | [zslice-multi] counts 3/2/1/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo fills most of the eggshell with a complex, elongated pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows multiple bright bands/layers consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no worm extending outside the eggshell). | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY projection shows two main body lobes forming a hairpin/U-shape with moderate eggshell filling. Dark space remains within the eggshell boundary. The XZ view shows two bright bands consistent with two parallel body segments. This matches 2fold references rather than pretzel, which would show denser filling and more complex overlapping coils. Consistent with previous T77 classification. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, particularly visible in the XZ view which shows complex, multi-layered internal structure. The YZ view shows a swirled/ring-like pattern indicating multiple overlapping coils. This matches pretzel reference images better than 2fold, which would show a simpler hairpin with more empty space. Consistent with previous T78 pretzel classification. | [zslice-multi] counts 2/2/1/3/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, irregularly shaped body with multiple overlapping coils/segments visible. The eggshell is densely filled with signal in the XZ view, showing complex internal structure with multiple layers. The body appears to have 3+ folds creating an intricate pattern. This matches the pretzel reference images well, and is consistent with the previous two observations being pretzel. The morphology shows clear advancement beyond 2fold with multiple overlapping body segments. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ projection shows at least 3 distinct bright bands indicating multiple overlapping body folds. The eggshell is moderately-to-densely filled. The complex folding pattern matches pretzel references better than 2fold. T78 and T79 were pretzel, and development doesn't reverse, so the T80 classification as 2fold was likely an error. | [zslice-multi] counts 2/2/2/3/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see a clear figure-8 or hourglass shape with two distinct lobes of signal connected by a constriction in the middle. This suggests two parallel body segments forming a hairpin/U-shape, characteristic of 2fold. The eggshell is moderately filled - there is still visible dark space around the embryo body, particularly above and below the constriction. This is not densely packed enough for pretzel, where the shell would be more uniformly filled with multiple overlapping coils. The XZ view shows bright signal but with clear structure of approximately two layers rather than the complex multi-layered pattern of pretzel. Comparing to references, this matches the 2fold examples better than pretzel. While the previous observation was pretzel, the morphology here more closely matches 2fold, and given the rule to prefer the earlier stage when uncertain, I classify as 2fold. | [zslice-multi] counts 2/2/3/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, overlapping pattern showing multiple body segments. The XZ view (bottom-left) shows multiple bright bands/layers consistent with 3+ folds of the body. This matches the pretzel reference images well, with the dense fill and complex coiled pattern. Previous observations at T81 and T82 were also pretzel, consistent with the slow stage progression rule. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping body folds in all three views. Multiple body segments are visible, particularly in the XZ view which shows several layers. This matches pretzel reference images. T81-82 were pretzel, and development cannot regress, so this should remain pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little dark space remaining inside the shell boundary. The XZ view shows complex curved/looping internal structures suggesting multiple body folds (3+). This matches pretzel references better than 2fold, which would show more empty space and clearer two-segment structure. The fill fraction is clearly beyond moderate (2fold) and into dense (pretzel) territory. | [zslice-multi] counts 2/2/3/3/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal showing complex, overlapping coil patterns rather than simple parallel segments. The YZ view shows multi-lobed structure consistent with multiple body folds. Matches pretzel reference images and is consistent with T85 classification. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated, complex morphology with multiple overlapping body segments creating an irregular, lumpy shape. The eggshell is densely filled with signal - the XZ (bottom-left) view shows bright signal filling most of the eggshell area with complex internal structure suggesting multiple folded layers. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. Multiple parallel body segments are visible, indicating 3+ folds. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body segments (at least 3 bright bands visible in XZ view). This matches pretzel reference images rather than 2fold. T85 and T86 were pretzel; development doesn't reverse, so this should remain pretzel. The T87 2fold classification was likely an error. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible two-segment folded body structure in XY view. The XZ view shows a bilobed pattern consistent with 2fold. Not yet densely filled enough for pretzel - still notable dark space within the eggshell. Consistent with previous 2fold observations at T87-T88. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous timepoint T89 was pretzel. The eggshell fill is moderate-to-dense with some complex body structure visible. The XY view shows multiple body regions with a curved extension, and the XZ view shows layered signal consistent with multiple folds. While borderline with late 2fold, maintaining pretzel classification consistent with T89 since stages don't regress. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately-to-densely filled with signal. The XZ view shows multiple bright bands suggesting 3+ body folds overlapping. The pattern is more complex than a simple 2fold hairpin. Consistent with previous two timepoints classified as pretzel, and morphology matches early pretzel reference images. | [zslice-multi] counts 2/2/1/1/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows a complex, multi-lobed structure with multiple overlapping body segments filling most of the eggshell. The XZ view (bottom-left) shows a densely packed pattern with coiled structures visible. The YZ view (top-right) shows the characteristic swirled/complex pattern of a pretzel stage. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal, showing complex overlapping coils/body segments consistent with pretzel stage. Multiple body layers visible in XZ view. Matches pretzel reference images well. T90-91 were pretzel; the T92 2fold classification was likely erroneous since development cannot regress. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body extending across most of the eggshell with complex, overlapping structures. The XZ (bottom-left) view shows multiple layered bands of signal indicating multiple body folds/coils. The YZ view (top-right) shows several bright spots suggesting overlapping body segments. This matches the pretzel reference images well, with dense filling and complex coiled morphology. The previous observation was pretzel at T93, and the morphology is consistent with continuing in the pretzel stage. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping body segments rather than a clean two-segment hairpin. The XY view shows an elongated body with multiple overlapping coils, and the XZ view shows dense, complex internal structure. This matches pretzel references better than 2fold. Despite previous oscillation, the morphology here clearly shows progression beyond 2fold with multiple body folds visible. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - some dark space remains but complex internal structure is developing. The XZ view shows layered body segments consistent with 2fold. While the fill fraction is increasing toward pretzel levels, there is still visible empty space within the eggshell. Previous two timepoints were 2fold, and stages change slowly, so maintaining 2fold classification. | [zslice-multi] counts 2/1/1/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body spanning most of the eggshell with complex, overlapping structures. Multiple body segments/coils are visible, creating a tangled appearance. The XZ (bottom-left) view shows dense, layered signal filling the shell. Compared to the 2fold reference (which shows two parallel segments with moderate fill), this image shows more complexity and denser filling, consistent with pretzel stage. The previous observation at T96 was pretzel, and the morphology here is consistent with continuing in the pretzel stage. | [zslice-multi] counts 2/3/2/3/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the body shows multiple coiled segments filling most of the eggshell space, with relatively little dark/empty space remaining. The YZ view (top-right) shows a complex pattern with multiple overlapping layers. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple body folds creating a tangled appearance. The previous two timepoints were also classified as pretzel, consistent with stages changing slowly. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space, and multiple overlapping body segments are visible in the XY view creating a complex pattern. This matches pretzel reference images. T96 and T97 were also pretzel; the T98 2fold classification was likely an error as development doesn't reverse. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows complex looping/coiling patterns with multiple overlapping body segments, not a simple U-shaped hairpin. The eggshell is densely filled with signal. The morphology matches pretzel references better than 2fold, with multiple folds visible. T97 was also pretzel, and the morphology here is consistent with that stage. | [zslice-multi] counts 3/2/1/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous timepoint was pretzel. The XY view shows a moderately filled eggshell with complex folding pattern showing overlapping body segments. The XZ view shows multi-layered internal structure consistent with pretzel stage. While the fill fraction is not extremely dense, the folding complexity and consistency with T100 support maintaining the pretzel classification. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body segments/coils. The XY view shows complex, tangled morphology with little empty space inside the eggshell. The XZ view shows multiple layered bright bands. This matches pretzel references better than 2fold, which would show clearer two-parallel-segment structure with more empty space. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two distinct lobes/segments visible in XY view with a dark gap between them, consistent with a hairpin fold. Moderate eggshell fill fraction with visible dark space remaining. Matches 2fold references well. Not dense enough for pretzel. Consistent with previous two observations of 2fold. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments/coils visible in XY view, and multiple stacked bright bands in XZ view indicate 3+ folds. Matches pretzel reference images well. Consistent with T103 classification of pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space. Multiple overlapping body coils (>2 segments) are visible in the XY view, and the YZ view shows a ring/coil pattern. The XZ view shows multiple stacked bright bands. This matches pretzel reference images rather than 2fold, which would show only two parallel segments with more empty space. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body segments/coils. The XZ projection shows complex layered structure consistent with 3+ folds. This matches pretzel reference images much better than 2fold. T103 was pretzel, and development cannot reverse, so this remains pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ view shows complex looping/coiling patterns with multiple overlapping body segments, and the eggshell is densely filled with signal with relatively little empty dark space remaining. This matches the pretzel reference images better than 2fold, which typically shows clearer two-parallel-segment structure with more empty space. The transition from 2fold at T106 to pretzel at T107 is plausible. | [zslice-multi] counts 2/2/2/3/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the embryo body shows multiple overlapping coils/segments creating a complex, tangled pattern that fills most of the eggshell. The XZ view (bottom-left) shows complex internal structure with multiple overlapping layers. The YZ view (top-right) also shows a densely filled, round profile with bright spots throughout. This matches the pretzel reference images well, with 3+ body folds creating the dense fill pattern. The previous timepoint was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible - I can see at least 3 parallel tracks of nuclei creating a complex, tangled pattern. The YZ view shows the signal filling most of the oval cross-section with internal structure suggesting multiple overlapping layers. The XZ view also shows dense, complex signal. This matches the pretzel reference images well, with the eggshell being densely packed and little empty dark space remaining inside. Consistent with the previous two timepoints classified as pretzel. | [zslice-multi] counts 3/2/2/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the embryo shows multiple body segments with a complex, tangled pattern filling most of the eggshell. The XZ view (bottom-left) shows dense, layered signal with multiple overlapping structures. The YZ view (top-right) also shows a densely packed, complex pattern. This is consistent with the pretzel stage reference images showing 3+ folds. The previous three timepoints were all pretzel, and no sign of hatching (no elongated worm outside the eggshell) is visible. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping body segments visible in all three views. The XZ projection shows multiple layered bright bands indicating 3+ folds. This matches pretzel references better than 2fold. T108-T109 were pretzel; the T110 classification of 2fold was likely erroneous since stages don't regress. | [zslice-multi] counts 1/1/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, showing complex overlapping structures in the XY view. The XZ view shows multiple layered bright regions suggesting 3+ body folds. The fill fraction and complexity exceed the 2fold reference and match pretzel. Since T109 was pretzel, development cannot regress, supporting pretzel classification. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, particularly visible in the right portion of the XY view. The XZ view (bottom-left) shows distinct crossing/folded body segments. The fill fraction is moderate - not yet densely packed like pretzel references. This matches the 2fold reference images well. Previous three timepoints were all 2fold, and the morphology hasn't changed significantly enough to indicate progression to pretzel (which would show denser filling and more complex coiling). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal compared to the 2fold references. In the XY view, the body appears elongated and fills most of the eggshell with complex, overlapping structures rather than a clean two-parallel-segment hairpin. The XZ (bottom-left) view shows multiple layered bands of signal suggesting 3+ body folds, with a complex internal pattern resembling the pretzel reference images. The YZ view (top-right) also shows a complex, swirled pattern rather than a simple two-lobed structure. While previous timepoints were classified as 2fold, the morphology here has clearly progressed to show denser filling and more complex folding consistent with the pretzel stage. | [zslice-multi] counts 2/3/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 in the XY view, the body fills most of the eggshell with complex, overlapping structures and relatively little dark space inside the shell boundary. The XZ view shows multiple overlapping coils/layers creating a complex tangled pattern. This matches the pretzel reference images well, with multiple body folds visible. The previous timepoint was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with some dark space remaining. The XY view shows a folded body with approximately two parallel segments. While the XZ view hints at increasing complexity approaching pretzel, the fill fraction is still moderate rather than dense. Previous observation was 2fold, and at this borderline transition, defaulting to the earlier stage. | [zslice-multi] counts 2/2/3/1/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping body segments creating a complex, tangled pattern with bright signal covering most of the eggshell interior. The XZ view (bottom-left) also shows dense, complex signal filling the shell. The YZ view (top-right) shows layered bright signal. This dense fill pattern with multiple overlapping coils matches the pretzel reference images well. There are clearly more than 2 parallel body segments visible, ruling out 2fold. The previous observation was pretzel, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - multiple overlapping coils/body segments are visible in the XY view, creating a complex pattern. The XZ (bottom-left) view shows bright, complex overlapping structures filling most of the eggshell. The YZ (top-right) view also shows the eggshell nearly completely filled. There are more than 2 parallel body segments visible, consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous two timepoints being classified as pretzel. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments filling most of the eggshell interior. The YZ view (top-right) shows a ring-like pattern consistent with multiple coils. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the embryo shows a complex, tangled pattern with multiple body segments overlapping - characteristic of pretzel stage. The XZ view (bottom-left) shows multiple layers of bright signal stacked vertically, indicating 3+ folds. The YZ view (top-right) also shows complex internal structure. This is consistent with the previous three timepoints all classified as pretzel, and there is no sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/3/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible. In the XY view (top-left), the body shows multiple folded segments creating a tangled pattern typical of pretzel stage. The XZ view (bottom-left) shows bright, complex overlapping structures filling most of the eggshell. The YZ view (top-right) shows a dense, irregularly shaped mass. This is consistent with the previous three observations of pretzel stage, and there is no sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 3/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments and overlapping layers filling most of the eggshell. The YZ view (top-right) shows a ring-like pattern consistent with coiled body segments. The XZ view (bottom-left) shows multiple bright bands indicating several body folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 123, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-folded body with at least 3 overlapping segments visible, and the eggshell is moderately-to-densely filled. This matches pretzel reference images. Previous T120-T121 were pretzel; the T122 '2fold' classification was likely erroneous since stages don't regress. The morphology clearly shows multiple coils characteristic of pretzel stage. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 124, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ projection shows multiple (3+) bright bands indicating several body folds. The eggshell is densely filled with signal, with little empty dark space remaining. This matches pretzel references better than 2fold. T121 was also pretzel, suggesting the T122-T123 2fold calls may have been conservative. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 125, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex looping pattern visible. The eggshell is densely filled with signal - there's relatively little empty dark space inside the eggshell boundary. In the XZ view (bottom-left), the signal fills most of the eggshell area with complex internal structure. Multiple body segments (3+) can be traced in the XY projection, consistent with pretzel stage. This matches the pretzel reference images and is consistent with the previous T124 classification of pretzel. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 126, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled structure with multiple parallel segments - more than the two expected for 2fold. The XZ view (bottom-left) shows a complex looping pattern consistent with 3+ folds. The YZ view (top-right) shows an elongated pattern with internal structure suggesting overlapping body layers. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 127, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in all three views. The XY view shows multiple body segments creating a tangled pattern within the eggshell. The XZ view shows complex layered structure consistent with 3+ folds. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 128, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping coil patterns in all three views. Multiple body segments are visible with tangled/overlapping structure, particularly evident in the XZ view. This matches pretzel references well. Previous T125-T126 were pretzel; development cannot regress, so this remains pretzel. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 129, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping body folds. Multiple coiled segments are visible in the XY projection. The fill fraction is high with little empty space inside the eggshell. This matches pretzel references better than 2fold. T126 was correctly classified as pretzel; development cannot regress, so this remains pretzel. | [zslice-multi] counts 3/2/1/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 130, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with multiple overlapping body segments creating a complex, tangled pattern within the eggshell. The eggshell is densely filled with signal - there is relatively little dark/empty space inside the eggshell boundary. In the XZ (bottom-left) view, I can see multiple overlapping coils/layers of the body. The YZ view also shows a complex, filled pattern. This matches the pretzel reference images well, with 3+ body folds visible. The previous timepoint was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice-multi] counts 2/3/1/3/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 131, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body occupying most of the eggshell interior with complex, overlapping structures. The XZ (bottom-left) view shows multiple layers of bright signal filling the shell densely. There appear to be multiple overlapping coils/body segments visible, consistent with 3+ folds. This matches the pretzel reference images well, with the dense fill pattern and complex internal structure. Previous observations at T129 and T130 were pretzel, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 132, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately to densely filled with signal. The XY view shows complex folding with multiple body segments overlapping, and the XZ view shows layered internal structure consistent with 3+ folds. T129-T130 were pretzel, and development cannot regress, so this is consistent with pretzel stage. The T131 classification of 2fold was likely an error. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 133, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo shows an elongated, complex pattern with multiple overlapping body segments filling most of the eggshell. The YZ view (top-right) shows a ring-like pattern characteristic of coiled body segments seen in cross-section, consistent with pretzel stage. The XZ view (bottom-left) shows dense, complex signal filling the shell. Multiple body folds/coils are visible rather than just two parallel segments, ruling out 2fold. This matches the pretzel reference images well and is consistent with the previous T132 classification of pretzel. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 134, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little dark space remaining. Multiple overlapping body segments/coils are visible in both XY and XZ views, creating a complex tangled pattern. This matches pretzel reference images rather than 2fold, which would show clearer two-parallel-segment morphology with more empty space. The embryo has progressed beyond 2fold into pretzel stage. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 135, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping body segments visible in all three views. The XZ projection shows multiple curved bands suggesting 3+ folds. This matches pretzel references better than 2fold, and is consistent with T132 being pretzel - the embryo cannot regress to an earlier stage. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 136, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body coiled within the eggshell with multiple overlapping segments visible. The YZ view (top-right) shows a complex, ring-like pattern suggesting multiple body folds overlapping. In the XZ view (bottom-left), the signal fills most of the eggshell with complex internal structure. This matches the pretzel reference images well, with 3+ body folds creating a densely packed, tangled appearance. The previous timepoint was also classified as pretzel, consistent with slow stage progression. | [zslice-multi] counts 2/2/3/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 137, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal. In the XY view (top-left), the embryo body shows multiple overlapping coils/segments filling most of the eggshell interior, with complex looping patterns visible. The YZ view (top-right) shows multiple parallel bright bands (at least 3 distinct layers), indicating multiple body folds. The XZ view (bottom-left) also shows a complex, densely packed pattern. This matches the pretzel reference images well, with the eggshell being mostly filled and multiple overlapping body segments visible. Consistent with the previous two observations of pretzel stage. | [zslice-multi] counts 2/3/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 138, + "predicted_stage": "early", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Error: Error code: 429 - {'type': 'error', 'error': {'type': 'rate_limit_error', 'message': \"This request would exceed your organization's rate limit of 250,000,000 input tokens per minute (org: 88de94f7-8772-4d0b-8ac8-46ad57a86a44, model: claude-opus-4-6, model_group: claude_opus_4_5, qos: -5). For details, refer to: https://docs.claude.com/en/api/rate-limits. You can see the response headers for current usage. Please reduce the prompt length or the maximum tokens requested, or try again later. You may also contact sales at https://claude.com/contact-sales to discuss your options for a rate limit increase.\"}, 'request_id': 'req_011CaKMteMQBfw6tu24iBK3z'}", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1428.3205771446228, + "error": null, + "accuracy": 0.42857142857142855, + "adjacent_accuracy": 0.9642857142857143 + }, + { + "embryo_id": "embryo_2", + "predictions": [ + { + "timepoint": 45, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo body has elongated significantly compared to comma references, with sparse eggshell filling and the beginning of a fold-back visible. The shape is more elongated than comma but doesn't yet show two clear parallel segments. Matches early 1.5fold reference (T47). Transition from comma at T44 is consistent with expected timing. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body beginning to fold with sparse-to-moderate eggshell filling. The XY view shows early folding but not yet a clear two-parallel-segment hairpin. This matches 1.5fold references better than 2fold. The jump from comma at T44 to 2fold at T45 was likely premature; this timepoint is more consistent with 1.5fold morphology. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XZ side view shows two layers of signal suggesting a folded body. Eggshell fill is moderate with some dark space remaining. Consistent with previous 2fold classification at T45-T46. While it resembles the 1.5fold reference at T47, the side view layering and continuity with prior observations support early 2fold. | [zslice-multi] counts 2/2/1/2/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there's some dark space remaining but the embryo body occupies a substantial portion. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a 2fold stage. The fill fraction is moderate (not densely packed like pretzel), and the morphology closely matches the 2fold reference images. Previous three timepoints were all 2fold, and there's no clear evidence of additional folding that would indicate pretzel stage. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with fluorescent signal - there is some dark space remaining but the embryo body occupies a substantial portion of the eggshell interior. In the XY view (top-left), I can see an elongated body with what appears to be two parallel segments, consistent with a hairpin/U-shape fold. The XZ view (bottom-left) shows a moderately filled pattern with some structure visible. This matches the 2fold reference images well. The fill fraction is not yet dense enough for pretzel (still some dark gaps visible), and the morphology is consistent with the previous three timepoints all classified as 2fold. No clear advancement to pretzel stage is evident. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with the body folded back on itself, creating two parallel segments visible as a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the embryo occupies a substantial portion. The YZ view shows horizontal banding consistent with two parallel body layers. The XZ view shows structured signal with moderate fill. This matches the 2fold reference images well. The eggshell is not yet densely packed enough for pretzel stage, and the previous three timepoints were all 2fold, consistent with slow stage progression. | [zslice-multi] counts 3/2/1/1/1 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with visible dark spaces remaining inside the shell boundary. The body shows elongation with approximately two parallel segments but not the dense, multi-coil pattern characteristic of pretzel. Matches 2fold references better than pretzel. Preferring earlier stage given uncertainty, and T48-T49 were both 2fold. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "1.5fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Two parallel body segments visible in XY and XZ views with moderate eggshell filling. Some dark space remains inside the eggshell. Pattern matches 2fold references well - not dense enough for pretzel. Consistent with previous T51 classification of 2fold. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate-to-sparse eggshell fill with some dark space remaining. The XY view shows an elongated body with curvature but not a clear two-parallel-segment hairpin pattern. The XZ view shows early folding. Consistent with 1.5fold reference images and matches previous T52 classification. Not yet showing the distinct parallel segments and moderate fill of 2fold. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with some dark space remaining. Two parallel body segments visible in XY and XZ views forming a hairpin/U-shape. Matches 2fold reference images well. Not yet densely filled like pretzel. Consistent with previous T53 classification of 2fold. | [zslice-multi] counts 1/2/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows an elongated body with what appears to be two parallel segments visible - consistent with a 2fold stage. The eggshell is moderately filled with signal - there is some dark space remaining but less than in 1.5fold references. The XZ view (bottom-left) shows layered bright bands suggesting two body segments overlapping. Compared to the pretzel references, the eggshell is not yet densely filled and the pattern is not as complex/tangled. This matches the 2fold reference images well, and is consistent with the previous observations at T53-T54 being 2fold. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a clear folded morphology - two parallel body segments visible forming a hairpin/U-shape. The eggshell is moderately filled with signal but still has some dark space, consistent with 2fold stage. The XZ view shows two distinct bright bands separated by a darker region, indicating two parallel body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel). Previous three observations were all 2fold, and the morphology hasn't changed significantly enough to advance to pretzel. | [zslice-multi] counts 3/1/2/1/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous timepoint was pretzel, and stages don't regress. The XY view shows moderate-to-dense filling with some complex folding patterns. The XZ view shows multiple layers of signal. While the fill isn't as dense as later pretzel references, it's consistent with early pretzel stage, and since T56 was already classified as pretzel, maintaining this classification is appropriate. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with two visible parallel body segments forming a hairpin/U-shape in the XY view. Dark space still present within the eggshell, particularly on one side. Matches 2fold references well. Not yet showing the dense multi-coil filling characteristic of pretzel stage. Consistent with previous 2fold classification. | [zslice-multi] counts 3/2/1/1/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal in all three views, with complex overlapping structure visible in the XY projection. Multiple body layers appear to overlap, creating a tangled pattern. This matches pretzel reference images better than 2fold, which would show more distinct dark space and clearer two-segment structure. Consistent with previous pretzel classifications at T56 and T58. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with visible dark space remaining, two parallel body segments visible in XY view forming a hairpin/U-shape, consistent with 2fold reference images. Not yet showing the dense multi-coil filling characteristic of pretzel stage. | [zslice-multi] counts 3/2/2/2/1 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark space remaining inside the shell boundary. Two parallel body segments visible in XY and XZ views rather than the dense, complex multi-coil pattern of pretzel. The fill is not dense enough for pretzel - significant empty space remains. Previous observations oscillate between 2fold and pretzel, suggesting a transition zone; defaulting to earlier stage. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Looking at this image carefully: In the XY view (top-left), I see an elongated embryo with what appears to be two parallel body segments - a clear hairpin/U-shape structure. The eggshell is moderately filled but not densely packed - there's still noticeable dark space, particularly around the edges. In the XZ view (bottom-left), I can see approximately 2-3 layers of signal but with gaps between them. This image actually matches the 2fold reference image very closely (it appears to be the same T62 reference). The eggshell fill is moderate rather than dense, and I can distinguish two main parallel body segments rather than the complex overlapping coils of a pretzel. While previous observations were pretzel, the 'when in doubt choose earlier stage' rule applies, and this morphology is more consistent with 2fold than pretzel - the fill fraction is moderate, not dense. | [zslice-multi] counts 3/1/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous three timepoints were pretzel. The XY view shows a moderately complex folding pattern with multiple body segments visible. The XZ view shows layered structure consistent with multiple folds. While the eggshell fill fraction appears slightly less dense than some pretzel references, the morphological complexity and continuity with previous observations support maintaining the pretzel classification. | [zslice-multi] counts 3/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous three timepoints classified as pretzel. The eggshell shows moderately dense filling with complex body folding visible in XY and XZ views. While the fill fraction appears slightly less dense than typical pretzel references, stages don't regress, and the multiple overlapping body segments are consistent with pretzel stage. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo appears elongated and fills most of the eggshell with complex, overlapping structures. The XZ view (bottom-left) shows multiple overlapping body layers with a complex coiled pattern. The YZ view (top-right) shows a compact, bright structure with visible internal complexity. This matches the pretzel reference images well, with multiple folded body segments creating a dense, tangled appearance. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark spaces inside the shell boundary. Two parallel body segments visible in XY view forming a hairpin/U-shape fold. Matches 2fold reference images better than pretzel - lacks the dense, multi-coil filling characteristic of pretzel stage. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal showing complex internal structure with multiple overlapping body segments. The XY view shows an elongated form with tangled/folded body, and the XZ view shows layered structure consistent with 3+ folds. Matches pretzel reference images and is consistent with the most recent classification at T66. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell filling with visible dark space remaining, two parallel body segments forming a hairpin/U-shape in XY view, no evidence of three or more overlapping coils. Matches 2fold reference images. Previous stage was 2fold, and morphology has not clearly advanced to pretzel. | [zslice-multi] counts 1/1/2/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark spaces remaining. Two parallel body segments visible in XY view showing a clear fold/hairpin pattern. Matches 2fold reference images well. Consistent with previous T67-T68 classifications. Not dense enough filling for pretzel stage. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with a clear constriction/bend in the middle, forming two distinct lobes connected by a narrower region - this is consistent with a 2fold hairpin/U-shape with two parallel body segments. The eggshell is moderately filled - there is some dark space but the signal occupies a good portion of the eggshell interior. The XZ view (bottom-left) shows two bright masses consistent with two overlapping body segments. This matches the 2fold reference images well. The fill fraction is moderate (not yet densely packed like pretzel), and the previous three timepoints were all 2fold, so maintaining this classification is appropriate. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping body segments visible in both XY and XZ views. Multiple coils/folds are apparent rather than a simple two-segment hairpin. This matches pretzel references and is consistent with the T70 pretzel classification. The fill fraction is high with relatively little empty space inside the eggshell. | [zslice-multi] counts 3/1/2/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with multiple overlapping body segments creating a complex, tangled pattern. The eggshell is densely filled with signal - there's relatively little dark space inside the eggshell boundary. The XZ view shows multiple layers of bright signal stacked vertically, consistent with multiple body folds. The YZ view shows a compact, bright structure. This matches the pretzel reference images well, with 3+ body folds visible. Previous two timepoints were also pretzel, consistent with slow stage progression. | [zslice-multi] counts 2/1/3/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XZ (bottom-left) view shows the shell nearly completely filled with bright, complex overlapping structures. In the XY view (top-left), there are multiple overlapping body segments creating a complex, tangled pattern with at least 3 visible lobes/segments. The YZ view (top-right) also shows dense, bright filling. This matches the pretzel reference images well, with multiple coils filling the eggshell. Previous three timepoints were all pretzel, and there's no sign of hatching (no elongated worm outside the shell). | [zslice-multi] counts 3/2/2/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments creating a tangled appearance. The eggshell is densely filled with signal in the XZ view (bottom-left), showing multiple bright bands/layers consistent with 3+ folds. The YZ view (top-right) also shows dense, complex signal filling. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No signs of hatching are visible. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two main body segments in a hairpin/U-shape configuration with moderate eggshell filling. Dark space remains visible within the eggshell boundary. The XZ view confirms two parallel bright regions. This matches 2fold references well - not yet showing the dense, complex multi-coil pattern of pretzel stage. Consistent with previous T74 classification. | [zslice-multi] counts 3/2/1/3/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows a complex, elongated shape with multiple overlapping body segments and an irregular, lobed outline that extends across most of the eggshell. The eggshell is densely filled with signal - there is relatively little dark empty space within the eggshell boundary. The XZ view shows multiple bright layers/bands stacked vertically, indicating overlapping coils. This matches the pretzel reference images well, where multiple folds create a complex, tangled pattern. The previous observation at T75 was also pretzel, and stages change slowly, supporting this classification. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark spaces remaining, two parallel body segments visible in XY view. The XZ view shows layered structure but not yet the dense, complex coiling of pretzel stage. Matches late 2fold references better than pretzel. Previous observation was 2fold, and morphology hasn't clearly advanced to pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little dark space remaining. Multiple overlapping body segments are visible in the XY view, and the XZ projection shows several bright layers indicating 3+ folds. This matches pretzel references better than 2fold, which would show a clearer two-segment hairpin with more empty space. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, showing complex internal structure in the XZ view with multiple overlapping layers. The XY view shows a bilobed pattern with body segments folding over each other. This matches pretzel-stage references and is consistent with the previous timepoint (T78) classification of pretzel. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, and the XY and XZ views show multiple overlapping body segments (more than 2 parallel segments visible). The complex, tangled pattern with high fill fraction matches pretzel references better than 2fold. The YZ view shows multi-lobed structure indicating 3+ folds. This is consistent with the transition observed at T78. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty dark space remaining inside the shell boundary. Multiple overlapping body segments are visible in both XY and XZ views, creating a complex tangled pattern consistent with 3+ folds. This matches pretzel references better than 2fold, which should show clearer two-segment hairpin with more empty space. T78 was also pretzel, suggesting the embryo had already reached this stage. | [zslice-multi] counts 3/2/1/2/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal spans most of the eggshell with a complex, elongated pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows a dense, complex pattern with what appears to be multiple coiled layers. This matches the pretzel reference images well, with the dense fill fraction and complex overlapping structure characteristic of 3+ folds. The previous timepoint (T81) was also classified as pretzel, and stages change slowly, so maintaining pretzel is consistent. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell filling with some dark space remaining, particularly visible in XY view. Two parallel body segments visible in the fold pattern. Not yet showing the dense, complex multi-coil pattern of pretzel. Consistent with previous 2fold classification. | [zslice-multi] counts 1/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty space, consistent with pretzel stage. The YZ view shows a ring-like pattern suggesting multiple overlapping body coils. The complex, tangled appearance matches pretzel reference images. This is consistent with the previous T83 classification of pretzel. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining, two parallel body segments visible in XY view. The fill fraction and complexity don't yet match the densely packed pretzel references. Consistent with previous 2fold classification - transitional but not clearly pretzel yet. | [zslice-multi] counts 3/2/2/2/1 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body coils visible in the XZ and YZ views, creating complex layered patterns. Matches pretzel reference images well. Consistent with previous pretzel classifications at T83 and T85. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping body segments rather than a clean two-parallel-segment pattern. The XY view shows multiple coiled structures and the XZ view shows dense, tangled signal. This matches pretzel references better than 2fold, indicating the embryo has progressed to 3+ folds. The transition from 2fold at T86 to pretzel at T87 is consistent with the oscillation seen in recent timepoints suggesting the embryo is at this boundary. | [zslice-multi] counts 2/1/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, and the XZ projection shows complex internal structure with multiple overlapping body segments/coils rather than a simple two-segment hairpin. This matches the pretzel reference at T88 well. The fill fraction is high with little empty space inside the eggshell, and the body has clearly folded more than twice. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Multiple overlapping body segments visible in XY view with complex folded morphology. YZ view shows ring-like pattern indicating coiled body. Eggshell is densely filled with signal. Consistent with pretzel reference images and previous T88 classification. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with two main parallel body segments visible in XY view. Some dark space remains within the eggshell boundary. The complexity is increasing but not yet showing the dense, multi-layered coiling characteristic of pretzel. Previous observation was 2fold, and morphology is consistent with late 2fold stage. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space inside the shell boundary. Multiple overlapping body segments are visible in both XY and XZ views, creating a complex tangled pattern. This matches pretzel references better than 2fold, which would show clearer two-parallel-segment structure with more empty space. The T88 pretzel classification was likely correct, and this represents progression to/continuation of pretzel stage. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping coils/body segments creating a complex, tangled pattern rather than a simple hairpin (which would indicate 2fold). The YZ view (top-right) shows a complex, non-uniform pattern with multiple bright regions suggesting overlapping body layers. The XZ view (bottom-left) also shows dense, complex signal filling. This matches the pretzel reference images well, with 3+ body folds creating the dense, overlapping appearance. Consistent with the previous T91 classification of pretzel. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing complex, overlapping body segments (more than 2 parallel segments visible). The XY view shows a tangled pattern with multiple coils rather than a simple U-shaped hairpin. The XZ view confirms complex looping. This matches pretzel references better than 2fold, which would show clearer two-segment organization with more empty space. | [zslice-multi] counts 2/1/3/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the eggshell is densely filled with fluorescent signal showing complex, overlapping coiled structures with multiple body segments visible. There's relatively little dark/empty space within the eggshell boundary. The XZ view (bottom-left) shows a complex pattern with multiple overlapping layers. The YZ view (top-right) appears angular/irregular, consistent with multiple folded body segments. This matches the pretzel reference images well - the eggshell is densely packed with signal from multiple overlapping body folds (3+ folds). This is consistent with the previous observation of pretzel at T93. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing multiple overlapping body segments/coils visible in both XY and XZ views. The complex, tangled pattern with at least 3 body layers and relatively little empty space within the eggshell is more consistent with pretzel than 2fold. While previous observations oscillated, the morphology here clearly shows multiple folds beyond a simple hairpin. | [zslice-multi] counts 3/2/3/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body filling most of the eggshell with complex, overlapping structures. The XZ (bottom-left) view shows multiple layered bands of signal consistent with 3+ folds. The YZ view (top-right) shows a compact, complex pattern. This matches the pretzel reference images well, with multiple overlapping coils visible. The eggshell fill fraction is high (dense), consistent with pretzel stage. Previous observation was also pretzel, and stages change slowly, supporting this classification. | [zslice-multi] counts 2/2/1/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body filling most of the eggshell interior with complex, overlapping structures. Multiple body segments/coils are visible, creating a tangled pattern. The XZ view (bottom-left) shows dense, complex signal filling the shell. This matches the pretzel reference images well, with multiple overlapping folds. Previous two timepoints were also pretzel, consistent with slow stage progression. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo body forming a complex looped/coiled pattern with multiple overlapping segments visible within the eggshell, consistent with pretzel stage. The eggshell is densely filled with signal. The XZ view shows multiple layered bright bands. This matches pretzel references and is consistent with T95-96 being pretzel. The T97 classification of 2fold was likely an error since development doesn't reverse. | [zslice-multi] counts 1/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space. Multiple overlapping body segments create a complex, tangled pattern in both XY and XZ views. This matches pretzel references. Development cannot regress from pretzel (T96) back to 2fold, so the T97-T98 2fold classifications were likely errors. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see multiple overlapping coils/body segments creating a complex, tangled pattern with at least 3 visible body segments. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, with the dense fill fraction and multiple overlapping folds. The previous timepoint (T99) was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark space remaining. Multiple body segments are becoming visible but the fill fraction is not yet dense enough for pretzel. Previous observation was 2fold, and when uncertain between 2fold and pretzel, the earlier stage is preferred. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows a clear hairpin/U-shaped body with two parallel segments connected by a bend. Eggshell fill is moderate with some dark space remaining. Matches 2fold references well. Not dense enough or complex enough for pretzel. Consistent with previous T100-T101 classifications of 2fold. | [zslice-multi] counts 3/3/2/3/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, I can see multiple overlapping coils/body segments within the eggshell - there are clearly more than two parallel segments visible, with a complex folded pattern. The eggshell is densely filled with signal, though there are some darker gaps between the coils. The YZ view shows an irregular, complex pattern consistent with multiple overlapping folds. This matches the pretzel reference images well, with the multi-fold body creating a tangled appearance. The previous timepoint was also classified as pretzel, and stages change slowly, so this is consistent. | [zslice-multi] counts 2/2/3/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping body segments filling most of the eggshell. The eggshell is densely filled with signal, and the pattern shows multiple coils/folds rather than a simple hairpin (2fold). The XZ view also shows complex overlapping structures. This is consistent with the pretzel reference images and the previous two observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments, consistent with pretzel stage. The complex tangled pattern in XY and swirling pattern in XZ match pretzel references. T102 and T103 were pretzel; T104's 2fold classification was likely erroneous as development doesn't reverse. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex bilobed/figure-8 pattern with dense signal filling. The XZ view shows densely packed bright regions suggesting multiple overlapping body layers. The overall fill fraction is high and the pattern is complex, consistent with pretzel stage. Previous observations at T103 and T105 were also pretzel, supporting continuity. | [zslice-multi] counts 2/3/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body filling most of the eggshell with complex, overlapping structures. The XZ (bottom-left) view shows multiple layered body segments with a complex pattern. The YZ view shows a swirled/coiled pattern. This matches the pretzel reference images well, with multiple overlapping folds visible. The previous two timepoints were also classified as pretzel, and there's no sign of hatching. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments - more than the two parallel segments expected for 2fold. The complex, tangled pattern matches pretzel references. T105 and T106 were pretzel; development cannot reverse to 2fold, so this is consistent with continued pretzel stage. | [zslice-multi] counts 1/3/2/3/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XZ view (bottom-left) shows complex, overlapping structures filling most of the eggshell interior. In the XY view (top-left), the signal appears elongated with multiple overlapping body segments creating a complex pattern, consistent with 3+ folds. The YZ view (top-right) shows a densely packed, bright oval. This matches the pretzel reference images well, with the dense fill fraction and complex coiled morphology. The previous observation was pretzel at T108, and stages change slowly, so pretzel is consistent. | [zslice-multi] counts 3/3/1/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 110, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 111, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled folding patterns with multiple parallel segments - more than two distinct body segments can be traced. The XZ view (bottom-left) shows dense, complex internal structure with multiple layers. The YZ view (top-right) shows an irregular, multi-lobed pattern consistent with multiple body folds overlapping. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 112, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing complex, overlapping coiled body segments. In the XY view (top-left), the embryo shows multiple folded body segments with a tangled/complex pattern filling most of the eggshell. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. Several bright punctate nuclei are visible. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No evidence of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 113, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled morphology with multiple folded segments - more than two parallel segments are apparent. The XZ view (bottom-left) shows the characteristic pretzel pattern with overlapping bright regions. The YZ view (top-right) shows a complex, non-uniform pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 114, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body segments/coils. The XY view shows a complex folded pattern with at least 3 body layers visible, not a simple U-shape. The XZ view shows dense, complex internal structure. This matches pretzel references and is consistent with T111-T112 pretzel classifications. The T113 2fold call was likely erroneous as development doesn't reverse. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 115, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments are visible in the XY view, creating a complex pattern consistent with 3+ folds. The XZ view shows layered, wrapped signal. This matches pretzel reference images. Since T112 was pretzel, the embryo cannot regress to 2fold - the previous 2fold classifications at T113-T114 were likely errors. | [zslice-multi] counts 2/2/3/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 116, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the embryo body fills most of the eggshell with a complex, elongated pattern showing multiple overlapping structures. The XZ view (bottom-left) shows dense, bright signal filling the shell with complex internal structure suggesting multiple coiled body segments. The YZ view (top-right) shows a triangular/irregular shape with multiple bright clusters, consistent with overlapping body folds. This matches the pretzel reference images well, with dense fill and complex coiling. The previous timepoint was also classified as pretzel, and stages change slowly, so pretzel is consistent. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 117, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark spaces remaining, consistent with 2fold. The body shows folding but not the densely packed, multi-coiled pattern of pretzel. Previous observation was 2fold, and the morphology doesn't show clear advancement to pretzel. Following the rule to prefer the earlier stage when uncertain. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 118, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows an elongated, complex pattern filling most of the eggshell with little dark space inside. The XZ (bottom-left) view shows multiple overlapping body layers with a complex, coiled pattern. The YZ view (top-right) shows a ring-like or looped structure consistent with multiple folds. This matches the pretzel reference images well, with multiple body segments overlapping. The eggshell fill fraction is high (dense), consistent with pretzel stage rather than 2fold. Previous observation was pretzel, and morphology confirms this. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 119, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty dark space inside the shell boundary. The XY and XZ views show complex, overlapping body segments rather than a simple two-segment hairpin characteristic of 2fold. The pattern matches pretzel reference images with multiple overlapping coils filling the shell. While previous observation was 2fold, the morphology here clearly shows advancement to pretzel. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 120, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with little empty space. Multiple overlapping body segments are visible in both XY and XZ views, showing complex coiling patterns rather than a simple two-segment hairpin. This matches pretzel reference images. The earlier T117 pretzel classification was likely correct, and T118-T119 2fold classifications were likely underestimates. | [zslice-multi] counts 1/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 121, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see an elongated embryo with what appears to be two parallel body segments forming a hairpin/U-shape. The eggshell is moderately filled - there is some dark space remaining but the body occupies a good portion of the shell. The fill fraction is moderate, not yet densely packed like pretzel stage. The XZ view (bottom-left) shows a complex but not yet fully coiled pattern. Comparing to references, this matches the 2fold stage well - two parallel segments visible, moderate fill. The previous three observations were all 2fold, and while the embryo may be approaching pretzel, I don't see the dense, multi-coiled filling characteristic of pretzel stage yet. Following the rule to prefer the earlier stage when uncertain. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 122, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with a complex, somewhat tangled pattern rather than a simple two-parallel-segment hairpin. The XZ view (bottom-left) shows dense, overlapping signal filling the shell. Compared to the 2fold references, which show moderate fill with clear two-segment structure and more dark space, this image shows significantly more fill and complexity, matching the pretzel references. The transition from 2fold to pretzel is consistent with developmental progression at T122 given previous 2fold observations at T119-121. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1281.8214168548584, + "error": null, + "accuracy": 0.3717948717948718, + "adjacent_accuracy": 0.9615384615384616 + }, + { + "embryo_id": "embryo_3", + "predictions": [ + { + "timepoint": 39, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with a curved body shape and some dark space within the eggshell, consistent with comma stage. The body shows one curved band of nuclei with a constriction/indentation visible, but no clear parallel folded segments yet. The eggshell is not sparsely filled enough for early 1.5fold - there's still substantial signal but with some empty regions. Comparing to references, this matches the comma reference images (T40-T44) very well. The previous three timepoints were all comma, and there's no clear morphological change to 1.5fold yet (no J-shape or hairpin visible).", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 40, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo body that is beginning to curve but hasn't yet formed a clear fold-back. The eggshell still has some empty space, particularly visible in the XY projection where the body doesn't fill the entire shell. Compared to the 1.5fold reference, this image lacks the clear J-shape or partial hairpin structure - the body appears more as a single curved band. The morphology is consistent with the comma reference images, showing the characteristic C-shaped curvature. The previous three timepoints were all comma, and there's no clear evidence of progression to 1.5fold yet.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 41, + "predicted_stage": "comma", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo shows an elongated body with some curvature, but the eggshell still has noticeable empty space. While there's slightly more filling than earlier comma timepoints, there isn't a clear J-shape or partial hairpin fold characteristic of 1.5fold. Previous three timepoints were comma, and following the rule to prefer the earlier stage when uncertain, this remains comma.", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 42, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The embryo has elongated significantly compared to comma references, with the body extending along the full length of the eggshell. The fill fraction is sparse-to-moderate with dark space remaining, consistent with 1.5fold. The body shows early folding but not yet two clear parallel segments. This matches the 1.5fold reference images well and represents a clear morphological change from the previous comma stage. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 43, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is sparsely to moderately filled with signal, with dark space remaining especially on the right side of the XY view. The body appears elongated with early folding but lacks the clear two parallel segments characteristic of 2fold. Morphology matches 1.5fold references better than 2fold. The jump from comma (T41) to 2fold (T42) was likely premature; this timepoint is more consistent with 1.5fold. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold (overrode 1.5fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 44, + "predicted_stage": "2fold", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. XZ view shows two distinct lobes consistent with two parallel body segments (hairpin fold). Matches 2fold reference images well. No evidence of the dense, complex multi-fold pattern of pretzel stage. Consistent with previous 2fold classification. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 45, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with moderate eggshell filling - some dark space remains but the body clearly shows two parallel segments with a fold. The overall morphology matches the 2fold reference images well, with the body forming a hairpin/U-shape. The eggshell is moderately filled but not yet densely packed as in pretzel stage. Previous three observations were all 2fold, and there's no clear morphological change to suggest advancement to pretzel. | [zslice-multi] counts 1/2/1/1/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 46, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a bilobed body shape with moderate eggshell filling - significant dark space remains inside the shell boundary. Two main body segments are visible forming a hairpin-like fold, but the shell is not densely packed with multiple overlapping coils as expected for pretzel. The morphology matches 2fold references better than pretzel, and per rules, when uncertain I choose the earlier stage. | [zslice-multi] counts 2/2/1/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 47, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal with very little empty dark space inside. Multiple overlapping body segments create a complex pattern in the XY view. This matches pretzel reference images and is consistent with the previous two pretzel classifications. | [zslice-multi] counts 2/1/1/1/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 48, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal fills nearly the entire eggshell with a complex, tangled pattern of multiple overlapping body segments. The XZ view (bottom-left) also shows dense, bright signal filling the shell with multiple layers visible. This matches the pretzel reference images well, showing multiple coils/folds within the eggshell. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 49, + "predicted_stage": "pretzel", + "ground_truth_stage": "1.5fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous three timepoints were pretzel, and stages don't regress. While the bilobed appearance with constriction looks unusual, the XZ view shows complex internal structure consistent with a folded embryo. The YZ view shows textured signal throughout. Maintaining pretzel classification for continuity. | [zslice-multi] counts 3/1/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": false, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 50, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view (top-left), the embryo shows a bean/kidney-shaped mass that fills most of the eggshell with multiple overlapping body segments creating a complex pattern. The XZ view (bottom-left) shows multiple layers of bright signal with complex internal structure. The YZ view (top-right) shows the eggshell is well-filled with signal showing multiple bright spots at different positions, consistent with overlapping coils. This matches the pretzel reference images and is consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/2/1/1/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 51, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Previous three timepoints were pretzel. While the eggshell fill appears moderate rather than densely packed, the XZ view shows complex multi-band structure suggesting multiple folds. The YZ cross-section is well-filled. Stages don't regress, so maintaining pretzel classification consistent with previous observations. | [zslice-multi] counts 2/1/1/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 52, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows multiple layers of signal with a complex internal pattern suggesting multiple body folds. This matches the pretzel reference images well, with dense filling and multiple overlapping coils. Previous three timepoints were all pretzel, and there is no sign of hatching (no signal outside the eggshell). | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 53, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two body lobes/segments with a constriction between them, consistent with a hairpin fold. Eggshell fill is moderate - some dark space remains but not sparse. Matches 2fold reference images well. Not yet densely filled like pretzel. Consistent with previous T52 classification of 2fold. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 54, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY view shows two main body lobes/segments in a hairpin-like fold pattern with moderate eggshell filling. Significant dark space remains within the eggshell boundary. The pattern shows two parallel body segments connected by a bend, not the dense multi-coil overlapping pattern expected for pretzel. Matches 2fold reference images well. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 55, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), I can see complex, overlapping coiled structures with multiple body segments visible, consistent with 3+ folds. The XZ view (bottom-left) shows dense, layered signal filling most of the eggshell. This matches the pretzel reference images well, with the dense fill and complex tangled pattern. The previous two timepoints were also classified as pretzel, and stages change slowly, so continuing as pretzel is consistent. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 56, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space inside the eggshell boundary. In the XY view (top-left), the embryo shows complex, overlapping coiled structures with multiple body segments visible, consistent with 3+ folds. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and there is no indication of hatching (no elongated worm outside the shell). | [zslice-multi] counts 3/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 57, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the eggshell with a complex, tangled pattern showing multiple overlapping body segments. The XZ view (bottom-left) shows multiple bright layers/coils stacked within the shell. This matches the pretzel reference images well, with 3+ body folds creating overlapping coils. Previous three timepoints were all pretzel, and no morphological change toward hatching is evident. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 58, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. Two parallel body segments visible in XY view with a darker midline suggesting a hairpin fold. Matches 2fold references well. Not yet showing the dense, complex multi-coil pattern of pretzel stage. Consistent with previous T57 classification of 2fold. | [zslice-multi] counts 1/1/1/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 59, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "XY projection shows two distinct lobes of signal forming a hairpin/U-shape with a clear constriction between them, indicating two parallel body segments. Eggshell fill fraction is moderate with some dark space remaining. Morphology matches 2fold references and is consistent with previous 2fold classifications at T57-T58. Not yet densely filled enough for pretzel. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 60, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The YZ view shows a ring-like pattern indicating body coiling beyond a simple hairpin. The eggshell is moderately-to-densely filled with signal, and multiple body layers are visible in the XZ projection. This is consistent with early pretzel stage, continuing from the T59 pretzel classification. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 61, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows two parallel body segments with a dark gap between them forming a hairpin/U-shape. The eggshell is moderately filled but not densely packed like pretzel. No evidence of three or more overlapping coils. Matches 2fold references and is consistent with previous T60 classification. | [zslice-multi] counts 2/1/2/3/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 62, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal spans most of the eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows multiple layered body segments with a complex pattern suggesting 3+ folds. This matches the pretzel reference images well, with the dense fill and tangled appearance. The previous observation was pretzel at T61, and stages change slowly, consistent with remaining at pretzel. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 63, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping structures visible. In the XY view, the embryo body shows multiple coiled/folded segments filling most of the eggshell interior, with relatively little empty dark space. The XZ view (bottom-left) shows a complex, densely packed pattern with multiple layers of signal. This matches the pretzel reference images well, where 3+ folds create overlapping coils. The YZ view also shows a complex internal structure consistent with pretzel stage. Previous observations at T61 and T62 were pretzel, and stages change slowly, further supporting this classification. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 64, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, and the XY view shows multiple overlapping body segments creating a complex looped/coiled pattern rather than a simple two-segment hairpin. The XZ view confirms multiple layers. This matches pretzel references better than 2fold, and is consistent with T61-T62 being pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 65, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark spaces remaining. The XY view shows complex folding that could suggest early pretzel, but the fill fraction is not yet dense enough to clearly indicate pretzel. Multiple body segments are visible but the pattern is consistent with late 2fold. Previous timepoints were 2fold, and following the rule to prefer the earlier stage when uncertain. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 66, + "predicted_stage": "2fold", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal - there's still some dark space visible, particularly on the right side of the XY view, but the embryo is filling more of the shell than in 1.5fold. In the XY view, I can see what appears to be two parallel body segments with some internal structure/folding visible. The XZ (bottom-left) view shows layered bright bands consistent with a folded body. The fill fraction is moderate - not yet densely packed like pretzel references. This matches the 2fold reference images well, and is consistent with the previous three timepoints all being 2fold. No clear transition to pretzel (which would show denser filling and more complex coiling) is evident yet. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 67, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), I can see two parallel body segments forming a clear hairpin/U-shape, with a bend connecting them. The eggshell is moderately filled - there is some dark space remaining but the body occupies a substantial portion. The fill fraction is moderate, not yet densely packed like pretzel stage. This matches the 2fold reference images well. The previous three observations were all 2fold, and there's no clear morphological change to suggest progression to pretzel (which would show 3+ overlapping coils and dense filling). | [zslice-multi] counts 3/2/2/3/3 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 68, + "predicted_stage": "pretzel", + "ground_truth_stage": "2fold", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view, the embryo shows multiple overlapping coils/body segments within the eggshell - I can see at least 3 distinct body segments creating a complex, tangled pattern. The eggshell is densely filled with signal, with relatively little empty dark space inside the shell boundary. The XZ view also shows multiple layered body segments. This matches the pretzel reference images well, with the complex folding pattern characteristic of 3+ folds. The previous timepoint was also classified as pretzel, consistent with slow stage progression. | [zslice-multi] counts 3/2/1/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 69, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal showing multiple overlapping body segments. The XZ view shows several horizontal bands indicating 3+ body folds. The XY view shows a complex pattern with overlapping coils rather than a simple U-shape. Consistent with pretzel classification from T67-T68. | [zslice-multi] counts 2/2/3/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 70, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little empty/dark space inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern. The XZ view (bottom-left) shows multiple bright layers with complex overlapping structure. This matches the pretzel reference images well, with 3+ body folds visible. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 71, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body spanning most of the eggshell interior with complex, overlapping structures. The XZ (bottom-left) view shows multiple layers of bright signal filling the shell. There are multiple body segments visible with a complex, tangled pattern consistent with 3+ folds. The previous three timepoints were all pretzel, and the morphology here is consistent with that stage. The fill fraction is high (dense), matching pretzel rather than 2fold. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 72, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping coils/body segments - more than the two parallel segments expected for 2fold. The complex, tangled pattern matches pretzel references. T69 and T70 were pretzel; the T71 classification of 2fold was likely an error since development doesn't reverse. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 73, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is moderately filled with some dark space remaining, consistent with 2fold. Two parallel body segments visible in XY view. Not yet showing the dense, complex multi-coil pattern of pretzel. Matches 2fold reference images and is consistent with previous two observations at 2fold. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 74, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body segments in a complex pattern. More than two parallel segments are visible in the XY projection, consistent with 3+ folds. This matches pretzel reference images and is consistent with the T73 pretzel classification. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 75, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with complex, overlapping structures visible. The XZ view (bottom-left) shows multiple overlapping body layers creating a complex pattern with bright regions throughout. This dense filling pattern is consistent with the pretzel stage reference images, where 3+ folds create overlapping coils. The previous two timepoints were also classified as pretzel, and stages change slowly, supporting continuity. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 76, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 77, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the body occupying most of the eggshell interior with complex, overlapping structures. Multiple body segments/coils are visible, particularly evident in the XZ (bottom-left) view where several parallel layers of signal can be seen. The YZ view also shows multiple bright spots indicating overlapping body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/1/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 78, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal, with complex overlapping coil patterns visible in the XY view showing multiple body folds. This matches pretzel reference images. T75 and T76 were pretzel; the morphology here is consistent with continued pretzel stage. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 79, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible - there's a complex pattern with signal distributed around the periphery and through the center, creating a ring-like or pretzel-like appearance. The dark central region in the XY view suggests the body is coiled around the interior. The YZ view shows a ring-like pattern consistent with multiple body folds. The eggshell is densely filled overall, matching pretzel stage references. This is consistent with the previous T78 classification of pretzel. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 80, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill with some dark space remaining. The body shows complex folding that is approaching but not clearly exceeding two parallel segments. Previous timepoint was 2fold, and while this is at the transition to pretzel, the fill fraction is still moderate rather than dense, favoring the earlier stage classification. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 81, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little dark space remaining inside the shell boundary. Multiple overlapping body segments are visible in both XY and XZ views, creating a complex layered pattern rather than a simple two-segment hairpin. This matches pretzel reference images better than 2fold. The T78 observation was also pretzel, suggesting the earlier 2fold calls at T79-T80 may have been conservative. | [zslice-multi] counts 3/2/1/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 82, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), the body shows multiple overlapping coils/folds creating a complex pattern that fills most of the eggshell. There appear to be more than two parallel body segments visible, with a looping/coiled structure characteristic of the pretzel stage. The XZ view (bottom-left) also shows dense, complex signal filling the shell. This matches the pretzel reference images well and is consistent with the previous T81 classification of pretzel. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 83, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little dark space remaining inside the shell boundary. Multiple overlapping body segments are visible creating a complex pattern, consistent with 3+ folds. This matches pretzel reference images better than 2fold references, which show more empty space and simpler two-segment structure. The transition from 2fold to pretzel appears to be occurring around this timepoint. | [zslice-multi] counts 3/2/2/1/1 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 84, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a complex folded morphology with multiple body segments visible - there's a clear curved/looped structure with at least 3 overlapping body regions. The eggshell is densely filled with signal, though there is some dark space on the left side. The XZ view (bottom-left) shows multiple distinct bright regions indicating overlapping body layers. This matches the pretzel reference images well, showing the characteristic multiple coils/folds within the eggshell. The previous observation was also pretzel (T83), and stages change slowly, consistent with maintaining this classification. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 85, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the embryo densely filling the eggshell with multiple overlapping coils/body segments visible - I can see at least 3 parallel tracks of nuclei with complex folding patterns. The eggshell is densely filled with signal, with relatively little empty dark space inside the shell boundary. The XZ view also shows complex, multi-layered signal. This matches the pretzel reference images well, and is consistent with the previous two observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 86, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern within the eggshell. The XZ view shows complex internal structure with multiple layers. This matches the pretzel reference images well, and is consistent with the previous three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 87, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with complex overlapping coils visible in the XY view. Multiple body segments can be seen creating a tangled pattern. The XZ view shows bright, complex layered structure. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel stage. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 88, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 the body occupies most of the eggshell interior with complex, overlapping coils visible. In the XY view (top-left), the signal fills the elongated eggshell shape with multiple overlapping body segments creating a tangled pattern. The XZ view (bottom-left) shows complex internal structure with multiple bright layers. This matches the pretzel reference images well, showing 3+ folds within the eggshell. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 89, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows an elongated embryo with multiple overlapping coils/body segments visible within the eggshell - at least 3 parallel segments can be discerned. The eggshell is densely filled with signal, though some dark gaps remain between the coiled body segments. The XZ view shows complex, tangled body structure with multiple layers. This matches the pretzel reference images well, with the characteristic multiple-fold pattern. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 90, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/segments, consistent with pretzel stage. The complex tangled pattern with little empty space inside the shell matches pretzel references. T87-88 were pretzel, and development cannot regress, so the T89 2fold classification was likely erroneous. | [zslice-multi] counts 2/2/1/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 91, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal - the XY view shows the embryo body spanning most of the eggshell interior with relatively little dark/empty space. The XZ (bottom-left) view shows complex, overlapping layers of signal with multiple bright bands, consistent with multiple body folds. The YZ view (top-right) shows a complex pattern with multiple bright regions suggesting overlapping coils. This matches the pretzel reference images well, where the body has folded 3+ times creating a densely packed, complex pattern. The previous observation at T90 was also pretzel, and stages change slowly, further supporting this classification. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 92, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows a complex, elongated body with multiple overlapping coils/segments visible within the eggshell. The eggshell is densely filled with signal - there is very little dark empty space inside the eggshell boundary. In the XZ view (bottom-left), the signal fills most of the eggshell area with a complex, tangled pattern showing multiple body layers. The YZ view (top-right) also shows a complex, non-uniform pattern consistent with multiple overlapping folds. This is more than just two parallel segments (2fold) - there appear to be 3+ body segments overlapping, and the fill fraction is high. Comparing to references, this matches the pretzel stage examples much better than the 2fold examples. While the previous observation was 2fold, the morphology here clearly shows progression to pretzel with dense filling and multiple coils. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 93, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "In the XY view (top-left), the embryo shows multiple overlapping coils/body segments within the eggshell, with a complex folded pattern visible. The eggshell is densely filled with signal. In the XZ view (bottom-left), multiple parallel bright bands are visible (3+ segments), indicating multiple body folds. The YZ view (top-right) shows a complex, non-uniform pattern consistent with overlapping coils. This matches the pretzel reference images well, with multiple body folds creating a tangled appearance. The previous classification was pretzel at T92, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 94, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, and the XY projection shows multiple overlapping body segments creating a complex pattern rather than a simple two-segment hairpin. The morphology closely matches pretzel reference images with complex coiled structure. While previous observation was 2fold, the clear multi-fold pattern and dense fill fraction indicate transition to pretzel. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 95, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Eggshell is densely filled with fluorescent signal showing complex, multi-layered coiling pattern. Multiple overlapping body segments visible in both XY and XZ views. Matches pretzel reference images well. Consistent with previous pretzel classifications at T92 and T94. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 96, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with signal, with complex internal structure visible in all views. The XZ projection shows multiple overlapping bright bands suggesting 3+ body folds. The central dark region in XY with bright signal on both sides indicates complex coiling beyond a simple 2fold hairpin. Fill fraction is dense, matching pretzel references more than 2fold. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 97, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows the eggshell densely filled with fluorescent signal, with multiple overlapping coils/body segments visible creating a complex pattern. There are clearly more than 2 parallel body segments - I can see multiple curved bands of nuclei overlapping within the eggshell. The XZ view also shows a complex, densely packed pattern with multiple layers. This matches the pretzel reference images well, with the eggshell mostly filled and a tangled appearance. The previous observation at T96 was pretzel, and the morphology is consistent with continuing in this stage. | [zslice-multi] counts 2/3/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 98, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little empty/dark space remains inside the eggshell boundary. In the XY view (top-left), the signal fills most of the elongated eggshell with a complex, tangled pattern showing multiple overlapping body segments. The XZ view (bottom-left) also shows dense, complex signal filling the shell with visible coiling patterns. This matches the pretzel reference images well, with multiple folded body segments creating overlapping layers. The previous two timepoints were also classified as pretzel, consistent with the slow stage progression rule. | [zslice-multi] counts 3/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 99, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), the body shows complex, tangled patterns with multiple folded segments filling most of the eggshell interior. The XZ view (bottom-left) also shows dense, complex signal with multiple layers. This matches the pretzel reference images well, with 3+ body folds creating overlapping signal. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 100, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible in the XY view. The body shows complex, tangled folding patterns with 3+ parallel segments visible, particularly clear in the XZ (bottom-left) view where multiple bright bands are stacked. The YZ view (top-right) also shows a complex, multi-lobed pattern consistent with multiple body folds. This matches the pretzel reference images well, and is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 3/3/3/3/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 101, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows multiple overlapping coils of the embryo body within the eggshell, with a complex tangled pattern. The eggshell is densely filled with fluorescent signal. Multiple body segments are visible with overlapping loops, consistent with 3+ folds. This matches the pretzel reference images well. No sign of hatching (no worm body extending outside the eggshell). Consistent with previous observations at T98-T100. | [zslice-multi] counts 3/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 102, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal, with multiple overlapping coils visible. In the XY view (top-left), I can see multiple parallel body segments forming a complex, tangled pattern with at least 3 folds visible - the body wraps around the interior of the eggshell. The XZ view (bottom-left) also shows dense, layered signal. This matches the pretzel reference images well. Previous three timepoints were all pretzel, and there's no sign of hatching (no elongated worm outside the eggshell). | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 103, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal showing multiple overlapping body coils/folds - characteristic of pretzel stage. Complex tangled pattern visible in XY view with at least 3 body layers. Matches pretzel references well. T100 and T101 were also pretzel; the T102 '2fold' classification was likely erroneous as development doesn't reverse. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 104, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "Moderate eggshell fill fraction with visible dark spaces, two parallel body segments visible in XY view, and layered but not densely complex signal in XZ view. Matches 2fold references well. Consistent with previous T102-T103 classifications of 2fold. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 105, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal with very little empty space, and the XZ view shows multiple overlapping body layers/coils rather than a simple two-segment hairpin. This matches pretzel reference images. The morphology has clearly advanced beyond 2fold, with 3+ body segments visible in the projections. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 106, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is moderately filled with signal but still has noticeable dark space on one side, consistent with 2fold rather than pretzel. Two parallel body segments are visible but not the dense, multi-layered coiling characteristic of pretzel. The XZ view shows some layering but not the complex tangled pattern of pretzel references. Previous three timepoints were 2fold, and the morphology hasn't clearly transitioned to pretzel. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel (overrode 2fold)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 107, + "predicted_stage": "2fold", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The eggshell is densely filled with fluorescent signal \u2014 very little dark/empty space remains inside the eggshell boundary. In the XY view (top-left), multiple overlapping coils/body segments are visible, creating a complex, tangled pattern with at least 3 parallel segments visible. The XZ view (bottom-left) also shows dense, complex signal filling most of the eggshell. This matches the pretzel reference images well, with the dense fill and multiple overlapping body folds. Consistent with the previous T106 classification of pretzel. | [zslice-multi] counts 1/2/1/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": false, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 108, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex coiled/looping body pattern with multiple overlapping segments (more than 2 parallel segments), and the eggshell is densely filled with signal with little empty dark space. This matches pretzel reference images. The morphology has clearly advanced beyond 2fold, consistent with the transition seen in recent timepoints. | [zslice-multi] counts 3/3/2/2/2 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + }, + { + "timepoint": 109, + "predicted_stage": "pretzel", + "ground_truth_stage": "pretzel", + "is_transitional": false, + "transition_between": null, + "reasoning": "The XY view shows a complex, multi-lobed structure with multiple overlapping coils visible within the eggshell. The eggshell appears densely filled with signal, and the body shows multiple folded segments creating a tangled/pretzel-like appearance. The XZ view (bottom-left) shows dense, complex internal structure with multiple layers. This is consistent with the pretzel reference images and the previous classification at T108. The morphology clearly shows more than two parallel body segments, ruling out 2fold. | [zslice-multi] counts 1/2/2/2/3 max=3 -> pretzel", + "reasoning_trace": null, + "tool_calls": 0, + "tools_used": [], + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, + "verification_result": null, + "candidate_stages": null + } + ], + "duration_seconds": 1063.606009721756, + "error": null, + "accuracy": 0.4788732394366197, + "adjacent_accuracy": 0.9295774647887324 + }, + { + "embryo_id": "embryo_4", + "predictions": [], + "duration_seconds": 0.2796761989593506, + "error": null, + "accuracy": 0.0, + "adjacent_accuracy": 0.0 + } + ], + "started_at": "2026-04-22T19:04:19.044352", + "completed_at": "2026-04-22T20:07:13.072640", + "total_predictions": 233, + "overall_accuracy": 0.4248927038626609, + "metrics": { + "accuracy": 0.4248927038626609, + "adjacent_accuracy": 0.9527896995708155, + "per_stage": { + "1.5fold": { + "accuracy": 0.024390243902439025, + "n": 41 + }, + "2fold": { + "accuracy": 0.4406779661016949, + "n": 59 + }, + "pretzel": { + "accuracy": 0.5413533834586466, + "n": 133 + } + } + } +} \ No newline at end of file