diff --git a/data/results/chart_1.5fold+2fold+pretzel.png b/data/results/chart_1.5fold+2fold+pretzel.png index e984f0c..9c2c722 100644 Binary files a/data/results/chart_1.5fold+2fold+pretzel.png and b/data/results/chart_1.5fold+2fold+pretzel.png differ diff --git a/data/results/scientific_1.5fold+2fold+pretzel.json b/data/results/scientific_1.5fold+2fold+pretzel.json index e30fd92..a1009d3 100644 --- a/data/results/scientific_1.5fold+2fold+pretzel.json +++ b/data/results/scientific_1.5fold+2fold+pretzel.json @@ -12,7 +12,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a bean/comma-like shape with two lobes and the body occupies most of the visible eggshell area but without clear folding or parallel body segments. No hairpin is visible, matching the comma reference. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -29,7 +29,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a compact elongated mass with slight asymmetry between two lobes, similar to the comma reference. The eggshell is sparsely filled with significant dark space at the ends, and no clear parallel body segments or fold-back are visible. Consistent with previous comma observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -46,7 +46,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a single elongated mass filling moderately with some empty space at the ends of the eggshell. No clear parallel body segments or hairpin fold visible yet. Matches comma reference best, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -59,15 +59,15 @@ }, { "timepoint": 58, - "predicted_stage": "1.5fold", + "predicted_stage": "comma", "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows a single elongated body with a slight curve/constriction, occupying only part of the eggshell with clear empty space on the right. No parallel body segments are visible yet (no fold-back). The morphology matches the comma reference best \u2014 one curved band of nuclei, eggshell partially empty. Consistent with previous T55-T57 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, @@ -80,7 +80,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo body has elongated and fills more of the eggshell than a comma stage, with signs of folding beginning \u2014 body now extends across most of the length with some parallel structure emerging but still sparse fill. Matches 1.5fold reference better than comma.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -97,7 +97,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately-sparsely filled with some dark space remaining. The XY view shows elongated body with a partial fold visible, matching 1.5fold reference. Not yet showing clear two parallel segments of 2fold. Consistent with previous T59 observation.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -114,7 +114,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell moderately filled with some dark space remaining. Body is elongated with a partial fold visible \u2014 not yet forming two clearly parallel segments. Matches 1.5fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -127,15 +127,15 @@ }, { "timepoint": 62, - "predicted_stage": "2fold", + "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 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": "Eggshell is sparsely filled with significant dark space especially on the right side. XY shows elongated body with partial fold but not yet two clear parallel segments reaching the other end. Matches 1.5fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -144,15 +144,15 @@ }, { "timepoint": 63, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately filled with some dark space still visible, especially at the ends. The body shows partial folding but not yet clear parallel segments forming a hairpin. Morphology closely matches 1.5fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -161,15 +161,15 @@ }, { "timepoint": 64, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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 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": "The eggshell shows moderate-to-sparse fill with visible dark space at the periphery. The body shows partial folding but not yet two clearly parallel segments forming a full hairpin. Consistent with previous 1.5fold observations and matches the 1.5fold reference best.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -178,15 +178,15 @@ }, { "timepoint": 65, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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 the morphology shows two parallel segments rather than multiple overlapping coils. Consistent with previous observations at T62-T64.", + "reasoning": "The XY view shows a curved body with partial folding - the tail appears to be curling back but hasn't yet reached the head to form clear parallel segments. The eggshell is sparsely to moderately filled with visible dark space remaining, especially at the ends. This matches the 1.5fold reference better than 2fold, which would show clearer parallel body segments.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -195,15 +195,15 @@ }, { "timepoint": 66, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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 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": "Eggshell is sparsely to moderately filled with visible dark space in XZ view. Body shows elongated form with a slight fold but not yet clear two parallel segments meeting end-to-end. Matches 1.5fold reference better than 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -212,15 +212,15 @@ }, { "timepoint": 67, - "predicted_stage": "2fold", + "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 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": "The embryo fills a moderate portion of the eggshell with some empty space still visible, particularly at one end. The XY view shows an elongated shape with partial folding but no clear parallel body segments forming a hairpin. Consistent with previous 1.5fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -229,15 +229,15 @@ }, { "timepoint": 68, - "predicted_stage": "2fold", + "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 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": "Eggshell is moderately-to-sparsely filled with noticeable dark space around the body. The body shows elongation with a partial fold but not a clear two-parallel-segment hairpin yet. Consistent with ongoing 1.5fold stage from prior frames.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -246,15 +246,15 @@ }, { "timepoint": 69, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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 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": "The embryo shows moderate fill with some dark space still visible in the eggshell. The XY view shows an elongated body with a slight bend but not yet a clear hairpin with two parallel segments. Morphology matches 1.5fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -263,15 +263,15 @@ }, { "timepoint": 70, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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 observations were all 2fold, and the morphology is consistent with continuing in this stage.", + "reasoning": "The embryo body occupies only part of the eggshell with significant dark/empty space visible. Only one main curved body band is visible without clear parallel segments indicating a full hairpin. Matches 1.5fold reference; consistent with T67-T69.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -280,15 +280,15 @@ }, { "timepoint": 71, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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.", + "reasoning": "The XY view shows an elongated body with a partial fold \u2014 a dark gap visible in the upper portion indicates the tail has curled but not fully met the head. The eggshell is sparsely to moderately filled with significant dark space remaining. This matches 1.5fold morphology, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -301,7 +301,7 @@ "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 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": "The XY view shows two parallel body segments with a clear bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. This matches the 2fold reference better than 1.5fold, which had only one main curve.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -318,7 +318,7 @@ "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 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": "The XY view shows two parallel body segments with a bend, consistent with a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference better than pretzel (not densely packed/coiled) and consistent with previous T72 observation.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -335,7 +335,7 @@ "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. 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": "XY view shows two parallel body segments visible with bend between them. Eggshell is moderately filled with some dark space remaining at ends. Matches 2fold reference and consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -352,7 +352,7 @@ "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'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": "The eggshell is moderately filled with signal, with some dark space remaining (especially in the upper portion of XY view). Two parallel body segments appear visible in the XY projection, consistent with a hairpin/U-shape. The fill density is not yet dense enough for pretzel, and matches the 2fold reference well. Consistent with prior T72-T74 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -369,7 +369,7 @@ "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 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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in XY view with hairpin fold. Matches 2fold reference well; not dense/tangled enough for pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -386,7 +386,7 @@ "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 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": "Eggshell moderately filled with some dark space still visible at the tapered end. Two parallel body segments visible in XY view forming a hairpin shape. Not yet densely packed like pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -403,7 +403,7 @@ "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 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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in the XY view forming a hairpin shape. Matches 2fold references, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -420,7 +420,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in the XY view with a bend, consistent with a hairpin U-shape. Matches 2fold reference better than pretzel (not densely packed with multiple coils). Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -433,15 +433,15 @@ }, { "timepoint": 80, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments are visible in the XY view forming a hairpin/U-shape, consistent with 2fold. Not yet dense enough to be 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, @@ -450,15 +450,15 @@ }, { "timepoint": 81, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "XY view shows two parallel body segments with a clear bend, suggesting a hairpin shape. Eggshell is moderately filled with some dark space remaining \u2014 not densely packed like pretzel. Matches 2fold reference well, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -467,15 +467,15 @@ }, { "timepoint": 82, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space remaining, especially visible in the XY view where two parallel body segments with a bend can be seen. The XZ view shows hairpin-like folding. Not densely packed enough for pretzel. Consistent with prior 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -484,15 +484,15 @@ }, { "timepoint": 83, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "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 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": "Two parallel body segments visible in XY view with a clear hairpin shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -501,15 +501,15 @@ }, { "timepoint": 84, - "predicted_stage": "pretzel", + "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 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": "XY view shows two parallel body segments with visible dark gap between them (hairpin shape). Eggshell is moderately filled with some dark space remaining. Not yet densely packed like pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -518,15 +518,15 @@ }, { "timepoint": 85, - "predicted_stage": "pretzel", + "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 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": "XY view shows two parallel body segments (upper and lower) with a bend, characteristic hairpin U-shape. Eggshell is moderately filled with some dark space visible at the ends. XZ view shows clear parallel folds. Not yet dense/tangled enough for pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -535,15 +535,15 @@ }, { "timepoint": 86, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space remaining at the ends. The XY view shows two parallel body segments forming a hairpin shape. Matches 2fold reference best; not yet densely packed like 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, @@ -552,15 +552,15 @@ }, { "timepoint": 87, - "predicted_stage": "pretzel", + "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 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": "The embryo shows moderate eggshell fill with visible dark space around it, and the XY view shows two roughly parallel body segments forming a hairpin shape. This matches the 2fold reference better than pretzel (which would be densely filled).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -569,15 +569,15 @@ }, { "timepoint": 88, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Two parallel body segments are visible in the XY view forming a hairpin shape. Matches 2fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -586,15 +586,15 @@ }, { "timepoint": 89, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space visible (especially the central dark region in YZ view showing a clear bend/loop). Two parallel body segments are visible in the XY view with a U-shape/hairpin structure. Not yet densely filled enough for pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -603,15 +603,15 @@ }, { "timepoint": 90, - "predicted_stage": "pretzel", + "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 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": "The embryo shows a hairpin shape with moderate eggshell filling \u2014 some dark space remains around the body. The XY view shows two parallel body segments joined at a bend, matching the 2fold reference. Not dense enough to be 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, @@ -620,15 +620,15 @@ }, { "timepoint": 91, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with visible dark space at the ends. Two parallel body segments visible in XY view forming a hairpin shape. Matches 2fold reference, consistent with prior 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, @@ -637,15 +637,15 @@ }, { "timepoint": 92, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space still visible. XZ view shows two parallel body segments with a clear gap between them (hairpin U-shape), consistent with 2fold. Not yet dense/tangled enough for pretzel. Matches previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -654,15 +654,15 @@ }, { "timepoint": 93, - "predicted_stage": "pretzel", + "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. 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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in the XY view with a hairpin shape. Matches 2fold reference better than pretzel (not densely filled). Consistent 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, @@ -671,15 +671,15 @@ }, { "timepoint": 94, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space still visible at the ends. Two parallel body segments visible in the XY view with a hairpin shape. Signal density is not yet dense enough for pretzel. Matches 2fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -688,15 +688,15 @@ }, { "timepoint": 95, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with visible dark space at the periphery. The XY view shows two parallel body segments with a bend, consistent with a hairpin U-shape. Not densely coiled enough for pretzel. Matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -705,15 +705,15 @@ }, { "timepoint": 96, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space visible. XY shows an elongated body with visible parallel segments suggesting a hairpin fold. XZ view shows two parallel bands of nuclei with a gap. Consistent with 2fold references and 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, @@ -722,15 +722,15 @@ }, { "timepoint": 97, - "predicted_stage": "pretzel", + "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. 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": "The embryo shows moderate eggshell fill with some dark space still visible at the ends. Two parallel body segments are visible in the XY view creating a hairpin shape, matching the 2fold reference. Not yet dense enough to be 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, @@ -739,15 +739,15 @@ }, { "timepoint": 98, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with visible dark space remaining. Two parallel body segments visible in XY view suggesting a hairpin fold. Not dense enough for pretzel. Consistent with previous 2fold 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, @@ -756,15 +756,15 @@ }, { "timepoint": 99, - "predicted_stage": "pretzel", + "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. 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": "The XY view shows two parallel body segments with a clear hairpin/U-shape. The eggshell is moderately filled with some dark space remaining \u2014 not densely packed like pretzel. Matches the 2fold reference well, consistent 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, @@ -773,15 +773,15 @@ }, { "timepoint": 100, - "predicted_stage": "pretzel", + "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, 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": "The XZ view shows two clear parallel body segments connected by a bend, characteristic of a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining. No multiple overlapping coils visible yet. Consistent with previous 2fold 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, @@ -790,15 +790,15 @@ }, { "timepoint": 101, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space visible. XY shows two parallel body segments with a bend, characteristic hairpin shape. Not yet densely filled enough for pretzel. Matches 2fold references well.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -807,15 +807,15 @@ }, { "timepoint": 102, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "pretzel", "is_transitional": false, "transition_between": null, - "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": "The eggshell is moderately filled with some dark space visible at both ends. Two parallel body segments are visible in the XY view suggesting a hairpin/U-shape. Not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -824,15 +824,15 @@ }, { "timepoint": 103, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space still visible, especially at the edges. The XY view shows an elongated body with hairpin morphology typical of 2fold. Not yet densely packed like pretzel. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -845,7 +845,7 @@ "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 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": "The eggshell is densely filled with signal \u2014 multiple overlapping body segments are visible in the XY view (clear loop/coil structure), and the XZ view shows several parallel bands stacked together. This matches the pretzel reference more than 2fold, which had more dark space and only two parallel segments.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -862,7 +862,7 @@ "ground_truth_stage": "pretzel", "is_transitional": false, "transition_between": null, - "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": "Eggshell is densely filled with signal, very little dark space remaining. Multiple overlapping body segments are visible in the XZ view, indicating multiple folds. Consistent with previous pretzel classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -879,7 +879,7 @@ "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 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": "Eggshell is densely filled with signal, little dark space remaining. Multiple overlapping body segments visible creating a complex tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -896,7 +896,7 @@ "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 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": "Eggshell is densely filled with multiple overlapping coils visible especially in XZ view showing tangled parallel segments. Matches pretzel reference and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -913,7 +913,7 @@ "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, 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": "Eggshell is densely filled with signal, multiple overlapping body segments visible in both XY and XZ views creating a complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -930,7 +930,7 @@ "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 - 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": "Eggshell is densely filled with signal, multiple overlapping body segments visible creating a complex tangled pattern. Matches pretzel reference and continues from previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -947,7 +947,7 @@ "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 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": "The eggshell is densely filled with overlapping bright signal, and multiple body layers/coils are visible in the XZ view (bottom-left) showing complex overlapping structure. Consistent with previous pretzel classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -964,7 +964,7 @@ "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 shape outside the eggshell).", + "reasoning": "Eggshell is densely filled with overlapping bright signal, multiple body layers visible creating a complex tangled pattern. Matches pretzel reference and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -981,7 +981,7 @@ "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 (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": "Eggshell is densely filled with overlapping fluorescent signal, showing multiple body layers/coils with complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -998,7 +998,7 @@ "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. 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": "The eggshell is densely filled with bright signal, XZ view shows multiple overlapping body segments/coils creating a complex tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1015,7 +1015,7 @@ "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 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": "Eggshell is densely filled with complex overlapping signal, multiple body coils visible in XZ view with tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1032,7 +1032,7 @@ "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 previous three observations of pretzel.", + "reasoning": "The eggshell is densely filled with fluorescent signal, multiple overlapping coils visible especially in the XZ view showing tangled body segments. Matches pretzel reference well, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1049,7 +1049,7 @@ "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 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": "Eggshell is densely filled with bright fluorescent signal, multiple overlapping body segments visible in both XY and XZ views, complex tangled pattern consistent with pretzel stage. Matches previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1066,7 +1066,7 @@ "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": "Eggshell is densely filled with bright signal and little dark space remains. Multiple overlapping body segments visible in XY and XZ views creating a complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1083,7 +1083,7 @@ "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 is consistent with the previous three observations all being pretzel. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "Eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible creating a tangled coiled pattern. Matches pretzel reference well and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1100,7 +1100,7 @@ "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": "The eggshell is densely filled with overlapping bright signal showing multiple coiled body segments. The XY view shows two parallel body regions offset/overlapping, and the XZ view shows a complex tangled pattern with little dark space. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1117,7 +1117,7 @@ "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 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": "Eggshell is densely filled with bright fluorescent signal with multiple overlapping body segments visible, matching the pretzel reference. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1134,7 +1134,7 @@ "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": "Eggshell is densely filled with fluorescent signal with multiple overlapping body segments visible in the side views. Consistent with previous pretzel observations and matches pretzel reference morphology.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1151,7 +1151,7 @@ "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 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": "Eggshell is densely filled with multiple overlapping coils of bright signal. The XZ view shows multiple parallel body segments stacked, and the XY view shows a complex tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1168,7 +1168,7 @@ "ground_truth_stage": "pretzel", "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 (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": "The eggshell is densely filled with overlapping fluorescent signal showing multiple body layers. Complex tangled pattern with multiple overlapping segments visible, consistent with pretzel stage and matching previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1185,7 +1185,7 @@ "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 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": "Eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible creating a complex tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1202,7 +1202,7 @@ "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 multiple folded body segments creating an intricate pattern. Consistent with the previous three observations of pretzel stage.", + "reasoning": "The eggshell is densely filled with multiple overlapping coiled body segments visible in the XY view, showing the characteristic tangled pretzel pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1219,7 +1219,7 @@ "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": "Eggshell is densely filled with multiple overlapping body segments visible in all three views. The YZ and XZ views show multiple parallel curved bands indicating multi-fold coiling. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1236,7 +1236,7 @@ "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. 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": "Eggshell is densely filled with fluorescent signal showing multiple overlapping coils. YZ view shows multiple parallel body segments. Consistent with prior pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1253,7 +1253,7 @@ "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 elongated worm outside the eggshell). Consistent with the previous three observations of pretzel.", + "reasoning": "The eggshell is densely filled with signal showing multiple overlapping body segments. The XY view shows curved/coiled structure with multiple layers, and XZ shows a densely filled shape with overlapping bright bands. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1270,7 +1270,7 @@ "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 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": "Eggshell is densely filled with bright signal, multiple overlapping body segments visible creating a tangled/coiled appearance. Matches pretzel reference well, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1287,7 +1287,7 @@ "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": "The eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible in both XY and XZ views creating a complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1304,7 +1304,7 @@ "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, 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": "Eggshell is densely filled with overlapping signal, multiple body layers visible creating a complex tangled pattern. Matches pretzel reference well, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1321,7 +1321,7 @@ "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": "Eggshell is densely filled with multiple overlapping bright bands visible in both XY and XZ views, indicating multiple coiled body segments. The complex tangled pattern matches the pretzel reference, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1338,7 +1338,7 @@ "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 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 eggshell is densely filled with multiple overlapping coils visible in the XY view. Multiple body segments are visible, creating a complex tangled pattern consistent with pretzel stage. Matches previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1355,7 +1355,7 @@ "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 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": "The eggshell is densely filled with overlapping fluorescent signal showing multiple body segments/coils. XY view shows tangled overlapping bands, and XZ view shows multiple parallel layers of nuclei. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1372,7 +1372,7 @@ "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 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": "Eggshell is densely filled with overlapping fluorescent signal, multiple body layers visible with complex tangled pattern. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1389,7 +1389,7 @@ "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 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": "The eggshell is densely filled with overlapping coiled body segments. Multiple parallel bands visible in the XZ view indicate multiple folds. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1406,7 +1406,7 @@ "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 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": "Eggshell is densely filled with overlapping coils of fluorescent signal visible in XY view showing multiple body segments tangled together. Side view shows multiple layers stacked. Matches pretzel reference and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1423,7 +1423,7 @@ "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 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": "Eggshell is densely filled with fluorescent signal, multiple overlapping body segments visible creating a complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1435,9 +1435,9 @@ "candidate_stages": null } ], - "duration_seconds": 678.0339498519897, + "duration_seconds": 520.1384418010712, "error": null, - "accuracy": 0.75, + "accuracy": 0.7619047619047619, "adjacent_accuracy": 1.0 }, { @@ -1445,15 +1445,15 @@ "predictions": [ { "timepoint": 45, - "predicted_stage": "1.5fold", + "predicted_stage": "comma", "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a subtle constriction between two lobes, similar to bean/comma stage. The eggshell is not densely filled - significant dark space remains, especially in side views. Only one band of nuclei is visible, no parallel body segments or folding. Consistent with previous comma 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, @@ -1462,15 +1462,15 @@ }, { "timepoint": 46, - "predicted_stage": "1.5fold", + "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 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": "Eggshell is sparsely filled with significant dark space around the body. Single elongated mass with slight asymmetry, no clear folding or parallel segments visible. Matches comma reference closely and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -1483,7 +1483,7 @@ "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 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": "The image exactly matches the 1.5fold reference. The embryo shows elongation with partial folding - one curved body visible with sparse eggshell filling (notable dark space at the right end). The body has elongated beyond the compact comma stage but not yet formed the clear parallel hairpin of 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1500,7 +1500,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely to moderately filled with dark space visible especially at the right end. Body appears elongated with a partial fold but no clear parallel segments yet. Matches 1.5fold reference better than comma (more elongated) or 2fold (no clear hairpin).", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1517,7 +1517,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely to moderately filled with dark empty space still visible at the ends. The XY view shows a partially folded body with a developing curl but not yet a clear two-parallel-segment hairpin. Matches 1.5fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1534,7 +1534,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely-to-moderately filled with visible dark space, especially on the right side. The body shows elongation with a partial fold visible in the side view but no clear parallel hairpin segments yet. Matches 1.5fold reference best, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1551,7 +1551,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely filled with dark space visible at both ends; body shows a single elongated mass with partial curling, not yet forming two parallel segments. Matches 1.5fold reference and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1568,7 +1568,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely filled with dark space at the right end. The body shows one main elongated mass with partial folding but no clear two parallel segments. Matches 1.5fold reference closely, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1585,7 +1585,7 @@ "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, 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": "Eggshell is sparsely-to-moderately filled with visible dark space at the ends. Body shows elongation with a partial fold but not yet two clearly parallel segments. Matches 1.5fold reference and consistent with prior timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1602,7 +1602,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo body shows moderate elongation with one main curve, and the eggshell still has visible dark/empty space around the body (sparse-moderate fill). No clear parallel hairpin segments are yet visible. Matches the 1.5fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1619,7 +1619,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely filled with dark space still visible at the ends. No clear parallel body segments or hairpin visible \u2014 looks like a single elongated curved body. Matches 1.5fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1636,7 +1636,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely filled with significant dark space at edges. The body shows a single elongated mass with partial fold visible but no clear two parallel segments or hairpin. Consistent with previous 1.5fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1653,7 +1653,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely filled with dark space remaining, especially in lower right. XY view shows an elongated body with partial curve but not yet a clear hairpin with two fully parallel segments. Consistent with previous 1.5fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1670,7 +1670,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows elongation with partial folding visible. Eggshell is moderately filled with some dark space remaining, particularly at the ends. The XZ view shows two somewhat parallel layers but not tightly packed. Morphology matches 1.5fold reference - partial fold without full hairpin, and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1687,7 +1687,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The eggshell appears sparsely-to-moderately filled with noticeable dark space at the top. Body shows partial folding but not yet two clear parallel segments reaching end-to-end. Consistent with continuing 1.5fold progression from previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1704,7 +1704,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows a curved body with partial folding but not yet forming two clear parallel segments meeting end-to-end. The eggshell is sparsely filled with significant dark space remaining, especially at the top-right of the XY view. This matches the 1.5fold reference better than 2fold, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1721,7 +1721,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows elongated body with a visible bend/curve at the upper edge suggesting the tail has folded back near the head. The eggshell is moderately filled with some dark space remaining, and two parallel body segments appear visible. This matches the 2fold reference better than 1.5fold, consistent with progression from prior 1.5fold stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1738,7 +1738,7 @@ "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, 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": "Eggshell is moderately filled with dark space remaining at top. Two parallel body segments visible in XY forming a hairpin shape. Matches the 2fold reference closely.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1755,7 +1755,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "XY view shows two parallel body segments with a bend, matching 2fold reference. Eggshell is moderately filled with some dark space remaining. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1772,7 +1772,7 @@ "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 at this stage.", + "reasoning": "The XY view shows two parallel body segments with a clear bend, forming a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining. This matches the 2fold reference well, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1789,7 +1789,7 @@ "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 (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": "Eggshell is moderately filled with some dark space remaining. YZ view shows two parallel body segments stacked, indicating hairpin folding. Matches 2fold reference well and consistent with previous frames.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1806,7 +1806,7 @@ "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 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": "XY view shows two parallel body segments with a bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. Consistent with previous 2fold observations and matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1823,7 +1823,7 @@ "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 - 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": "The XY view shows two parallel body segments connected by a bend, consistent with a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining, not yet densely packed like pretzel. Matches 2fold reference well and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1840,7 +1840,7 @@ "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 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": "XY shows an elongated curved body with a slight arch, consistent with a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Matches 2fold reference well and consistent with prior timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1857,7 +1857,7 @@ "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 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": "XY view shows two parallel body segments (upper and lower band) with some dark space still visible at the ends of the eggshell \u2014 classic hairpin/U-shape. Fill is moderate, not densely packed like pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1874,7 +1874,7 @@ "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 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": "XY view shows two parallel body segments forming a hairpin/U-shape with a bend. Eggshell is moderately filled with some dark space remaining. No dense multi-coil tangle typical of pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1891,7 +1891,7 @@ "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 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": "XY view shows two parallel body segments (hairpin shape) with a visible gap between them. Eggshell is moderately filled with some dark space remaining at the ends. Not yet densely packed like pretzel. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1908,7 +1908,7 @@ "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 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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin pattern. Matches 2fold reference better than pretzel (not densely packed) and previous frames were 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1925,7 +1925,7 @@ "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 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": "Eggshell moderately filled with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin/U-shape. Matches 2fold reference closely, consistent with prior timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1942,7 +1942,7 @@ "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 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": "The XY view shows two parallel body segments with a clear hairpin bend, characteristic of 2fold. Eggshell fill is moderate with some dark space still visible. Matches 2fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1959,7 +1959,7 @@ "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 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": "The XY view shows two parallel body segments with a clear bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. Consistent with previous 2fold observations and matches the 2fold reference well.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1976,7 +1976,7 @@ "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 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": "The XY view shows two parallel body segments connected with a bend, characteristic of 2fold. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference closely and consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1993,7 +1993,7 @@ "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 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": "XY view shows two parallel body segments with a bend, consistent with a hairpin/U-shape. Moderate eggshell fill with some dark space remaining \u2014 not yet densely packed like pretzel. Matches 2fold reference closely.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2006,15 +2006,15 @@ }, { "timepoint": 78, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "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 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": "XY view shows two parallel body segments separated by a dark gap (hairpin/U-shape), with moderate eggshell fill \u2014 some dark space remains at the ends. Matches 2fold reference closely, consistent with prior timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2023,15 +2023,15 @@ }, { "timepoint": 79, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately filled with some dark space remaining, especially at the ends. Two parallel body segments visible in XY view with a bend, consistent with a hairpin U-shape. Matches 2fold reference better than pretzel (not densely packed with multiple coils). Consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2040,15 +2040,15 @@ }, { "timepoint": 80, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments appear visible in the XY view with a bend, consistent with a hairpin shape. Not yet densely packed like pretzel. Matches 2fold reference well and is consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2057,15 +2057,15 @@ }, { "timepoint": 81, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space remaining, particularly around the edges. Two parallel body segments appear visible in the XY view with a hairpin structure. Not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -2078,7 +2078,7 @@ "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": "The eggshell is densely filled with fluorescent signal with very little dark empty space remaining. The XZ view shows multiple overlapping body segments/coils, and the overall brightness is high from overlapping layers. This matches the pretzel reference closely.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2095,7 +2095,7 @@ "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 stage.", + "reasoning": "Eggshell is densely filled with fluorescent signal, very little dark space remaining. Multiple overlapping body segments are visible in the XZ view showing the characteristic coiled pattern. Matches pretzel reference closely, and consistent with previous T82 classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2108,15 +2108,15 @@ }, { "timepoint": 84, - "predicted_stage": "pretzel", + "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/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": "The eggshell is moderately filled with visible dark spaces, particularly in the lower-left region of XY view. Two parallel body segments appear visible with a hairpin curve. The signal density is less than typical pretzel (which would be densely filled with overlapping coils). Given previous frames were labeled pretzel, but this image shows notable empty space, it better matches 2fold morphology.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2125,15 +2125,15 @@ }, { "timepoint": 85, - "predicted_stage": "pretzel", + "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 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": "The XY view shows two clearly parallel body segments (upper and lower bands) connected by a bend, forming a hairpin/U-shape. The eggshell is moderately filled with some dark space still visible, especially at the ends. This matches the 2fold reference better than pretzel, which would show denser filling and multiple overlapping coils.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2142,15 +2142,15 @@ }, { "timepoint": 86, - "predicted_stage": "pretzel", + "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/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": "Eggshell is moderately filled with some dark space still visible around the body. YZ view shows two parallel body segments clearly. XZ side view shows a U-shape/hairpin with two layers. Matches 2fold reference better than densely-filled 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, @@ -2159,15 +2159,15 @@ }, { "timepoint": 87, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space still visible at the edges. Two parallel body segments visible in the XZ view (bottom-left) with a hairpin U-shape. Signal density is not yet pretzel-like dense. Consistent with prior 2fold 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, @@ -2176,15 +2176,15 @@ }, { "timepoint": 88, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space remaining. XZ view shows clear parallel body segments (hairpin/U-shape visible). Not yet densely filled enough for pretzel. Consistent with previous 2fold 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, @@ -2193,15 +2193,15 @@ }, { "timepoint": 89, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space still visible, particularly at the edges. Two parallel body segments are visible in the XY view with a bend, consistent with a hairpin U-shape. The signal density is higher than 1.5fold but not as dense/tangled as pretzel. Matches 2fold reference best.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2210,15 +2210,15 @@ }, { "timepoint": 90, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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 (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": "The eggshell is moderately filled with clear dark space remaining at top and corners. Two parallel body segments visible in XY view connected by a bend, forming a U/hairpin shape. Not densely packed enough for pretzel. Consistent with previous 2fold 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, @@ -2227,15 +2227,15 @@ }, { "timepoint": 91, - "predicted_stage": "pretzel", + "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/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": "Eggshell is moderately filled with some dark space still visible at ends. XY view shows two parallel body segments with a bend. XZ side view clearly shows two stacked parallel body layers, consistent with 2fold hairpin. Not yet dense/tangled enough for 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, @@ -2244,15 +2244,15 @@ }, { "timepoint": 92, - "predicted_stage": "pretzel", + "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, 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": "The eggshell is moderately filled with some dark space still visible at the ends. Two parallel body segments are visible in XY view forming a hairpin/U-shape. Not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -2261,15 +2261,15 @@ }, { "timepoint": 93, - "predicted_stage": "pretzel", + "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/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": "The XY view shows two parallel body segments forming a clear hairpin/U-shape with a bend. Eggshell is moderately filled with some dark space still visible, not densely packed like pretzel. Matches 2fold reference well.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2278,15 +2278,15 @@ }, { "timepoint": 94, - "predicted_stage": "pretzel", + "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. 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": "The XY view shows two parallel body segments with a bend, forming a hairpin shape. Eggshell is moderately filled with dark space remaining at the ends, not densely packed like pretzel. Matches 2fold reference best, consistent 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, @@ -2295,15 +2295,15 @@ }, { "timepoint": 95, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space remaining, particularly visible in the XZ view. Two parallel body segments appear visible in the XY view forming a hairpin shape. Signal density is not yet dense enough for pretzel, consistent with continued 2fold 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, @@ -2312,15 +2312,15 @@ }, { "timepoint": 96, - "predicted_stage": "pretzel", + "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 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": "The XY view shows two parallel body segments with a bend, characteristic of a hairpin 2fold shape. The eggshell is moderately filled with visible dark space remaining, not densely packed as in pretzel. Consistent with previous 2fold 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, @@ -2329,15 +2329,15 @@ }, { "timepoint": 97, - "predicted_stage": "pretzel", + "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. 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": "The eggshell is moderately filled with some dark space visible (especially center in XY). Two parallel body segments visible along the long axis forming a U-shape. Matches 2fold reference better than pretzel (which would be densely filled with multiple coils). Consistent with previous 2fold 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, @@ -2346,15 +2346,15 @@ }, { "timepoint": 98, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows two parallel body segments forming a hairpin shape with moderate eggshell fill - dark space still visible at top and bottom. Not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -2363,15 +2363,15 @@ }, { "timepoint": 99, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Two parallel body segments appear visible in the XY and XZ views suggesting a hairpin/U-shape. Consistent with previous 2fold 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, @@ -2380,15 +2380,15 @@ }, { "timepoint": 100, - "predicted_stage": "pretzel", + "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. 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": "XY view shows two parallel body segments with visible curvature/bend. Eggshell is moderately filled with some dark space still visible at the poles and edges. Not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -2397,15 +2397,15 @@ }, { "timepoint": 101, - "predicted_stage": "pretzel", + "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. 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": "Eggshell is moderately filled with some dark space remaining at ends. Two parallel body segments visible in XY view with a bend connecting them. Not yet densely packed enough for pretzel. Consistent with prior 2fold 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, @@ -2414,15 +2414,15 @@ }, { "timepoint": 102, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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 - 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": "XY view shows two parallel body segments connected by a bend (hairpin shape). Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Consistent with previous 2fold 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, @@ -2431,15 +2431,15 @@ }, { "timepoint": 103, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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 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": "The XY view shows a clear hairpin with two parallel body segments and a visible curve/bend at one end. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Consistent with previous 2fold 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, @@ -2448,15 +2448,15 @@ }, { "timepoint": 104, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space still visible, particularly at the ends. Two parallel body segments visible in the XY view with a curve, consistent with a hairpin U-shape. Not densely packed enough for pretzel. Matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2465,15 +2465,15 @@ }, { "timepoint": 105, - "predicted_stage": "pretzel", + "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. 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": "XY shows two parallel body segments with a bend forming a hairpin shape. Moderate eggshell fill with some dark space visible at ends. Not yet densely packed/coiled like pretzel. Matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2482,11 +2482,11 @@ }, { "timepoint": 106, - "predicted_stage": "hatching", + "predicted_stage": "2fold", "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 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": "The XY view shows two lobes/parallel segments with a bend, and the eggshell has moderate fill with visible dark space. Pattern matches 2fold reference, not densely filled enough for pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2499,11 +2499,11 @@ }, { "timepoint": 107, - "predicted_stage": "hatching", + "predicted_stage": "2fold", "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 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": "Eggshell is moderately filled with some dark space remaining at top. Two parallel body segments visible in XY view with a clear hairpin fold. Pattern matches 2fold reference - not yet densely packed enough to be pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2516,11 +2516,11 @@ }, { "timepoint": 108, - "predicted_stage": "hatching", + "predicted_stage": "2fold", "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 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": "The XY view shows two parallel body segments visible as upper and lower bands with some dark space between them and at the ends. The eggshell is moderately filled, not densely packed with overlapping coils as in pretzel. This matches the 2fold reference best, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2533,11 +2533,11 @@ }, { "timepoint": 109, - "predicted_stage": "hatching", + "predicted_stage": "2fold", "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 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": "The eggshell is moderately filled with some dark gaps visible, and two parallel body segments are visible in the XY view connected by a bend. This matches the 2fold reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2550,11 +2550,11 @@ }, { "timepoint": 110, - "predicted_stage": "hatching", + "predicted_stage": "2fold", "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 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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments are visible in the XY view with a bend, matching the 2fold reference. Not dense enough for pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2567,15 +2567,15 @@ }, { "timepoint": 111, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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 deforming the eggshell. The previous three timepoints were all classified as hatching, and stages change slowly. The morphology is consistent with continued hatching.", + "reasoning": "The eggshell is densely filled with signal with very little dark/empty space remaining. Multiple overlapping body segments are visible in the XY view, and the XZ view shows the complex tangled pattern characteristic of pretzel stage. This matches the pretzel reference better than 2fold, which has more empty space.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2584,15 +2584,15 @@ }, { "timepoint": 112, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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 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": "Eggshell is densely filled with overlapping bright signal and little dark empty space. Multiple overlapping body layers visible in XZ view showing coiled/tangled pattern. Consistent with prior pretzel classification at T111.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2601,15 +2601,15 @@ }, { "timepoint": 113, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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": "Eggshell is densely filled with signal, showing multiple overlapping body layers in both XY and XZ views. The XZ view reveals parallel coils characteristic of pretzel folding. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2618,15 +2618,15 @@ }, { "timepoint": 114, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "ground_truth_stage": "pretzel", "is_transitional": false, "transition_between": null, - "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": "The eggshell is densely filled with overlapping bright signal, showing multiple coils/folds. The XZ view shows complex tangled pattern with multiple body layers. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2635,15 +2635,15 @@ }, { "timepoint": 115, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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 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": "Eggshell is densely filled with multiple overlapping bright bands visible in XY view, showing complex coiled morphology. Multiple parallel segments visible indicating 3+ folds. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2652,15 +2652,15 @@ }, { "timepoint": 116, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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 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": "The eggshell is densely filled with signal showing multiple overlapping body layers, consistent with pretzel stage. The XZ view shows multiple parallel bands indicating a coiled body. Continues from previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2669,15 +2669,15 @@ }, { "timepoint": 117, - "predicted_stage": "hatching", + "predicted_stage": "pretzel", "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 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": "Eggshell is densely filled with bright signal, multiple overlapping body segments visible in XY and XZ views showing complex coiled pattern. Matches pretzel reference well, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2686,16 +2686,16 @@ }, { "timepoint": 118, - "predicted_stage": "early", + "predicted_stage": "pretzel", "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_011CaK4L8QTnb5FTeRzixvzH'}", + "reasoning": "Eggshell is densely filled with multiple overlapping coils of bright signal. YZ and XZ views show multiple parallel body segments stacked, matching pretzel reference. Continues from previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, - "is_adjacent_correct": false, + "is_correct": true, + "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, "verification_result": null, @@ -2707,7 +2707,7 @@ "ground_truth_stage": "pretzel", "is_transitional": false, "transition_between": null, - "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": "Eggshell is densely filled with signal, multiple overlapping body segments visible in the XY view creating a complex tangled pattern. The side view shows layered bright bands consistent with multiple coils. Matches pretzel references and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2724,7 +2724,7 @@ "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 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": "Eggshell densely filled with overlapping coils, multiple body layers visible in both XY and XZ views, consistent with prior pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2741,7 +2741,7 @@ "ground_truth_stage": "pretzel", "is_transitional": false, "transition_between": null, - "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": "The eggshell is densely filled with multiple overlapping layers of signal, showing complex tangled pattern with multiple parallel body segments visible in the XZ view. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2758,7 +2758,7 @@ "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 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": "Eggshell is densely filled with overlapping bright segments; multiple body coils visible in both XY and XZ views, with tangled/complex pattern typical of pretzel stage. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2770,10 +2770,10 @@ "candidate_stages": null } ], - "duration_seconds": 822.9110968112946, + "duration_seconds": 485.11695528030396, "error": null, - "accuracy": 0.7948717948717948, - "adjacent_accuracy": 0.9871794871794872 + "accuracy": 0.5897435897435898, + "adjacent_accuracy": 1.0 }, { "embryo_id": "embryo_3", @@ -2784,7 +2784,7 @@ "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 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": "The embryo shows a single elongated mass filling most of the eggshell with a slight curvature visible. No clear folding or parallel body segments are present. Morphology matches the comma reference - one curved band of nuclei, no hairpin fold yet. Consistent with previous T36-T38 comma observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2797,15 +2797,15 @@ }, { "timepoint": 40, - "predicted_stage": "comma", + "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 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": "The embryo has elongated along the eggshell with signal extending further than comma. In the XY view, a curved darker gap in the middle suggests the body has begun folding back - a J-shape with partial fold visible. The eggshell is sparsely-to-moderately filled with some dark space remaining. This matches the 1.5fold reference better than comma, which shows a more compact mass with empty eggshell space.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2814,15 +2814,15 @@ }, { "timepoint": 41, - "predicted_stage": "comma", + "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 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": "The embryo fills most of the eggshell with moderate density. Compared to comma (more empty space around a clear curved body), this shows a more elongated body with partial folding. No clear two parallel segments of a full hairpin yet, so not 2fold. Matches 1.5fold reference best, consistent with previous T40 observation.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -2835,7 +2835,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately-to-densely filled but still shows some structure with a visible diagonal seam suggesting a partial fold (J-shape). Not yet clear two parallel segments nor complex multi-coil pretzel pattern. Consistent with progression from previous 1.5fold frames.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2852,7 +2852,7 @@ "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 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": "The embryo fills most of the eggshell length but shows a partial fold visible in the XY view \u2014 one main curved body with a beginning hairpin. Not yet two clearly parallel segments. Consistent with prior 1.5fold timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2869,7 +2869,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely-to-moderately filled with dark space still visible at the ends. The body appears as a single elongated mass without clear parallel segments or a hairpin fold. Matches the 1.5fold reference closely, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2886,7 +2886,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows moderate-to-sparse fill with some dark space around the edges of the eggshell. Body has elongated with a slight constriction visible but no clear parallel segments or hairpin fold yet. Matches 1.5fold reference well; consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2899,15 +2899,15 @@ }, { "timepoint": 46, - "predicted_stage": "1.5fold", + "predicted_stage": "comma", "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, 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": "The embryo body shows a single elongated curved mass with a slight bend, filling only a portion of the eggshell (significant dark space at the ends). No clear parallel body segments or fold-back is visible yet. Morphology matches comma reference best \u2014 still one curved band of nuclei without a clear J-shape 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, @@ -2920,7 +2920,7 @@ "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 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": "Eggshell is moderately-to-sparsely filled with some dark space at top. The embryo shows elongation with a hint of folding but no clear two parallel segments yet. Body occupies most of the shell length, more elongated than comma but not a full hairpin. Matches 1.5fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2937,7 +2937,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is moderately filled with some dark space visible at the ends. XY shows a curved body with partial folding but no clear two parallel segments reaching full length. Matches 1.5fold reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2954,7 +2954,7 @@ "ground_truth_stage": "1.5fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows elongation with a partial curve/fold visible in XY view. Eggshell is sparsely to moderately filled with dark space remaining. No clear two-parallel-segment hairpin yet. Consistent with previous 1.5fold timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2971,7 +2971,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows an elongated body with a slight curve/partial fold beginning \u2014 one main body band with some bulging suggesting the tail is starting to curl back. The eggshell is sparsely filled with significant dark space around the body. No clear two parallel segments yet, consistent with 1.5fold and matching previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2988,7 +2988,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a curved body with a notch/indentation at the top-left (partial fold forming). Eggshell is sparsely filled with significant dark space remaining. Only one main curve visible with partial tail curl, not yet forming a full hairpin. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3001,15 +3001,15 @@ }, { "timepoint": 52, - "predicted_stage": "1.5fold", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The eggshell is moderately-to-densely filled with signal, and in the XY view two parallel body segments are visible with a clear central gap/fold between them, indicating the tail has folded back toward the head. This matches the 2fold reference better than 1.5fold where the eggshell still had significant empty space.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3022,7 +3022,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The eggshell is moderately-sparsely filled with dark space still visible at the ends. XY view shows a curved body with what appears to be a partial fold but not yet two fully parallel segments. Given previous T52 was 2fold, this looks similar - borderline 1.5fold/2fold, but the gap between segments and incomplete elongation suggests still transitioning. Given T52 was marked 2fold, maintaining 2fold is reasonable, but the morphology here with visible dark ends of eggshell looks more like 1.5fold/early 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3039,7 +3039,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "XY view shows a clear constriction with two lobes but not yet two parallel elongated body segments. Eggshell is sparsely filled with significant dark space at the ends. Morphology matches 1.5fold references better than 2fold, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3056,7 +3056,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows an elongated body with a visible dark space/gap in the middle suggesting a partial fold (J-shape), but not two clearly parallel segments. The eggshell is sparsely-to-moderately filled with significant dark space around the embryo. Consistent with previous 1.5fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3069,15 +3069,15 @@ }, { "timepoint": 56, - "predicted_stage": "1.5fold", + "predicted_stage": "2fold", "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows two clear parallel body segments with a dark gap between them (hairpin shape), indicating the tail has folded back to meet the head. The eggshell is moderately filled with some dark space still visible. This matches the 2fold reference better than 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, @@ -3090,7 +3090,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell is sparsely/moderately filled with clear dark space at the right end. The body appears as a single elongated mass with some asymmetric bulging but no clear parallel segments or hairpin fold. This matches the 1.5fold reference better than 2fold. The previous T56 '2fold' call may have been premature.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3107,7 +3107,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "Eggshell shows sparse-to-moderate fill with visible dark space, especially a dark gap in the center of XY view suggesting one curve with partial fold. No clear two parallel body segments yet. Matches 1.5fold reference best, consistent with previous T57.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3124,7 +3124,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The embryo shows a curved body with sparse eggshell filling - significant dark space remains within the eggshell boundary. The morphology shows partial folding without clear parallel segments, consistent with the 1.5fold reference. Matches the trajectory from previous T57-T58.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3141,7 +3141,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "The XY view shows two clear parallel body segments with a dark gap between them (hairpin/U-shape), indicating the tail has folded back to approximately reach the head. The eggshell is moderately filled with some dark space remaining. This matches the 2fold reference better than 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3158,7 +3158,7 @@ "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 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": "XY view shows two parallel body segments with a dark gap between them (hairpin/U-shape). Eggshell is moderately filled with some dark space remaining. Consistent with 2fold progression from prior 1.5fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3175,7 +3175,7 @@ "ground_truth_stage": "2fold", "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 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": "The eggshell is moderately filled with two parallel body segments visible in the XY view, consistent with 2fold. Not yet densely packed enough for pretzel, and consistent with previous T60-T61 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3192,7 +3192,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "XY view shows two parallel body segments with a dark gap between them (hairpin shape), tail approximately reaching head. Eggshell is moderately filled with some dark space remaining. Consistent with previous 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3209,7 +3209,7 @@ "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 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": "XY view shows two clear parallel body segments separated by a dark gap in the middle \u2014 classic hairpin/U-shape. The eggshell is moderately filled with some dark space remaining at the ends and center. Matches 2fold reference; consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3226,7 +3226,7 @@ "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 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": "The XY view shows an elongated body with two parallel segments visible (top and bottom bands with a slight gap/bend). Eggshell is moderately filled with some dark space remaining. Matches the 2fold reference closely, consistent with previous T62-T64 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3243,7 +3243,7 @@ "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 is consistent with continuing in this stage.", + "reasoning": "Two parallel body segments visible in XY view forming a hairpin shape, with moderate eggshell fill (some dark space remaining at top/bottom). Matches 2fold reference closely, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3260,7 +3260,7 @@ "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 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": "Eggshell is moderately filled with some dark space remaining. The XY view shows an elongated body with a visible bend/fold structure, consistent with two parallel body segments. Matches 2fold reference best; not yet densely packed like pretzel.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3277,7 +3277,7 @@ "ground_truth_stage": "2fold", "is_transitional": false, "transition_between": null, - "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": "XY view shows a clear hairpin with two parallel body segments and a dark interior gap (the fold loop). Eggshell is moderately filled with some dark space remaining. Matches 2fold reference closely.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3294,7 +3294,7 @@ "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 hasn't changed significantly.", + "reasoning": "The eggshell is moderately filled with signal, with some dark space still visible at the ends. Two parallel body segments appear visible in the XY view suggesting a hairpin fold. Matches the 2fold reference best, consistent with previous T66-T68 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3311,7 +3311,7 @@ "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. 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": "The XY view shows two parallel body segments connected by a bend with a visible dark gap between them (hairpin shape). The eggshell is moderately filled with some empty space remaining \u2014 not densely packed like pretzel. Consistent with prior 2fold observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3328,7 +3328,7 @@ "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 forming a hairpin pattern, consistent with 2fold references. Not yet densely packed enough for pretzel. Continuous with previous 2fold classifications at T68-T70.", + "reasoning": "The eggshell is moderately filled with some dark space remaining. The XY view shows two parallel body segments forming a hairpin/U-shape, consistent with 2fold. Matches the 2fold reference well, and previous timepoints were 2fold.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3341,15 +3341,15 @@ }, { "timepoint": 72, - "predicted_stage": "pretzel", + "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 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": "XY view shows two parallel body segments with a clear gap/bend between them (hairpin shape). The eggshell is moderately filled with some dark space remaining, not densely packed. This matches 2fold morphology, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3358,15 +3358,15 @@ }, { "timepoint": 73, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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 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": "Eggshell is moderately filled with some dark space still visible, especially in the XY view where the body occupies most but not all of the shell. Two parallel body segments are visible in both XY and XZ views, with a hairpin fold. This matches the 2fold reference better than pretzel (which would show denser filling and multiple overlapping coils). Consistent with previous 2fold 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, @@ -3375,15 +3375,15 @@ }, { "timepoint": 74, - "predicted_stage": "pretzel", + "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 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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in XY view forming a hairpin/U-shape. Consistent with previous 2fold observations and matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3392,15 +3392,15 @@ }, { "timepoint": 75, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space remaining, especially in the lower portion of the XY view. Two parallel body segments are visible in the XZ view, suggesting a hairpin/U-shape configuration. This matches the 2fold reference best, and is consistent 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, @@ -3409,15 +3409,15 @@ }, { "timepoint": 76, - "predicted_stage": "pretzel", + "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. 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": "Eggshell is moderately filled with some dark space remaining. The XY view shows two parallel body segments connected by a bend, consistent with a hairpin/U-shape. Matches 2fold reference well; not yet densely coiled like 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, @@ -3426,15 +3426,15 @@ }, { "timepoint": 77, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space visible (central darker region in XY view suggests a hairpin fold with two parallel body segments). Not dense enough for pretzel. Consistent with previous 2fold 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, @@ -3443,15 +3443,15 @@ }, { "timepoint": 78, - "predicted_stage": "pretzel", + "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 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": "The XY view shows two parallel body segments with a clear dark gap between them (hairpin shape). Eggshell is moderately filled with some dark space still visible, not densely packed as pretzel. Consistent with previous 2fold 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, @@ -3460,15 +3460,15 @@ }, { "timepoint": 79, - "predicted_stage": "pretzel", + "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 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": "XY view shows a clear hairpin/U-shape with two parallel body segments around a central dark gap \u2014 characteristic of 2fold. Eggshell is moderately filled with visible dark space between folds, not densely packed as in pretzel. Consistent with previous 2fold 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, @@ -3477,15 +3477,15 @@ }, { "timepoint": 80, - "predicted_stage": "pretzel", + "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. 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": "The XY view shows two parallel body segments with a clear dark gap/hairpin bend between them, characteristic of 2fold. The eggshell is moderately filled with some dark space remaining. Consistent with previous 2fold 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, @@ -3494,15 +3494,15 @@ }, { "timepoint": 81, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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 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": "Eggshell is moderately filled with some dark space still visible (especially at ends and center). Two parallel body segments visible in XY view with a bend, consistent with 2fold hairpin. Not yet densely packed like pretzel. Matches 2fold reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3511,15 +3511,15 @@ }, { "timepoint": 82, - "predicted_stage": "pretzel", + "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), 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": "XY view shows a clear hairpin/U-shape with two parallel body segments and a dark gap between them. Eggshell is moderately filled with some dark space remaining, not densely packed as in pretzel. Matches 2fold reference well.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3528,15 +3528,15 @@ }, { "timepoint": 83, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space visible at the ends. Two parallel body segments are visible in the XY view forming a hairpin/U-shape. Signal density matches 2fold reference, not yet densely packed like pretzel. Consistent with previous 2fold 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, @@ -3545,15 +3545,15 @@ }, { "timepoint": 84, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows a clear hairpin with two parallel body segments connected by a bend at the left end, forming a U-shape. The eggshell is moderately filled with some dark space visible in the center of the loop. This matches the 2fold reference best, not yet the dense filling of 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, @@ -3562,15 +3562,15 @@ }, { "timepoint": 85, - "predicted_stage": "pretzel", + "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, 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": "XY view shows two parallel body segments with a clear bend \u2014 a hairpin/U-shape. Eggshell is moderately filled with visible dark space at the ends, not densely packed like pretzel. Matches 2fold reference closely.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3579,15 +3579,15 @@ }, { "timepoint": 86, - "predicted_stage": "pretzel", + "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. 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": "The XY view shows a clear hairpin with two parallel body segments and a visible internal dark loop/gap, characteristic of 2fold. The eggshell is moderately filled \u2014 not densely packed like pretzel, and dark space remains at the ends. Consistent with progression from prior 2fold frames.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": false, "phase_count": 1, @@ -3600,7 +3600,7 @@ "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": "The eggshell is densely filled with signal, with little dark space remaining. Multiple overlapping body segments visible in XY view, and the XZ view shows a complex tangled pattern with overlapping layers. This matches the pretzel reference better than 2fold, which had more visible dark space and clearer parallel segments.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3617,7 +3617,7 @@ "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.", + "reasoning": "Eggshell is densely filled with signal, and the XY view shows multiple overlapping body segments forming a coiled pattern. The XZ view shows complex tangled structure consistent with pretzel stage. Follows progression from previous pretzel classification.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3634,7 +3634,7 @@ "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 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": "Eggshell is densely filled with overlapping bright signal, especially visible in the XZ view showing multiple stacked layers. The YZ view shows a compact, bright, filled cross-section. Multiple overlapping body segments are visible, consistent with pretzel stage and following previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3651,7 +3651,7 @@ "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, with 3+ folds creating overlapping body segments. Consistent with previous observations at T87-T89.", + "reasoning": "Eggshell is densely filled with overlapping fluorescent signal. Multiple parallel body segments visible in the XZ view indicating multiple coils. Matches pretzel reference closely and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3668,7 +3668,7 @@ "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 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": "Eggshell is densely filled with overlapping bright signal throughout; multiple coiled body segments visible with little dark space inside shell. Matches pretzel reference and consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3685,7 +3685,7 @@ "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) 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": "The eggshell is densely filled with overlapping bright signal showing multiple body layers/coils in both the XY and XZ views. The complex tangled pattern with multiple overlapping segments matches the pretzel reference, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3702,7 +3702,7 @@ "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": "Eggshell is densely filled with multiple overlapping coils visible in the XY view, showing complex tangled pattern consistent with pretzel stage. Continues from prior pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3719,7 +3719,7 @@ "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 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": "The eggshell is densely filled with multiple overlapping coils visible in the XY view, showing the tangled multi-fold pattern characteristic of pretzel stage. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3736,7 +3736,7 @@ "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 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": "The eggshell is densely filled with signal showing multiple overlapping body segments. The XY view shows complex tangled pattern with multiple layers visible, and XZ shows dense fill across the shell. Consistent with previous pretzel classifications.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3753,7 +3753,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments visible in both XY and XZ views. The complex tangled pattern with coils matches the pretzel reference. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3770,7 +3770,7 @@ "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, 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 signal showing multiple overlapping body segments/coils. The XY view shows complex tangled pattern with multiple parallel bands visible. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3787,7 +3787,7 @@ "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": "Eggshell is densely filled with signal, multiple overlapping body segments visible creating a complex tangled pattern. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3804,7 +3804,7 @@ "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 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": "Eggshell is densely filled with overlapping bright signal, multiple coiled body layers visible in all views, consistent with continued pretzel stage following T96-T98.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3821,7 +3821,7 @@ "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) 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": "The eggshell is densely filled with multiple overlapping body layers visible in the XY view, showing complex coiled pattern consistent with pretzel stage. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3838,7 +3838,7 @@ "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": "The eggshell is densely filled with multiple overlapping coils visible in the XY view, showing complex tangled pattern with multiple body segments. Matches pretzel reference closely and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3855,7 +3855,7 @@ "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 - 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": "The eggshell is densely filled with signal, showing multiple overlapping body segments visible in the XY view (parallel coils with a curved band). The pattern is complex and consistent with previous pretzel observations at T99-T101.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3872,7 +3872,7 @@ "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": "The eggshell is densely filled with fluorescent signal with multiple overlapping body segments visible, particularly clear in the XZ view showing several parallel coils. Very little dark space remains inside the shell, consistent with pretzel stage and previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3889,7 +3889,7 @@ "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 three observations of pretzel stage. No sign of hatching (no elongated worm outside the eggshell).", + "reasoning": "Eggshell is densely filled with multiple overlapping body layers visible in all three views. The XZ view shows multiple parallel segments tangled together, consistent with pretzel stage. Follows previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3906,7 +3906,7 @@ "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 elongated worm outside the shell). Consistent with previous three observations of pretzel.", + "reasoning": "Eggshell is densely filled with overlapping body segments, multiple coils visible in XY view. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3923,7 +3923,7 @@ "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 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": "Eggshell is densely filled with fluorescent signal with multiple overlapping body segments visible in the XY view. The complex tangled pattern and high fill fraction match the pretzel reference. Consistent with previous pretzel observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3940,7 +3940,7 @@ "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 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": "Eggshell is densely filled with signal, multiple overlapping body segments visible creating a complex tangled pattern. Matches pretzel reference and consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3957,7 +3957,7 @@ "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 of pretzel stage.", + "reasoning": "The eggshell is densely filled with multiple overlapping coils/body segments visible in the XY view, showing the complex tangled pattern characteristic of pretzel stage. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3974,7 +3974,7 @@ "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. 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": "The XY view shows multiple overlapping coils with a complex tangled pattern. The eggshell is densely filled with signal, and multiple body layers overlap creating the bright tangled appearance characteristic of pretzel stage. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3986,38 +3986,38 @@ "candidate_stages": null } ], - "duration_seconds": 598.227730512619, + "duration_seconds": 441.5914149284363, "error": null, - "accuracy": 0.7746478873239436, + "accuracy": 0.6056338028169014, "adjacent_accuracy": 1.0 }, { "embryo_id": "embryo_4", "predictions": [], - "duration_seconds": 0.1755971908569336, + "duration_seconds": 0.27407050132751465, "error": null, "accuracy": 0.0, "adjacent_accuracy": 0.0 } ], - "started_at": "2026-04-22T15:13:18.235955", - "completed_at": "2026-04-22T15:48:17.584886", + "started_at": "2026-04-27T19:19:51.376592", + "completed_at": "2026-04-27T19:43:58.498053", "total_predictions": 233, - "overall_accuracy": 0.7725321888412017, + "overall_accuracy": 0.6566523605150214, "metrics": { - "accuracy": 0.7725321888412017, - "adjacent_accuracy": 0.9957081545064378, + "accuracy": 0.6566523605150214, + "adjacent_accuracy": 1.0, "per_stage": { "1.5fold": { - "accuracy": 0.6585365853658537, + "accuracy": 0.8048780487804879, "n": 41 }, "2fold": { - "accuracy": 0.6101694915254238, + "accuracy": 0.8135593220338984, "n": 59 }, "pretzel": { - "accuracy": 0.8796992481203008, + "accuracy": 0.5413533834586466, "n": 133 } } diff --git a/data/results/zslice_multi_1.5fold+2fold+pretzel.json b/data/results/zslice_multi_1.5fold+2fold+pretzel.json index f3758c0..c506111 100644 --- a/data/results/zslice_multi_1.5fold+2fold+pretzel.json +++ b/data/results/zslice_multi_1.5fold+2fold+pretzel.json @@ -12,7 +12,7 @@ "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": "The embryo shows a bean/comma-like shape with a slight constriction in the middle. The eggshell is only moderately filled with two lobes visible but no clear folding or parallel body segments. This matches the comma reference closely, consistent with prior T52-T54 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -29,7 +29,7 @@ "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": "The embryo shows a slight asymmetric elongated mass with moderate fill but still has empty space at both ends of the eggshell. Only one band of nuclei is visible without clear folding, matching the comma reference. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -42,35 +42,35 @@ }, { "timepoint": 57, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The embryo fills moderately but still shows a single elongated mass without clear parallel body segments or hairpin fold. The XY view shows one elongated curved body, and XZ shows a single thick band. Consistent with comma stage transitioning toward 1.5fold, but no clear fold yet.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 58, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The XY view shows a single elongated mass with slight asymmetry/curvature, occupying moderate portion of eggshell with some empty space on the right. No clear parallel body segments or fold visible. Signal density and morphology match the comma reference best, consistent with previous observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, @@ -80,7 +80,7 @@ "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": "The embryo body fills more of the eggshell compared to comma, with elongation and some asymmetric thickening on one side suggesting the tail has started to curl back. Still some dark space in the shell, not yet a clear two parallel hairpin. Matches 1.5fold reference. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -97,7 +97,7 @@ "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": "The eggshell is moderately-sparsely filled with some dark space at top and bottom. The embryo shows elongation with a partial fold visible but not yet two clear parallel segments reaching each other. Morphology matches 1.5fold reference better than 2fold (which shows clearer parallel segments). | [zslice-multi] counts 1/1/1/1/2 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -114,7 +114,7 @@ "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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments are visible in the XY and XZ views, connected by a bend \u2014 consistent with a hairpin/U-shape. Matches 2fold reference well, and is consistent with prior T59-T60 observations. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -127,15 +127,15 @@ }, { "timepoint": 62, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "Eggshell is moderately filled with some dark space remaining at the ends. Two parallel body segments are visible in the XY view, consistent with a 2fold hairpin. Matches 2fold reference best, and previous frames were also 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": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -148,7 +148,7 @@ "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": "The eggshell is moderately filled with signal, and two parallel body segments are visible in the XY view with a bend at one end, matching the 2fold reference. Consistent with prior 2fold observations at T60-T61. | [zslice-multi] counts 1/1/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -165,7 +165,7 @@ "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": "The eggshell is moderately filled with signal, showing two parallel body segments in the XY view with a bend \u2014 consistent with a U-shape/hairpin. Some dark space remains but less than pretzel. Matches 2fold reference and is consistent with neighboring timepoints. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -178,16 +178,16 @@ }, { "timepoint": 65, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The XY view shows two parallel body segments with a visible bend, consistent with a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining. Matches the 2fold reference well, consistent with previous timepoints. | [zslice-multi] counts 3/1/1/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, + "is_adjacent_correct": false, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -199,7 +199,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, particularly at the right end. Two parallel body segments appear visible in the XY view with a bend. The morphology matches the 2fold reference better than pretzel, which shows denser filling and multiple overlapping coils. T65 pretzel call may have been premature. | [zslice-multi] counts 2/1/1/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -216,7 +216,7 @@ "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": "The XY view shows an elongated shape with visible bending/parallel segments but the eggshell is only moderately filled with a clear tapered end and some empty space. The signal density and morphology match the 2fold reference more closely than pretzel (which would be densely filled with multiple overlapping coils). Previous pretzel calls at T65-66 may have been premature; this frame shows 2fold morphology. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -233,7 +233,7 @@ "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": "The eggshell is moderately filled with visible dark space at the ends and top. Two parallel body segments appear visible in the XY view with a bend, matching the 2fold reference. Not dense enough for pretzel. | [zslice-multi] counts 3/2/2/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -246,15 +246,15 @@ }, { "timepoint": 69, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The XY view shows an elongated body with visible nuclei still resolvable as individual dots, not densely overlapping. There's clear dark space within the eggshell on both ends. Two parallel body segments visible with a bend. Matches 2fold reference better than pretzel (which is denser and more tangled). Earlier T67 was also 2fold, suggesting T68 pretzel may have been premature. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -263,15 +263,15 @@ }, { "timepoint": 70, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The XY view shows two lobes/parallel body segments with a slight bend, consistent with a hairpin shape. The eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Given previous timepoints oscillating around this stage (T67=2fold), this frame best matches 2fold morphology. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -280,15 +280,15 @@ }, { "timepoint": 71, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The XY view shows two parallel body segments with a clear dark gap between them (upper and lower bands), indicating a hairpin fold where the tail has reached the head. The eggshell is moderately filled with some dark space remaining. This matches the 2fold reference better than 1.5fold (which shows one main curve) or pretzel (densely filled). | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -297,15 +297,15 @@ }, { "timepoint": 72, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The XY view shows two parallel body segments forming a clear hairpin/U-shape, with the body curving back on itself. The eggshell is moderately filled but still has some dark space. This matches the 2fold reference better than 1.5fold, suggesting progression from the previous timepoints. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -314,15 +314,15 @@ }, { "timepoint": 73, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The XY view shows an elongated body with visible parallel segments suggesting a hairpin fold - the tail has elongated along the body. Eggshell fill is moderate, with dark space still visible at the right end and top. Not yet densely packed like pretzel. Two parallel body segments visible in XZ view. Matches 2fold reference better than pretzel (which shows denser filling) or 1.5fold (which shows less elongation). | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -331,15 +331,15 @@ }, { "timepoint": 74, - "predicted_stage": "pretzel", + "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 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": "The XY view shows two parallel body segments with a visible gap/bend between them \u2014 characteristic hairpin shape of 2fold. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference better than 1.5fold (which has more sparse filling) or pretzel (which is densely packed). | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -352,7 +352,7 @@ "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": "The XY view shows an elongated body with what appears to be two parallel segments visible (upper brighter band and a lower dimmer band). The eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. The morphology closely matches the 2fold reference. | [zslice-multi] counts 3/1/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -365,15 +365,15 @@ }, { "timepoint": 76, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately filled with some dark space still visible, especially at the ends. Two parallel body segments appear visible in the XY view with a bend, consistent with a hairpin/U-shape. Not yet densely filled enough for pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -386,7 +386,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, especially at the right end. Two parallel body segments appear visible in the XY view forming a U/hairpin shape. Signal density is not as dense as pretzel reference. Consistent with T74 and T76 observations of 2fold. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -399,15 +399,15 @@ }, { "timepoint": 78, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XY view shows two parallel body segments with a bend, forming a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining, not densely packed as in pretzel. Matches 2fold reference closely and is consistent with previous T76-T77 observations. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -420,7 +420,7 @@ "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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in XY with a bend, consistent with hairpin 2fold. Not yet densely packed like pretzel. Matches previous observations and 2fold reference. | [zslice-multi] counts 1/1/1/3/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -433,15 +433,15 @@ }, { "timepoint": 80, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The XY view shows a body with two parallel segments connected at one end (hairpin/U-shape). The eggshell is moderately filled with some dark space still visible around the body, not densely packed as in pretzel. This matches 2fold morphology better than pretzel. The previous T79 'pretzel' may have been a misclassification given T77-78 were 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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -454,7 +454,7 @@ "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": "The XY view shows two roughly parallel body segments with a visible bend, and the eggshell is moderately filled with some dark space still present. The pattern matches the 2fold reference better than pretzel (not densely packed with multiple coils) or 1.5fold (more filled than sparse J-shape). Given progression around T78-81, 2fold is consistent. | [zslice-multi] counts 1/2/3/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -467,15 +467,15 @@ }, { "timepoint": 82, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XY view shows two parallel body segments with a bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. XZ view shows two parallel bands consistent with 2fold stage. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -484,15 +484,15 @@ }, { "timepoint": 83, - "predicted_stage": "2fold", + "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 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": "The XY view shows two clear parallel body segments separated by a horizontal dark gap - the hallmark hairpin/U-shape of 2fold. The eggshell is moderately filled with some dark space remaining between the folded segments. Not yet dense enough for pretzel (no multiple overlapping coils visible). | [zslice-multi] counts 3/1/1/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -501,15 +501,15 @@ }, { "timepoint": 84, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments in the XY view with a complex tangled pattern. The XZ view shows dense fill across the full shell length. This matches pretzel stage, consistent with T81 and T83. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -522,7 +522,7 @@ "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": "Eggshell is densely filled with signal, multiple overlapping body segments visible in XY and XZ views showing complex folding pattern. Consistent with previous pretzel classifications. | [zslice-multi] counts 3/2/1/3/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -535,15 +535,15 @@ }, { "timepoint": 86, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "Eggshell is densely filled with signal, multiple overlapping body layers visible in XY and XZ views creating a complex tangled pattern. Consistent with previous pretzel observations and matches pretzel reference. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -552,15 +552,15 @@ }, { "timepoint": 87, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The embryo shows a bilobed/hairpin shape with visible dark space within the eggshell (moderate fill, not dense). Two parallel body segments are visible in XY and XZ views with a clear bend. Signal is not dense enough for pretzel - significant empty space remains. Matches 2fold reference best. | [zslice-multi] counts 2/2/3/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -573,7 +573,7 @@ "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": "The XY view shows an elongated body with a clear bend, and the XZ view shows two parallel stacked segments with some dark space still visible within the eggshell. Fill is moderate rather than dense \u2014 not enough overlapping coils for pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -586,15 +586,15 @@ }, { "timepoint": 89, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is densely filled with signal, with multiple overlapping body segments visible in XY and a ring-like structure in YZ indicating coiling. The XZ view shows bright, tangled overlapping layers. This matches pretzel better than 2fold, which would show only two parallel segments with more dark space. | [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_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -603,15 +603,15 @@ }, { "timepoint": 90, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XY view shows an elongated body with moderate eggshell filling - some dark space remains at the ends. Two parallel body segments are suggested in the XZ view. This matches 2fold references better than pretzel (which would show denser filling and more overlapping coils). Consistent with previous T89 observation. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -620,15 +620,15 @@ }, { "timepoint": 91, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately filled with some dark space still visible at the ends. Two parallel body segments appear visible in the XY view with a hairpin-like shape. Not yet densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -641,7 +641,7 @@ "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": "Eggshell moderately filled with some dark space remaining, especially visible in XZ view showing two parallel body segments with a bend. Signal not dense enough for pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -658,7 +658,7 @@ "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": "Eggshell is moderately filled with some dark space visible at the ends. Two parallel body segments visible in the XY view with a bend. Matches 2fold reference better than pretzel (not densely packed with multiple coils). | [zslice-multi] counts 2/1/2/3/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -675,7 +675,7 @@ "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": "The eggshell is densely filled with fluorescent signal, with multiple overlapping body segments visible in both XY and XZ views. The pattern looks complex and tangled with little dark space remaining, consistent with pretzel stage. Follows progression from T93. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -692,7 +692,7 @@ "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": "The XY view shows an elongated body with some dark space remaining at the top of the eggshell, indicating moderate fill rather than dense. Two parallel segments are suggested but not heavily overlapping coils. This matches the 2fold reference better than the dense pretzel pattern. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -709,7 +709,7 @@ "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": "Eggshell is moderately filled with some dark space still visible, especially around edges. XZ view shows two parallel body segments with a bend, characteristic of a hairpin/U-shape. Consistent with previous 2fold observations at T94-T95. | [zslice-multi] counts 1/1/1/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -722,15 +722,15 @@ }, { "timepoint": 97, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space still visible around the body, especially at the top and bottom of the XY view. Two parallel body segments are visible in the XZ projection, consistent with 2fold hairpin. Not yet densely filled like pretzel reference. | [zslice-multi] counts 1/2/2/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -743,7 +743,7 @@ "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": "The eggshell is moderately filled with some dark space visible, especially at the ends. Two parallel body segments appear visible in the XY view connected by a bend. Not dense enough for pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -760,7 +760,7 @@ "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": "The eggshell is densely filled with signal, with multiple overlapping body segments visible in both XY and XZ views. The pattern shows complex tangled coiling characteristic of pretzel stage, with little dark space remaining inside the shell. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -777,7 +777,7 @@ "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": "The XZ view shows two parallel body segments forming a clear hairpin/U-shape. The eggshell is moderately filled with some dark space still visible, not densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -790,15 +790,15 @@ }, { "timepoint": 101, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is densely filled with fluorescent signal with multiple overlapping body layers visible in the XY and XZ views. The pattern shows complex tangled coils consistent with pretzel stage, matching the previous T100 observation. | [zslice-multi] counts 3/1/2/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -807,15 +807,15 @@ }, { "timepoint": 102, - "predicted_stage": "2fold", + "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/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": "The eggshell is densely filled with signal showing multiple overlapping body segments in the XZ view (bottom-left), consistent with pretzel stage. Previous frames were pretzel, and morphology matches pretzel references with complex tangled pattern filling most of the shell. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -828,7 +828,7 @@ "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": "Eggshell is densely filled with bright signal and multiple overlapping body layers are visible in the XZ view, consistent with pretzel stage and matching previous observations. | [zslice-multi] counts 2/1/1/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -845,7 +845,7 @@ "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": "Eggshell is densely filled with fluorescent signal showing multiple overlapping coils/folds. The XZ view shows multiple parallel body segments stacked, indicating the body has folded three or more times. Matches pretzel reference and consistent with previous timepoints. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -862,7 +862,7 @@ "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": "The eggshell is densely filled with fluorescent signal with little dark empty space. The XZ view shows multiple overlapping body segments/layers (3+ parallel bands visible), indicating multiple folds. This matches the pretzel reference better than 2fold, and is consistent with T102-103 pretzel classification. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -879,7 +879,7 @@ "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": "The eggshell is densely filled with fluorescent signal, with multiple overlapping body segments visible in the XY view and the XZ view showing complex overlapping coils. Very little dark empty space remains inside the shell, matching the pretzel reference pattern. | [zslice-multi] counts 1/1/1/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -896,7 +896,7 @@ "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": "The XZ view shows two parallel body segments with dark space between them, characteristic of a hairpin fold. The eggshell is moderately filled with visible dark regions, not densely packed as in pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/1/3/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -913,7 +913,7 @@ "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": "The eggshell is densely filled with signal, with multiple overlapping body segments visible in the XY and XZ views. The XZ view shows multiple parallel layers of nuclei indicating multiple folds. Consistent with pretzel stage following T107. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -926,15 +926,15 @@ }, { "timepoint": 109, - "predicted_stage": "pretzel", + "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 - 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": "Eggshell is densely filled with signal, multiple overlapping body segments visible in XY view forming a complex coiled pattern, consistent with pretzel stage and matches previous observations. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -947,7 +947,7 @@ "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": "The eggshell is densely filled with fluorescent signal with multiple overlapping body layers visible, especially in the XZ view showing complex tangled pattern. The XY view shows overlapping segments suggesting multiple folds. Consistent with pretzel at T107-108. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -964,7 +964,7 @@ "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": "The XY view shows an elongated body with visible parallel segments and a bend, consistent with a hairpin shape. The eggshell is moderately filled with some dark space remaining, not densely packed as in pretzel. Matches 2fold reference best, consistent with prior T109-T110. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -981,7 +981,7 @@ "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": "Eggshell is moderately filled with some dark space still visible, especially at the ends. Two parallel body segments visible in XY view with a bend, consistent with 2fold hairpin. Not yet densely packed like pretzel. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -998,7 +998,7 @@ "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": "Eggshell is moderately filled with some dark space visible at the ends. XZ view shows two parallel body segments forming a hairpin/U-shape. Matches 2fold reference well; not yet dense enough for pretzel. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1015,7 +1015,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, particularly visible in the XZ view showing two parallel body layers with a gap between them. The XY view shows an elongated body with a bend. This matches the 2fold reference with two parallel segments and moderate fill, consistent with previous timepoints. | [zslice-multi] counts 2/3/2/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1028,15 +1028,15 @@ }, { "timepoint": 115, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "Eggshell is densely filled with signal, minimal dark space. XZ view shows multiple overlapping body segments/coils. Matches pretzel references, consistent with progression from T114. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1049,7 +1049,7 @@ "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": "Eggshell is densely filled with bright signal throughout, minimal dark empty space. Multiple overlapping body segments create a complex tangled pattern. Consistent with prior pretzel classification. | [zslice-multi] counts 3/2/2/1/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1062,15 +1062,15 @@ }, { "timepoint": 117, - "predicted_stage": "pretzel", + "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 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": "Eggshell is densely filled with bright signal, multiple overlapping body layers visible, consistent with prior pretzel observations. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1079,15 +1079,15 @@ }, { "timepoint": 118, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "Eggshell is densely filled with signal, very little dark space remains. Multiple overlapping body layers visible in XY view with complex tangled pattern. Matches pretzel reference better than 2fold - prior timepoints were pretzel, consistent with ongoing 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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1100,7 +1100,7 @@ "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": "XY view shows two parallel body segments forming a hairpin shape with moderate eggshell fill and some dark space remaining. Consistent with previous 2fold observations. | [zslice-multi] counts 3/1/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1113,15 +1113,15 @@ }, { "timepoint": 120, - "predicted_stage": "pretzel", + "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 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": "Eggshell is densely filled with overlapping fluorescent signal, with multiple parallel body segments visible in the XY view suggesting 3+ folds. Matches pretzel reference with complex tangled appearance and bright overlapping layers. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1130,15 +1130,15 @@ }, { "timepoint": 121, - "predicted_stage": "pretzel", + "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 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": "Eggshell is densely filled with signal and the XZ view shows multiple overlapping body segments (more than two parallel bands), indicating multiple coils. Overall brightness and complexity match pretzel references better than 2fold. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1151,7 +1151,7 @@ "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": "The eggshell is densely filled with signal, very little dark space remaining inside. Multiple overlapping body segments are visible in the XY view forming a complex coiled pattern, and the XZ view shows multiple parallel layers. This matches the pretzel reference better than 2fold, which would show more empty space. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1168,7 +1168,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, especially at the right end. Two parallel body segments are visible in the XY view with a bend, consistent with a hairpin/U-shape. Not dense enough for pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1181,15 +1181,15 @@ }, { "timepoint": 124, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in the XY view with a bend. Matches 2fold reference best, consistent with previous observations. | [zslice-multi] counts 2/2/2/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1198,15 +1198,15 @@ }, { "timepoint": 125, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows two parallel body segments connected by a bend (hairpin/U-shape). The eggshell is moderately filled with some dark space still visible, not densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 1/2/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1219,7 +1219,7 @@ "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": "Eggshell is moderately filled with some dark space remaining. YZ view shows two parallel body segments with a bend, characteristic of a hairpin/U-shape. Not yet densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/2/1/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1232,15 +1232,15 @@ }, { "timepoint": 127, - "predicted_stage": "2fold", + "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). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning": "The eggshell is densely filled with signal showing multiple overlapping body segments. The YZ view shows multiple parallel bands of signal indicating multiple coils. Consistent with T126 pretzel classification and matches pretzel reference. | [zslice-multi] counts 1/1/1/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1253,7 +1253,7 @@ "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": "The eggshell is densely filled with multiple overlapping body segments visible in the XY view, showing the tangled coil pattern characteristic of pretzel. Consistent with previous pretzel observations. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1266,15 +1266,15 @@ }, { "timepoint": 129, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is densely filled with signal, showing multiple overlapping body layers creating a complex tangled pattern. The XY view shows coiled segments and the XZ view shows dense filling with minimal dark space. This matches the pretzel reference better than 2fold, which would show clearer parallel segments 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": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1287,7 +1287,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body layers visible in the XY view with parallel segments. The XZ view shows complex tangled pattern characteristic of pretzel stage with multiple folds. | [zslice-multi] counts 2/2/3/3/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1304,7 +1304,7 @@ "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": "The eggshell appears densely filled with fluorescent signal with multiple overlapping body segments visible, especially in the XZ view showing complex tangled pattern. Consistent with previous pretzel classification at T130. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1321,7 +1321,7 @@ "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": "XY view shows multiple overlapping curved body segments with a visible internal loop/coil pattern. The eggshell is densely filled with signal across most of its interior, with complex tangled morphology characteristic of pretzel stage. Given progression past 2fold, this is pretzel. | [zslice-multi] counts 2/1/1/2/4 max=4 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1338,7 +1338,7 @@ "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": "Eggshell is densely filled with overlapping fluorescent signal showing multiple body layers/coils. XY view shows complex tangled pattern with multiple body segments visible. Consistent with pretzel stage, matching previous timepoints. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1351,16 +1351,16 @@ }, { "timepoint": 134, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments in both XY and XZ views. The XZ view shows a complex pattern with multiple layers of signal stacked, and the XY view shows overlapping curved bands suggesting 3+ folds. Fill fraction is high with little empty space, consistent with pretzel stage. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, + "is_adjacent_correct": false, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -1372,7 +1372,7 @@ "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": "The eggshell is densely filled with fluorescent signal throughout, with multiple overlapping body layers visible in the XZ view showing parallel segments. The pattern is complex/tangled matching pretzel reference. Given prior observations cycling through stages (likely a late embryo moving), the dense fill strongly indicates pretzel. | [zslice-multi] counts 1/2/2/3/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1385,15 +1385,15 @@ }, { "timepoint": 136, - "predicted_stage": "pretzel", + "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 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": "Eggshell is densely filled with signal showing multiple overlapping body segments/coils. The XY view shows a ring-like pattern suggesting folded coils, and the XZ view shows multiple parallel bright bands. Consistent with prior T135 pretzel classification. | [zslice-multi] counts 1/1/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1406,7 +1406,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments forming a complex coiled pattern in XY view. Parallel bands visible with bright tangled structure consistent with pretzel stage. | [zslice-multi] counts 2/1/1/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1419,61 +1419,61 @@ }, { "timepoint": 138, - "predicted_stage": "early", + "predicted_stage": "pretzel", "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": "Eggshell is densely filled with overlapping bright signal, multiple body layers visible creating a tangled complex pattern. Consistent with previous pretzel observations. | [zslice-multi] counts 1/2/3/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, - "is_adjacent_correct": false, - "verification_triggered": false, - "phase_count": 1, + "is_correct": true, + "is_adjacent_correct": true, + "verification_triggered": true, + "phase_count": 2, "verification_result": null, "candidate_stages": null } ], - "duration_seconds": 1428.3205771446228, + "duration_seconds": 851.6330795288086, "error": null, - "accuracy": 0.42857142857142855, - "adjacent_accuracy": 0.9642857142857143 + "accuracy": 0.34523809523809523, + "adjacent_accuracy": 0.9523809523809523 }, { "embryo_id": "embryo_2", "predictions": [ { "timepoint": 45, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The embryo shows a single elongated body with slight asymmetry/constriction between two lobes, consistent with comma stage. The eggshell is only partially filled with significant dark space remaining, and no clear folding or parallel body segments are visible. Matches the comma reference closely, consistent with prior T42-T44 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 46, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The embryo shows a single elongated mass with slight asymmetry/constriction, filling less than half the eggshell with significant dark space remaining. No parallel body segments visible. Morphology matches the comma reference closely and is consistent with previous T43-T45 observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, @@ -1483,7 +1483,7 @@ "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": "The image matches the 1.5fold reference almost exactly. The embryo shows elongation with sparse eggshell filling \u2014 noticeable dark space remains at the ends. One curved band with partial folding visible, not yet two clear parallel segments. Matches 1.5fold reference better than comma. | [zslice-multi] counts 1/1/1/2/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1500,7 +1500,7 @@ "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": "The embryo fills the eggshell moderately with some dark space remaining, especially at the ends. The XY view shows an elongated body without clear parallel segments - suggesting a partial fold rather than a full hairpin. This matches the 1.5fold reference better than 2fold. The previous T47 call of 2fold may have been slightly early; morphology here shows sparse-to-moderate fill with a single curved body. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1513,15 +1513,15 @@ }, { "timepoint": 49, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "Eggshell is sparsely-to-moderately filled with clear empty space at one end. The embryo shows elongation with a partial fold but not clearly two parallel segments. Previous T47/T48 labeled 2fold seems premature given T46 was comma - this looks like 1.5fold morphology with partial curvature and significant dark space in the shell. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1530,16 +1530,16 @@ }, { "timepoint": 50, - "predicted_stage": "pretzel", + "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 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": "The eggshell is sparsely to moderately filled with clear dark empty space at the right end. The XZ view shows two parallel bands suggesting a partial fold, but the tail has not fully extended to meet the head. Consistent with previous 1.5fold observation and matches 1.5fold reference. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, - "is_adjacent_correct": false, + "is_correct": true, + "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -1547,15 +1547,15 @@ }, { "timepoint": 51, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "Eggshell is sparsely to moderately filled with dark space at the ends. The body shows partial elongation with one main curve visible, no clear parallel hairpin segments yet. Matches 1.5fold reference and continues the previous trend. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1568,7 +1568,7 @@ "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": "Eggshell is sparsely filled with significant dark space at the right end. Body shows elongation with partial fold but not full hairpin - matches 1.5fold reference. Consistent with previous timepoints. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1581,15 +1581,15 @@ }, { "timepoint": 53, - "predicted_stage": "2fold", + "predicted_stage": "1.5fold", "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": "Eggshell is moderately-sparsely filled with dark space still visible at the ends and edges. The XY view shows a single elongated body with subtle folding but no clear two parallel segments. Matches 1.5fold reference best, consistent with previous timepoints. | [zslice-multi] counts 1/1/1/1/1 max=1 -> 1.5fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1602,7 +1602,7 @@ "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": "The eggshell is sparsely-to-moderately filled with visible empty space at the top. One main elongated curved body is visible with partial folding but no clear two parallel segments. Matches 1.5fold reference, consistent with prior timepoints. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1619,7 +1619,7 @@ "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": "Eggshell is sparsely to moderately filled with noticeable dark space especially at the right end. Only one main body mass is visible without clear parallel folded segments, consistent with 1.5fold rather than 2fold. Matches 1.5fold reference. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1636,7 +1636,7 @@ "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": "The XY view shows two parallel body segments with a bend, and the eggshell is moderately filled with dark space still visible at the ends. This matches the 2fold reference well, consistent with prior T54-T55 observations. | [zslice-multi] counts 3/1/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1649,16 +1649,16 @@ }, { "timepoint": 57, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is moderately filled with clear dark space at both ends, and the XY view shows two parallel body segments with a bend - a hairpin/U-shape. The signal density is not yet dense enough for pretzel (which would fill the eggshell). This matches the 2fold reference better than pretzel. | [zslice-multi] counts 2/3/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, + "is_adjacent_correct": false, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -1666,16 +1666,16 @@ }, { "timepoint": 58, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately filled with visible dark space at the ends and top, not densely packed as in pretzel. The XY view shows an elongated body with two parallel segments visible. Given the earlier T55 was 2fold, this frame looks more consistent with 2fold morphology than pretzel - the previous pretzel calls at T56-57 may have been premature. | [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": false, + "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -1687,7 +1687,7 @@ "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": "Eggshell is sparsely to moderately filled with visible dark space at the ends. Signal appears as a single elongated band without clear multiple parallel segments or complex coiling. Given previous observations were likely overestimated (pretzel at T56-57 seems premature), this looks most like 1.5fold/2fold transition. The moderate fill and lack of multiple distinct overlapping layers suggest 1.5fold. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1704,7 +1704,7 @@ "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": "XY view shows two parallel body segments with a clear bend \u2014 hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Matches 2fold reference well, consistent with previous observations. | [zslice-multi] counts 2/3/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1717,15 +1717,15 @@ }, { "timepoint": 61, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell shows moderate filling with visible dark space around the body, particularly at the ends. The XY view shows an elongated body with visible curvature but not densely packed coils. This matches 2fold morphology better than pretzel. The previous T60 pretzel call may have been premature. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1734,15 +1734,15 @@ }, { "timepoint": 62, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "Eggshell is moderately filled with visible dark space at the ends and top. The XY view shows two parallel body segments with a hairpin bend. Matches 2fold reference closely, consistent with prior T61 observation. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1755,7 +1755,7 @@ "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": "The XY view shows two parallel body segments with a visible indent between them (hairpin shape). Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Matches 2fold reference best and consistent with previous T62 observation. | [zslice-multi] counts 2/3/2/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1772,7 +1772,7 @@ "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": "The XY view shows two parallel body segments with dark space between them and empty eggshell space at the ends \u2014 a clear hairpin/U-shape. The eggshell is moderately filled, not densely packed with multiple overlapping coils as in pretzel. The previous T63 'pretzel' call appears premature; this matches 2fold references best. | [zslice-multi] counts 3/3/1/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1789,7 +1789,7 @@ "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": "Eggshell is moderately filled with some dark space still visible at top and edges. Two parallel body segments are visible in the XY view (upper and lower bands). Not dense enough for pretzel - matches 2fold reference better. Previous pretzel calls at T63-64 may have been premature. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1806,7 +1806,7 @@ "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": "The XY view shows two parallel body segments with a clear bend, forming a hairpin/U-shape. Eggshell is moderately filled with noticeable dark space at the ends, not densely packed like pretzel. Matches 2fold reference best. | [zslice-multi] counts 3/3/1/3/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1823,7 +1823,7 @@ "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": "The XY view shows two parallel body segments with some dark space between them and at the ends of the eggshell, indicating moderate fill. The body is clearly folded into a hairpin but not densely coiled like pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/2/1/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1840,7 +1840,7 @@ "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": "XY shows a curved elongated body with visible hairpin/U-shape \u2014 two parallel segments connected by a bend. Eggshell is moderately filled with some dark space remaining (not densely packed like pretzel). Consistent with T67 2fold. | [zslice-multi] counts 1/2/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1857,7 +1857,7 @@ "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": "XY view shows two parallel body segments (upper and lower bands) with a bend, indicating a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining, not densely packed as in pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1874,7 +1874,7 @@ "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": "The XY view shows two parallel body segments forming a hairpin/U-shape with a clear bend. The eggshell is moderately filled with some dark space still visible, consistent with 2fold rather than the denser pretzel stage. Matches the 2fold reference well and continues from prior T67-T69. | [zslice-multi] counts 2/3/2/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1887,15 +1887,15 @@ }, { "timepoint": 71, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with two parallel body segments visible in XY view (upper and lower bands separated by a faint gap). Some dark space remains at the ends of the eggshell. This matches the 2fold reference better than pretzel, which would show denser filling and multiple overlapping coils. The prior T70 pretzel call may have been premature. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1904,15 +1904,15 @@ }, { "timepoint": 72, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows two parallel body segments with some dark space still visible within the eggshell, particularly at the lower edge. Fill is moderate, not densely packed like pretzel. Matches 2fold reference well and consistent with T69/T71. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1925,7 +1925,7 @@ "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": "Eggshell is moderately filled with some dark space remaining. XY view shows two parallel body segments connected by a bend \u2014 classic hairpin/U-shape. Matches 2fold reference better than pretzel (not densely filled, no multiple overlapping coils). | [zslice-multi] counts 3/1/2/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1938,15 +1938,15 @@ }, { "timepoint": 74, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "XY view shows two parallel body segments with a clear bend \u2014 a hairpin/U-shape characteristic of 2fold. The eggshell still has visible dark space at both ends (not densely filled as pretzel would be). T73 pretzel call was likely premature; morphology here matches 2fold references better. | [zslice-multi] counts 3/2/2/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1955,15 +1955,15 @@ }, { "timepoint": 75, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XY view shows two lobes with visible dark/empty space between and around them within the eggshell \u2014 not densely filled like pretzel. Two parallel body segments are suggested by the bilobed appearance. The eggshell is moderately filled with notable dark regions, matching 2fold rather than pretzel. Previous pretzel calls at T73-74 may have been premature. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -1976,7 +1976,7 @@ "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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in XY view with a bend, consistent with 2fold hairpin shape. Matches 2fold reference better than the densely filled pretzel. | [zslice-multi] counts 1/1/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -1989,15 +1989,15 @@ }, { "timepoint": 77, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The embryo shows moderate eggshell fill with some dark space remaining. Two parallel body segments are visible in the XY view with a clear hairpin shape, matching the 2fold reference. Consistent with prior 2fold observations. | [zslice-multi] counts 2/3/2/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2006,15 +2006,15 @@ }, { "timepoint": 78, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is densely filled with signal, and the XY view shows multiple overlapping body segments with a complex tangled pattern. The side view shows dense fill with little empty space. Consistent with pretzel stage, matching reference. | [zslice-multi] counts 1/1/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2027,7 +2027,7 @@ "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": "Eggshell is moderately filled with some dark space remaining, particularly at the ends. XY view shows two parallel body segments with a bend, matching 2fold reference. Not densely packed enough for pretzel. Consistent with prior T78 observation. | [zslice-multi] counts 1/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2044,7 +2044,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, particularly at the ends. Two parallel body segments are visible in the XY view with a clear hairpin/U-shape. The fill pattern matches the 2fold reference better than pretzel (which shows denser, more tangled filling). Consistent with previous T78-T79 observations. | [zslice-multi] counts 1/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2061,7 +2061,7 @@ "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": "Eggshell is moderately filled with some dark space still visible at the ends and middle. Two parallel body segments visible in the XZ view (bottom-left), consistent with hairpin/U-shape. Not yet densely packed as pretzel. Matches 2fold reference. | [zslice-multi] counts 3/2/1/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2078,7 +2078,7 @@ "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": "The eggshell is densely filled with bright signal with very little empty space. Multiple overlapping body segments are visible in the XZ view, creating a complex tangled pattern. This matches the pretzel reference closely, consistent with previous T81 pretzel classification. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2091,15 +2091,15 @@ }, { "timepoint": 83, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "Eggshell is moderately filled with some dark space at the ends. XZ view shows two parallel body segments with a visible gap between them, characteristic of a hairpin/U-shape. Not dense enough for pretzel (no multiple overlapping coils). Matches 2fold reference. | [zslice-multi] counts 1/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2112,7 +2112,7 @@ "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": "The eggshell is moderately filled with some dark space still visible at the edges. Two parallel body segments appear visible in the XY view with a bend, consistent with a hairpin/U-shape. Not densely packed enough to be pretzel. Matches 2fold reference. | [zslice-multi] counts 2/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2125,15 +2125,15 @@ }, { "timepoint": 85, - "predicted_stage": "pretzel", + "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 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": "XY view shows two clear parallel body segments (hairpin shape) with visible dark space between them. Eggshell is moderately filled, not densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2146,7 +2146,7 @@ "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": "Eggshell is moderately filled with some dark space remaining. Two parallel body segments visible in the XY and XZ views, forming a hairpin shape. YZ view shows the characteristic folded cross-section. Matches 2fold reference better than pretzel which would be densely filled. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2163,7 +2163,7 @@ "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": "Eggshell is moderately filled with some dark space remaining at the ends. Two parallel body segments visible in the XZ view forming a hairpin/U-shape. Not yet densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/1/1/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2180,7 +2180,7 @@ "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": "The eggshell is moderately filled with some dark space visible, especially at the ends. The XZ view shows two parallel body segments forming a hairpin/U-shape. The fill density is not yet dense enough for pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/1/3/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2197,7 +2197,7 @@ "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": "The eggshell is densely filled with fluorescent signal with multiple overlapping body segments visible in the XY view, showing complex folded pattern. Little dark space remains inside the eggshell. Matches pretzel reference well, consistent with T88 classification. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2210,15 +2210,15 @@ }, { "timepoint": 90, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is moderately filled with visible dark space, and the XY view shows two parallel body segments forming a hairpin/U-shape. Not dense enough to be pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2231,7 +2231,7 @@ "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": "Eggshell is densely filled with signal, very little dark space remaining. Multiple overlapping body segments visible in XY view and side projection shows complex coiling pattern. Matches pretzel reference well, consistent with previous pretzel observations. | [zslice-multi] counts 3/2/1/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2248,7 +2248,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments in both the XY and XZ views. The complex tangled pattern with little dark space inside the shell matches the pretzel reference, consistent with previous T90-T91 observations. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2265,7 +2265,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments in the XY view with a clear coiled/folded pattern. Little dark space remains inside the shell. Given prior timepoints were pretzel, and morphology matches pretzel references better than 2fold. | [zslice-multi] counts 1/2/1/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2278,15 +2278,15 @@ }, { "timepoint": 94, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The XY view shows two parallel body segments stacked (hairpin shape) with some dark space still visible in the eggshell. The fill is moderate, not densely packed like pretzel. Matches 2fold reference morphology best. | [zslice-multi] counts 1/3/3/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2299,7 +2299,7 @@ "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": "The eggshell is densely filled with bright fluorescent signal, especially visible in the XZ view showing multiple overlapping body layers. The XY view shows complex tangled structure with multiple coils. Consistent with previous pretzel classifications at T93-T94. | [zslice-multi] counts 2/3/2/3/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2316,7 +2316,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments in the XZ view (bottom-left) with a characteristic coiled/tangled pattern. The YZ view shows multiple stacked layers. This matches the pretzel reference and continues from previous pretzel observations. | [zslice-multi] counts 2/2/3/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2333,7 +2333,7 @@ "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": "The eggshell is densely filled with multiple overlapping bright bands visible in both XY and XZ views, indicating multiple coiled body segments. Consistent with previous pretzel timepoints. | [zslice-multi] counts 1/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2346,15 +2346,15 @@ }, { "timepoint": 98, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is densely filled with signal showing multiple overlapping body segments. The XY view shows complex tangled coils, and the XZ view reveals two parallel body layers with bright signal filling most of the shell. This matches the pretzel reference better than 2fold, which has more empty space. Given T95-96 were pretzel, this is consistent. | [zslice-multi] counts 1/3/2/1/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2367,7 +2367,7 @@ "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": "The eggshell is densely filled with overlapping fluorescent signal, with multiple body layers visible in YZ and XZ views. The complex tangled pattern and bright overlapping coils match the pretzel reference. Consistent with surrounding timepoints. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2384,7 +2384,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments/coils in both XY and XZ views. Complex tangled pattern with little dark space, consistent with pretzel stage and matches previous observations. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2401,7 +2401,7 @@ "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": "The eggshell is densely filled with overlapping bright signal, little dark space visible inside. Multiple overlapping body segments are visible in the XY view and XZ view shows complex tangled pattern. Matches pretzel reference best. T100 '2fold' was likely a misclassification given T98/T99 were pretzel. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2418,7 +2418,7 @@ "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": "XY view shows two parallel body segments with a clear bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2431,15 +2431,15 @@ }, { "timepoint": 103, - "predicted_stage": "pretzel", + "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 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": "The XY view shows multiple overlapping coils with curved/folded body segments visible. The eggshell is densely filled with signal, especially in the XZ view showing bright tightly packed nuclei filling most of the shell interior. Consistent with pretzel stage following T102. | [zslice-multi] counts 2/1/2/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2448,15 +2448,15 @@ }, { "timepoint": 104, - "predicted_stage": "2fold", + "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 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": "The eggshell appears densely filled with signal, especially visible in the XZ view showing multiple overlapping bright bands. The XY view shows complex tangled structure with multiple body segments overlapping. Given the progression (previously oscillating between 2fold/pretzel), the dense fill and multi-layered appearance matches pretzel best. | [zslice-multi] counts 1/1/3/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2469,7 +2469,7 @@ "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": "Eggshell is densely filled with multiple overlapping coils visible in XY view. Multiple parallel body segments visible in XZ projection. Consistent with previous pretzel observations. | [zslice-multi] counts 2/3/2/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2482,15 +2482,15 @@ }, { "timepoint": 106, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XZ view (bottom-left) shows the eggshell densely filled with multiple overlapping bright bands, consistent with multiple body folds. The XY view shows complex overlapping structure rather than a clean hairpin. Following T104-T105 pretzel classifications, this continues in 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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2499,15 +2499,15 @@ }, { "timepoint": 107, - "predicted_stage": "2fold", + "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 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": "The eggshell is densely filled with fluorescent signal - very little dark space remains inside. Multiple overlapping body layers are visible in both XY and XZ views, suggesting multiple folds/coils. This matches the pretzel reference better than 2fold, which would show clearer parallel segments with moderate filling. Given T104-105 were pretzel, this is likely continued pretzel stage. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2520,7 +2520,7 @@ "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": "The eggshell is densely filled with signal, and multiple parallel body segments/coils are visible in the XY and XZ views, indicating multiple folds. Matches pretzel reference. | [zslice-multi] counts 1/3/2/2/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2537,7 +2537,7 @@ "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": "The eggshell is densely filled with signal showing multiple overlapping body segments visible in both XY and XZ views. The complex, tangled pattern with little dark space inside the shell matches pretzel references. Consistent with previous pretzel observations. | [zslice-multi] counts 3/2/2/1/1 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2550,15 +2550,15 @@ }, { "timepoint": 110, - "predicted_stage": "pretzel", + "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. 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": "The eggshell is densely filled with signal across multiple overlapping body segments visible in the XY and XZ projections. Complex tangled pattern consistent with pretzel stage, matching previous observations. | [zslice-multi] counts 1/1/2/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2567,15 +2567,15 @@ }, { "timepoint": 111, - "predicted_stage": "pretzel", + "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 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": "The eggshell is densely filled with fluorescent signal with very little dark/empty space. Multiple overlapping body layers are visible in the XY and XZ views, and the YZ view shows complex stacked coils. This matches the pretzel reference, consistent with T108-109. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2584,15 +2584,15 @@ }, { "timepoint": 112, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell appears densely filled with overlapping bright signal, with multiple body layers visible in the XZ view suggesting multiple coils. Little dark/empty space remains. Given prior pretzel observation at T109 and the dense fill pattern, this matches pretzel morphology. | [zslice-multi] counts 2/1/2/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2605,7 +2605,7 @@ "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": "The XZ view clearly shows two parallel body segments with a central dark gap between them, characteristic of a hairpin/U-shape. The eggshell is moderately filled with some dark space remaining, not densely packed as in pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2622,7 +2622,7 @@ "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": "XY view shows two parallel body segments forming a hairpin shape with moderate eggshell fill. Not yet densely packed/coiled like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2639,7 +2639,7 @@ "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": "XY view shows two parallel body segments forming a hairpin/U-shape. Eggshell is moderately filled with some dark space still visible, especially at the right end. No complex overlapping coils indicating pretzel. Matches 2fold reference. | [zslice-multi] counts 2/1/3/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2652,15 +2652,15 @@ }, { "timepoint": 116, - "predicted_stage": "2fold", + "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 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": "The eggshell is densely filled with signal across all views, with multiple overlapping body layers visible in the XZ view showing complex coiling. Previous observation was already pretzel, and morphology matches pretzel reference. | [zslice-multi] counts 1/2/1/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2673,7 +2673,7 @@ "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": "Eggshell is densely filled with signal, multiple overlapping body segments visible in XY view with complex tangled pattern. Consistent with previous pretzel classifications. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2690,7 +2690,7 @@ "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": "The eggshell is densely filled with bright fluorescent signal, with multiple overlapping body segments visible in both XY and XZ views. The YZ view shows stacked coils indicating multiple folds. Consistent with previous pretzel observations. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2707,7 +2707,7 @@ "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": "The eggshell is densely filled with signal - the XY view shows bright fluorescence throughout the shell with multiple overlapping body layers visible. The XZ view shows stacked parallel layers characteristic of multiple folds. Given prior pretzel observations and high fill fraction, this is pretzel stage. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2724,7 +2724,7 @@ "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": "The eggshell is densely filled with signal throughout, showing multiple overlapping body segments in both XY and XZ views. The complex tangled pattern with little dark space remaining matches the pretzel reference better than 2fold, which would show a cleaner U-shape with more empty space. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2737,15 +2737,15 @@ }, { "timepoint": 121, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "XY view shows two parallel body segments (hairpin shape) with some dark space still visible within the eggshell. Fill is moderate, not dense/tangled enough for pretzel. Matches 2fold reference. | [zslice-multi] counts 3/1/2/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -2758,7 +2758,7 @@ "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": "Eggshell is densely filled with signal with multiple overlapping body segments visible, especially in the XZ view showing complex coiling. Consistent with progression from 2fold to pretzel. | [zslice-multi] counts 1/2/2/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2770,10 +2770,10 @@ "candidate_stages": null } ], - "duration_seconds": 1281.8214168548584, + "duration_seconds": 814.2777233123779, "error": null, - "accuracy": 0.3717948717948718, - "adjacent_accuracy": 0.9615384615384616 + "accuracy": 0.47435897435897434, + "adjacent_accuracy": 0.9743589743589743 }, { "embryo_id": "embryo_3", @@ -2784,7 +2784,7 @@ "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": "The embryo shows a subtle constriction/curve with a single elongated body occupying most of the eggshell width but still appearing as one band without clear folding. No parallel body segments visible. Matches comma reference with slight asymmetry between ends. Consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2797,33 +2797,33 @@ }, { "timepoint": 40, - "predicted_stage": "comma", + "predicted_stage": "2fold", "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": "The embryo now fills most of the eggshell length with moderate density, and a faint second band/curve is visible beneath the main body in the XY view, suggesting the tail has begun folding back (J-shape). This is more elongated than the comma references but not yet showing two clear parallel segments of a 2fold. | [zslice-multi] counts 2/1/2/2/1 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": false, - "phase_count": 1, + "verification_triggered": true, + "phase_count": 2, "verification_result": null, "candidate_stages": null }, { "timepoint": 41, - "predicted_stage": "comma", + "predicted_stage": "bean", "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": "The embryo fills most of the eggshell as a single elongated mass with subtle constriction/asymmetry. No clear curve or folded body segments visible. Eggshell is densely packed but this is because the embryo hasn't elongated/separated from the shell yet \u2014 characteristic of bean stage. The previous 'comma' and '2fold' labels may have been premature; this frame best matches bean morphology.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, + "is_adjacent_correct": false, "verification_triggered": false, "phase_count": 1, "verification_result": null, @@ -2831,101 +2831,101 @@ }, { "timepoint": 42, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The embryo shows a single curved band of nuclei with a subtle diagonal constriction visible in the XY view. The eggshell is moderately filled but shows one main elongated body, not multiple parallel segments. This matches the comma stage morphology best, consistent with T39. The previous T40/T41 labels appear inconsistent \u2014 this frame shows clear comma-stage features.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 43, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "The XY view shows an elongated curved body with a visible dorsal indentation/curvature typical of comma stage. The eggshell is moderately filled but still shows the single curved body band, not parallel folded segments. Matches comma reference best, consistent with previous T42 observation.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 44, - "predicted_stage": "2fold", + "predicted_stage": "comma", "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": "Eggshell moderately filled with a single elongated mass, slight asymmetry with one end tapering. No parallel body segments or folding visible. Matches comma reference and consistent with previous T42-T43 comma observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 45, - "predicted_stage": "pretzel", + "predicted_stage": "comma", "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": "The embryo shows a single elongated body with slight asymmetry/constriction, occupying a moderate portion of the eggshell with visible dark space. Only one band of nuclei is visible without clear folding. Matches comma reference best, consistent with previous timepoints.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": false, - "verification_triggered": true, - "phase_count": 2, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 46, - "predicted_stage": "pretzel", + "predicted_stage": "comma", "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": "The embryo body appears as a single elongated mass with slight curvature, occupying a moderate portion of the eggshell with dark space still visible around it. No clear folding or parallel segments are visible yet. Matches comma reference closely and follows previous comma observations.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": false, - "verification_triggered": true, - "phase_count": 2, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 47, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The embryo fills most of the eggshell now, more than in comma stage. A faint curve/partial fold is visible in the XY view suggesting the tail has begun curling back but has not reached the head. No clear parallel body segments yet, so not 2fold. Matches 1.5fold reference best. | [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": false, + "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -2933,16 +2933,16 @@ }, { "timepoint": 48, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately-to-densely filled with signal. In the XY view, I can see two roughly parallel bands of nuclei with a curved boundary between them, consistent with a partial fold. However, the fold is not as complete as a clear 2fold hairpin \u2014 there is still some dark space visible. Given the previous progression (comma at T45-46, then 2fold at T47), and the morphology matching the 1.5fold references, this appears to be 1.5fold. But considering T47 was already called 2fold and stages progress forward, this could be early 2fold. The clear parallel segments visible in XY support 2fold. | [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": false, + "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, "verification_result": null, @@ -2950,18 +2950,18 @@ }, { "timepoint": 49, - "predicted_stage": "pretzel", + "predicted_stage": "comma", "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": "The XY view shows a single curved/kidney-shaped body with a notch at the top, still occupying less than half the eggshell with significant empty space. No parallel body segments visible yet \u2014 this matches comma morphology better than 2fold. The previous 2fold labels at T47-48 were likely premature; T49 shows clear comma shape.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": false, - "verification_triggered": true, - "phase_count": 2, + "is_adjacent_correct": true, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, @@ -2971,7 +2971,7 @@ "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": "The embryo shows elongation with a subtle fold/bend visible in the XY view \u2014 an upper bulge suggesting the head curling back. The eggshell is sparsely-to-moderately filled with dark space still visible at the ends. No clear two parallel segments yet, but more elongated than comma. Matches 1.5fold reference best. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -2984,18 +2984,18 @@ }, { "timepoint": 51, - "predicted_stage": "pretzel", + "predicted_stage": "bean", "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": "The embryo shows a clear constriction in the middle with two lobes visible in the XY view, matching bean stage morphology. The shape is a solid mass filling most of the eggshell with a slight waist \u2014 no curved body, no folding, no parallel segments. Previous observations (comma/pretzel) appear inconsistent; this image clearly resembles the bean reference.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "is_adjacent_correct": false, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, @@ -3005,7 +3005,7 @@ "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": "Eggshell is moderately filled with some dark space visible (notably a dark curve/gap in the middle of XY view suggesting a folded body). The signal shows an elongated body beginning to fold back on itself \u2014 one main curve with a partial hairpin, not yet two fully parallel segments. Matches the 1.5fold reference better than 2fold (less dense) or comma (body now fills more of shell). | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3018,15 +3018,15 @@ }, { "timepoint": 53, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is sparsely to moderately filled with dark empty space visible at both ends. XY view shows a curved embryo body with a beginning fold but not clear parallel segments. Matches 1.5fold reference better than 2fold (which shows clearer hairpin with two parallel segments). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3035,32 +3035,32 @@ }, { "timepoint": 54, - "predicted_stage": "pretzel", + "predicted_stage": "bean", "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": "The embryo shows a two-lobed bean-like shape with a subtle constriction in the middle. The mass fills most of the eggshell uniformly with no clear curved body, no parallel segments, and no folding visible. This matches the bean reference best. The previous '2fold' labels appear inconsistent with morphology \u2014 this image shows pre-elongation bean/early-comma stage.", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], "is_correct": false, - "is_adjacent_correct": true, - "verification_triggered": true, - "phase_count": 2, + "is_adjacent_correct": false, + "verification_triggered": false, + "phase_count": 1, "verification_result": null, "candidate_stages": null }, { "timepoint": 55, - "predicted_stage": "pretzel", + "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), 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": "The XY view shows two parallel body segments with a dark gap between them (characteristic hairpin shape of 2fold). The eggshell is moderately filled with some dark space remaining. This matches the 2fold reference and is consistent with previous T52-T53 observations. | [zslice-multi] counts 1/1/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3069,15 +3069,15 @@ }, { "timepoint": 56, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows two parallel body segments with a dark gap between them (hairpin shape). Eggshell is moderately filled with some dark space remaining. Matches 2fold reference well, consistent with previous T55 observation. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3090,7 +3090,7 @@ "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": "The embryo shows a single elongated body with a subtle constriction but no clear parallel folded segments. Significant dark space remains within the eggshell, particularly at the right end. The pattern matches the 1.5fold reference better than 2fold (no clear hairpin with two parallel segments) or bean (body is clearly elongated). The previous 2fold calls at T55-56 may have been premature; this frame shows morphology consistent with 1.5fold. | [zslice-multi] counts 1/2/2/2/2 max=2 -> 2fold (overrode 1.5fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3107,7 +3107,7 @@ "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": "The eggshell is moderately filled with some dark space remaining, particularly visible in the XY view where there's a darker region in the upper-middle area suggesting two parallel body segments with space between them. The YZ view shows a U-shape. This matches the 2fold reference better than pretzel (which would be denser) and consistent with previous timepoints. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3124,7 +3124,7 @@ "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": "The XY view shows two lobes/parallel body segments with a visible bend, consistent with a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining \u2014 not densely packed like pretzel. Matches 2fold reference well and consistent with previous timepoints. | [zslice-multi] counts 2/2/2/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3141,7 +3141,7 @@ "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": "XY view shows a clear hairpin/U-shape with two parallel body segments connected by a bend, and there's still visible dark space in the eggshell. This matches 2fold rather than pretzel which would show denser filling with multiple overlapping coils. The previous pretzel call at T59 was likely premature. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3158,7 +3158,7 @@ "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": "The XY view shows two parallel body segments with a visible dark gap between them (hairpin U-shape). Eggshell is moderately filled with some dark space remaining around the body. Only two parallel bands are visible, not multiple overlapping coils, so this is 2fold, not pretzel. Consistent with T60. | [zslice-multi] counts 2/1/1/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3175,7 +3175,7 @@ "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": "The eggshell is moderately filled with some dark space remaining at both ends. Two parallel body segments are visible in the XY projection forming a hairpin-like shape. This matches the 2fold reference better than pretzel, which would show denser filling and more overlapping coils. | [zslice-multi] counts 2/1/1/3/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3192,7 +3192,7 @@ "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": "The XY view shows two parallel body segments with a clear bend forming a hairpin/U-shape, with visible dark space in the middle. The eggshell is moderately filled, not densely packed as in pretzel. Previous pretzel calls at T61-62 may have been premature; this clearly shows 2fold morphology. | [zslice-multi] counts 1/2/2/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3209,7 +3209,7 @@ "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": "The XY view shows two clear parallel body segments separated by a dark gap in the middle (hairpin/U-shape), with moderate eggshell fill. This matches 2fold morphology rather than pretzel (which would have denser, more coiled fill). Consistent with T63. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3226,7 +3226,7 @@ "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": "Eggshell is moderately filled with some dark space remaining, particularly at the ends. Two parallel body segments visible in XY view suggesting a hairpin fold. Consistent with previous 2fold observations and matches 2fold reference better than pretzel (not densely packed). | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3243,7 +3243,7 @@ "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": "The XY view shows two parallel body segments (upper and lower bands) forming a hairpin shape, with moderate eggshell fill and some dark space remaining. Matches 2fold reference. Consistent with previous timepoints. | [zslice-multi] counts 2/2/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3256,15 +3256,15 @@ }, { "timepoint": 67, - "predicted_stage": "pretzel", + "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-multi] counts 3/2/2/3/3 max=3 -> pretzel (overrode 2fold)", + "reasoning": "Eggshell is moderately filled with some dark space remaining. The XY view shows an elongated body with a visible bend/fold suggesting two parallel segments. Matches 2fold reference morphology and consistent with previous timepoints. | [zslice-multi] counts 2/2/1/1/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3277,7 +3277,7 @@ "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": "XY view shows a clear hairpin with two parallel body segments and a dark loop interior. Eggshell is moderately filled with some dark space remaining. Matches 2fold reference. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3290,15 +3290,15 @@ }, { "timepoint": 69, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is moderately filled with some dark space still visible (particularly at the ends and top). Two parallel body segments are visible in the XY view with a clear bend, matching 2fold reference. Not yet densely packed as in pretzel. T68 may have been slightly premature; this frame looks consistent with late 2fold. | [zslice-multi] counts 1/1/2/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3311,7 +3311,7 @@ "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": "The XY view shows two parallel body segments with a clear bend/gap between them, forming a hairpin shape. The eggshell is moderately filled with some dark space still visible. This matches the 2fold reference better than pretzel (which would show denser, more complex coiling). Consistent with surrounding timepoints T67/T69. | [zslice-multi] counts 1/1/2/1/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3328,7 +3328,7 @@ "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": "The XY view shows two parallel body segments with moderate eggshell fill - dark space still visible at top and ends. XZ view shows clear two-layer stacking typical of 2fold. Not densely packed enough for pretzel. Matches 2fold reference best. | [zslice-multi] counts 2/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3345,7 +3345,7 @@ "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": "The XY view shows two parallel body segments with a clear gap/bend between them, forming a hairpin U-shape. The eggshell is moderately filled with some dark space still visible between the folds. This matches the 2fold reference rather than the densely-filled pretzel stage. Consistent with previous 2fold observations at T69 and T71. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3362,7 +3362,7 @@ "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": "Eggshell is moderately filled with some dark space visible, especially along the top of the XY view. YZ view shows two distinct parallel layers (hairpin cross-section). Matches 2fold reference more than pretzel which would be more densely packed. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3375,15 +3375,15 @@ }, { "timepoint": 74, - "predicted_stage": "pretzel", + "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 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": "The XY view shows two parallel body segments with a visible central gap/loop, indicating a hairpin shape. The eggshell is moderately filled with some dark space still visible around the body. This matches 2fold better than pretzel, which would show denser filling and multiple overlapping coils. Previous T73 pretzel call may have been premature. | [zslice-multi] counts 1/1/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3392,15 +3392,15 @@ }, { "timepoint": 75, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space visible at the ends and between body segments. Two parallel body segments are visible in the XY view forming a hairpin/U-shape. Matches 2fold reference better than pretzel (which would be densely packed). Consistent with previous T72, T74 observations. | [zslice-multi] counts 2/2/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3409,15 +3409,15 @@ }, { "timepoint": 76, - "predicted_stage": "pretzel", + "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. 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": "The eggshell is moderately filled with some dark space remaining, especially visible in the XY view where there's a curved shape with two parallel segments suggesting a hairpin fold. Signal density is higher than 1.5fold but not as tightly packed as pretzel. Consistent with previous 2fold observations at T74-T75. | [zslice-multi] counts 1/1/1/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3430,7 +3430,7 @@ "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": "XY view shows two parallel body segments forming a hairpin/U-shape with a visible dark gap between them, consistent with 2fold. Eggshell is moderately filled with some dark space remaining\u2014not densely packed like pretzel. Matches 2fold reference. | [zslice-multi] counts 1/2/2/2/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3447,7 +3447,7 @@ "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": "Eggshell is moderately filled with a visible dark gap/bend in the middle of the XY view, showing two parallel body segments (hairpin shape). Not yet densely packed enough for pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/2/2/1/2 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3464,7 +3464,7 @@ "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": "The XY view shows a clear ring/loop pattern with multiple overlapping body segments forming a coil. The eggshell is densely filled with signal, with bright overlapping layers. This matches pretzel morphology, consistent with progression from T78. | [zslice-multi] counts 1/2/2/1/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3477,15 +3477,15 @@ }, { "timepoint": 80, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The XY view shows a clear hairpin with two parallel body segments and a dark gap between them \u2014 eggshell is moderately filled with some dark space remaining. Not yet the dense, tangled pattern of pretzel. Consistent with prior 2fold observations. | [zslice-multi] counts 3/1/1/2/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3498,7 +3498,7 @@ "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": "Eggshell is densely filled with signal, with multiple overlapping body segments visible in both XY and XZ views. The YZ view shows stacked parallel bands indicating multiple folds. Consistent with pretzel stage and previous observations. | [zslice-multi] counts 2/2/2/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3511,15 +3511,15 @@ }, { "timepoint": 82, - "predicted_stage": "2fold", + "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 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": "The XY view shows a closed loop/coil pattern with multiple overlapping body segments forming a ring-like shape. The eggshell is densely filled with signal and the pattern is complex with overlapping tissue layers, matching pretzel stage. Consistent with previous T80-T81 pretzel observations. | [zslice-multi] counts 3/2/1/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3528,15 +3528,15 @@ }, { "timepoint": 83, - "predicted_stage": "pretzel", + "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 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": "Eggshell is densely filled with overlapping bright signal, multiple coiled body segments visible in XY and XZ views, matching pretzel reference. Consistent with prior timepoints. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3545,15 +3545,15 @@ }, { "timepoint": 84, - "predicted_stage": "pretzel", + "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 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": "The XY view shows a clear looping/coiled body outline with multiple overlapping segments forming a closed-loop pattern. The eggshell is densely filled with signal and multiple body layers overlap, matching the pretzel reference better 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": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3562,15 +3562,15 @@ }, { "timepoint": 85, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "XY view shows two parallel body segments with a bend, forming a hairpin/U-shape. Eggshell is moderately filled with some dark space remaining, not densely packed like pretzel. Matches 2fold reference. | [zslice-multi] counts 1/2/2/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3583,7 +3583,7 @@ "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": "XY view shows a clear hairpin/U-shape with two parallel body segments and a visible internal dark gap between them. Eggshell is moderately filled with some dark space remaining \u2014 not densely packed like pretzel. Matches 2fold references. | [zslice-multi] counts 2/1/2/2/3 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3600,7 +3600,7 @@ "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": "The eggshell is densely filled with bright signal, showing multiple overlapping body segments in both XY and XZ views. The pattern is complex and tangled with little dark space remaining inside the shell, consistent with pretzel stage and following the previous pretzel observation. | [zslice-multi] counts 3/2/3/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3613,15 +3613,15 @@ }, { "timepoint": 88, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments with a complex coiled/tangled pattern visible in the XY view. Consistent with previous pretzel classification at T86-T87. | [zslice-multi] counts 2/1/2/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3630,15 +3630,15 @@ }, { "timepoint": 89, - "predicted_stage": "2fold", + "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. Consistent with the previous three observations of pretzel stage. | [zslice-multi] counts 2/1/2/2/2 max=2 -> 2fold (overrode pretzel)", + "reasoning": "The eggshell is densely filled with fluorescent signal - the XZ view shows multiple overlapping bright bands (at least 3 parallel body segments visible), indicating multiple coils. Very little dark space remains inside the shell. This matches the pretzel reference with its complex, tangled, densely-filled appearance rather than a simple 2fold hairpin. | [zslice-multi] counts 2/2/2/3/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3647,15 +3647,15 @@ }, { "timepoint": 90, - "predicted_stage": "pretzel", + "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/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": "Eggshell is densely filled with signal with little dark space. Multiple overlapping body layers visible in XZ view showing complex tangled pattern. Matches pretzel reference well, consistent with surrounding timepoints. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3668,7 +3668,7 @@ "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": "The eggshell is densely filled with fluorescent signal with little dark empty space. Multiple overlapping body layers visible in XY view showing complex folded pattern. The XZ view shows dense bright signal throughout. This matches the pretzel reference better than 2fold, which would have more visible dark space and only two parallel segments. | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3681,15 +3681,15 @@ }, { "timepoint": 92, - "predicted_stage": "pretzel", + "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 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": "The eggshell is moderately filled with some dark space visible, particularly at the ends and bottom. Two parallel body segments are visible in the XY view forming a hairpin/U-shape. This matches the 2fold reference better than pretzel (which would be densely filled with multiple overlapping coils). | [zslice-multi] counts 2/2/2/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3702,7 +3702,7 @@ "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": "The eggshell is densely filled with signal, showing multiple overlapping body segments/coils in the XY view. The complex tangled pattern with little dark space and multiple parallel layers visible matches the pretzel reference better than 2fold. | [zslice-multi] counts 1/2/1/2/2 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3715,15 +3715,15 @@ }, { "timepoint": 94, - "predicted_stage": "pretzel", + "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 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": "XY view shows two parallel body segments forming a hairpin/U-shape with moderate eggshell fill. Some dark space remains, not yet densely packed like pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": true, + "is_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3736,7 +3736,7 @@ "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": "XY view shows two parallel body segments with a dark gap between them (clear hairpin/U-shape), characteristic of 2fold. The eggshell has moderate fill with visible dark space in the middle, not densely packed like pretzel. Matches 2fold reference. | [zslice-multi] counts 1/2/1/2/2 max=2 -> 2fold", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3753,7 +3753,7 @@ "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": "The eggshell is moderately filled with some dark space remaining. Two parallel body segments are visible in the XY and XZ views, indicating a hairpin U-shape. Not yet densely packed enough to be pretzel. Consistent with previous 2fold observations. | [zslice-multi] counts 3/1/1/1/1 max=3 -> pretzel (overrode 2fold)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3766,15 +3766,15 @@ }, { "timepoint": 97, - "predicted_stage": "pretzel", + "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 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": "The eggshell is densely filled with overlapping signal, and multiple parallel body segments/coils are visible in the XY view. This matches the pretzel reference with complex tangled morphology, consistent with the progression from T96. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3787,7 +3787,7 @@ "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": "The eggshell is densely filled with signal, with two parallel bands visible in the XY view and multiple overlapping segments in the XZ view. The pattern is complex with little empty space, matching the pretzel reference better than 2fold which shows more dark space. | [zslice-multi] counts 3/3/1/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3804,7 +3804,7 @@ "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": "Eggshell is densely filled with fluorescent signal with multiple overlapping body segments visible in the side view. High overall brightness and complex tangled pattern matches pretzel reference. Consistent with surrounding timepoints. | [zslice-multi] counts 3/1/1/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3821,7 +3821,7 @@ "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": "The eggshell is densely filled with bright signal with multiple overlapping body segments visible in the XY view (upper and lower coils). The XZ view shows dense, complex overlapping structure. Matches pretzel reference well, consistent with T98-T99 progression. | [zslice-multi] counts 2/2/2/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3838,7 +3838,7 @@ "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": "The eggshell is densely filled with multiple overlapping coils visible in the XY view, showing complex tangled pattern. Signal fills most of the shell interior with multiple parallel body segments. Matches pretzel reference and continues from previous pretzel observations. | [zslice-multi] counts 3/1/1/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3851,15 +3851,15 @@ }, { "timepoint": 102, - "predicted_stage": "2fold", + "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, 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": "Eggshell is densely filled with signal showing multiple overlapping body segments (visible folds in XY view with parallel bright bands). Complex tangled pattern consistent with pretzel stage, matching previous timepoints. | [zslice-multi] counts 2/2/3/1/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3872,7 +3872,7 @@ "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": "Eggshell is densely filled with fluorescent signal with multiple overlapping body layers visible in the XY and XZ projections. No clear empty space, complex tangled pattern consistent with pretzel stage, matching previous observations. | [zslice-multi] counts 2/1/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3885,15 +3885,15 @@ }, { "timepoint": 104, - "predicted_stage": "2fold", + "predicted_stage": "pretzel", "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": "The eggshell is densely filled with fluorescent signal, with multiple overlapping layers visible in the XY view and complex tangled pattern in XZ. Little dark space remains inside the shell, consistent with pretzel stage. Given previous T101-T102 were pretzel, this matches the ongoing stage. | [zslice-multi] counts 2/2/1/2/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], - "is_correct": false, + "is_correct": true, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3906,7 +3906,7 @@ "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": "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 view shows complex tangled structure filling the shell. Consistent with pretzel stage. | [zslice-multi] counts 2/2/1/1/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3923,7 +3923,7 @@ "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": "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 the XY view, and the XZ view shows complex tangled pattern filling the shell. This matches the pretzel reference better than 2fold, which typically shows more dark space and clearer hairpin structure. | [zslice-multi] counts 3/2/2/2/2 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3940,7 +3940,7 @@ "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": "The eggshell is densely filled with signal, multiple overlapping body layers visible in XY and XZ views with complex tangled pattern. Matches pretzel reference well and consistent with previous T106. | [zslice-multi] counts 1/1/1/2/1 max=2 -> 2fold (overrode pretzel)", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3953,15 +3953,15 @@ }, { "timepoint": 108, - "predicted_stage": "pretzel", + "predicted_stage": "2fold", "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": "The XY view shows multiple overlapping coiled body segments with complex folding pattern. The eggshell is densely filled with signal with little empty space, and multiple parallel/curved segments are visible indicating 3+ folds. This matches pretzel stage better than 2fold, which would show only two parallel segments with more dark space. | [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_correct": false, "is_adjacent_correct": true, "verification_triggered": true, "phase_count": 2, @@ -3974,7 +3974,7 @@ "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": "The XY view shows multiple overlapping coils with a tangled appearance. The eggshell is densely filled with signal with little dark space visible. Multiple body segments overlap creating the complex pattern characteristic of pretzel stage. | [zslice-multi] counts 1/2/1/1/3 max=3 -> pretzel", "reasoning_trace": null, "tool_calls": 0, "tools_used": [], @@ -3986,38 +3986,38 @@ "candidate_stages": null } ], - "duration_seconds": 1063.606009721756, + "duration_seconds": 661.8691613674164, "error": null, - "accuracy": 0.4788732394366197, - "adjacent_accuracy": 0.9295774647887324 + "accuracy": 0.4225352112676056, + "adjacent_accuracy": 0.9577464788732394 }, { "embryo_id": "embryo_4", "predictions": [], - "duration_seconds": 0.2796761989593506, + "duration_seconds": 0.27806735038757324, "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", + "started_at": "2026-04-27T19:43:58.512476", + "completed_at": "2026-04-27T20:22:46.571088", "total_predictions": 233, - "overall_accuracy": 0.4248927038626609, + "overall_accuracy": 0.41201716738197425, "metrics": { - "accuracy": 0.4248927038626609, - "adjacent_accuracy": 0.9527896995708155, + "accuracy": 0.41201716738197425, + "adjacent_accuracy": 0.9613733905579399, "per_stage": { "1.5fold": { - "accuracy": 0.024390243902439025, + "accuracy": 0.17073170731707318, "n": 41 }, "2fold": { - "accuracy": 0.4406779661016949, + "accuracy": 0.5423728813559322, "n": 59 }, "pretzel": { - "accuracy": 0.5413533834586466, + "accuracy": 0.42857142857142855, "n": 133 } } diff --git a/perception/_base.py b/perception/_base.py index 72b9e2b..32e996a 100644 --- a/perception/_base.py +++ b/perception/_base.py @@ -20,7 +20,7 @@ logger = logging.getLogger(__name__) # Default model for single-call perception functions -DEFAULT_MODEL = "claude-opus-4-6" +DEFAULT_MODEL = "claude-opus-4-7" # Developmental stages in order (C. elegans) STAGES = ["early", "bean", "comma", "1.5fold", "2fold", "pretzel", "hatching", "hatched"] @@ -85,7 +85,6 @@ async def call_claude( client.messages.create, model=model, max_tokens=max_tokens, - temperature=temperature, system=system_blocks, messages=[{"role": "user", "content": content}], ) @@ -134,7 +133,6 @@ async def call_claude_conversation( client.messages.create, model=model, max_tokens=max_tokens, - temperature=temperature, system=system_blocks, messages=messages, ) diff --git a/perception/scientific.py b/perception/scientific.py index fd46116..2713362 100644 --- a/perception/scientific.py +++ b/perception/scientific.py @@ -58,13 +58,11 @@ 1. **Compare to references first**, then use the descriptions above. -2. **Stages change slowly** — each lasts many timepoints (10-60+). Default \ -to the same stage as previous observation unless morphology clearly changed. +2. **Stages change slowly** — each lasts many timepoints (10-60+), so \ +consecutive frames are usually the same stage. Use the previous observation \ +as context, but classify based on the morphology in THIS image. -3. **When in doubt, choose the EARLIER stage.** The most common error is \ -classifying too advanced. - -4. **KEY DISCRIMINATOR: eggshell fill fraction.** How much of the eggshell \ +3. **KEY DISCRIMINATOR: eggshell fill fraction.** How much of the eggshell \ interior is filled with bright signal? - Sparse (lots of dark space inside shell) → 1.5fold or earlier - Moderate (some dark space) → 2fold @@ -91,16 +89,6 @@ async def perceive_scientific( history_text = build_history_text(history) if history_text: content.append({"type": "text", "text": history_text}) - last_stage = history[-1].get("stage", "unknown") if history else "unknown" - content.append({ - "type": "text", - "text": ( - f"The most recent observation was '{last_stage}'. " - f"Remember: stages change slowly. The current stage is most likely " - f"'{last_stage}' unless you see a clear morphological change. " - f"When uncertain, prefer the earlier stage." - ), - }) content.append( {