feat: napari auto-loads in-store labels + single-GPU dashboard - #17
Merged
Conversation
When labels= is omitted and the image is a .zarr, overlay every label image registered under labels/<name>/ (where tile_process writes them by default) as its own multi-scale Labels layer. So view_in_napari( "scan.zarr") just shows image + segmentation. Docs the Imaris-pyramid rebuild behaviour too. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
On a GPU run with no existing client, start a 1-worker/1-thread in-process LocalCluster: GPU evals stay serial (no VRAM contention) but a Dask dashboard is exposed and its URL logged, so progress is visible. Falls back to the threaded scheduler if distributed/bokeh are absent; a user-provided cluster is used as-is. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Two UX/observability features, docs updated alongside each.
napari auto-loads labels
view_in_napari("scan.zarr")— with nolabels=— now auto-overlays every label image registered underscan.zarr/labels/<name>/(wheretile_processwrites them by default), each as its own multi-scale Labels layer. Falls back to image-only if there are none.Live dashboard on a single GPU
A GPU run (no existing client) starts a 1-worker/1-thread in-process
LocalCluster: evals stay serial (no VRAM contention) but a Dask dashboard is exposed and its URL logged, so you can watch tiles stream through. Graceful fallback to the threaded scheduler ifdistributed/bokeharen't installed; a user cluster is used as-is.Docs: napari guide (auto-load + Imaris-pyramid-rebuild note), performance guide (dashboard section). Tests: label discovery + resolution. 29 passed, ruff + mkdocs --strict clean.
🤖 Generated with Claude Code