Document the segmentation pipeline - #10
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Add a tutorial notebook that carries an OME-TIFF through InstanSeg nucleus segmentation to a SpatialData zarr, and register it in the docs. Name the zarr store for the slide's stem (`slide.ome.tif` -> `slide.zarr`) instead of the full filename, via a new `slide_stem` helper. Untrack the SLURM scripts; they are cluster-specific scratch.
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Add the segmentation steps to Getting started and both optional extras to Installation. Restore the trailing newline in .gitignore, which end-of-file-fixer rejected in CI.
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Documentation and tutorial update for the segmentation pipeline added in #9, which shipped without docs.
Tutorial
docs/notebooks/segment_nuclei.ipynbpicks up whereconvert_to_ometiff.ipynbleaves off: it takes an OME-TIFF throughsegment_wsiandgeojson_to_spatialdatato a written SpatialData zarr, then reads the store back and plots the nuclei over the H&E.Executed end-to-end on a kidney H&E (867 MB, 1239 tiles, 83,554 nuclei), so the committed outputs are real.
Registered in
tutorials.md,index.md,api.md(new Segmenting section) andinstallation.md(thesegmentationextra).convert_to_ometiff.ipynbnow links forward to it.Zarr store naming
The store is now named for the slide's stem rather than its full filename:
Path.stemalone does not do this (slide.ome.tif→slide.ome), so this adds aslide_stemhelper incore/utils.pyand adefault_zarr_pathinsegmentation/to_spatialdata.py. The.zarr.zipsibling and the skip-existing check follow automatically.Stores written under the old convention are no longer recognised by the skip-existing check, so a re-run would rebuild them. A rename snippet is in the
geojson_to_spatialdata.pymodule docstring.Also
The SLURM scripts are untracked — they are cluster-specific scratch, not part of the package surface.
Checks
pytest— 100 passedsphinx-build -W— build succeededruff check/ruff format --check— clean