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Add experimental Pyxa (Stellaromics) reader - #425

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ckmah:pyxa-reader

Open

Add experimental Pyxa (Stellaromics) reader#425
ckmah wants to merge 37 commits into
scverse:mainfrom
ckmah:pyxa-reader

Commits on Sep 24, 2026
- Add PyxaKeys constants for Pyxa reader
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- Add subsampled Pyxa test fixture
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- Add _validate_columns helper for Pyxa reader
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- Add _get_points loader for Pyxa reader
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- Add _get_table loader for Pyxa reader
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- Add _get_shapes loader for Pyxa reader
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- Add pyxa() reader function
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- Add pyxa CLI command and register as experimental reader
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- Document Pyxa in README experimental readers section
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- Apply pre-commit fixes (isort, pyupgrade, line endings)
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- Untrack uv.lock
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- Add optional mosaic image support to pyxa reader
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- Adapt pyxa reader to upstream CLI, mypy and ruff conventions
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- Convert Pyxa shapes to micrometers and test against public xsmall data
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- Split Pyxa shapes into footprints and z-planes, load all mosaic scales
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Commits on Sep 25, 2026
- pyxa: optional inputs (studio clusters, transcripts, shapes, images) with required counts and metadata
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Commits on Sep 28, 2026
- pyxa: sparse counts; keys for the mosaic file and cell labels
  
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- pyxa: find the mosaic in the directory, zipped or not; image= replaces image_path
  
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- pyxa: mosaic grid shared by image and labels; integer label ids from cell_id
  
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- pyxa tests: sort imports, drop unused import
  
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- pyxa: decode segmentation polygons into rings on the mosaic grid
  
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- pyxa: empty rings for an empty segmentation file
  
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- pyxa: plan label tiles and draw them lazily, one dask task per tile
  
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- pyxa: multiscale 3D cell labels on the mosaic grid
  
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- pyxa: coarse label levels are strided views of level 0
  
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- pyxa tests: cover the short-level guard
  
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- pyxa: labels= rasterizes 3D cell labels annotated by the table; shapes= option
  
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Commits on Sep 29, 2026
- pyxa: decode polygon row groups in worker processes
  
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- pyxa: decode polygons in batches to bound memory
  
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- pyxa: assign tiles from padded bounds so seams match
  
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- pyxa tests: type-clean labels tests for mypy
  
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- pyxa: configurable worker pool, shut down after decode
  
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- pyxa: sample coarse labels at voxel centres
  
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- pyxa: docs, changelog, logging, CLI conflict, zip root
  
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- pyxa: keep the reader in one module
  
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- pyxa: coarse label steps from the mosaic's OME scales
  
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  32bc0e5
- pyxa tests: fetch the xsmall fixture when the CI artifact lacks it; mypy-clean
  
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  9a85304

Commits

Commits on Sep 24, 2026

Commits on Sep 25, 2026

Commits on Sep 28, 2026

Commits on Sep 29, 2026