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Add experimental Pyxa (Stellaromics) reader - #425

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ckmah:pyxa-reader

Commits on Sep 24, 2026

Add PyxaKeys constants for Pyxa reader
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35946aa
Add subsampled Pyxa test fixture
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ab8c165
Add _validate_columns helper for Pyxa reader
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667649f
Add _get_points loader for Pyxa reader
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88cc5fa
Add _get_table loader for Pyxa reader
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3cd1ce2
Add _get_shapes loader for Pyxa reader
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0d32578
Add pyxa() reader function
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48ee184
Add pyxa CLI command and register as experimental reader
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5b5e4ad
Document Pyxa in README experimental readers section
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01983c2
Apply pre-commit fixes (isort, pyupgrade, line endings)
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571fa19
Untrack uv.lock
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ca3245f
Add optional mosaic image support to pyxa reader
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9390a2a
Adapt pyxa reader to upstream CLI, mypy and ruff conventions
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18c2d98
Convert Pyxa shapes to micrometers and test against public xsmall data
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47ed13e
Split Pyxa shapes into footprints and z-planes, load all mosaic scales
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2e01fe7

Commits on Sep 25, 2026

pyxa: optional inputs (studio clusters, transcripts, shapes, images) with required counts and metadata
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d7bc44f

Commits on Sep 28, 2026

pyxa: sparse counts; keys for the mosaic file and cell labels

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30bf5c4
pyxa: find the mosaic in the directory, zipped or not; image= replaces image_path

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86d5d6b
pyxa: mosaic grid shared by image and labels; integer label ids from cell_id

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06353c1
pyxa tests: sort imports, drop unused import

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9aa9032
pyxa: decode segmentation polygons into rings on the mosaic grid

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b90a534
pyxa: empty rings for an empty segmentation file

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9d98693
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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197d1af
pyxa: coarse label levels are strided views of level 0

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cc6ed0e
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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d6373af

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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bf13de5
pyxa tests: type-clean labels tests for mypy

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ba0fa39
pyxa: configurable worker pool, shut down after decode

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cb1ec64
pyxa: sample coarse labels at voxel centres

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dbbd4e0
pyxa: docs, changelog, logging, CLI conflict, zip root

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8517749
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