feat: Updates for 10x Genomics Atera bundles

[stephenwilliams22]

Adds a native reader for 10x Genomics Atera datasets: cell-by-gene expression table, cell/nucleus segmentation labels and boundary polygons, per-transcript locations, and morphology images.

• Table (cell_feature_matrix.zarr.zip/csc_cell_feature_matrix.zarr.zip) is read directly with anndata's own zarr IO (anndata.io.read_elem/ anndata.io.sparse_dataset), with X lazily backed by dask.
• Cell/nucleus labels are lazily backed by dask; boundary polygons are read via shapely.from_ragged_array, with an optional tiled/pyramided partial-read path (read_cell_boundaries) for large bundles.
• Transcripts are read lazily per spatial tile via dask-delayed.
• Morphology images are read via tifffile's native OME-TIFF tile grid, avoiding materializing full-resolution planes.
• An example notebook with a finalized tiny atera output bundle is provided for testing. This can be found in the atera_example.ipynb for testing.

Enables massive datasets on a basic laptop (2M cells, 11 billion transcripts). Basic analysis workflow (loading, plotting, HVG, PCA, normalization, clustering, etc) max memory usage was 7GB on a new mac in ~15min.

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Codecov Report

❌ Patch coverage is 23.29317% with 382 lines in your changes missing coverage. Please review.
✅ Project coverage is 60.17%. Comparing base (261578f) to head (91ed96d).

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/_atera_common.py	14.78%	242 Missing ⚠️
src/spatialdata_io/readers/atera.py	15.66%	140 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (261578f) and HEAD (91ed96d). Click for more details.

HEAD has 5 uploads less than BASE

Flag	BASE (261578f)	HEAD (91ed96d)
	8	3

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #426      +/-   ##
==========================================
- Coverage   65.79%   60.17%   -5.63%     
==========================================
  Files          26       28       +2     
  Lines        3263     3761     +498     
==========================================
+ Hits         2147     2263     +116     
- Misses       1116     1498     +382     

Files with missing lines	Coverage Δ
src/spatialdata_io/__init__.py	100.00% <ø> (ø)
src/spatialdata_io/_constants/_constants.py	100.00% <100.00%> (ø)
src/spatialdata_io/readers/atera.py	15.66% <15.66%> (ø)
src/spatialdata_io/readers/_atera_common.py	14.78% <14.78%> (ø)

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[Zethson]

@stephenwilliams22 could you please always ensure that the pre-commit checks are green? Ideally a PR should always have green CI before anyone has a look.

Thanks!

[stephenwilliams22]

@stephenwilliams22 could you please always ensure that the pre-commit checks are green? Ideally a PR should always have green CI before anyone has a look.

Thanks!

@Zethson sorry about that. we should be good to go now.