Feat: Support for Visium HD cell segmentation in Space Ranger 4.0

[stephenwilliams22]

This pr adds support for cell segmentation in Visium HD which was added in Space Ranger 4.0.

Features include

• Updating and refactoring the visium_hd function
• Default loading of Visium HD cell segmentations
• New parameters
  • load_segmentations_only which disables bin loading
  • load_nucleus_segmentations which loads nucleus segmentations and calculates a nucleus only expression matrix

spatial data structure will look something like

SpatialData object
├── Images
│     ├── 'hd_hires_image': DataArray[cyx] (3, 5394, 6000)
│     └── 'hd_lowres_image': DataArray[cyx] (3, 540, 600)
├── Shapes
│     ├── 'hd_cell_segmentations': GeoDataFrame shape: (612, 2) (2D shapes)
│     └── 'hd_nucleus_segmentations': GeoDataFrame shape: (950, 2) (2D shapes)
└── Tables
      ├── 'cell_segmentations': AnnData (612, 32285)
      └── 'nucleus_segmentations': AnnData (950, 32285)
with coordinate systems:
    ▸ 'hd_downscaled_hires', with elements:
        hd_hires_image (Images), hd_cell_segmentations (Shapes), hd_nucleus_segmentations (Shapes)
    ▸ 'hd_downscaled_lowres', with elements:
        hd_lowres_image (Images), hd_cell_segmentations (Shapes), hd_nucleus_segmentations (Shapes)

To do based on submission guidelines

• Function tests
• Provided tiny test data
• CLI support
• Centroid support?
• "how to" notebook
  • Example: here feat: visium hd cell segmentation example spatialdata-notebooks#152

[codecov-commenter]

Codecov Report

❌ Patch coverage is 93.37748% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.20%. Comparing base (0e891ec) to head (301650e).
⚠️ Report is 59 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/visium_hd.py	92.95%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #328      +/-   ##
==========================================
+ Coverage   48.24%   55.20%   +6.95%     
==========================================
  Files          26       26              
  Lines        2794     2806      +12     
==========================================
+ Hits         1348     1549     +201     
+ Misses       1446     1257     -189     

Files with missing lines	Coverage Δ
src/spatialdata_io/__main__.py	86.18% <100.00%> (+0.15%)	⬆️
src/spatialdata_io/_constants/_constants.py	100.00% <100.00%> (ø)
src/spatialdata_io/readers/visium_hd.py	76.53% <92.95%> (+61.09%)	⬆️

... and 1 file with indirect coverage changes

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[stephenwilliams22]

@LucaMarconato please let me know if my vignette should go someplace else but I thought it would be good to have one.

[LucaMarconato]

Thanks @stephenwilliams22! We can review the vignette here, but before merging please move it to the spatialdata-notebooks repo, in this folder.

If you would like we could add the vignette in gallery in the docs.

[stephenwilliams22]

Thanks @stephenwilliams22! We can review the vignette here, but before merging please move it to the spatialdata-notebooks repo, in this folder.

If you would like we could add the vignette in gallery in the docs.

Perfect. moved here scverse/spatialdata-notebooks#152

[stephenwilliams22]

@LucaMarconato tests updated. Let me know what you think!