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Feat: Support for Visium HD cell segmentation in Space Ranger 4.0 #328

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@stephenwilliams22 stephenwilliams22 commented Oct 6, 2025 •
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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

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codecov-commenter commented Oct 6, 2025 •
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Codecov Report

❌ Patch coverage is 8.38323% with 153 lines in your changes missing coverage. Please review.
✅ Project coverage is 48.24%. Comparing base (595eea7) to head (0e891ec).
⚠️ Report is 8 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_io/readers/visium_hd.py 4.37% 153 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #328      +/-   ##
==========================================
- Coverage   49.06%   48.24%   -0.83%     
==========================================
  Files          26       26              
  Lines        2686     2794     +108     
==========================================
+ Hits         1318     1348      +30     
- Misses       1368     1446      +78
Files with missing lines Coverage Δ
src/spatialdata_io/__main__.py 86.03% <ø> (ø)
src/spatialdata_io/_constants/_constants.py 100.00% <100.00%> (ø)
src/spatialdata_io/readers/visium_hd.py 15.43% <4.37%> (+0.29%) ⬆️

... and 1 file with indirect coverage changes

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@stephenwilliams22 stephenwilliams22 mentioned this pull request Oct 6, 2025
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@stephenwilliams22 stephenwilliams22 marked this pull request as draft October 6, 2025 17:54
@quentinblampey quentinblampey mentioned this pull request Oct 7, 2025
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@LucaMarconato please let me know if my vignette should go someplace else but I thought it would be good to have one.

stephenwilliams22
stephenwilliams22 commented Oct 10, 2025
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tests/test_visium_hd.py
Comment on lines +47 to +71

# TODO: Replace with the actual Visium HD test dataset folder name
# This dataset name is used to locate the test data in the './data/' directory.
# See https://github.com/scverse/spatialdata-io/blob/main/.github/workflows/prepare_test_data.yaml
# for instructions on how to download and place the data on disk.
DATASET_FOLDER = "Visium_HD_Mouse_Brain_Chunk"
DATASET_ID = "visium_hd_tiny"


@skip_if_below_python_version()
def test_visium_hd_data_extent() -> None:
"""Check the spatial extent of the loaded Visium HD data."""
f = Path("./data") / DATASET_FOLDER
if not f.is_dir():
pytest.skip(f"Test data not found at '{f}'. Skipping extent test.")

sdata = visium_hd(f, dataset_id=DATASET_ID)
extent = get_extent(sdata, exact=False)
extent = {ax: (math.floor(extent[ax][0]), math.ceil(extent[ax][1])) for ax in extent}

# TODO: Replace with the actual expected extent of your test data
expected_extent = "{'x': (1000, 7000), 'y': (2000, 8000)}"
assert str(extent) == expected_extent


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Need to update these once tiny test is added

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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.

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stephenwilliams22 commented Oct 13, 2025 •
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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

@LucaMarconato LucaMarconato mentioned this pull request Oct 22, 2025
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