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

stephenwilliams22 · 2025-10-06T16:51:44Z

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 · 2025-10-06T16:53:34Z

Codecov Report

❌ Patch coverage is 94.11765% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.13%. Comparing base (7cccdd1) to head (62c3f9f).
⚠️ Report is 27 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/readers/visium_hd.py	92.85%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #328      +/-   ##
==========================================
+ Coverage   49.06%   55.13%   +6.06%     
==========================================
  Files          26       26              
  Lines        2686     2802     +116     
==========================================
+ Hits         1318     1545     +227     
+ Misses       1368     1257     -111

Files with missing lines	Coverage Δ
src/spatialdata_io/__main__.py	`86.03% <100.00%> (ø)`
src/spatialdata_io/_constants/_constants.py	`100.00% <100.00%> (ø)`
src/spatialdata_io/readers/visium_hd.py	`76.36% <92.85%> (+61.23%)`	⬆️

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review-notebook-app · 2025-10-10T18:02:27Z

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stephenwilliams22 · 2025-10-10T18:05:43Z

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

stephenwilliams22 · 2025-10-10T19:19:15Z

tests/test_visium_hd.py

+
+# 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
+
+


Need to update these once tiny test is added

LucaMarconato · 2025-10-13T15:28:59Z

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 · 2025-10-13T15:52:16Z

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

for more information, see https://pre-commit.ci

pyproject.toml

stephenwilliams22 · 2025-10-29T19:00:34Z

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

stephenwilliams22 added 4 commits September 24, 2025 13:24

feat: suppor for spaceranger4.0

b1e6d06

make nuc segmentation and cut dup code

a6d7e9f

use only in_nucleus

31379c8

make local functions

34ac722

stephenwilliams22 requested a review from LucaMarconato October 6, 2025 16:51

stephenwilliams22 mentioned this pull request Oct 6, 2025

Add support for Space Ranger cell segmentation data #323

Open

stephenwilliams22 marked this pull request as draft October 6, 2025 17:54

stephenwilliams22 added 2 commits October 6, 2025 11:11

ruff

b7848fa

typing

ae43fe7

quentinblampey mentioned this pull request Oct 7, 2025

new version of Visium HD data with segmentation from SpaceRanger V4 gustaveroussy/sopa#326

Closed

stephenwilliams22 added 3 commits October 7, 2025 15:45

nuc seg cli

31c76fd

tests

9134c94

add vignette

42028ce

update BARCODE_MAPPINGS_PATH and calc centroids

b269d32

stephenwilliams22 commented Oct 10, 2025

View reviewed changes

stephenwilliams22 and others added 2 commits October 13, 2025 16:01

delete vignette. moved to new PR

0e891ec

Merge branch 'main' into stephen/spaceranger4.0

c9674ca

LucaMarconato mentioned this pull request Oct 22, 2025

temp PR: Visium HD 4.0 #333

Draft

pre-commit-ci bot and others added 4 commits October 22, 2025 13:03

[pre-commit.ci] auto fixes from pre-commit.com hooks

49d3e7e

for more information, see https://pre-commit.ci

wip code review visium hd

30e4076

wip code review

cc9dc68

initial review pass

e5c2d16

LucaMarconato mentioned this pull request Oct 27, 2025

Add visium hd test datasets #336

Merged

LucaMarconato added 2 commits October 27, 2025 20:10

Merge branch 'main' into stephen/spaceranger4.0

ab3611b

pin pyarrow

8cecbf3

LucaMarconato and others added 7 commits October 27, 2025 21:09

fix docstring

4b8a41f

code review simplification

39ffde5

fix typo

01583e0

fix unnecessary check

8bb3ab9

fix unnecessary check

3098486

fix docstring

955a9a6

update tests

6f6459c

stephenwilliams22 marked this pull request as ready for review October 29, 2025 18:58

stephenwilliams22 commented Oct 29, 2025

View reviewed changes

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stephenwilliams22 added 3 commits October 29, 2025 19:24

revert python change and update pytest

0d11d26

test precommit

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ruff

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