scverse/spatialdata

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An open and interoperable data framework for spatial omics data

Stars: 394
Forks: 95
Open beginner issues: 10
Indexed issues: 308
Avg merge: 4d 3h
Merged PRs (30d): 7

Dominant language: Python
License: BSD-3-Clause
Last GitHub push: Sep 11, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

308 open issues indexed

Invalid "selection" values in "read_zarr()" should raise an error Open

needs: triage priority: low

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

scverse/spatialdata#1172 · 2 comments · Opened Aug 3, 2026
Transformation on large image results in very large chunks Open

needs: triage priority: medium

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/spatialdata#1161 · 3 comments · Opened Jul 8, 2026
Add SPEC-0 badge Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

scverse/spatialdata#1153 · 1 comment · 1 reaction · Opened Jun 22, 2026
Output spatially ordered `anndata` object Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/spatialdata#1145 · 6 comments · Opened Jun 17, 2026
Allow customization of suffix separator when concatenating SpatialData objects Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/spatialdata#1139 · Opened May 29, 2026
Proseg v3 transcript dataframe issue Open

needs: triage priority: medium

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/spatialdata#1137 · 2 comments · Opened May 22, 2026
`attributes/ome/omero/channels/label` gets incorrectly coerced to integer Open

needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/spatialdata#1136 · 1 comment · 1 reaction · Opened May 21, 2026
Unable to save SpatialData object to zarr Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 62/100

scverse/spatialdata#1135 · 2 comments · Opened May 21, 2026
Lack of symmetry between shapes and points in on-disk format Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/spatialdata#1134 · 2 comments · Opened May 21, 2026
Clarify uniqueness of index for points and shapes Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/spatialdata#1130 · Opened May 15, 2026
Index name not preserved after read-write for points and shapes? Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/spatialdata#1126 · 6 comments · Opened May 12, 2026
Refactor and speed-up SpatialData query funtions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/spatialdata#1101 · 2 comments · 1 reaction · Opened Mar 26, 2026
join_spatialelement_table crashes when obs index name matches an existing column Open

needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

scverse/spatialdata#1099 · 2 comments · Opened Mar 25, 2026
PointsModel warning Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

scverse/spatialdata#1098 · 3 comments · Opened Mar 24, 2026
More informative error when subsetting results in no observations retained in Visium HD Open

needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 67/100

scverse/spatialdata#1096 · 1 comment · Opened Mar 17, 2026
MuData Table for SpatialData object Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/spatialdata#1085 · 5 comments · 3 reactions · Opened Mar 2, 2026
Align pyramid downscaling with `ome-zarr-py` (`nearest` for labels; tighten tests) Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/spatialdata#1070 · Opened Feb 11, 2026
Dask 2026.1.2 breaks ome-zarr-py support Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

scverse/spatialdata#1059 · 3 comments · Opened Jan 31, 2026
cannot import name 'ConsolidatedMetadataStore' from 'zarr.storage' Open

needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 58/100

scverse/spatialdata#1058 · 5 comments · Opened Jan 30, 2026
match_sdata_to_table removes layers Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/spatialdata#1051 · 2 comments · Opened Jan 16, 2026
Improve CI speed by reducing the number of warnings Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/spatialdata#1044 · Opened Jan 6, 2026
Find faster way to infer categories in `PointsModel.parse()` Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/spatialdata#1042 · Opened Jan 3, 2026
Possible deadlock on `map_raster()`? Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/spatialdata#1040 · Opened Jan 3, 2026
Improve dev workflows around benchmarks Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/spatialdata#1036 · 1 comment · Opened Jan 2, 2026
Transform dimensions are changed when writing to zarr store Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/spatialdata#1029 · 2 comments · Opened Dec 11, 2025
Scale transform changes aggregate results Open

needs: triage priority: low

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

scverse/spatialdata#1028 · 2 comments · Opened Dec 11, 2025
Improve compatibility of cell segmentation output formats with downstream analysis tools Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/spatialdata#1026 · 1 comment · 1 reaction · Opened Nov 24, 2025
Merging multiple samples into a single SpatialData object + single merged table Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/spatialdata#1025 · 1 comment · Opened Nov 21, 2025
Writing multiscale element to disk fails when configuring Dask to uses "processes" Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

scverse/spatialdata#1024 · 6 comments · Opened Nov 20, 2025
Writing results of polygon query as Zarr Open

needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/spatialdata#1023 · 5 comments · Opened Nov 19, 2025
Image models fail with the latest `multiscale-spatial-image` release Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

scverse/spatialdata#1020 · Opened Nov 15, 2025
Don't use empty `asserts` Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

scverse/spatialdata#1019 · 2 reactions · Opened Nov 15, 2025
Use scverse template Open

maint 🏗️

scverse/spatialdata#1018 · 2 assignees · Opened Nov 14, 2025
polygon_query returns only rectangles Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/spatialdata#1017 · 1 comment · Opened Nov 10, 2025
`pip install "spatialdata[extra]"` not working with Python 3.11 Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/spatialdata#1016 · 1 comment · 1 reaction · Opened Nov 7, 2025
Can not import the package using jupyter notebook in Visual Studio Code Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/spatialdata#1014 · 1 comment · Opened Nov 5, 2025
Reading and writing issues on Mac with external disk Open

needs: triage priority: low

Difficulty 4/5 3-5 days Newbie friendliness 52/100

scverse/spatialdata#1013 · 1 comment · Opened Nov 4, 2025
`ShapesModel.parse()`, for `.geojson` files, ignores non-geometry colums. Open

needs: triage priority: low

Difficulty 3/5 1-2 days Newbie friendliness 68/100

scverse/spatialdata#1008 · 1 comment · Opened Oct 27, 2025
Concatenate from dictionary Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/spatialdata#998 · 1 comment · Opened Oct 15, 2025
Renaming of feature_key column of points Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 70/100

scverse/spatialdata#996 · 1 comment · Opened Oct 10, 2025
[Suggestion] Allow strings for method when constructing multiscale Image2DModel Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

scverse/spatialdata#995 · 1 comment · Opened Oct 9, 2025
Using `functools.partial` in an unsupported way that’ll break in a future Python version Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

scverse/spatialdata#993 · 1 comment · 1 reaction · Opened Oct 6, 2025
query.bounding_box not cropping the table Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/spatialdata#992 · 1 comment · Opened Oct 1, 2025
Non linear alignment - warpy Open

Difficulty 5/5 Over a week Newbie friendliness 38/100

scverse/spatialdata#991 · 2 comments · Opened Oct 1, 2025
Add installation tests for direct dependents (BioC-style) Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/spatialdata#990 · Opened Sep 30, 2025
exceeding rasterize's maximum label index Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 65/100

scverse/spatialdata#987 · 3 comments · Opened Sep 22, 2025
Move ngff transformations to separate repo? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/spatialdata#976 · 2 comments · 3 reactions · Opened Aug 25, 2025
Some suggestions and proposals for annotations in SpatialData Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/spatialdata#975 · 2 comments · Opened Aug 24, 2025
Easily enable sorting points along a Z-order curve Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/spatialdata#974 · 2 comments · 3 reactions · Opened Aug 22, 2025
Add tests for read / write on azure Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/spatialdata#972 · Opened Aug 20, 2025

scverse/spatialdata

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