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

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308 open issues indexed

ArrowInvalid: offset overflow while concatenating arrays Open

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

scverse/spatialdata#970 · 7 comments · Opened Aug 19, 2025
rasterize messes up label to shape mapping when rastering only a subset of shapes Open

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

scverse/spatialdata#966 · Opened Aug 10, 2025
Should 2.5D data (points, images, labels) be stored in one 3D Element or multiple 2D Elements? Open

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

scverse/spatialdata#961 · Opened Jul 23, 2025
Clarify how to store "additional information" for Points Open

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

scverse/spatialdata#960 · Opened Jul 23, 2025
Include name of index column for Parquet tables in `spatialdata_attrs` for shapes/points Open

Difficulty 4/5 3-5 days Newbie friendliness 40/100

scverse/spatialdata#958 · Opened Jul 18, 2025
Option to delay scale_factors downsampling along Z dimension for 3D images Open

scverse/spatialdata#954 · 1 reaction · 2 assignees · Opened Jul 10, 2025
`concatenate` on points should just contain multiple tables instead of concatenating them Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/spatialdata#953 · Opened Jul 10, 2025
Error in aggregate over Image2DModel by Labels2DModel when transform is more complex than translation Open

needs: triage priority: medium

Difficulty 3/5 1-2 days Newbie friendliness 72/100

scverse/spatialdata#950 · 3 comments · Opened Jul 3, 2025
Reported issue with bounding box query and rotated images Open

method: query

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

scverse/spatialdata#949 · 1 comment · Opened Jul 2, 2025
Error when applying `spatialdata.transform` to multiscale images (related to scale handling) Open

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

scverse/spatialdata#947 · Opened Jul 1, 2025
Add dedicated API/CLI for validation of on-disk data Open

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

scverse/spatialdata#940 · Opened May 25, 2025
write_element and delete_element_from_disk are very slow when SpatialData object contains large number of elements Open

needs: triage priority: low

Difficulty 4/5 3-5 days Newbie friendliness 68/100

scverse/spatialdata#938 · 2 comments · Opened May 21, 2025
Read xenium data get TypeError: unhashable type: 'list' Open

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

scverse/spatialdata#937 · 1 comment · Opened May 21, 2025
get_centroids() slow on on labels elements Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/spatialdata#936 · 1 reaction · Opened May 19, 2025
Deal with the case when `.attrs`/`.uns` are not JSON-serializable Open

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

scverse/spatialdata#933 · Opened May 12, 2025
Large spatial transcriptomics datasets best practices Open

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

scverse/spatialdata#932 · Opened May 12, 2025
Uncaught error during pretty print Open

bug 🚨

scverse/spatialdata#926 · 2 comments · 1 assignee · Opened Apr 18, 2025
sd.concatenate throws ValidationError on queried sdatas Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/spatialdata#924 · Opened Apr 9, 2025
Keep polygon interior during vectorization Open

needs: triage priority: medium

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

scverse/spatialdata#920 · 1 comment · Opened Apr 2, 2025
[Feature Request] Convert from LabelsModel to ShapesModel Open

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

scverse/spatialdata#917 · Opened Apr 1, 2025
`render_points` with column coloring throws error when there are too many points Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

scverse/spatialdata#910 · Opened Mar 21, 2025
New features of polygon queries Open

enhancement ✨ method: query

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

scverse/spatialdata#908 · Opened Mar 18, 2025
Rename SpatialData elements Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/spatialdata#906 · 2 comments · 5 reactions · Opened Mar 18, 2025
tests: racoon dataset generation is flaky on arm mac Open

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

scverse/spatialdata#900 · 1 comment · Opened Mar 17, 2025
Can I speed up the spatialdata.polygon_query when dealing with really big datasets? Open

method: query performance 🚀

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

scverse/spatialdata#893 · 2 comments · Opened Feb 28, 2025
Image2DModel.parse() forgetting about scale_factors if chunking Open

needs: triage priority: medium

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

scverse/spatialdata#886 · 2 comments · 2 reactions · Opened Feb 25, 2025
Improve docs re data types for the Elements Open

docs 📜

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

scverse/spatialdata#885 · 1 comment · Opened Feb 25, 2025
Spatialdata object from remote .zarr store merges multiple tables during reading Open

remote ☁️

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

scverse/spatialdata#880 · Opened Feb 14, 2025
Spatialdata object created from remote .zarr store does not preserve "path" property Open

remote ☁️

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

scverse/spatialdata#879 · Opened Feb 14, 2025
Reading remote .zarr store has issue with reading shapes.parquet file Open

remote ☁️

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/spatialdata#878 · 3 comments · Opened Feb 14, 2025
Mismatch between local and remote pre-commits Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

scverse/spatialdata#875 · Opened Feb 11, 2025
Improve substitute of `rechunk('auto')` after `bounding_box.query` Open

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

scverse/spatialdata#872 · 1 comment · Opened Feb 11, 2025
Quirks installing spatialdata with pixi Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

scverse/spatialdata#870 · 4 comments · Opened Feb 11, 2025
Feature request, write_element does not materialize computation in in-memory SpatialData Object Open

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

scverse/spatialdata#866 · 7 comments · 3 reactions · Opened Feb 10, 2025
Unrecognized zarr version for example dataset in tutorial Open

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

scverse/spatialdata#863 · 7 comments · Opened Feb 4, 2025
Check for regular chunks before writing Open

models

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

scverse/spatialdata#862 · Opened Feb 4, 2025
Tests fails with `dask==2024.12.0` and `dask==2024.12.1` Open

dependencies 🐣

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

scverse/spatialdata#860 · Opened Feb 4, 2025
read_zarr from s3 Open

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

scverse/spatialdata#859 · 1 comment · Opened Feb 4, 2025
Efficient whole slide imaging IO Open

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

scverse/spatialdata#856 · 1 comment · 4 reactions · Opened Jan 31, 2025
Enable partial reading for specific subsets of elements Open

I/O 💿

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

scverse/spatialdata#855 · 1 comment · 2 reactions · Opened Jan 30, 2025
Shape mismatch in dataloader when rasterization is not used. Open

needs: triage priority: medium

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

scverse/spatialdata#854 · 1 comment · Opened Jan 30, 2025
`JoinTypes.__members__` empty in Python 3.13 Open

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

scverse/spatialdata#852 · Opened Jan 30, 2025
`RasterModel.parse()` should accept also `DataTree`. Open

models tiledb-soma

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

scverse/spatialdata#847 · Opened Jan 26, 2025
Cases uncaught from validation for raster data Open

models needs: triage priority: low tiledb-soma

Difficulty 3/5 1-2 days Newbie friendliness 64/100

scverse/spatialdata#846 · 1 comment · Opened Jan 25, 2025
Incremental reading APIs Open

I/O 💿

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

scverse/spatialdata#843 · Opened Jan 24, 2025
Save custom `.attrs` in SpatialElements to disk Open

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

scverse/spatialdata#839 · 8 comments · Opened Jan 21, 2025
v0.2.6 broken due to updates in Dask Open

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

scverse/spatialdata#835 · 4 comments · 2 reactions · Opened Jan 17, 2025
Importing ROIs and transformations from QuPath Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/spatialdata#834 · 2 comments · Opened Jan 17, 2025
Enhancement: Local SpatialData object with remotely accessed pyramidal OME-ZARR image Open

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

scverse/spatialdata#831 · 4 comments · 2 reactions · Opened Jan 15, 2025
Jupyter kernel crashing with sdata.write Open

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

scverse/spatialdata#827 · 4 comments · Opened Jan 14, 2025

scverse/spatialdata

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