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

Missing filtered table in polygon_query() of MERFISH data Open

bug 🚨 method: query

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

scverse/spatialdata#633 · 7 comments · Opened Jul 11, 2024
Improvement to the docs Open

docs 📜

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

scverse/spatialdata#631 · 6 comments · Opened Jul 9, 2024
Drop `region` (`region_key` and `instance_key` are enough) Open

element: table 📑

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

scverse/spatialdata#629 · Opened Jul 9, 2024
Issue with aggregation when `.attrs` is replaced instead of `.attrs['transform']` Open

method: transforms 🔃

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

scverse/spatialdata#600 · Opened Jun 25, 2024
multiprocessing for dataloader Open

method: dataloader needs: triage priority: medium

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

scverse/spatialdata#590 · 3 comments · Opened Jun 18, 2024
Invalid shapes during vectorization Open

element: shapes ▲ method: vectorize ◃ needs: triage priority: medium

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

scverse/spatialdata#583 · 1 comment · Opened Jun 12, 2024
Querying points doesn't filter the associated table Open

element: points ⊙ method: query

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

scverse/spatialdata#567 · 1 comment · Opened May 24, 2024
`polygon_query()` with `filter_table=True` on labels should filter the table. Open

method: query needs: triage priority: medium

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

scverse/spatialdata#564 · 1 comment · Opened May 23, 2024
Test aggregation of vector data by vector data when `agg_func` is a `list` of `str` Open

method: aggregation 🔢 needs: triage priority: low

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

scverse/spatialdata#561 · 1 comment · Opened May 16, 2024
Extract Image features from VisiumHD and Squidpy Open

enhancement ✨ question ❓

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

scverse/spatialdata#548 · 2 comments · Opened Apr 19, 2024
Cannot aggregate Labels2DModel by ShapesModel Open

method: aggregation 🔢 question ❓

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

scverse/spatialdata#546 · 1 comment · Opened Apr 17, 2024
Parameter name `(target_|to_)?coordinate_system(s)?` Open

method: transforms 🔃

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

scverse/spatialdata#534 · Opened Apr 3, 2024
Mixed polygon/multipolygon geometry types from disk Open

element: shapes ▲ I/O 💿

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

scverse/spatialdata#529 · Opened Mar 30, 2024
Missing `dtype` validation for labels? Open

element: labels 🏷️

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

scverse/spatialdata#527 · Opened Mar 30, 2024
`_get_unique_label_values_as_index()` should be included as a case of `get_values()` Open

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

scverse/spatialdata#522 · 1 comment · Opened Mar 28, 2024
Allow reloading of particular elements, and add `reload: bool` parameter to write functions Open

I/O 💿

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

scverse/spatialdata#521 · Opened Mar 27, 2024
Different cell ids selected in regions: spatialdata vs Xenium explorer Open

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

scverse/spatialdata#507 · 4 comments · Opened Mar 25, 2024
Parse and validate against `POLYGON Z` (same for points and multipolygons) in the `ShapesModel` Open

element: shapes ▲

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

scverse/spatialdata#505 · Opened Mar 23, 2024
Check for uniqueness of names also across the file storage Open

I/O 💿

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

scverse/spatialdata#504 · Opened Mar 23, 2024
Proposal: simplify data model for Points Open

element: points ⊙ element: table 📑

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

scverse/spatialdata#503 · 1 comment · Opened Mar 22, 2024
`join_sdata_spatialelement_table()` fails with non-unique `AnnData` obs Open

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

scverse/spatialdata#494 · 1 reaction · Opened Mar 20, 2024
Opening remote data store is inconsistent Open

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

scverse/spatialdata#488 · 1 reaction · Opened Mar 14, 2024
Replace some `AssertionError` with other exceptions Open

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

scverse/spatialdata#483 · Opened Mar 13, 2024
Spatialdata does not seem to be interoperable with squidpy image pipelines Open

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

scverse/spatialdata#463 · Opened Feb 22, 2024
Reduce import time Open

needs: triage priority: low

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

scverse/spatialdata#456 · 2 comments · 1 reaction · Opened Feb 13, 2024
Allowing pd.DataFrame as table would be super convenient for me! Open

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

scverse/spatialdata#452 · 1 comment · Opened Feb 6, 2024
Backed multiscale image, problems with scales and dims Open

method: transforms 🔃

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

scverse/spatialdata#446 · Opened Jan 30, 2024
Support for private remote object storage Open

format

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

scverse/spatialdata#441 · 7 comments · 2 reactions · Opened Jan 26, 2024
Helper functions around the pixel size in units Open

method: transforms 🔃

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

scverse/spatialdata#436 · 2 comments · 1 reaction · Opened Jan 18, 2024
Check validity of shapely geometries in `ShapesModel.parse()` Open

element: shapes ▲ needs: triage priority: low

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

scverse/spatialdata#429 · 1 comment · Opened Jan 15, 2024
`chunks` needs to be passed to `to_multiscale` otherwise it's ignored Open

needs: triage priority: low

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

scverse/spatialdata#421 · 1 comment · Opened Jan 7, 2024
Remove `region` from `adata.uns['spatialdata_attrs']` Open

element: table 📑

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

scverse/spatialdata#419 · 1 comment · Opened Jan 5, 2024
Simplify `read_table_and_validate()` for S3 storages Open

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

scverse/spatialdata#418 · Opened Jan 4, 2024
Expand to desired bounding box Open

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

scverse/spatialdata#416 · 1 comment · Opened Dec 18, 2023
Windows CI Open

CI ∫

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

scverse/spatialdata#413 · Opened Dec 14, 2023
Concurrency-save writing to SpatialData Open

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

scverse/spatialdata#412 · 2 reactions · Opened Dec 11, 2023
Rechunk dask image if not using multi-scales Open

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

scverse/spatialdata#406 · 2 comments · Opened Nov 24, 2023
Consider adding `.uns` or `.attrs` to `SpatialData` Open

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

scverse/spatialdata#404 · Opened Nov 23, 2023
Better support for visualising highly multiplexed images Open

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

scverse/spatialdata#401 · 2 comments · 2 reactions · Opened Nov 15, 2023
ome-zarr-py labels logging still appears Open

needs: triage priority: low

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

scverse/spatialdata#400 · 3 comments · Opened Nov 13, 2023
Support for nested hierarchies in NGFF stores Open

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

scverse/spatialdata#398 · 2 comments · Opened Nov 8, 2023
Use `GeoDataFrame` for points Open

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

scverse/spatialdata#396 · 1 comment · Opened Nov 8, 2023
[Proposal] Rename Sequence transformation to avoid clashes Open

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

scverse/spatialdata#382 · 1 comment · Opened Oct 24, 2023
AttributeError: type object 'MultiscaleSpatialImage' has no attribute 'from_dict' Open

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

scverse/spatialdata#380 · 1 comment · Opened Oct 23, 2023
Adding image to same slot for backed sdata Open

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

scverse/spatialdata#374 · 1 comment · Opened Oct 10, 2023
Using Dask `GeoDataFrame` for lazy representation of shapes. Open

element: points ⊙ element: shapes ▲ I/O 💿

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

scverse/spatialdata#359 · 1 comment · Opened Sep 25, 2023
Adding a pixel size in OMERO metadata Open

method: transforms 🔃

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

scverse/spatialdata#357 · 3 comments · Opened Sep 19, 2023
`sdata.write()` broken -> Reason why GH actions fail Open

bug 🚨

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

scverse/spatialdata#352 · 1 comment · Opened Sep 11, 2023
Channel Equivalent For `Labels2DModel` Open

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

scverse/spatialdata#338 · 3 comments · Opened Aug 20, 2023
Question - distance measurements Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

scverse/spatialdata#334 · 1 comment · Opened Aug 8, 2023

scverse/spatialdata

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