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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19 beginner-friendly issues open

aggregate(values, by=<multiscale labels>) crashes with AttributeError despite DataTree being a declared input type Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#1249 · Opened Sep 13, 2026
unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster Open

bug 🚨 element: images 🌌 element: labels 🏷️ needs: triage

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

scverse/spatialdata#1239 · Opened Sep 11, 2026
spatialdata.models.force_2d() silently drops interior rings (holes) of polygons Open

bug 🚨 element: shapes ▲ models needs: triage priority: medium

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

scverse/spatialdata#1234 · Opened Sep 11, 2026
aggregate(image, by=labels) crashes when the labels have no background (no zero pixels) Open

bug 🚨 element: labels 🏷️ method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#1230 · Opened Sep 11, 2026
TableModel rejects int8/uint8 instance-key columns although the error message promises 'uint equivalents' (breaks aggregate/to_circles on uint8 labels) Open

bug 🚨 element: labels 🏷️ element: table 📑 models needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1229 · Opened Sep 11, 2026
Substring matching of element names against a single-region table (`element_name in regions` with `regions: str`) Open

bug 🚨 element: table 📑 method: query needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1228 · Opened Sep 11, 2026
Case-insensitive element-name uniqueness check only works when the existing name is lowercase Open

API bug 🚨 I/O 💿 needs: triage priority: medium

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

scverse/spatialdata#1221 · Opened Sep 11, 2026
relabel_sequential() fails for every unsigned dtype: OverflowError: Python integer -1 out of bounds for uint16 Open

bug 🚨 element: labels 🏷️ needs: triage priority: high

Difficulty 2/5 1-3 hours Newbie friendliness 76/100

scverse/spatialdata#1215 · Opened Sep 11, 2026
_filter_labels_element rebuilds set(ids_to_keep) inside a comprehension: O(n_labels × n_keep) in right/inner joins with filter_label_pixels=True Open

bug 🚨 element: labels 🏷️ method: query needs: triage performance 🚀 priority: high

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

scverse/spatialdata#1208 · Opened Sep 11, 2026
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
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
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
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
`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
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
Test aggregation when shapes touch but not overlap Open

method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#301 · 1 comment · Opened Jun 19, 2023
`value_key` is ignored in `aggregate()` for images Open

method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#274 · 1 comment · Opened May 22, 2023
Filtering by coordinate system that doesn't exist returns an empty SpatialData object Open

needs: triage priority: low

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

scverse/spatialdata#239 · 3 comments · Opened May 4, 2023
Fix typo in argument names in `align_elements_using_landmarks()` Open

needs: triage priority: low

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

scverse/spatialdata#229 · 1 comment · Opened Apr 18, 2023

scverse/spatialdata

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