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

Bug: `get_values()` gives an error when asking annotations of labels Open

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

scverse/spatialdata#332 · Opened Aug 7, 2023
transparent `ShapesModel.parse` geometry arguments Open

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

scverse/spatialdata#315 · 1 comment · 1 reaction · Opened Jun 30, 2023
Coordinate transformations refactoring Open

method: transforms 🔃

scverse/spatialdata#308 · 4 comments · 2 reactions · 1 assignee · Opened Jun 22, 2023
Aggregation and multiple tables Open

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

scverse/spatialdata#305 · Opened Jun 20, 2023
Improvement to aggregation (`by_key`) Open

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

scverse/spatialdata#304 · Opened Jun 20, 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
Add `resolution` parameter to `circles_to_polygons()` Open

enhancement ✨ method: aggregation 🔢

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

scverse/spatialdata#300 · Opened Jun 19, 2023
No reloading after saving Open

scverse/spatialdata#297 · 1 assignee · Opened Jun 14, 2023
Refactoring the io and in-memory lazy vs non-lazy representation Open

format

scverse/spatialdata#293 · 6 comments · 1 assignee · Opened Jun 9, 2023
CI to make small datasets for interoperability testing Open

scverse/spatialdata#292 · 3 comments · 1 assignee · Opened Jun 9, 2023
Refactor `get_elements()` from `spatialdata-plot` and push upstream Open

enhancement ✨

scverse/spatialdata#289 · 1 assignee · Opened Jun 8, 2023
`deepcopy` doesn't deepcopy `.attrs['transform']` in `GeoDataFrame` Open

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

scverse/spatialdata#286 · 3 comments · Opened Jun 6, 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
Spatial query with `target_coordinate_system` not in element Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

scverse/spatialdata#273 · Opened May 19, 2023
Validate transformations when calling `set_transformation` Open

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

scverse/spatialdata#266 · Opened May 17, 2023
Overwriting issue when rerunning code Open

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

scverse/spatialdata#265 · 1 comment · Opened May 17, 2023
Helper function (or modify parser) to selectively copy metadata between objects Open

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

scverse/spatialdata#258 · Opened May 15, 2023
Aggregate: buffering only points, not points and polygons/multipolygons Open

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

scverse/spatialdata#251 · Opened May 10, 2023
ome-zarr labels source metadata Open

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

scverse/spatialdata#244 · 1 comment · 1 reaction · Opened May 8, 2023
Do not convert arrays to dask Open

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

scverse/spatialdata#243 · 2 comments · Opened May 8, 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
[Request] More informative error message when len nodes != 1 Open

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

scverse/spatialdata#237 · Opened May 4, 2023
Make the models callable (and call the parser) Open

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

scverse/spatialdata#235 · Opened Apr 28, 2023
on-disk representation becomes ambigious when shapes contains circles and polygons Open

needs: triage priority: low

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

scverse/spatialdata#234 · 2 comments · Opened Apr 27, 2023
Geopandas vs pandas for points Open

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

scverse/spatialdata#233 · 2 comments · Opened Apr 27, 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
Refactoring query functions Open

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

scverse/spatialdata#225 · 3 comments · 1 reaction · Opened Apr 13, 2023
`Image2DModel` gives wrong name to the image Open

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

scverse/spatialdata#223 · Opened Apr 11, 2023
Table `region_key` column is not `categorical` anymore after `concatenate()` Open

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

scverse/spatialdata#221 · Opened Apr 11, 2023
Method to validate the relationship between elements Open

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

scverse/spatialdata#218 · 1 comment · Opened Apr 5, 2023
Bug with `INSTANCE_KEY` for points? Open

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

scverse/spatialdata#217 · Opened Apr 5, 2023
Cases not currently covered by the aggergation Open

method: aggregation 🔢

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

scverse/spatialdata#216 · 1 comment · Opened Apr 5, 2023
Aggregation with multiscale objects Open

method: aggregation 🔢 needs: triage priority: medium

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

scverse/spatialdata#215 · 1 comment · Opened Apr 5, 2023
Models: mixed types for the same shape column Open

element: shapes ▲ needs: triage priority: low

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

scverse/spatialdata#214 · 1 comment · Opened Apr 5, 2023
Aggregation and multipolygons Open

method: aggregation 🔢

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

scverse/spatialdata#213 · Opened Apr 5, 2023
Aggregation case: a shape in `values` intersects two shapes in `by` Open

method: aggregation 🔢

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

scverse/spatialdata#211 · Opened Apr 5, 2023
Aggregate points by shapes lazily Open

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

scverse/spatialdata#210 · 2 comments · 1 reaction · Opened Apr 5, 2023
Aggregate points by labels Open

method: aggregation 🔢

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

scverse/spatialdata#209 · Opened Apr 5, 2023
New features for the CLI Open

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

scverse/spatialdata#190 · 2 comments · Opened Mar 16, 2023
convert integers indexes to `int32` Open

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

scverse/spatialdata#187 · 2 comments · 1 reaction · Opened Mar 14, 2023
Extend functionality of the tiling Open

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

scverse/spatialdata#184 · Opened Mar 11, 2023
Increase test coverage of rasterization Open

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

scverse/spatialdata#177 · Opened Mar 8, 2023
Explicit intrinsic coordinate system for points and shapes Open

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

scverse/spatialdata#169 · 11 comments · Opened Mar 6, 2023
Interpolation when resampling images Open

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

scverse/spatialdata#166 · 1 comment · Opened Mar 1, 2023
Offset when rasterizing data Open

element: images 🌌 element: labels 🏷️ method: rasterization method: transforms 🔃 needs: triage priority: medium

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

scverse/spatialdata#165 · 14 comments · 1 reaction · Opened Mar 1, 2023
type and storage of `instance_key` issues Open

element: table 📑 I/O 💿

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

scverse/spatialdata#158 · 16 comments · Opened Feb 27, 2023
Let PointsModel be a dask or pandas dataframe Open

enhancement ✨

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

scverse/spatialdata#153 · 5 comments · 1 reaction · Opened Feb 24, 2023
Rename `maintain_positioning` parameter of `BaseTransformation.tranform()` Open

Difficulty 2/5 1-3 hours Newbie friendliness 32/100

scverse/spatialdata#148 · 1 comment · Opened Feb 22, 2023
Shapes element parser should have an easy way to set the axes for the coordinates Open

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

scverse/spatialdata#146 · 1 comment · 1 reaction · Opened Feb 20, 2023
Currently considering only scale in the transformations for multiscales Open

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

scverse/spatialdata#125 · Opened Feb 2, 2023

scverse/spatialdata

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