Issues

• ci: check docstring parameters against signatures

  scverse/spatialdata#1303 · Filter by author jan-glx opened on Nov 6, 2026

• docs: re-enable nitpicky so broken cross-references fail the docs build

  scverse/spatialdata#1302 · Filter by author jan-glx opened on Nov 6, 2026

• to_polygons() on labels is not pixel-exact: half-pixel shift, cut corners, filled holes, chunk-dependent output

  Bug

  scverse/spatialdata#1301 · Filter by author MeyerBender opened on Nov 6, 2026

• Py3.14: fsspec[s3] can resolve ancient s3fs 0.3.5; suggest s3fs>=2024.1 floor

  scverse/spatialdata#1293 · Filter by author cursor opened on Oct 28, 2026
  1

• Affine transformations are written to disk different from how they are stored in memory

  Enhancement

  scverse/spatialdata#1284 · Filter by author MeyerBender opened on Oct 23, 2026
  5

• bounding_box_query slows down with string cell IDs in newest spatialdata release

  Bug

  scverse/spatialdata#1279 · Filter by author sophiamaedler opened on Oct 19, 2026

• Integration Testing CI Install Failure on python 3.12

  scverse/spatialdata#1276 · Filter by author scverse-issue-creator opened on Oct 16, 2026

• bounding_box_query(filter_table=True) restores dropped categories but not their colors in uns

  scverse/spatialdata#1271 · Filter by author Marius1311 opened on Oct 9, 2026

• SpatialData 0.8.0 permits Zarr versions that do not provide ArrayNotFoundError

  scverse/spatialdata#1256 · Filter by author Darlokt opened on Sep 22, 2026

• Document that spatial queries on MultiPolygon keep also the components outside the queried region

  docs 📜element: shapes ▲method: querypriority: low
  scverse/spatialdata#1255 · Filter by author LucaMarconato opened on Sep 21, 2026

• aggregate(values, by=<labels with no non-background instance>) raises a misleading 'regions do not match' error

  bug 🚨element: labels 🏷️method: aggregation 🔢needs: triagepriority: low
  scverse/spatialdata#1250 · Filter by author LucaMarconato opened on Sep 13, 2026

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

  bug 🚨element: labels 🏷️method: aggregation 🔢needs: triagepriority: medium
  scverse/spatialdata#1249 · Filter by author LucaMarconato opened on Sep 13, 2026

• bounding_box_query(filter_table=True) crashes if the SpatialData object contains an orphan table

  bug 🚨element: table 📑method: queryneeds: triagepriority: medium
  scverse/spatialdata#1248 · Filter by author LucaMarconato opened on Sep 13, 2026

• Collection of minor issues found by an automated bug hunt (validation edge cases, misleading errors, small inefficiencies)

  bug 🚨needs: triage
  scverse/spatialdata#1244 · Filter by author LucaMarconato opened on Sep 11, 2026

• repr(sdata) reports the parquet row count for any points element that shares backing files, even after lazy filtering

  APIbug 🚨element: points ⊙needs: triage
  scverse/spatialdata#1243 · Filter by author LucaMarconato opened on Sep 11, 2026

• Joins on an element with duplicated index values duplicate rows (inner/right) instead of erroring

  bug 🚨element: shapes ▲method: queryneeds: triage
  scverse/spatialdata#1242 · Filter by author LucaMarconato opened on Sep 11, 2026

• concatenate(): orphan tables crash the dict form; a generator input gives a misleading error

  bug 🚨method: concatenateneeds: triage
  scverse/spatialdata#1241 · Filter by author LucaMarconato opened on Sep 11, 2026

• validate_table_in_spatialdata: the instance-key dtype-mismatch TypeError can never fire (dtype is str)

  bug 🚨element: table 📑needs: triage
  scverse/spatialdata#1240 · Filter by author LucaMarconato opened on Sep 11, 2026

• unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster

  bug 🚨element: images 🌌element: labels 🏷️needs: triage
  scverse/spatialdata#1239 · Filter by author LucaMarconato opened on Sep 11, 2026

• Multi-box bounding_box_query works on elements but crashes on a SpatialData object (TypeError: Unsupported type list)

  bug 🚨method: queryneeds: triage
  scverse/spatialdata#1238 · Filter by author LucaMarconato opened on Sep 11, 2026

• write_element(name, overwrite=True) can never overwrite an existing element, even purely in-memory tables/shapes

  APIenhancement ✨I/O 💿needs: triage
  scverse/spatialdata#1237 · Filter by author LucaMarconato opened on Sep 11, 2026

• rasterize(labels, value_key=...) crashes for categorical table columns and for labels absent from the table

  bug 🚨element: labels 🏷️method: rasterizationneeds: triagepriority: medium
  scverse/spatialdata#1236 · Filter by author LucaMarconato opened on Sep 11, 2026

• to_polygons(labels) turns a label containing a hole into an invalid MultiPolygon with the hole counted as area

  bug 🚨element: labels 🏷️method: vectorize ◃needs: triagepriority: medium
  scverse/spatialdata#1235 · Filter by author LucaMarconato opened on Sep 11, 2026
  2

• spatialdata.models.force_2d() silently drops interior rings (holes) of polygons

  bug 🚨element: shapes ▲modelsneeds: triagepriority: medium
  scverse/spatialdata#1234 · Filter by author LucaMarconato opened on Sep 11, 2026

• get_extent(circles, exact=True) (the default) is wrong for anisotropic/shearing transformations, while exact=False is right

  bug 🚨element: shapes ▲method: transforms 🔃needs: triagepriority: medium
  scverse/spatialdata#1233 · Filter by author LucaMarconato opened on Sep 11, 2026