Issues

• 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

• 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

• bounding_box_query on circles ignores the radius (only the centre is tested), polygon_query does not

  bug 🚨element: shapes ▲method: queryneeds: triagepriority: medium
  scverse/spatialdata#1232 · Filter by author LucaMarconato opened on Sep 11, 2026

• A failing aggregate() leaves the internal __ones_column / __areas_column on the user's shapes element

  bug 🚨element: shapes ▲method: aggregation 🔢needs: triage
  scverse/spatialdata#1231 · Filter by author LucaMarconato opened on Sep 11, 2026

• aggregate(image, by=labels) crashes when the labels have no background (no zero pixels)

  bug 🚨element: labels 🏷️method: aggregation 🔢needs: triagepriority: medium
  scverse/spatialdata#1230 · Filter by author LucaMarconato opened on Sep 11, 2026

• TableModel rejects int8/uint8 instance-key columns although the error message promises 'uint equivalents' (breaks aggregate/to_circles on uint8 labels)

  bug 🚨element: labels 🏷️element: table 📑modelsneeds: triagepriority: medium
  scverse/spatialdata#1229 · Filter by author LucaMarconato opened on Sep 11, 2026

• Substring matching of element names against a single-region table (element_name in regions with regions: str)

  bug 🚨element: table 📑method: queryneeds: triagepriority: medium
  scverse/spatialdata#1228 · Filter by author LucaMarconato opened on Sep 11, 2026

• match_sdata_to_table / filter_by_table_query crash for how='left_exclusive' and how='right_exclusive'

  bug 🚨element: table 📑method: queryneeds: triagepriority: medium
  scverse/spatialdata#1227 · Filter by author LucaMarconato opened on Sep 11, 2026

• Joins crash (IndexError / KeyError: None) when the element and the table share no instance

  bug 🚨element: table 📑method: queryneeds: triagepriority: medium
  scverse/spatialdata#1226 · Filter by author LucaMarconato opened on Sep 11, 2026

• inner join on a Labels element returns table=None even with filter_label_pixels=True

  bug 🚨element: labels 🏷️element: table 📑method: queryneeds: triagepriority: medium
  scverse/spatialdata#1225 · Filter by author LucaMarconato opened on Sep 11, 2026