Issues

• Improve dev workflows around benchmarks

  scverse/spatialdata#1036 · Filter by author LucaMarconato opened on Jan 2, 2026
  1

• Transform dimensions are changed when writing to zarr store

  needs: triagepriority: medium
  scverse/spatialdata#1029 · Filter by author MSHelm opened on Dec 11, 2025
  2

• Scale transform changes aggregate results

  needs: triagepriority: low
  scverse/spatialdata#1028 · Filter by author MSHelm opened on Dec 11, 2025
  2

• Improve compatibility of cell segmentation output formats with downstream analysis tools

  scverse/spatialdata#1026 · Filter by author asmlgkj opened on Nov 24, 2025
  1

• Merging multiple samples into a single SpatialData object + single merged table

  scverse/spatialdata#1025 · Filter by author Rafael-Silva-Oliveira opened on Nov 21, 2025
  1

• Writing multiscale element to disk fails when configuring Dask to uses "processes"

  scverse/spatialdata#1024 · Filter by author ArneDefauw opened on Nov 20, 2025
  6

• Writing results of polygon query as Zarr

  needs: triagepriority: low
  scverse/spatialdata#1023 · Filter by author SFD5311 opened on Nov 19, 2025
  5

• Image models fail with the latest multiscale-spatial-image release

  scverse/spatialdata#1020 · Filter by author LucaMarconato opened on Nov 15, 2025

• Don't use empty asserts

  scverse/spatialdata#1019 · Filter by author timtreis opened on Nov 15, 2025

• Use scverse template

  maint 🏗️
  Task

  scverse/spatialdata#1018 · Filter by author Zethson opened on Nov 14, 2025
  

• polygon_query returns only rectangles

  needs: triagepriority: medium
  scverse/spatialdata#1017 · Filter by author MathysHub opened on Nov 10, 2025
  1

• pip install "spatialdata[extra]" not working with Python 3.11

  scverse/spatialdata#1016 · Filter by author LucaMarconato opened on Nov 7, 2025
  1

• Can not import the package using jupyter notebook in Visual Studio Code

  scverse/spatialdata#1014 · Filter by author amina2500 opened on Nov 5, 2025
  1

• Reading and writing issues on Mac with external disk

  needs: triagepriority: low
  scverse/spatialdata#1013 · Filter by author LouisK92 opened on Nov 4, 2025
  1

• ShapesModel.parse(), for .geojson files, ignores non-geometry colums.

  needs: triagepriority: low
  scverse/spatialdata#1008 · Filter by author LucaMarconato opened on Oct 27, 2025
  1

• Concatenate from dictionary

  scverse/spatialdata#998 · Filter by author revalescente opened on Oct 15, 2025
  1

• Renaming of feature_key column of points

  needs: triagepriority: medium
  scverse/spatialdata#996 · Filter by author LouisK92 opened on Oct 10, 2025
  1

• [Suggestion] Allow strings for method when constructing multiscale Image2DModel

  scverse/spatialdata#995 · Filter by author conradfoo opened on Oct 9, 2025
  1

• Using functools.partial in an unsupported way that’ll break in a future Python version

  scverse/spatialdata#993 · Filter by author flying-sheep opened on Oct 6, 2025
  1

• query.bounding_box not cropping the table

  scverse/spatialdata#992 · Filter by author PerrineGilloteaux opened on Oct 1, 2025
  1

• Non linear alignment - warpy

  scverse/spatialdata#991 · Filter by author revalescente opened on Oct 1, 2025
  2

• Add installation tests for direct dependents (BioC-style)

  scverse/spatialdata#990 · Filter by author LucaMarconato opened on Sep 30, 2025

• exceeding rasterize's maximum label index

  needs: triagepriority: medium
  scverse/spatialdata#987 · Filter by author LouisK92 opened on Sep 22, 2025
  3

• Move ngff transformations to separate repo?

  scverse/spatialdata#976 · Filter by author jo-mueller opened on Aug 25, 2025
  2

• Some suggestions and proposals for annotations in SpatialData

  scverse/spatialdata#975 · Filter by author selmanozleyen opened on Aug 24, 2025
  2