Issues

• Visium HD: empty dataset_id default produces an unnamed coordinate system that napari-spatialdata can't select

  bug
  scverse/spatialdata-io#422 · Filter by author alihamraoui opened on Sep 16, 2026

• AI-generated: macsima() uses the OME plane positions as pixel padding widths, truncated

  scverse/spatialdata-io#419 · Filter by author LucaMarconato opened on Sep 9, 2026
  1

• MCMICRO reader does not support new nf-core/mcmicro output formats

  scverse/spatialdata-io#409 · Filter by author adamjtaylor opened on Jul 22, 2026

• Visium in matrix market format

  scverse/spatialdata-io#408 · Filter by author LinearParadox opened on Jul 15, 2026

• Feature request: lazy parsing of the pyramidal OME-TIFF morphology focus in Xenium

  xenium
  scverse/spatialdata-io#407 · Filter by author LucaMarconato opened on Jul 12, 2026

• CosMx Reader Incorrectly Assumes Image Dimension Order

  scverse/spatialdata-io#403 · Filter by author SFD5311 opened on Jun 4, 2026
  2

• Xenium Fails to read third party segmentation

  bugxenium
  scverse/spatialdata-io#402 · Filter by author annasaax-rgb opened on May 29, 2026
  1

• Xenium transcript dask DataFrame has non-unique index; transcript_id is the natural unique key

  xenium
  scverse/spatialdata-io#397 · Filter by author LucaMarconato opened on May 15, 2026

• Handling of case-variant column names in CosMx data

  scverse/spatialdata-io#393 · Filter by author SFD5311 opened on Apr 28, 2026
  1

• filtered_counts_file parameter for cell-segmented matrices

  visium-hd
  scverse/spatialdata-io#390 · Filter by author dennisdharmawan opened on Apr 8, 2026

• Add Xenium Explorer GeoJSON import

  scverse/spatialdata-io#385 · Filter by author wlason opened on Mar 12, 2026
  1

• BMKS300

  scverse/spatialdata-io#384 · Filter by author ogandril opened on Mar 10, 2026
  2

• spatialdata.write fails on Xenium sdata in env with pandas 3.0.0

  xenium
  scverse/spatialdata-io#364 · Filter by author EmielGeeraerts opened on Feb 3, 2026
  4

• Error reading Xenium data: morphology file missing

  xenium
  scverse/spatialdata-io#362 · Filter by author enric-bazz opened on Feb 1, 2026
  2

• Error with spatialdata_io.xenium() reader

  xenium
  scverse/spatialdata-io#361 · Filter by author enric-bazz opened on Jan 30, 2026
  2

• visium_hd reader: load_segmentations_only = False still loads segmentation results

  scverse/spatialdata-io#359 · Filter by author julienmortier opened on Jan 22, 2026
  4

• Anndata compatible version with spatialdata-io 5.1/5.0

  scverse/spatialdata-io#346 · Filter by author AtlasMaroc opened on Nov 18, 2025
  1

• Improve the contribution guide by adding some examples

  scverse/spatialdata-io#340 · Filter by author LucaMarconato opened on Nov 1, 2025

• PyArrow OSError: Unexpected end of stream

  scverse/spatialdata-io#334 · Filter by author LucaMarconato opened on Oct 27, 2025
  4

• proposal for friendly spatialdata_io.stereoseq function

  scverse/spatialdata-io#355 · Filter by author l-zh007 opened on Sep 17, 2025
  1

• Xenium read error

  scverse/spatialdata-io#325 · Filter by author SirKuikka opened on Sep 17, 2025
  9

• How to read BGI's STOmics spatial transcriptomics data?

  scverse/spatialdata-io#322 · Filter by author timtreis opened on Sep 7, 2025

• Recommended approach for reading multiple Xenium slides with mutual panel at once

  scverse/spatialdata-io#319 · Filter by author matt-sd-watson opened on Sep 2, 2025
  1

• ENHANCEMENT: to_legacy_anndata support with region > 1

  scverse/spatialdata-io#318 · Filter by author gboscagli opened on Sep 1, 2025
  12

• Cosmx reader: CellOverlay is skipped

  scverse/spatialdata-io#313 · Filter by author StevenWijnen opened on Aug 11, 2025
  1