Published May 6, 2026 | Version v0.7.0
Software Open

scverse/spatialdata-io: v0.7.0

Authors/Creators

  • 1. European Molecular Biology Laboratory
  • 2. Cure51 and Gustave Roussy Institute
  • 3. MPI of Biochemistry
  • 4. @lizard-bio
  • 5. @10XGenomics
  • 6. University Heidelberg @SchapiroLabor
  • 7. @nvidia @scverse @theislab
  • 8. Wellcome Sanger Institute
  • 9. Iber Lab - ETH Zürich
  • 10. Boehringer Ingelheim
  • 11. CRUK Scotland Institute-Beatson Building
  • 12. Institute for Computational Biomedicine

Description

<!-- Release notes generated using configuration in .github/release.yml at main -->

What's Changed

Added

  • Add spatialdata-io version and reader name to attrs by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/360
  • Allow overriding scale_factor in visium hd by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/394

Changed

  • Xenium: cache zip store opening; vectorize cell id encoding by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/370
  • Faster imports by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/373
  • Improve Xenium performance, fix multinucleate cells bug by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/376
  • Refactor xenium reader by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/386
  • feat: add support for non-gex data in visium hd by @stephenwilliams22 in https://github.com/scverse/spatialdata-io/pull/391
  • Use scanpy for reading matrixes by @cgeyskens in https://github.com/scverse/spatialdata-io/pull/292

Fixed

  • Faster xenium points parsing by precomputing categories by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/363
  • Faster xenium polygon parsing via ragged arrays by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/365
  • Xenium avoid calling get_element_instances(); fix deprecation warning by @LucaMarconato in https://github.com/scverse/spatialdata-io/pull/369
  • fix codex reader - table by @nilchia in https://github.com/scverse/spatialdata-io/pull/377
  • fix visium_hd reader by @Mira-Kreuzer in https://github.com/scverse/spatialdata-io/pull/389
  • Fixes #298: Repeatedly appending parent path to flatFiles by @mayank-singh-sikarwar in https://github.com/scverse/spatialdata-io/pull/305
  • adjusted docstrings in steinbock reader py file by @LukasHats in https://github.com/scverse/spatialdata-io/pull/165
  • Handle autofluorescence channels and pass through unknown image types by @MSHelm in https://github.com/scverse/spatialdata-io/pull/368
  • Align CLI arguments with reader APIs for full parameter consistency by @Copilot in https://github.com/scverse/spatialdata-io/pull/321

New Contributors

  • @nilchia made their first contribution in https://github.com/scverse/spatialdata-io/pull/377
  • @Mira-Kreuzer made their first contribution in https://github.com/scverse/spatialdata-io/pull/389
  • @mayank-singh-sikarwar made their first contribution in https://github.com/scverse/spatialdata-io/pull/305
  • @LukasHats made their first contribution in https://github.com/scverse/spatialdata-io/pull/165
  • @cgeyskens made their first contribution in https://github.com/scverse/spatialdata-io/pull/292
  • @Copilot made their first contribution in https://github.com/scverse/spatialdata-io/pull/321

Full Changelog: https://github.com/scverse/spatialdata-io/compare/v0.6.0...v0.7.0

Files

scverse/spatialdata-io-v0.7.0.zip

Files (155.0 kB)

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Additional details

Related works

Is supplement to
Software: https://github.com/scverse/spatialdata-io/tree/v0.7.0 (URL)

Software

Repository URL
https://github.com/scverse/spatialdata-io