All pull requests

Pull requests

• fix: tile-invariant featurization (positions, truncation, multiscale, granularity) + lower output memory

  #1295·timtreis opened Sep 21, 2026·

  ·
  1

• chore(deps): bump the actions-deps group across 1 directory with 8 updates

  dependenciesgithub_actions
  #1294·dependabot[bot] opened Sep 21, 2026·

  ·
  1

• fix: preserve SpatialData input when copying spatial neighbors

  #1292·Georicl opened Sep 14, 2026·

  ·
  1

  1

• feat: add sort_order to spatial_scatter

  #1291·Georicl opened Sep 14, 2026·

  ·
  1

  1

• docs: correct img_res_key references in spatial plotting

  #1290·Georicl opened Sep 13, 2026·

  ·
  1

  1

• refactor: restructure the api docs (4/4)

  #1287·selmanozleyen opened Sep 3, 2026·4/4·

  ·

• chore: replace two enums with literals (3/4)

  #1286·selmanozleyen opened Sep 3, 2026·3/4·

  ·
  1

• Incorporating feedback on niche refactor

  #1284·shashkat opened Sep 1, 2026·

  ·
  1

  20

• [pre-commit.ci] pre-commit autoupdate

  #1283·pre-commit-ci[bot] opened Aug 31, 2026·

  ·
  1

• refactor: add StainReference transform methods (2/4)

  #1280·selmanozleyen opened Aug 28, 2026·2/4·

  ·
  1

• refactor: convert experimental parameters to TypedDicts (1/4)

  #1279·selmanozleyen opened Aug 28, 2026·1/4·

  ·
  5

• feat: automatic K selection (CellCharter's ClusterAutoK)

  #1276·selmanozleyen opened Aug 22, 2026·

  ·
  1

  9

• Emergent-seam cut-cell detection for calculate_tiling_qc (dense tissue / wide gaps / single-sided cuts)

  #1255·timtreis opened Aug 6, 2026·

  ·
  1

• Multi-slide pooled fit_stain_reference

  #1209·timtreis opened Jun 14, 2026·

  ·
  9

  

• feat: stalign api and landmark alignment

  release-added
  #1195·selmanozleyen opened Jun 1, 2026·

  ·
  19

  

• Add spatialdata-plot delegation backend (gated by feature flag)

  #1173·timtreis opened May 12, 2026·

  ·
  1

  

• Draft: add contour-based ring density and smooth signed-distance density for SpatialData

  #1163·hutaobo opened Apr 16, 2026·

  ·
  1

  4

• Feat/gene imputation

  #1161·MDLDan opened Apr 16, 2026·

  ·
  2

• Add pluggable backend dispatch system

  #1151·Intron7 opened Apr 7, 2026·

  ·
  16

• Improved sliding windows

  #1116·schrf opened Feb 10, 2026·

  ·
  1

  12

  

• Add new spatial graph features and tests (closes #901)

  #1091·luckyy14 opened Jan 3, 2026·

  ·
  1

• Add Pytest Benchmarks Feature

  pytest-benchmark
  #1070·selmanozleyen opened Dec 1, 2025·

  ·
  1

• Use the correct image for scatter plots with alternate spatial bases

  #1032·obriencshl opened Sep 8, 2025·

  ·
  5

• Adding Benchmarks

  benchmarkenhancement ✨
  #1016·selmanozleyen opened Jul 10, 2025·

  ·
  5

  

• sq.pp.filter_cells for SpatialData

  #1011·selmanozleyen opened Jun 18, 2025·

  ·
  1

  1