Issues

• Integration Testing CI Test Failure on python 3.12

  scverse/squidpy#1312 · Filter by author scverse-issue-creator opened on Oct 12, 2026

• Integration Testing CI Test Failure on python 3.14

  scverse/squidpy#1311 · Filter by author scverse-issue-creator opened on Oct 12, 2026

• Request: Tutorial for ImageContainer -> SpatialData conversion

  scverse/squidpy#1305 · Filter by author timtreis opened on Sep 29, 2026
  

• Integration Testing CI Test Failure on python 3.14 with prerelease dependencies

  scverse/squidpy#1301 · Filter by author scverse-issue-creator opened on Sep 26, 2026

• Bugs and problems in calculate_niche and in unreleased main.

  scverse/squidpy#1293 · Filter by author selmanozleyen opened on Sep 15, 2026

• In place shuffle dedup

  scverse/squidpy#1289 · Filter by author selmanozleyen opened on Sep 10, 2026
  1

  

• Extensibility API for niche calling

  scverse/squidpy#1285 · Filter by author grst opened on Sep 2, 2026
  10

• using TypedDict instead of frozen dataclasses for the kwargs

  scverse/squidpy#1275 · Filter by author selmanozleyen opened on Aug 21, 2026
  

• spatial_autocorr crashes when the graph contains singletons

  scverse/squidpy#1256 · Filter by author durr1602 opened on Aug 10, 2026
  

• Add automatic K selection (CellCharter's ClusterAutoK) for the cellcharter niche flavor

  scverse/squidpy#1244 · Filter by author selmanozleyen opened on Jul 19, 2026
  1

  

• Radial kernel + cutoff for neighborhood graph

  scverse/squidpy#1241 · Filter by author durr1602 opened on Jul 7, 2026

• Tutorial request: Stereo-seq (BGI STOmics) analysis — bin vs cellbin

  scverse/squidpy#1228 · Filter by author asmlgkj opened on Jun 24, 2026

• Add persistence diagrams for persistent homology analysis

  scverse/squidpy#1225 · Filter by author a12dongithub opened on Jun 22, 2026

• pl.ligrec does not match pvaule table output

  scverse/squidpy#1201 · Filter by author LukasNbio opened on Jun 4, 2026
  1

• speed up _resolve_data in spatial neighbors when working with spatialdata

  scverse/squidpy#1199 · Filter by author grst opened on Jun 3, 2026
  10

• Public api change: rename adata to data and make it positional only

  scverse/squidpy#1180 · Filter by author selmanozleyen opened on May 15, 2026

• spatial_neighbour_x should have serializable internals to avoid uns formats

  scverse/squidpy#1174 · Filter by author selmanozleyen opened on May 12, 2026

• Why does co_occurence not use a pre-calculated spatial graph

  scverse/squidpy#1165 · Filter by author grst opened on Apr 23, 2026

• Feature request: contour-based inward/outward ring density for cells and transcripts around polygon annotations

  scverse/squidpy#1160 · Filter by author hutaobo opened on Apr 16, 2026
  1

• n-hop neighbors in spatial graph

  scverse/squidpy#1159 · Filter by author grst opened on Apr 14, 2026
  5

• rectangle as shape

  scverse/squidpy#1155 · Filter by author MathildaStigenberg opened on Apr 10, 2026
  1

• Bring minimal stalign function

  squidpy2.0
  scverse/squidpy#1146 · Filter by author selmanozleyen opened on Apr 2, 2026
  1

  

• We shouldn't use assert_adata_equal

  scverse/squidpy#1143 · Filter by author selmanozleyen opened on Mar 16, 2026
  1

• Control verbosity, like Scanpy

  scverse/squidpy#1141 · Filter by author alam-shahul opened on Mar 12, 2026
  2

• replace manual variable checks with wrapper functions across codebase

  scverse/squidpy#1137 · Filter by author timtreis opened on Mar 3, 2026