Issues

• [Bug] Fix voronoi_frames for shapely 2.2 and remove the shapely<2.2 pin

  bug
  Bug

  prism-oncology/sopa#452 · Filter by author alihamraoui opened on Oct 8, 2026
  1

• [Bug]

  prism-oncology/sopa#439 · Filter by author jonasmac16 opened on Jul 29, 2026
  3

• nf-core/sopa maintenance

  Task

  prism-oncology/sopa#436 · Filter by author quentinblampey opened on Jul 15, 2026
  

• Stiching of Patches

  prism-oncology/sopa#434 · Filter by author YashdeepMul opened on Jul 12, 2026
  1

• Support segger as a segmentation method

  Feature

  prism-oncology/sopa#431 · Filter by author EliHei2 opened on Jun 24, 2026
  15

  

• [Bug] Issue when saving as Xenium

  prism-oncology/sopa#420 · Filter by author lguerard opened on May 13, 2026
  4

• Custom Segmentation Error

  prism-oncology/sopa#407 · Filter by author hallumg opened on Apr 2, 2026
  1

• [Bug] sopa.segmentation.cellpose falls back to CPU despite gpu=True and valid torch.cuda context

  Bug

  prism-oncology/sopa#382 · Filter by author rushilp7 opened on Feb 1, 2026
  5

• [Bug] Xenium explorer conversion for large PhenoCycler image

  Bug

  prism-oncology/sopa#378 · Filter by author rayanelkholdi opened on Jan 13, 2026
  6

• segmentation combine between two spatialdata objects

  prism-oncology/sopa#369 · Filter by author PietroD opened on Dec 16, 2025
  1

• [Feature] Add numpy array mask from external tool to sopa's spatialdata

  prism-oncology/sopa#361 · Filter by author PietroD opened on Dec 2, 2025
  1

• Issue CosMx reader and polygons

  prism-oncology/sopa#357 · Filter by author ccruizm opened on Nov 21, 2025
  1

• [Feature] Singular g4x support

  prism-oncology/sopa#339 · Filter by author derrik-gratz opened on Oct 20, 2025
  1

• Can sopa take as input COMET data ?

  prism-oncology/sopa#331 · Filter by author reJELIN opened on Oct 6, 2025
  3

• [Bug] Local run looking for conda activate (I use uv)

  prism-oncology/sopa#317 · Filter by author josenimo opened on Sep 15, 2025
  2

• Using xenium_aligned_image for multi-channel (20 channel) IF images

  prism-oncology/sopa#300 · Filter by author quentinblampey opened on Aug 27, 2025

• Cell ID mismatch when using proseg

  prism-oncology/sopa#299 · Filter by author ccruizm opened on Aug 27, 2025
  10

• [Bug]ComSeg segmentation infinite loop

  prism-oncology/sopa#292 · Filter by author jonas2612 opened on Aug 14, 2025
  18

• [Bug] Issue with dask segmentation on Windows

  prism-oncology/sopa#256 · Filter by author lguerard opened on May 13, 2025
  11

• [Bug] Issue with transcripts.csv when doing patches

  prism-oncology/sopa#224 · Filter by author lguerard opened on Mar 13, 2025
  6

• Reading a slide image while retaining channel data?

  prism-oncology/sopa#213 · Filter by author austinv11 opened on Feb 17, 2025
  8

• Obtaining transcript confidence and assignment_confidence from baysor segmentation

  prism-oncology/sopa#149 · Filter by author pngai1 opened on Nov 4, 2024
  4

• [Bug] Isse with running Baysor segmentation on some but not all patches

  prism-oncology/sopa#123 · Filter by author marsdenl opened on Sep 12, 2024
  27

• [Bug]"Could not find element with name ['cell_circles']"

  prism-oncology/sopa#117 · Filter by author Yifan-debug opened on Sep 2, 2024
  7

• [Feature] General reader for non-commercial datasets

  prism-oncology/sopa#116 · Filter by author lopollar opened on Sep 2, 2024
  3