Issues

• Docker location should no longer be hardcoded on Mac

  bugneeds verification
  CellProfiler/CellProfiler-plugins#318 · Filter by author apurvag28 opened on Sep 22, 2026
  1

• ExportToAnnData

  CellProfiler/CellProfiler-plugins#315 · Filter by author koalive opened on Sep 4, 2026
  5

• Error with runilastic plugin on CellProfiler

  CellProfiler/CellProfiler-plugins#309 · Filter by author DrAwesome32 opened on May 22, 2026
  5

• torch/cuda hard-coded bug in RunCellpose.py (running Cellpose 4 with Cellprofiler 4.2.8 on M1max)

  CellProfiler/CellProfiler-plugins#300 · Filter by author davewabbo opened on Mar 19, 2026

• CellProfiler plugins (RunCellpose and Runilastik) working only in test mode and not in analysis mode using Docker Desktop in Windows computer

  CellProfiler/CellProfiler-plugins#298 · Filter by author ShataDg opened on Jan 15, 2026
  2

• RunCellpose crashes when 'show probability image' is on

  CellProfiler/CellProfiler-plugins#295 · Filter by author kate-bowers-broad opened on Oct 14, 2025

• RunCellpose crashes when using Podman with GPU in Mac

  CellProfiler/CellProfiler-plugins#293 · Filter by author emiglietta opened on Sep 24, 2025
  5

• Add URL custom model download to RunCellpose

  enhancement
  CellProfiler/CellProfiler-plugins#280 · Filter by author ErinWeisbart opened on Jul 31, 2025

• CallBarcodes - add warning if Barcodes.csv is sparse matrix

  enhancement
  CellProfiler/CellProfiler-plugins#268 · Filter by author ErinWeisbart opened on Jan 10, 2025
  

• Runilastik doesn't work with multichannel input images

  CellProfiler/CellProfiler-plugins#260 · Filter by author bethac07 opened on Sep 10, 2024

• Unit test failed

  CellProfiler/CellProfiler-plugins#253 · Filter by author binliunls opened on Aug 8, 2024

• RunCellpose_Issues with GPU memory share setting

  CellProfiler/CellProfiler-plugins#236 · Filter by author sugan89 opened on Mar 1, 2024
  4

• RunCellpose error on Mac related to CUDA

  CellProfiler/CellProfiler-plugins#233 · Filter by author olasabet opened on Feb 14, 2024

• RunCellpose and CUDA out of memory

  CellProfiler/CellProfiler-plugins#230 · Filter by author obruck opened on Jan 18, 2024

• Crop representative cells plugin

  feature request
  CellProfiler/CellProfiler-plugins#209 · Filter by author fefossa opened on Jun 26, 2023

• RunDeepProfiler doesn't run in analysis mode on Windows, only on mac

  CellProfiler/CellProfiler-plugins#208 · Filter by author fefossa opened on Jun 26, 2023
  3

• stardist plugin does not free gpu memory

  CellProfiler/CellProfiler-plugins#196 · Filter by author sunyi000 opened on May 31, 2023

• Create test pipelines

  CellProfiler/CellProfiler-plugins#188 · Filter by author ErinWeisbart opened on May 5, 2023

• Example pipeline for compensatecolors

  CellProfiler/CellProfiler-plugins#179 · Filter by author gwaybio opened on Feb 15, 2023
  8

  

• Implementing a DeepProfiler Plugin

  enhancement
  CellProfiler/CellProfiler-plugins#171 · Filter by author jenna-tomkinson opened on Nov 28, 2022
  5

• Module names must match file/class names for plugins to work from compiled binary

  CellProfiler/CellProfiler-plugins#165 · Filter by author hinerm opened on Oct 7, 2022

• Error in sys.excepthook while running cellprofiler in headless mode with CellPose as a plugin

  CellProfiler/CellProfiler-plugins#160 · Filter by author bethac07 opened on Sep 1, 2022
  2

• TypeError in RunCellpose in GPU mode

  CellProfiler/CellProfiler-plugins#154 · Filter by author braymp opened on Apr 15, 2022
  5

• CP3->CP4: Change in use of add_module_for_tst

  CellProfiler/CellProfiler-plugins#108 · Filter by author votti opened on Oct 2, 2020

• CompensateColors should sort channel names to make sure cycles stay in order

  CellProfiler/CellProfiler-plugins#102 · Filter by author bethac07 opened on Jul 1, 2020