Issues

• [BUG] make_train.py - Tiff label support and mask saving bug

  bug
  MouseLand/cellpose#1495 · Filter by author s-udisha opened on Sep 14, 2026

• test_loss scale/behavior changed between v4.0.8 and latest (v4.2.1.1) when fine-tuning cpsam

  bug
  MouseLand/cellpose#1493 · Filter by author reinavi74 opened on Sep 11, 2026

• [FEATURE] Region Specific Segmentation GUI

  enhancement
  MouseLand/cellpose#1492 · Filter by author RichardSantos256 opened on Sep 10, 2026

• LLSM generated 3D images: Compatibility with cpsam_v2 training data requirement

  bug
  MouseLand/cellpose#1491 · Filter by author s-udisha opened on Sep 9, 2026

• [BUG] Distributed_eval segmentation issue

  bug
  MouseLand/cellpose#1489 · Filter by author methornton opened on Aug 20, 2026

• [BUG] Flow generation is perturbed by neighboring cells

  bug
  MouseLand/cellpose#1486 · Filter by author remi-pigache opened on Aug 4, 2026

• [BUG] cellpose 3.1.1.1 declares numpy<2.1 but runs on numpy 2.3.5 under Python 3.13 — please relax the pin

  bug
  MouseLand/cellpose#1484 · Filter by author Gable404 opened on Jul 23, 2026

• [BUG] Stiching fails silently when running distributed cellpose on 2D images

  bug
  MouseLand/cellpose#1482 · Filter by author sbamopoulos opened on Jun 27, 2026

• [BUG]New models cpdino and cpdino-vitb don't work with 4.2.1.1

  bug
  MouseLand/cellpose#1476 · Filter by author JensWendt opened on Jun 17, 2026
  3

• [BUG] cpdino models do not run

  bug
  MouseLand/cellpose#1474 · Filter by author jimmib78 opened on Jun 16, 2026
  1

• Problem with GPU (MPS)

  install
  MouseLand/cellpose#1468 · Filter by author paularandamar opened on Jun 10, 2026
  3

• [BUG] Occasional glitchy mask during dynamics

  bug
  MouseLand/cellpose#1459 · Filter by author mmuunniiaakk opened on May 22, 2026
  3

• [BUG] Filter button not correctly filtering image

  bug
  MouseLand/cellpose#1452 · Filter by author mrariden opened on May 13, 2026

• [FEATURE] Remote server support for Cellpose GUI inference, training, and annotation

  enhancementlow priority
  MouseLand/cellpose#1424 · Filter by author bobqianic opened on Mar 31, 2026
  2

• [FEATURE] Speed-up for multiple ROI deletion

  enhancement
  MouseLand/cellpose#1419 · Filter by author chenyenchung opened on Mar 24, 2026
  1

  

• [FEATURE] Add CLAHE as an Optional Preprocessing Step

  enhancement
  MouseLand/cellpose#1376 · Filter by author xuefei-wang opened on Nov 27, 2025
  1

  

• Zarr 3 support for distributed

  distributedenhancement
  MouseLand/cellpose#1375 · Filter by author felixS27 opened on Nov 27, 2025
  1

• [INSTALL] issues with numpy > 2.0

  install
  MouseLand/cellpose#1350 · Filter by author totoro7034 opened on Oct 19, 2025
  5

• [FEATURE] Does distributed_segmentation supports 2D-multi channel image?

  distributedenhancement
  MouseLand/cellpose#1348 · Filter by author YueXia-natsu opened on Oct 16, 2025
  2

• Mask outlines appear fragmented on XZ and YZ projections

  enhancementGUI
  MouseLand/cellpose#1333 · Filter by author tomermilo opened on Sep 29, 2025
  1

• [BUG] Gaps in interphase and mitotic 3D nuclei when gradXY flows and cell probability look fine

  bug
  MouseLand/cellpose#1296 · Filter by author derekthirstrup opened on Aug 5, 2025
  4

• process_block, mismatched shape in zarr

  bugdistributedenhancement
  MouseLand/cellpose#1292 · Filter by author Elena983 opened on Aug 4, 2025

• [BUG] cellpose causing numerical issues in unrelated code in same process.

  bug
  MouseLand/cellpose#1253 · Filter by author klondenberg-bioptimus opened on Jun 24, 2025
  4

  

• Add Native 3-D Volume Training Mode and 3-D + T mask stitching to Cellpose-SAM

  enhancement
  MouseLand/cellpose#1219 · Filter by author derekthirstrup opened on Jun 2, 2025

• [FEATURE] Support for AMD gpu's (and others) on windows

  enhancement
  MouseLand/cellpose#1169 · Filter by author Teranis opened on May 13, 2025
  6