Owner

MouseLand

5 indexed repositories · View on GitHub

cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

Python · 2369 stars
Kilosort
Fast spike sorting with drift correction

Python · 627 stars
suite2p
cell detection in calcium imaging recordings

Python · 473 stars
stringer-pachitariu-et-al-2018b
Responses of 10,000 neurons to 2,800 natural images

MATLAB · 74 stars
stringer-pachitariu-et-al-2018a
Recordings of 10k neurons during spontaneous behaviors

MATLAB · 55 stars

Beginner friendly Everything

Open All

Unable to open RunSuite2p GUI Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

MouseLand/suite2p#1273 · Opened Sep 17, 2026
[BUG] make_train.py - Tiff label support and mask saving bug Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 68/100

MouseLand/cellpose#1495 · Opened Sep 14, 2026
`test_loss` scale/behavior changed between v4.0.8 and latest (v4.2.1.1) when fine-tuning cpsam Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

MouseLand/cellpose#1493 · Opened Sep 11, 2026
[FEATURE] Region Specific Segmentation GUI Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 38/100

MouseLand/cellpose#1492 · Opened Sep 10, 2026
LLSM generated 3D images: Compatibility with cpsam_v2 training data requirement Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

MouseLand/cellpose#1491 · Opened Sep 9, 2026
anatomical.select_rois applies the spatial high-pass twice (duplicated line since v1.0.0.1) Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

MouseLand/suite2p#1270 · Opened Sep 2, 2026
baseline='constant' subtracts the minimum over all neurons rather than a per-trace constant Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

MouseLand/suite2p#1269 · Opened Sep 2, 2026
BUG: bidiphase correction corrupts odd scan lines since the torch registration path (v1.0.0.1) Open

Difficulty 2/5 1-3 hours Newbie friendliness 83/100

MouseLand/suite2p#1265 · Opened Sep 2, 2026
DOC: Kilosort 2.5/3 rezToPhy writes a scaled identity as whitening_mat.npy (KS2.0 wrote the real Wrot) Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

MouseLand/Kilosort#1047 · Opened Sep 1, 2026
BUG (KS2/2.5/3): get_whitening_matrix normalizes covariance by ceil((Nbatch-1)/nSkipCov) but accumulates floor(..)+1 batches Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

MouseLand/Kilosort#1046 · Opened Sep 1, 2026
BUG: clusters with <=10 spikes export ContamPct = 0.0, the best possible score Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

MouseLand/Kilosort#1044 · Opened Sep 1, 2026
BUG: Typo in swarmsplitter.check_CCG that disables the refractoriness gate Open

Difficulty 1/5 Under an hour Newbie friendliness 78/100

MouseLand/Kilosort#1042 · Opened Aug 21, 2026
[BUG] Distributed_eval segmentation issue Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

MouseLand/cellpose#1489 · Opened Aug 20, 2026
BUG: flipping ROIs removes lam weighting Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MouseLand/suite2p#1263 · Opened Aug 5, 2026
[BUG] Flow generation is perturbed by neighboring cells Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 74/100

MouseLand/cellpose#1486 · Opened Aug 4, 2026
BUG: Left settings panel gets clipped and controls become inaccessible unless window is fullscreen Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

MouseLand/Kilosort#1041 · Opened Jul 31, 2026
Feature request: Controls and Help buttons open external docs instead of showing help in the GUI Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

MouseLand/Kilosort#1040 · 1 comment · Opened Jul 31, 2026
BUG: make_pc_features can associate PC features with the wrong channel IDs when multiple final clusters share a detection template Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

MouseLand/Kilosort#1039 · 1 comment · Opened Jul 26, 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 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 62/100

MouseLand/cellpose#1484 · Opened Jul 23, 2026
[BUG] Stiching fails silently when running distributed cellpose on 2D images Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

MouseLand/cellpose#1482 · Opened Jun 27, 2026
BUG: Array must not contain infs or NaNs Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

MouseLand/suite2p#1252 · Opened Jun 20, 2026
[BUG]New models `cpdino` and `cpdino-vitb` don't work with 4.2.1.1 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

MouseLand/cellpose#1476 · 3 comments · 1 reaction · Opened Jun 17, 2026
[BUG] cpdino models do not run Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MouseLand/cellpose#1474 · 1 comment · Opened Jun 16, 2026
Unknown " input and output size" error with suite2p v0.99rc0 Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

MouseLand/suite2p#1251 · Opened Jun 13, 2026
Problem with GPU (MPS) Open

install

Difficulty 4/5 3-5 days Newbie friendliness 45/100

MouseLand/cellpose#1468 · 3 comments · Opened Jun 10, 2026
BUG: force_sktiff does not work in tiff.ome_to_binary Open

Difficulty 3/5 1-2 days Newbie friendliness 56/100

MouseLand/suite2p#1250 · Opened Jun 9, 2026
Registration in version 1.0 seems to perform worse Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MouseLand/suite2p#1246 · Opened Jun 5, 2026
[BUG] Occasional glitchy mask during dynamics Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

MouseLand/cellpose#1459 · 3 comments · Opened May 22, 2026
BUG: Crash during registration if Bidiphase = -1 Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

MouseLand/suite2p#1239 · 1 comment · Opened May 18, 2026
[BUG] Filter button not correctly filtering image Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

MouseLand/cellpose#1452 · Opened May 13, 2026
BUG: Input buffer size wasn't large enough. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

MouseLand/suite2p#1237 · 2 comments · Opened Apr 28, 2026
DOC: Request for additional, explicit information about tau parameter in the documentation Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

MouseLand/suite2p#1236 · Opened Apr 27, 2026
[FEATURE] Remote server support for Cellpose GUI inference, training, and annotation Open

enhancement low priority

Difficulty 5/5 Over a week Newbie friendliness 30/100

MouseLand/cellpose#1424 · 2 comments · Opened Mar 31, 2026
[FEATURE] Speed-up for multiple ROI deletion Open

enhancement

MouseLand/cellpose#1419 · 1 comment · 1 assignee · Opened Mar 24, 2026
Dendrites detection Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

MouseLand/suite2p#1215 · Opened Feb 24, 2026
Code design: function arguments like db=default_db() are only evaluated at function definition time, not each time the function is called Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

MouseLand/suite2p#1212 · Opened Feb 20, 2026
BUG: Nonrigid registration with a single block along one dimension fails. Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

MouseLand/suite2p#1211 · Opened Feb 19, 2026
BUG: Output overwrite when saving reg_tiff for 2 channels Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

MouseLand/suite2p#1208 · Opened Feb 19, 2026
Suite2p with Qaudro M2000 on Windows Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

MouseLand/suite2p#1207 · Opened Feb 18, 2026
[FEATURE] Add CLAHE as an Optional Preprocessing Step Open

enhancement

MouseLand/cellpose#1376 · 1 comment · 1 assignee · Opened Nov 27, 2025
Zarr 3 support for distributed Open

distributed enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

MouseLand/cellpose#1375 · 1 comment · 1 reaction · Opened Nov 27, 2025
[INSTALL] issues with numpy > 2.0 Open

install

Difficulty 4/5 3-5 days Newbie friendliness 42/100

MouseLand/cellpose#1350 · 5 comments · Opened Oct 19, 2025
[FEATURE] Does distributed_segmentation supports 2D-multi channel image? Open

distributed enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

MouseLand/cellpose#1348 · 2 comments · Opened Oct 16, 2025
Mask outlines appear fragmented on XZ and YZ projections Open

enhancement GUI

Difficulty 3/5 1-2 days Newbie friendliness 45/100

MouseLand/cellpose#1333 · 1 comment · Opened Sep 29, 2025
Suite2p GUI shows images “blown out” (too bright) for Thorlabs Bergamo TIFFs, even at minimum slider setting Open

GUI

MouseLand/suite2p#1192 · 1 comment · 1 assignee · Opened Aug 22, 2025
FEATURE: Implementation of KS2.5 Prediction and Residual plots Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

MouseLand/Kilosort#971 · 1 comment · Opened Aug 8, 2025
[BUG] Gaps in interphase and mitotic 3D nuclei when gradXY flows and cell probability look fine Open

bug

Difficulty 5/5 Over a week Newbie friendliness 35/100

MouseLand/cellpose#1296 · 4 comments · Opened Aug 5, 2025
process_block, mismatched shape in zarr Open

bug distributed enhancement

Difficulty 3/5 1-2 days Newbie friendliness 52/100

MouseLand/cellpose#1292 · Opened Aug 4, 2025
FEATURE: Saving variables to disk between major steps Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

MouseLand/Kilosort#960 · 1 comment · Opened Jul 9, 2025
[BUG] cellpose causing numerical issues in unrelated code in same process. Open

bug

MouseLand/cellpose#1253 · 4 comments · 3 reactions · 1 assignee · Opened Jun 24, 2025

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