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

2

I have found in my testing that the main branch Cellpose 4.0.6 has a bug where 3-D mask z slices can “disappear” in single or range of z-planes even when...

derekthirstrup

Update gui.py for

2

fix: GUI flow visualization indexing and gradZ contrast bugs - Fix IndexError when viewing flows with different array layouts (C,Z,Y,X) - Add robust Z-axis slicing for flow views with _pick_z_image()...

derekthirstrup

[BUG] 3D GUI: selecting gradZ view breaks Z navigation (IndexError in gui.py:update_plot, followed by pyqtgraph data.shape[2] error)

1

Environment Cellpose: 4.0.6 OS: Windows (win32) Python: 3.13.0 Torch: 2.7.1+cu128 (CUDA detected and used) Repro image: 3D TIFF, 17 Z planes, shape reported by GUI: (17, 58, 45, 3) What...

derekthirstrup

When running distributed_eval() from cellpose.contrib.distributed_segmentation on a 3D Zarr input (channels, H, W), I encountered a shape mismatch error during block processing. Specifically, output_zarr[tuple(crop)] = segmentation fails due to a...

Elena983

[FEATURE] trouble detecting the "brightest" cells in image

3

Hi, I'm using cellpose 3.1.1.2 to detect my cells but got some trouble. After training with my own 26 images and masks, it successfully improved precision, but couldn't detect the...

EdwardNeuro

fix: handle 403 Forbidden in download_url_to_file

1

#### What changed? 1. Extended HTTP headers to fully simulate a browser request (added Accept, Accept-Language, etc.), solving 403 Forbidden caused by incomplete headers. 2. Added retry logic for HTTPError:...

codinglearner121

**Is your feature request related to a problem? Please describe.** I applied the cellpose on one tif stack containing many cells. The saved tif image is in 32-bit format, which...

gaole2019

…r the README

SethSterling22