[BUG] Anisotropy is ignored in CLI, creates an error in the GUI

[RpfR2000]

If I enter a value >1 for the anisotropy flag in the CLI (for a zstack), cellpose still analyzes the image as if the zstack were isotropic (no resizing is done). When using the GUI, the analysis seems to treat the stack correctly and make it isotropic prior to segmentation, but then I get an opencv error related to resizing at the mask creation step. This is using v4.0.3. This is the error message:

2025-05-20 08:41:31,452 [WARNING] Resizing is depricated in v4.0.1+ 2025-05-20 08:41:32,596 [INFO] masks created in 5.33s GUI_INFO: resizing flows to original image size ERROR: OpenCV(4.11.0) D:\a\opencv-python\opencv-python\opencv\modules\imgproc\src\resize.cpp:3845: error: (-215:Assertion failed) !dsize.empty() in function 'cv::hal::resize'

[mrariden]

Hi @RpfR2000 can you share the exact command you use in the CLI and the parameters you are trying to use in the GUI? Also the image stack shape?

[RpfR2000]

This was the CLI command: python3 -m cellpose --use_gpu --do_3D --diameter 15 --anisotropy 7.7 --save_tif --dir cellpose_test. In the GUI, I used all the default parameter values, but with diameter=15, anisotropy=7.7. The image stack shape is (31, 750, 750) (z,y,x). It is being read in as (31, 750, 750, 3) by the GUI (I presume RGB).

[mrariden]

@RpfR2000 I think I identified and fixed the bug. Can you test out the fix for me? Install the new version of the code with:

pip install git+https://github.com/MouseLand/cellpose.git@ansiotropy_fix

[RpfR2000]

Indeed, that works for the GUI, but it doesn't work for the CLI command I tested.

[mrariden]

@RpfR2000 Glad to hear the GUI is resolved. But I'm not able to replicate your CLI error. Can you first try installing everything into a fresh environment?

If that doesn't work please give me the output of the welcome message to cellpose containing the OS, torch version, python version. Also give me the output of pip list.

[RpfR2000]

Apologies! I was using "python3" instead of "python", which I think caused me to use a different python version and hence a different cellpose version. I will close this now