carsen-stringer

do you mean the flows? and by evaluate what do you mean? you can use your model on the command line with `python -m cellpose --dir /path/to/images --pretrained_model name_in_gui`

you can get it in the same way, the flows are saved in the `_seg.npy` file as a dictionary key, after you run the new model

just to clarify here, you made a new environment with `conda create --name cellpose python=3.8`?

thanks for the help, I'll provide this info in the readme

can you provide more context on your input images? is this on the command line or in a notebook?

closing due to inactivity

do you have an image you can post as an example? I'd recommend maybe retraining the model if cellpose is merging your masks. you can alternatively use a decreased diameter...

closing due to inactivity

are you using a clean conda environment? sometimes the installed conda version has issues

(clean meaning `conda create --name cellpose python=3.8`, this makes an environment with only python)