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kevinjohncutler / omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation
https://omnipose.readthedocs.io
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HTTP Error 500: INTERNAL SERVER ERROR #7

Closed rdemets closed 2 years ago

rdemets commented 2 years ago

Hi,

I have a conda environment that I used for cellpose 2.0, and I thought it would be quite straightforward to use the same environment for omnipose (I only did a pip install omnipose since).

First, I am getting a HTTP Error 500: INTERNAL SERVER ERROR when I try to run the line model = models.Cellpose(gpu=use_GPU, model_type='bact_omni') from the run_cellpose_GPU notebook.

Secondly, if I try to run it using one model that I already downloaded, I am getting an error eval() got an unexpected keyword argument 'omni' at the line masks, flows, styles, diams = model.eval(imgs_2D, diameter=None, flow_threshold=None, channels=channels, omni=True)

Am I missing anything ? Is there any other way to download the model and drag and drop it with the other models ? Should I have a dedicated environment without cellpose ? It seems like an easy to fix problem, I am a bit clueless on the procedure to use Omnipose properly.

Thanks for your help. Regards, R.

rdemets commented 2 years ago

Nevermind, I found the problem. It's indeed the cellpose version. I uninstall cellpose and pip install cellpose==1.0.2

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