Example1 notebook not working

[cnstt]

When executing the example1 notebook, I discovered several "issues":

• [x] Maybe it would be cool to indicate to the user at the beginning, that he should install cellpose, or insert a !pip install cellpose
• [x] from cellpose import iois missing when wanting to import the images from the test_files folder
• [x] The import of these files is failing with the error get_image_files() missing 1 required positional argument: 'mask_filter'
• [x] omni=True for the normalize99 function does not work (so I just removed it to make it work...)
• [x] 'bact_phase_omni' doesn't seem to be available anymore (I get HTTP Error 500: INTERNAL SERVER ERROR and it isn't displayed in the MODELS_NAMES...

For the first 2 I could open a PR to correct it ;)

[cnstt]

For the import error I encountered just changing it to files = io.get_image_files(basedir, "") works :)

[kevinjohncutler]

Thanks @cnstt! I'll make these changes. Some of the functions have been updated and that's the source of these errors. I'll have to do some more digging for the model download error.

[alix-pham]

Hi!

I'm trying to use Omnipose for bacterial segmentation and the last issue mentioned here is quite problematic for me. Is there one of the current models that can replace the 'bact_phase_omni' model? ('cyto', 'nuclei', 'tissuenet', 'livecell', 'cyto2', 'general', 'CP', 'CPx', 'TN1', 'TN2', 'TN3', 'LC1', 'LC2', 'LC3', 'LC4')

EDIT: I tried with 'general' but then, most of the keyword arguments do not exist anymore in cellpose.models.eval—I would guess because everything moved to the omnipose repo? I can see them (OMNI_MODELS) in core.py but I don't understand how to use the different functions to generate the masks (compute_masks? get_masks?)

Or is there somewhere the versions of cellpose and/or omnipose that were using that model (the one used in the Omnipose paper, I would guess)

Thank you very much in advance, Best,

Alix

[kevinjohncutler]

Sorry I didn't post here that those tasks have been completed for some time, thanks @cnstt. @alix-pham, those models are part of Cellpose2.0 and I have not yet made them available in Omnipose. This should be as simple as updating the name list in my Cellpose fork. You should be able to see bact_phase_omni, and if not, that means you do not have the latest version of Omnipose installed (use pip install git+...). I will eventually get the PyPi release updated, it just means that all my forked dependencies also need to be released on PyPi - and that's just been too much to juggle. Git installs don't care if dependencies are on GitHub or PyPi.