No module named 'imcsegpipe' error

[honeybee-224]

I already ran this pipeline on the example data, and it worked, but now that I tried again with my own data, I get the following error:

What should I do to resolve this issue? I already tried redownloading the pipeline and trying again and double checked the conda environment in use is the "imcsegpipe," I've only used the new pipeline so I know, the old "imctools" environment isn't accidentally being used.

[honeybee-224]

It also seems the "panel.csv" file is not recognized. Is the "deepcell" column that the example data had necessary for the panel file to be recognized?

[nilseling]

Hi @honeybee-224, the deepcell column is not needed. The panel file specification can be seen here: https://bodenmillergroup.github.io/ImcSegmentationPipeline/prepro.html. You could also post the error here so that I can have a look what's going on. As for the environment, could you please post the output of !conda list here?

[honeybee-224]

[honeybee-224]

[nilseling]

It seems like you are not working within the imcsegpipe conda environment. Could you please follow point 5 in the readme here: https://github.com/BodenmillerGroup/ImcSegmentationPipeline. And the issue with the panel file comes from the fact that the file cannot be found in the location that you specified. Please check that the panel file exist, maybe it's worth using full paths instead of relative paths.

[honeybee-224]

I just tried it again and ran into the same issue.

[honeybee-224]

I removed the imcsegpipe conda environment, reinstalled it, and I am still getting the same error message.

[nilseling]

Hmm, that's strange. You mean the error that the imvsegpipe module can't be found? Did you get any error messages when you installed the environment?

[honeybee-224]

It worked! Thank you for your help.