Jupyter notebook error: no module named 'imctools'

[SteveBoothHLI]

Hi everyone, I am working on a windows machine and I am having an error right at the start of the imc_preprocessing jupyter notebook.

I downloaded the segmentation pipeline folder from here: https://github.com/BodenmillerGroup/ImcSegmentationPipeline

Then I extracted the folder & started Anaconda Navigator GUI. To install the imctools environment I did the following: Environments -> Import -> selected the 'conda_imctools.yml' file from the downloaded folder. The environment imports successfully. Then in the anaconda prompt I did: activate imctools jupyter notebook

Navigated to the imc_preprocessing jupyter notebook. And in the first part of the code I receive the following error "ModuleNotFoundError: No module named 'imctools'".

If anyone can help me out trying to troubleshoot this error it would be greatly appreciated! Thanks, Steve

[votti]

Hey there,

As per the terminal screenshot I think you need to type 'conda activate imctools' in the terminal before writing 'jupyter notebook'.

Please let me know if it works!

I will update the guide once I am back from holidays.

Best, Vito

On Oct 1, 2018 5:09 AM, "SteveBoothHLI" notifications@github.com wrote:

Hi everyone, I am working on a windows machine and I am having an error right at the start of the imc_preprocessing jupyter notebook.

I downloaded the segmentation pipeline folder from here: https://github.com/BodenmillerGroup/ImcSegmentationPipeline

Then I extracted the folder & started Anaconda Navigator GUI. To install the imctools environment I did the following: Environments -> Import -> selected the 'conda_imctools.yml' file from the downloaded folder. The environment imports successfully. Then in the anaconda prompt I did: activate imctools jupyter notebook

Navigated to the imc_preprocessing jupyter notebook. And in the first part of the code I receive the following error "ModuleNotFoundError: No module named 'imctools'".

If anyone can help me out trying to troubleshoot this error it would be greatly appreciated! Thanks, Steve [image: error ss] https://user-images.githubusercontent.com/33731370/46264247-5188e300-c4cf-11e8-8325-8fc181484715.jpg

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[SteveBoothHLI]

Hi Vito, thanks for your quick reply!

In the screenshot you can see that I executed "activate imctools" then I executed the jupyter notebook from the activated imctools env.

I also just tried this with "conda activate imctools" then jupyter notebook and the error persists.

Steve

[votti]

Hey,

A sorry, I looked at it on a mobile phone - you sure are doing things right!

Two things to try: a) Reinstall the imctools environment (first use conda env remove imctools) then install it again using using: conda env create -f conda_imctools.yml - are there any errors during installation? b) try within the environment pip install git+https://github.com/BodenmillerGroup/imctools.git@develop-test Are there any errors? c) register the conda kernel as ipython kernel for jupyter specifically : activate imctools environment, then `python -m ipykernel install --user --name imctools --display-name "Python (imctools) " then select this env as active kernel in the notebook.

Let me know if/what helped! Best, Vito

[SteveBoothHLI]

Hi Vito, thanks so much.

It tried option A first and that alone did not work. However I then tried B & C and now the issue is resolved.

Thanks for your help! Enjoy the rest of your vacation, Steve

[votti]

Hm strange! I tested this several times on Ubuntu & Windows and everything seemed to work just with the conda install - I guess I need to investigate further and figure a procedure that works more reliable.

Glad that it worked after all!