Minian Installation/Kernel Problem

[Carlos]

Hi everyone, 

I have been trying use minian for miniscope data analysis but there are some installation problems. 

After installation, the jupyter notebook does not have the correct kernel "minian", nor does this option exist under "change kernel" (I have attached the screenshot). It only has the standard Python 3 (ipykernel), which leads to other errors in the code due to the wrong kernel.

Does anyone know how to fix the kernel in minian?

Thank you in advance!

Best wishes,

Carlos

For more context, I have installed Anaconda, then after opening the python project of "minian8" under conda, I have used the following in the python terminal (python version 3.8.16):

(minian8) PS C:\Users\miniscope\PycharmProjects\minian8> git clone https://github.com/DeniseCaiLab/minian.git
(minian8) PS C:\Users\miniscope\PycharmProjects\minian8> cd minian/
(minian8) PS C:\Users\miniscope\PycharmProjects\minian8\minian> conda env create -n minian -f environment.yml
(minian8) PS C:\Users\miniscope\PycharmProjects\minian8\minian> conda activate minian
(minian) PS C:\Users\miniscope\PycharmProjects\minian8\minian> jupyter notebook

[Florian Steenbergen]

Hi Carlos,

you have to run an additional line if you want to use a virtual environment in jupyter-notebooks.

For a full description see e.g. here:

https://janakiev.com/blog/jupyter-virtual-envs/

Basically, if I recall correctly, all you have to do is go to your anaconda prompt, activate the virtual environment and then run the following two lines:

pip install --user ipykernel

python -m ipykernel install --user --name=myenv

make sure to change the name (here myenv) to the name you want in the jupyter-notebook.

I guess you have to restart the jupyter-notebook before it is visible.

Hope that helps!

Best,

Florian

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[Carlos]

Thanks Florian, this made it work!

Best,

Carlos