search

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

First steps in Jupyter for MCD pre-processing? #83

Closed DOCroit closed 2 years ago

DOCroit commented 2 years ago

Greetings!

I am essentially foreign to coding outside of R and have been trying to process our MCD data on a Mac using your pipeline. I believe that I have successfully gotten initialized Jupyter, but I am really not sure how to proceed from there.

When I type in this code:

"from imctools.converters import ome2analysis from imctools.converters import ome2histocat from imctools.converters import mcdfolder2imcfolder from imctools.converters import exportacquisitioncsv"

I get an error 'var.mail.imctools.converters' not found

I've also treated the zipped MCD files as described in your instruction but then cannot find the path to them on Jupyter's terminal either.

Some additional details around these steps for an absolute n00b would be very very appreciated.

Thank you so much for your help

nilseling commented 2 years ago

Hi @DOCroit

could you please post the imctools version you are using: From your jupyter notebook, could you please report the output of conda list?

You won't need to access the MCD files directly from jupyter notebook but rather use the absolute path for reading them in. The "start-up" folder of jupyer notebook is always the folder in which you opened jupyter (where you used the command jupyter notebook). So if you want to have access to everything in your home directory type:

cd ~
jupyter notebook
nilseling commented 2 years ago

Closing due to inactivity. Please reopen if this issue persists.