search

BodenmillerGroup / ImcSegmentationPipeline

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

Errors setting up with example data #101

Closed honeybee-224 closed 2 years ago

honeybee-224 commented 2 years ago

I'm trying to use the example data provided to run the pipeline. I'm having trouble converting the mcd files into tiff files (e.g. patient1, patient 2, etc.) Do we need to use input, or are the regions of interest already selected? Every time I try to generate an output, I get an error message.

nilseling commented 2 years ago

Hi @honeybee-224,

could you please post the error here. Please also let us know the output of

!conda list
honeybee-224 commented 2 years ago
Screen Shot 2022-07-12 at 12 07 55 PM
nilseling commented 2 years ago

I still can't see where this error is raised and can't reproduce it. Could you please try to clone the repository again and follow the instructions to set up the environment? https://bodenmillergroup.github.io/ImcSegmentationPipeline/#getting-started

In the last code block of imc_preprocessing.ipynb there is a line !conda list. Could you please execute it and send me the output?