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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
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Error "FileNotFound" in the last step #112

Closed aleixrius closed 1 year ago

aleixrius commented 1 year ago

Hi, I am performing the cell segmentation as I did already a few times. In the last Jupyter step, after the mask has been generated, I run the cell to add the mask in the Histocat folder. But it appears the error "FileNotFound". Which could be the issue? I imagine that it is something easy because half year ago it was working. image

Thanks so much. Best, Aleix

nilseling commented 1 year ago

Hi @aleixrius,

thanks for reaching out! Could you please let us know which version of the pipeline you are using? And I believe you have checked that the directory structure exists?

aleixrius commented 1 year ago

Hi @nilseling, thanks so much for your answer. I am using one of the first versions of the pipeline (2019). The directories should be correct because all the steps before worked without any error. Best, Aleix

nilseling commented 1 year ago

Ok, so here you are trying to copy the masks into the histocat folder, right? I'm unfortunately not very familiar with the first version of the pipeline. Could you please send me a screenshot of the code chunk where you specify the paths?

nilseling commented 1 year ago

Closing due to inactivity - please reopen if this is still an issue.