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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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Issue converting mcd containing folders into imc zip folders #33

Closed cassandraman closed 4 years ago

cassandraman commented 4 years ago

Hello,

I've been getting the following error when running the step to convert mcd containing folders into imc zip folders.

ERROR:root:Error in ../example_data/SP11_1305A4.zip Traceback (most recent call last): File "", line 11, in File "/opt/anaconda3/envs/imctools/lib/python3.6/site-packages/imctools/scripts/convertfolder2imcfolder.py", line 35, in convert_folder2imcfolder assert(len(mcd_files) == 1) AssertionError

Would you recommend any way to troubleshoot this in Jupiter notebook, or is this an issue related to the zipped files itself?

Really appreciate your help, Cassandra

votti commented 4 years ago

Hi Cassandra, The reason for this error is that there are multiple .mcd files in the zip folder.

From the documentation: Data requirements: This scripts assume that each .mcd acquisition - and optionally all .txt files corresponding to this '.mcd' acquisition - are saved in one a seperate .zip folder.

Can you check if this is the case for your data? Cheers, Vito

cassandraman commented 4 years ago

Hi Vito,

Thanks for your quick response! I checked the file content of the zip, and found that additional .mcd files had been generated in during compression. I was able to resolve this issue.

Thanks for your help! Cassandra