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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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histocat doesn't open output histocat file #31

Closed minhtran1309 closed 4 years ago

minhtran1309 commented 4 years ago

Hi,

I run your pipeline and complete the segmentation part. Everything works like charm. Until I try to visualize the output of this function ome2micat.omefolder2micatfolder with histocat. I am not too sure if the problem is histocat or there is something missing in the /output/histocat. A quick look at the folder I try to open, it contains all the tiff file of different channel listed in acquisition.csv file. ~metal channel + antibody clone. tiff and a _mask.tiff with the same name as the parent folder name. After I opened it with Load Sample, directed to the directory with histcat, nothing happened at all. Thanks

votti commented 4 years ago

Hi minhran,

The format should be the correct one for histocat.

I was checking with some histocat experts and I think a problem could be some special characters in the file names. Could this be the issue?

If not: do you get any specific error message from histocat?

minhtran1309 commented 4 years ago

hi @votti

I assume the problem is on HistoCat. The naming has no special character since I used the dataset provided from the link in the tutorial and the same things happened. I posted the issue to HistoCat repo already. Thanks for your response.