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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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Nd145 not in list error when generating image stacks #127

Closed Yanira1208 closed 1 year ago

Yanira1208 commented 1 year ago

Hello! When I try to run my files through pre-processing with our panel I get the error that Nd145 is not in list. When I delete this tag from the list I don't get any issues but would it be possible to have this metal tag included? It contains a target we're interested in looking at. Thanks! Screenshots with issue and panel attached. IMC Panel ND145 not in list Screenshot 2023-03-14 164330

nilseling commented 1 year ago

Hi @Yanira1208 Are you using the newest version of the scripts? We adjusted some of the functions last week to support pre-processing.

Yanira1208 commented 1 year ago

I am running the newest version

nilseling commented 1 year ago

Hmm, ok, could you please send me one of the CSV files of one of the ometiff folders?

Yanira1208 commented 1 year ago

Just checked the ometiff files and I had the wrong tag, our CD33 marker isn't under Nd145 but Dy163. No wonder it wasn't working (: Thank you!

nilseling commented 1 year ago

No problem. I'm happy that the pipeline catches the issue. Closing now