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BodenmillerGroup / ImcSegmentationPipeline

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

Panel import with manually opened channels #63

Closed lecords closed 2 years ago

lecords commented 3 years ago

Hi,

before in the imctools, when one had opened channels manually in the CyTOF software, those dind't have be added to the panel.csv file when one didn't want to use those for the analysis and they would subsequently be omitted when generating the tiffs and ometiffs. Now however, one has to add all channels manually to the panel. Is there a way of going back to the first version regarding this matter? That would reduce the effort of including all other metal channels a lot.

Thanks.

nilseling commented 2 years ago

@jwindhager do you know how this is currently handled?

jwindhager commented 2 years ago

Not sure I understand the question, sorry :see_no_evil: Could you maybe clarify at what step exactly you specify the panel file and how this differs in the current version from the previous one? Thanks

nilseling commented 2 years ago

The question is if you need to add all opened channels to the panel file or if channels that are not listed in the panel file are ignored by default? Expected behaviour: OME-TIFF files: all channels are exported; TIFF files: only the channels indicated by 1 are exported. If the channel is not listed in the panel file, it's not being exported. And I think this is also the case, just double checking

nilseling commented 2 years ago

Closing as I think this is addressed.