Select ROIs for analysis

BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline

https://bodenmillergroup.github.io/ImcSegmentationPipeline/

MIT License

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Select ROIs for analysis #98

Closed Jeffchingg closed 2 years ago

Jeffchingg commented 2 years ago

Hi, is there anyway I can only pick up some ROIs from original MCD file for further processing? Our lab tech mis-input some channels in first serval ROI acquisition then corrected the mistakes for the others, which caused some channels were not collected in the first a few ROIs. This leads to error message showing the acquired signals are not consistent in pre-processing step. I don't if there is anyway I can get rid of those 'bad' ROIs when processing data. Thanks a lot!

nilseling commented 2 years ago

You can just delete the .ome.tiff files of these ROIs and proceed with the pre-processing script.

Jeffchingg commented 2 years ago

it works. Thank you for suggestion. @nilseling