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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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Presence of undefined channels during conversion from MCD to ome-TIFF #130

Closed petesfew closed 1 year ago

petesfew commented 1 year ago

Hi,

I am relatively new to the IMC platform and has been practicing the data pre-processing techniques as described in the imcsegpipe. After conversion of MCD to ome-TIFF, I realise that the omeTIFF contains channels that are not defined by the panel.csv. For example, there are signals for ArAr80, Xe131, Xe134 and others. These unlabelled channels are ultimately eliminated when converting omeTIFF to a full analysis TIFF stack.

My question is whether these signals arise from potential spillover or other technical artefacts and whether we have to deal with these (even though they are eliminated in the analysis stack)?

Milad4849 commented 1 year ago

Hi @petesfew,

Those channel are open during acquisition, so they are part of the MCD and the resulting ome-TIFF, but there are no corresponding metal-tagged antibodies. Such channels are typically used for detection of issues such as contaminations of the Argon gas used in IMC. Only the channels defined in the panel.csv file are relevant for the downstream analysis.

petesfew commented 1 year ago

Hi @Milad4849

Thanks for the explanation!