Looking for 201805_cp_segmentation_example imc_full_sm.tiff about imcsegmentationpipeline

[votti]

Hi arcolombo,
I am really sorry for the belated answer - I thought I already answered but must have missed to send the answer :/
Anyways: You can and have to generate an imc_full_sm.tiff specific to your antibody pannel & channel selection using the following script from the compensation paper: https://github.com/BodenmillerGroup/cyTOFcompensation/blob/master/scripts/imc_adaptsm.Rmd
Using a *_full.csv file generated via this pipeline during the analysis stack production step.

[arcolombo]

Hi Vito,

in the cp3_compensate pipeline, the compensation process creates a spill corrected "full.tiff" and exports the object level data as an excel sheet. How can we convert the spill correct full.tiff to an ome.tiff so we can view each channel in MCDViewer and examine the spill corrections ?

Thank you again Vito

AC

[nilseling]

Spillover correction has now been moved to https://bodenmillergroup.github.io/IMCDataAnalysis/spillover-correction.html