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BodenmillerGroup / cytomapper

R package for visualization of highly multiplexed imaging data
https://bodenmillergroup.github.io/cytomapper/
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Normalizing individual channels with different inputRanges #24

Closed JanaFischer closed 4 years ago

JanaFischer commented 4 years ago

When using the normalize function the same inputRange values are applied to all channels of the image but occasionally a certain channel needs to be enahnced more than others. A work around is to adjust the contrast in the bcg parameter for specific channels.

nilseling commented 4 years ago

My suggestion would be to add the option for a list input: inputRange = list(H3 = c(0, 130), CD8a = c(0, 50)) to specify the clipping range for individual channels. All channels that are not specified will not be altered

nilseling commented 4 years ago

This is now a feature. E.g. cur_images <- normalize(pancreasImages, inputRange = list(H3 = c(0, 70), CD99 = c(0, 100)))