BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
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Add option to remove the first acquisition row in IMC images. #204

Open nathansteenbuck opened 1 year ago

nathansteenbuck commented 1 year ago

Due to the laser, we often observe higher intensities in the first row (X = 1) of IMC images. I would suggest to add an argument for the preprocess functionality to remove the first row from the image (e.g. rm_first or remove_first). By default it should be set as False.

jwindhager commented 1 year ago

Note: IIRC this happens because, for the first row, the laser does not just ablate the "stage delta", but the full spot size.