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qbic-pipelines / root-tissue-analysis

Pipeline for pH analysis of A. thaliana root tissue
MIT License
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Change "brightfield" for correct channel name in codebase #16

Closed luiskuhn closed 1 year ago

luiskuhn commented 2 years ago

Since we know the input for segmentation (and what the fiji macro writes down) is not the brightfield channel, we need to change this name throughout the codebase, i.e. renaming variables using the correct name for that channel.

https://github.com/qbic-pipelines/root-tissue-analysis/blob/c56d579fc8972593b566a059a358799cf353f3ad/modules/local/rootseg/main.nf#L16

luiskuhn commented 1 year ago

It turns out it is the brightfield channel for excitation at 405 nm. Then this is not an issue