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mal-boisestate / Immunostained_Image_Analysis

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Fix channel name verification #49

Open ninanikitina opened 1 year ago

ninanikitina commented 1 year ago

With a new confocal upgrade nucleus mask name can vary, for example, I tried to run an analysis but it failed because the nucleus channel name is "DAPI-T2" not "DAPI", so we need to include a check if the channel name has a "DAPI" substring instead of == "DAPI"

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ninanikitina commented 1 year ago

Added changes in the find_channel() function in the BioformatReader.py file.

ninanikitina commented 1 year ago

Changed draw_and_save_cnts_for_channels() in ImageData as well so the function can save verification images