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I'm working with microscopy samples that feature a 'web' of dark lines. I want convert the images to binary so only the dark portions show up, but I'm uncertain of how to standardize this process. The images have varying brightness and contrast so just picking a single numerical threshold won't work. I could standardize the brightness and contrast across the entire images, but some of the samples have more dark lines than others, so in my ideal standardization scheme these samples actually should have lower overall brightness. I was thinking about selecting regions on each of the samples that are free of lines, and standardizing the brightness and contrast for these regions but I'm not sure how to best accomplish this and at any rate I would prefer to have a fully automated process with no room for human inconsistencies. Any advice? I've been working with Fiji / ImageJ thus far.

R. H.
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You can make use of adaptive threshold for your initial problem. It appears there is even an ImageJ plugin which implments it: https://sites.google.com/site/qingzongtseng/adaptivethreshold

TimeS
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