Hello everyone!
Please tell me how best to solve the problem. I have a z-stack with nerve fibers, I need to calculate their area. I use the threshold function in FIJI to highlight these fibers. However, I have a decrease in signal as the z-stack progresses and accordingly this leads to a change in the threshold. Using HistogramMatcher aligns the fluorescence in the z-stack to the desired slice, but I'm not sure if this is correct because the background also increases. Please advise how to correctly align the signal in the z-stack so that the threshold for all images becomes the same, but without loss of information or its distortion?
Thank you=)
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