I’m using Fiji and I’m a beginner. I have a set of images from an experiment, put them in a stack and then do a dynamic reslice, around the middle of the stack. In the reslice I want to extract the thin line over the larger black “line” (shown by the arrow in the image) and my problem is that I can’t extract the line successfully.

Example of dynamic reslice

I think the lighting in my experiment is the problem, because the pixel value of the line is quite similar to that of the background.

I’ve tried a few things, like playing with the brightness/contrast or the threshold, and I can get the big black one by applying a variance filter (see image below), but that’s not the line I want ^^’.

Result for the bigger black line

My question is, do you have any idea how to get the line I want, or is it impossible for this experiment?