I’m very new at ImageJ (Fiji) and I’m currently analyzing some scans from a micro-CT. My sample is cylinder-shaped, 20 mm in diameter and 3 mm thick, and I’m scanning the sample with the thickness in the z-direction.
I’m supposed to analyze the density profile (how the density differs through the sample thickness).
I think one way to do that is just to draw a line through the thickness and plot a line profile with Gray value vs. Distance(pixels). Another way is to measure the area fraction of each scan through the sample and plot Area fraction vs. Distance.
I think the last idea is the best, and I know how to measure the fraction for each scan in Fiji, but can I do some commando or something to automatically measure the fraction throughout the sample? And hopefully plot it as well.
The next problem is where do I start the measurement, my sample is a bit rough. Is there any function I can use that tells me where my sample top/bottom surfaces are and in which slices it is “good to start” with?