Hello! I am working with SEM images of collagen fibers in mice skulls and am trying to quantify my results. Does CellProfiler have a module to measure the anisotropy of a bundle of fibers, or a different way I can measure the relative alignments of the fibers compared to one another?
Also, I was wondering if the modules from the WormToolbox could be applied to images that are not worms. I explored around the Worm tutorial in attempt to learn how to individualize different collagen fibers using the software; however, I realized this may not be the best module to be using. Two of the main difficulties we are experiencing are due to the depth of field of the images and the amounts of calcium crystals in the images. Does CellProfiler enable a user to establish a "foreground" to simply identify fibers in the front of the image? Is there a way we could either disregard these calcium crystals in the SEM images, or perhaps electronically measure the mass or amounts of these fibers too?
Thank you in advance!