SEM images of Collagen Fibers


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!


There are definitely ways to measure orientation in CP, though not anisotropy per se. Masking out individual regions is definitely possible, whether manually using IdentifyObjectsManually or with something automated like the worm toolbox (which certainly CAN be used for other non-linear objects)

It’s hard to know how to specifically do that for your images though without seeing them- check out are tips for things to include for a list of things that make it easier for us to help you get started.