I have been working on a pipeline in CellProfiler to characterize the neurite network of my neurons. I’ve built it based on a paper that did something similar in ImageJ (https://onlinelibrary.wiley.com/doi/full/10.1002/cyto.a.22408)
The pipeline is divided into 3 steps: 1) nuclei segmentation, 2) soma detection and 3) neurite segmentation. I detect the neurite network using two masks that I combine together with ImageMath. I am pretty satisfied with the detection of the neurites. However, when I try to “skeletonize” the image (with MorphologicalSkeleton or Morph (skelpe)), I only get dots instead of continuous lines.
Therefore, my measurements with MeasureObjectSkeleton or MeasureImageSkeleton makes no sense. I have spent quite some time reading on blogs and forums; tried Smoothing/filters and EnhanceFeatures, but now it seems that I’m stuck.
I would like to measure: total neurite area, neurite length, and number of branching points
I’m using MeasureImageAreaOccupied to determine total neurite area, but I get an error message saying that my input image is not binary. My input image was generated in ImageMath: isn’t it a binary image?