Axon detection in confocal microscopy


I recently started using CellProfiler, and I could really use any help or advice
with my problem.
I’m working on images like the ones I attached. I need to segment the axons in the images
(the black filaments) and then take some measurements (length, number of branches,…) on
them. I tried inverting the images and using the IdentifyPrimaryObjects
module for the segmentation, but its not working.

Do you have any suggestions?

Thanks for your time


I’m attaching a pipeline to get you started. Unfortunately, your images are not very high contrast, so the pipeline does not work well yet. Perhaps with some additional adjustment, you can detect the full axons.

If you can detect the axon as a single object, you can use MeasureObjectSizeShape to obtain morphological parameters. The final module “skeletonizes” the object, i.e., reduces it to an object one pixel width, so the area measurement is equivalent to the total length. We have a MeasureNeurons module but it requires that there be one set of objects representing the nuclei and another for the axons.

2011_06_17.cp (4.81 KB)