How to count neurons? DAPI and Beta 3 Tubulin Staining




I am very new to Cell Profiler (I’m an undergraduate). I have been tasked with counting a large dataset of neuron images (1000+ images). I have attempted to simply create a pipeline to identify the primary object of the neuron cell body.

At minimum, I would like neuron cell body count. If possible, I would like axons counted as secondary objects and also a count on the number of axons that are degenerated (i.e the axon is not a continuous line)

In the pipeline I’ve started, CP keeps identifying straight axons as objects (see attached screenshot). Is there a way to force CP to look for circular objects?

Any advice for my other goals?

Very much appreciated, thank you!

NeuronCounting.cppipe (5.3 KB)


Note: there are many more cells in this image than just neurons