Measuring Neurites


apologies for the question question. I am new to CP and have read the other related posts but still cannot solve my issue. .I use CP3 and want to measure the length of neurites and the number of branches. I identify the neurites and then make an image skeleton and count the branches but I am not sure what he sees as branches as the numbers is wrong. Also, I am unsure how to get it to count the neurite lengths and see them as individual neurites.

Thanks for all the help!

Here is my pipeline:
neurites.cpproj (784.6 KB)

And here is a test image:



Can you explain in a bit more detail what specifically you don’t think is being measured accurately?



If you see the test image, there are only a handful of neurites (the branches from the cell body) but from my pipeline it identifies thousdands of them. i think it starts counting a new neurite at every change in intensity along the neurites. If that makes sense. As he counts thousands of branches.