Hello dear Vaa3D users,

I was wondering if anyone could help me with neurite tracing in Z-stack images? I have included example pictures and files.
In short, I would like to evaluate the growth of DRG sensory neurons on biomaterial fibers. Therefore I am interested in the total length of neuronal processes growing on a single fiber and in its environment. I would also like to make a statement about growth direction by looking at the angle fibers grow at in comparison to the orientation of the fiber and if there is directional growth without any structures. Lastly, I would like to measure soma size and number of neurons in the image, so that I can relate them to the length of neurites, but that can most likely be done manually.
There are a few challenges with my images. The fibers I use are often fluorescent themselves, as you can see in the example images and the antibody used for neuron staining is creating artifacts in form of small dots.
I think it should be possible to overcome these problems through reconstruction, but I am inexperienced with Vaa3D. I managed to do somewhat solid tracings with a demo of Neurolucida360 though.
If anyone has an idea on what tracing plug-ins or functions to use I would greatly appreciate the support. Please feel free to reach out to me.

Robin

(I have also uploaded the example via our university's filesharing service (please remove spaces): https://gigamove.   rz.rwth-aachen  .de/d/id/QT6fHkNMJE9Yhy?7&id=QT6fHkNMJE9Yhy  )