help > RE: Help needed in neurite tracing
Dec 3, 2019  10:12 AM | Hanchuan Peng
RE: Help needed in neurite tracing
To measure the neurite processes' length is straightforward, you can either use the Matlab toolbox for vaa3d to load swc file and sum up the distances of all adjacent nodes along a neurite, or right-click the specific neurite segment in Vaa3D's 3D viewer directly (assume you have first decompose a neuron into segments using the 'editing' menu when you right-click on the neuron) and then  select the 'profile'. You can follow the instructions in the Nature Protocols 2014 paper.

To measure the growth direction (or any angles), you can do that using the Matlab toolbox to load swc files and then calculate whatever you like.

To measure the soma size, you will have to either segment the soma literally (depending on how precise you want the measurement to be ), or in a simple way, go to check the radius of the measured soma node.

To count the # of the neurons, well, really depending on what exactly you want to do. If you have traced multiple neurons all at once and mix them in one swc file, then it could be tricky to use the swc files' info directly. But if you only look at the image directly, it is very simple, just click how many somas in the image using virtual finger function of vaa3d, typically you get the numbers of neurons within seconds.


Originally posted by Robin Karge:
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.


(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  )

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Robin Karge Dec 2, 2019
RE: Help needed in neurite tracing
Hanchuan Peng Dec 3, 2019