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help > Advanced axon tracing techniques and analysis
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Sep 30, 2020 08:09 PM | Shane Simo - Mcmaster
Advanced axon tracing techniques and analysis
Hi folks,
I have been using Vaa3D for several months. I primarily use Vaa3D to trace axons. I am very competent with the basics, but I want to make sure I get good with some of the advanced concepts too. I have a few questions:
1.) Is there a comprehensive, advanced guide specifically for axon/neurite tracing? I want run my axon through a quality control of sorts. It would be helpful if there was a tutorial for the neurontoolbox funciton menu.
2.) I haven't been able to find a Sholl analysis in Vaa3D and I've been having trouble getting SNT to work on FIJI. I saw in the forum that you folks were working on a Sholl analysis plugin. What's the status of that? Is it available to users? I would like to avoid using SNT if possible.
3.) Are there any other useful pluggins for analysis of axons?
4.) I saw this question pop up a couple of times in the forum, but how do I know what the scalebar means on the 3D viewer? I have a voxel size of about 200nm * 200nm * 500nm from my confocal collection. How does that translate to Vaa3D? I saw that Vaa3D is in voxel space. What does that mean?
Thank you for your help! I really enjoy using Vaa3D so far, but I want to become a Vaa3D expert! I also posted this in the other forum, but this might be a better place for it.
Shane Simon
I have been using Vaa3D for several months. I primarily use Vaa3D to trace axons. I am very competent with the basics, but I want to make sure I get good with some of the advanced concepts too. I have a few questions:
1.) Is there a comprehensive, advanced guide specifically for axon/neurite tracing? I want run my axon through a quality control of sorts. It would be helpful if there was a tutorial for the neurontoolbox funciton menu.
2.) I haven't been able to find a Sholl analysis in Vaa3D and I've been having trouble getting SNT to work on FIJI. I saw in the forum that you folks were working on a Sholl analysis plugin. What's the status of that? Is it available to users? I would like to avoid using SNT if possible.
3.) Are there any other useful pluggins for analysis of axons?
4.) I saw this question pop up a couple of times in the forum, but how do I know what the scalebar means on the 3D viewer? I have a voxel size of about 200nm * 200nm * 500nm from my confocal collection. How does that translate to Vaa3D? I saw that Vaa3D is in voxel space. What does that mean?
Thank you for your help! I really enjoy using Vaa3D so far, but I want to become a Vaa3D expert! I also posted this in the other forum, but this might be a better place for it.
Shane Simon
Oct 2, 2020 01:10 PM | Lorena Arancibia
RE: Advanced axon tracing techniques and analysis
Originally posted by Shane Simo:
Lorena
Hi folks,
2.) I haven't been able to find a Sholl analysis in Vaa3D and I've been having trouble getting SNT to work on FIJI. I saw in the forum that you folks were working on a Sholl analysis plugin. What's the status of that? Is it available to users? I would like to avoid using SNT if possible.
Hello, I am not sure there is a Sholl
analysis plugin for Vaa3D yet. I wrote a Matlab code for 3D Sholl
analysis which I used with traces generated in Vaa3D
which may be of help to you. You can download it from
here: https://github.com/AttwellLab/Microglia (It's the
GUISHoll folder). I hope it is useful.2.) I haven't been able to find a Sholl analysis in Vaa3D and I've been having trouble getting SNT to work on FIJI. I saw in the forum that you folks were working on a Sholl analysis plugin. What's the status of that? Is it available to users? I would like to avoid using SNT if possible.
Lorena