Hi, 

First of all, thank you very much for all the efforts and time to make this program accessible to all the biologists and neuroscientists. 

I'm working with NeuroGPS-tree tool from the official source(https://www.nature.com/articles/nmeth.36...), as the plug-in from vaa3D crashes on every platform that I've tried (Windows and Linux) with segmentation fault (same as in https://www.nitrc.org/forum/message.php?...). I used a swc file. 

The official tool requires the soma location as a swc format, and I'd like to use the landmarking function from vaa3D to mark these locations and export them as a SWC file. So far from what I've read, it looks like there's no tool to convert the marker file to swc. Is there any function from Vaa3D for this? 

Best,
Peter

Hi Peter Park!
I have run the NeuroGPS-tree plug on Windows in Vaa3D successfully. For your question, if you want to use the NeuroGPS-tree plugin and have problems in choosing marker file,the following steps may help you.

Choose the default option"NULL" when the pop-up window "Input soma position file path" occur，Click Ok, the tracing swc file will be generated , and just drag into Vaa3D.

Hope this can help you!

Thanks for the quick reply! It sounds like your steps involve not specifying soma positions. I don't think that's what's in the instruction from the original paper (as I want instance segmentation, I do think soma locations would be necessary to tell each individual neuron apart). Also the plug-in still crashes, with the version 3.2 (from this nitrc distribution). My machine is a freshly installed Windows 10 PC. Any tips for this?

Best,
Peter 

Originally posted by Lingli Zhang:

Hi Peter Park!
For the Vaa3D version, you can go to the (https://github.com/Vaa3D/release) to download the latest version.

For the marker file, you have to change ".marker" file into ".swc" file ,and the swc file format need to be"##n type x y z r parent" . you can changed it manually or write a script to change it. (the attached file was an example swc file which I changed it from the .marker file, all I did was copy the "x y z" from marker file).

And for Autu-tracing purpose, I think you can  try the Vaa3D plugin "Vaa3D_Neuron_APP2",the article addresses  (http://home.penglab.com/papersall/docpdf...) , we use it more often and you can compare the result.

Hope this can help you!

Originally posted by Peter Park:
Hi Peter,

Indeed there is a Vaa3D plugin that converts markers into the swc representation.
Refer to the attached image for the location of the plugin.

Best,
Yimin