help > Exporting neuron tracing and statistics
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May 31, 2017 12:05 PM | Gladys Lau
Exporting neuron tracing and statistics
Dear sir,
I would like to ask:
Is there a straightforward way to export Vaa3D neuron2 App2 tracings (which are swc files) for analysis in imagej, and also matlab?
Also, may I ask whether there's a way to export statistics calculated in Vaa3D (e.g. those made from "compute global features" under "neuron utilities" in the plugin menu)?
Thanks a lot for your help.
I would like to ask:
Is there a straightforward way to export Vaa3D neuron2 App2 tracings (which are swc files) for analysis in imagej, and also matlab?
Also, may I ask whether there's a way to export statistics calculated in Vaa3D (e.g. those made from "compute global features" under "neuron utilities" in the plugin menu)?
Thanks a lot for your help.
May 31, 2017 03:05 PM | Zhi Zhou
RE: Exporting neuron tracing and statistics
In FIji(ImageJ), there is a plugin can be used to import swc file
directly, please check their websit. In Matlab, please check here https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
You can use command line to run Vaa3D plugin and then copy the output from terminal. How to use command line, please check here https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
You can use command line to run Vaa3D plugin and then copy the output from terminal. How to use command line, please check here https://github.com/Vaa3D/Vaa3D_Wiki/wiki...
Jun 2, 2017 09:06 AM | Lorena Arancibia
Exporting neuron tracing and statistics
Hiya! Just so you know, ever since a FIJI update at some point late
last year, Simple Neurite Tracer has not been able to import
Vaa3D-created swc files. This appears to be due to it not
recognising the node type (second column in an swc numbers matrix).
It turns out that if you use Matlab, for example, to replace all
the numbers in that column (normally 274) to 0 then FIJI will
easily open the swc. Hope this helps.
Jul 8, 2017 08:07 AM | Gladys Lau
RE: Exporting neuron tracing and statistics
Noted. Thank you all for your help.