I want to quantify the number of vessels in my 3D images. First I run the Neuron Tracing utility of Vaa3D, this gives a swc file which looks quite acceptable. But the quantification options as described in the Nat. Protocol article are not available in Vaa3D, so it was suggested to use L-measure for this.
However L-measure is not able to read the swc format generated by Vaa3D. Most likely because the type values (2nd column) are not compatible with the original swc format in which the type value is an integer ranging from 0-7 (http://research.mssm.edu/cnic/swc.html). Could you help me to get the quantification working?
Kind regards,
Tonny

Attached my swc file.

Use the global neuron features plugin will generate L-measure compatible scores.

-Hanchuan

you can goto the vaa3d source repo and build from there. if you do not know how to build, you can either build from the instructions at vaa3d's google code site, or leave info here about your operating system etc so that we may be able to build one for you when we find time.


Originally posted by Hanchuan Peng:

Unofortunately I have not been able to figure out how to build the global neuron features plugin. If you would be able to construct it, that would be great. I am using a laptop with Windows 8.1, i7-4702MQ CPU processor with 32 GB RAM, 64 bits.
Thanks in advance! Tonny


Originally posted by Hanchuan Peng:

I attached the global_neuron_feature plugin.  You need to create a "global_neuron_feature" folder inside "plugins" folder first. And then put the attached file into \plugins\global_neuron_feature\ folder.

Zhi

Thanks! It seems to work, great.
Tonny

Sorry, again a question regarding the global_neuron-feature; is there a way to export the data to a file? (csv, txt or whatsoever)
I get al the desired features in a seperate window, but the only thing which I can do with it is to click it away; but I would like to save the data of each analysis.
Best, Tonny

You can select the text in that window and copy and paste to another place as you like...

You can also run the vaa3d plugin from command line, where you can specify a file or any place to export.

This is an open source project, you are encouraged to write a few lines of code to export (or even format) as you like.

Hope this helps.

-Hanchuan


Originally posted by Tonny Lagerweij:

Thank you for the clarifications above.
Being a computational biology novice, I am having trouble running L-Measure.
The software would load, but upon clicking "go" nothing happens.

Alternatively, the Vaa3D neuron profiling works wonders. However, the displayed numerical data, I cant copy it. It wouldnt allow.

Is there any other way to export the reported data?

Thank you again

Sam

You can use sorting plugin to sort the swc file first. The plugin is under "Plug-In" --> "neuron_utilities" --> "sort_neuron_swc"