I am trying to repeat the steps of Nature Protocols, vol 9-1, 2014 for the reconstruction and quantification of 3D.
The 3D reconstruction of a blood vessel structure works quite nice, but for the quantification I can not find the global_neuron_feature anywhere. Does anybody knows how to calculate the morphological features?
Kind regards, Tonny Lagerweij
VUmc, Amsterdam

Hi Tonny

Have you tried Plug-in->neuron_utilities->global_neuron_feature? L-measure is another useful software for calculating morphological features.

Cheers
Ajay

For windows version only, it might not be in the current version of the downloadable binary (need to double check), but it is in the previous version of Windows releases.

You can also find the src code from code repo. we use it a lot.

This plugin is basically a reimplementation of L-measure global features. Thanks Ajay for also pointing it out.

-Hanchuan

Originally posted by Tonny Lagerweij:

Sorry for my late reply, but thanks for your and Ajay's quick reply..
Unfortunately I still don't know how to get any quantifictation of the vessel structures which I see in the *.swc file. I have downloaded the L-measure program, but when I try to open the swc file which I created with Vaa3d, the L-measure program gives an error;"Given file type is not supported!!, Unable to create Neuron:E:\ filename.. . swc !".

Furthermore  I don't know what you mean with 'the src code from code repo'. In the neuron_utilities plugin, I don't find the global_neuron features (see attached screen print).
Hope you are still willing to help me out with this.
Tonny

Originally posted by Hanchuan Peng:

somehow NITRC stops to send us the notification when new msg is posted, :-(( need to fix that soon!


Originally posted by Tonny Lagerweij:

Is it possible to reconstruct the bloood vessel using 2 x-ray views? Please let me know

You can try our different BigNeuron tracing plugins. Here is the detailed information about different tracing plugins: https://github.com/BigNeuron/BigNeuron-Wiki/wiki/Neuron-Reconstruction-Algorithms