Volume 12 Supplement 1
Detailed visualization and morphometric analysis of reconstructed neurons using Blender and Python
© Aguiar and Szucs; licensee BioMed Central Ltd. 2011
Published: 18 July 2011
Topology and functional features are two related aspects in a neuron. Understanding and measuring the neuron's topology is therefore an important step in inferring and constraining its functional properties. Unfortunately the sheer complexity of most neuron's structures makes it virtually impossible to describe the topology richness in just a handful of parameters. Ultimately, the best way to describe a neuron's topology is by plainly performing reconstruction and visualizing it in a virtual 3D space. Here we present a collection of scripts, written in python programming language, which use Blender for 3D visualization. Blender is a well established free open source 3D content creation suite, available for all major operating systems under the GNU General Public
In addition to the main script, a collection of python functions were created to perform measurements and calculations on the parsed neuron data. These functions are accessible through an interactive python command window and they allow, among other things, calculation of varicosities densities, fiber lengths and inter-spine distances. The scripts can easily be extended to incorporate new functions.
This work was supported in part by Fundação para a Ciência e a Tecnologia (FCT) through the Centro de Matemática da Universidade do Porto (http://www.fc.up.pt/cmup/).
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.