Detailed visualization and morphometric analysis of reconstructed neurons using Blender and Python

Abstract

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 License. The main script is able to read the ASC file format from Neurolucida (MicroBrightField, Inc.), the most commonly used system for single neuron recon-struction, and parse the following structures: cell body contour, axonal trees, dendritic trees, spines and varic-osities. The script offers several options for rendering