3D reconstruction of neurons from confocal image stacks and visualization of computational modeling experiments

Abstract

In this study we perform precise geometrical 3D reconstructions of high complex neuronal architectures. First, confocal microscopy was used to scan neurons with submicron resolution. Second, we extracted the center-lines and diameters of the neuron by means of our reconstruction method, and third we used these metric data to generate compartment models that were transported into the proprietary format of modeling software such as NEURON or GENESIS. Fourth, routines were developed in the scripting language of the respective modeling program to perform computational modeling, and finally we transferred the modeling results to the visualization program AMIRA (Indeed Visual Concepts GmbH).