Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis

Frontiers in Computational Neuroscience
Stephan GreinGillian Queisser

Abstract

Neuron classification is an important component in analyzing network structure and quantifying the effect of neuron topology on signal processing. Current quantification and classification approaches rely on morphology projection onto lower-dimensional spaces. In this paper a 3D visualization and quantification tool is presented. The Density Visualization Pipeline (DVP) computes, visualizes and quantifies the density distribution, i.e., the "mass" of interneurons. We use the DVP to characterize and classify a set of GABAergic interneurons. Classification of GABAergic interneurons is of crucial importance to understand on the one hand their various functions and on the other hand their ubiquitous appearance in the neocortex. 3D density map visualization and projection to the one-dimensional x, y, z subspaces show a clear distinction between the studied cells, based on these metrics. The DVP can be coupled to computational studies of the behavior of neurons and networks, in which network topology information is derived from DVP information. The DVP reads common neuromorphological file formats, e.g., Neurolucida XML files, NeuroMorpho.org SWC files and plain ASCII files. Full 3D visualization and projections of the density to 1D a...Continue Reading

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Software Mentioned

NLMorphologyConverter
Matlab
Neurolucida system MicroBrightField
VRLP
Netbeans
studio
Gradle
NeuroMorpho
Windows
ProjectToXYZAxisDensityDecorator

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