neuroVIISAS: Approaching Multiscale Simulation of the Rat Connectome
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ORIGINAL ARTICLE
neuroVIISAS: Approaching Multiscale Simulation of the Rat Connectome Oliver Schmitt · Peter Eipert
Published online: 15 February 2012 © Springer Science+Business Media, LLC 2012
Abstract neuroVIISAS is a generic platform which allows the integration of neuroontologies, mapping functions for brain atlas development, and connectivity data administration; all of which are required for the analysis of structurally and neurobiologically realistic simulations of networks. What makes neuroVIISAS unique is the ability to integrate neuroontologies, image stacks, mappings, visualizations, analyzes and simulations to use them for modelling and simulations. Based on the analysis of over 2020 tracing studies, atlas terminologies and registered histological stacks of images, neuroVIISAS permits the definition of neurobiologically realistic networks that are transferred to the simulation engine NEST. The analysis on a local and global level, the visualization of connectivity data and the results of simulations offer new possibilities to study structural and functional relationships of neural networks. This paper describes the major components and techniques of how to analyse, visualize and simulate with neuroVIISAS shown on a model network at a coarse CNS level (106 regions, 1566 connections) out of 13681 regions and 134043 connections of the left and right part of the CNS. This network of major components of the left and right hemisphere has smallworld properties of the Watts-Strogatz model. Furthermore, synchronized subpopulations, oscillations of
Electronic supplementary material The online version of this article (doi:10.1007/s12021-012-9141-6) contains supplementary material, which is available to authorized users. O. Schmitt (B) · P. Eipert Department of Anatomy, Gertrudenstraße 9, 18055 Rostock, Germany e-mail: [email protected]
rate distributions and a time shift of population activities of the left and right hemisphere were observed in the neurocomputational simulations. In summary, a generic platform has been developed that realizes dataanalysis-visualization integration for the exploration of network dynamics on multiple levels. Keywords Nervous systems · Brainmapping · Neuroimaging · Connectivity · Terminology · Ontology · Stereotactic atlas · Information retrieval · Visualization · Data integration · Data analysis · Mouse brain · Rat brain · Human brain · MRI · Cell atlas · Modeling · Simulation · Computational neuroscience Abbreviations ac AC AD AVCN BSTam hrs neuroVIISAS
CC cc C. elegans CNS CPu ihf IT LH
Anterior commissure Amygdaloid complex Aqua destillata Anteroventral cochlear nucleus Bed nucleus of the stria terminalis anterior division anteromedial nucleus Hours neuro Visualization, Information, Image, Simulation and Analysis System Central canal Corpus callosum Caenorhabditis elegans Central nervous system Caudate putamen Interhemispheric fissure Implicit terminologies Lateral hypothalamic area
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LT MPO min PAG PB pc pcf PHL resp ROI SN SNR SNC VNTB VTK
Neuroinform (2012
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