neuroVIISAS: The Integration of Atlases and Connectomes for Modeling
-
1
University of Rostock, Anatomy, Germany
Modeling supports the understanding of complex biological systems like nervous systems and whole organisms. The building blocks to generate models of organisms are heterogeneous and involve multiple structures (organs and their subdivisions, regions of the CNS and their connections) and functions (motor action, perception, dynamics of the stimulus-response behavior). neuroVIISAS (neuro Visualization, Imagemapping, Information System for Analysis and Simulation) is build to allow the integration of structures in terms of 3D-reconstructions, connections and modeling of neuron populations (Schmitt and Eipert, 2012). It is an open environment with regard to import and export of data and a generic tool that can be used for the development of digital atlases, brain mapping, connectome and simulation projects of all types of nervous systems. For the modeling of populations of neurons the NEural Simulation Tool (NEST v 2.2.1) is used (Gewaltig and Diesmann, 2007). This approach enables the modeler to use more realistic connectome data for an accurate definition of connections between populations of neurons in NEST. How this is achieved will be demonstrated with examples of basal ganglia networks (Fig. 1). Furthermore, the interactions of visualization, simulation and analysis of complex neuronal networks will be shown. In addition to high level analysis and visualization functions of neuroVIISAS the import of connectivity data will be explained. The software can be downloaded from http://neuroviisas.med.uni-rostock.de/index-Dateien/Page455.htm.
Figure 1: The bilateral basal ganglia network. The hierarchical triangle visualization shows the subdivision of regions. The adjacency matrix shows color coded weights of connections. The smart organic graph layout with orthogonal bus router and symmetry option displays the color coded bilateral connections.
References
Gewaltig M-O, Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2(4):1430.
Schmitt O, Eipert P (2012) neuroVIISAS: approaching multi-scale simulation of the rat connectome. Neuroinformatics 10: 243-67.
Keywords:
connectome,
atlasing,
Simulations,
neuroontology,
visualization
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Demo
Topic:
Computational neuroscience
Citation:
Eipert
P and
Schmitt
O
(2013). neuroVIISAS: The Integration of Atlases and Connectomes for Modeling.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00016
Copyright:
The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers.
They are made available through the Frontiers publishing platform as a service to conference organizers and presenters.
The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated.
Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed.
For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions.
Received:
04 Mar 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Prof. Oliver Schmitt, University of Rostock, Anatomy, Rostock, 18057, Germany, schmitt@med.uni-rostock.de