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Neuroinformatics

, Volume 10, Issue 3, pp 243–267 | Cite as

neuroVIISAS: Approaching Multiscale Simulation of the Rat Connectome

  • Oliver Schmitt
  • Peter Eipert
Original Article

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 small-world properties of the Watts-Strogatz model. Furthermore, synchronized subpopulations, oscillations of 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 data-analysis-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

Anterior commissure

AC

Amygdaloid complex

AD

Aqua destillata

AVCN

Anteroventral cochlear nucleus

BSTam

Bed nucleus of the stria terminalis anterior division anteromedial nucleus

hrs

Hours

neuroVIISAS

neuro Visualization, Information, Image, Simulation and Analysis System

CC

Central canal

cc

Corpus callosum

C. elegans

Caenorhabditis elegans

CNS

Central nervous system

CPu

Caudate putamen

ihf

Interhemispheric fissure

IT

Implicit terminologies

LH

Lateral hypothalamic area

LT

List of terms

MPO

Medial preoptic area

min

Minute

PAG

Periaqueductal gray

PB

Phosphate buffer

pc

Posterior commissure

pcf

Precommissural fornix

PHL

Peripeduncular lateral hypothalamus

resp

respective

ROI

Region of interest

SN

Substantia nigra

SNR

Substantia nigra pars reticulata

SNC

Substantia nigra pars compacta

VNTB

Ventral nucleus of the trapezoid body

VTK

Visualization Toolkit

Notes

Acknowledgements

The authors thank Manfred Tasche of the Department of Mathematics of the University of Rostock for sharing his expertise and superior help in preparing the manuscript. We appreciate Andreas Wree of the Department of Anatomy for his critical discussions about the rat and mouse brain neuroanatomy. The authors extend their special thanks to Klaus-Peter Schmitz (Department of Biomedical Engineering, University of Rostock) for the support of the neuroVIISAS project. We thank Frauke Winzer, Susanne Lehmann, Hannah Ormanns, Konstanze Phillip and Richard Kettlitz for their faithful work on extending the database and mappings. We would like especially to thank Heidi Schumann and Christian Tominsky (Department of Computergraphics, University of Rostock) for introducing CGV for visualizing neuronal connectivities and Erik Virtel for realizing motif analysis. Sönke Langner (Baltic Imaging Center, University of Greifswald) supported the MRI measurements. All work was supported by the Faculty of Mathematics and Natural Sciences and of the Faculty of Medicine of the University of Rostock.

Supplementary material

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© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of AnatomyRostockGermany

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