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This article is part of the supplement: Sixteenth Annual Computational Neuroscience Meeting: CNS*2007

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iBrain: a simulation and visualization tool for activation of brain areas on a realistic 3D brain image

Tohru Suzuki1, Norio Fujimaki2 and Kazuhisa Ichikawa1*

Author Affiliations

1 Department of Brain and Bioinformation Science, Kanazawa Institute of Technology, Hakusan, Ishikawa, Japan

2 Biological ICT Group, Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, Kobe, Hyougo, Japan

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BMC Neuroscience 2007, 8(Suppl 2):P13  doi:10.1186/1471-2202-8-S2-P13

The electronic version of this article is the complete one and can be found online at:

Published:6 July 2007

© 2007 Suzuki et al; licensee BioMed Central Ltd.


Many computer models have been developed to simulate a neuron, neural networks, and activation of brain areas aimed at the elucidation of mechanisms of brain functions. In this track there is one clear direction of modeling from a single cell to the whole brain [1]. We developed a simulation and visualization tool, "iBrain", by which we could construct, simulate and visualize a model of the transition of brain activation on a realistic brain anatomical atlas.


The modeling and simulation parts were constructed by modifying the software tool for a biological cell, "A-Cell". Users can construct a Brodmann area-level model through A-Cell like GUI. The simulation algorithm is the same as that in A-Cell. In the visualization part, an anatomical atlas of human brain was constructed from the data of "Talairach Daemon Client" superimposing them on the human brain MRI volume of "ICBM template" from LONI. This allows users to see the shape and position of various anatomical regions of the brain from mm to hemisphere resolution in the realistic 3D brain (Fig. 1). The activation patterns calculated in the simulation are visualized on this brain image.

thumbnailFigure 1. An example of Brodmann area display in "iBrain".


To test the simulator, we tried to reproduce the activation patterns of a human's word processing which were measured by MEG (magneto-encephalogram). The reproduced patterns were roughly matched to the patterns from the experiment and we could see them visually on the iBrain.


Simulation and visualization of spatio-temporal activation of brain areas on a realistic 3D brain image can be realized by iBrain. We believe this software can help us to understand the brain function at macroscopic level.


  1. Markram H: The blue brain project.

    Nat Rev Neurosci 2006, 7:153-160. PubMed Abstract | Publisher Full Text OpenURL