Cx3D is a tool for simulating the growth of cortex in 3D developed at the Institute of Neuroinformatics of the University of Zürich and ETH Zürich.
New: A public Beta release of a
parallelized version of Cx3D, known as Cx3Dp is now available on
request from Andreas Hauri.
Cx3Dp scales with the number of cores and machines available, in speed
and in the size of simulation possible; the complete memory and processing
power of the available machines can be exploited. It allows the simulation of
millions of cells that interact with each other both biochemically and
physically.
The following figure taken from
Frédéric Zubler's PhD thesis shows the
results of a cortical development simulation. In a laminated structure representing the
cortical layers, various cells extend axons and dendrites, reproducing the typical
branching patterns of five different types of cortical neurons.
From left to right: a layer 2/3 pyramidal cell; a layer 4 spiny stellate cell;
a layer 5 pyramidal cell; a layer 6 pyramidal cell; and a layer 2/3 basket cell.
The top row shows the individual cells;
the bottom row shows the cells in the context of the cortical layers.
The following video generated from Cx3D was shown at the BIO-ICT Convergence Workshop in Brussels on 25th February 2010.
It shows the simulation of the lamination of a column of mouse cerebral cortex.
We simulated the production of a laminated column of mouse cerebral cortex starting with one single precursor cell, which contains the instruction code. In the first stage, the cell divides symmetrically and forms the neural epithelium. Cells of the neural epithelium undergo asymmetrical divisions to generate layer I cells (yellow) and then subplate cells (light grey), whereas the cells at the bottom differentiate into radial glial cells and generate growing fibers.
In the second phase, dividing cells in the ventricular zones differentiate into sub-populations of excitatory neurons and migrate along the radial glial fibers into the cortical plate. The neurons follow a guidance cue secreted by the cells in Layer I, which causes the inside-out formation of the different Layers (VI-V-IV-II/III).
Once the laminar structure is layed out, we simulate the tangential migration of a few inhibitory cells. Both excitatory and inhibitory cells grow neurites according to their specific cell type and the chemicals found in their local environment.
For further videos, follow this link.
Tutorial
Original Research Article:
Zubler, F. and Douglas, R. (2009) A framework for modeling the growth and development of neurons and networks.
Front. Comput. Neurosci. 3:25. doi:10.3389/neuro.10.025.2009
Sample code included in the source that produces the figures in the paper
Google groups discussion group http://groups.google.com/group/cx3d
A comparison of Cx3D and another simulation tool, called NETMORPH, was published by an independant group:
J. Aćimović, T. Mäki-Marttunen, R. Havela, H. Teppola, and M.-L. Linne,
"Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D",
EURASIP Journal on Bioinformatics and Systems Biology, vol. 2011, Article ID 616382, 13 pages, 2011. doi:10.1155/2011/616382
cx3d-0.03.zip
ICJNN.zip - source code for simulation presented at WCCI 2010
Cx3D is written in Java, which can be downloaded
here.
Cx3D is distributed under the
GNU General Public License version 3:
Cx3D is a tool for simulating the growth of cortex in 3D.
Copyright (C) 2009, 2010 Universität Zürich, Eidgenossische Technische Hochschule (ETH) Zürich, Andreas Hauri, Roman Bauer, & Toby Weston.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
All enquiries about Cx3D should be directed to Andreas Hauri.
Cx3D has been developed with the support of the
SECO EU Project (EU grant 216593).
