Cx3D: Cortex simulation in 3D

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: Cx3Dp, a parallelized version of Cx3D, is now available for download, see below. 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.

Cx3D Simulation Examples

Lamination of a Column of Mouse Cerebral Cortex

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.

Video 9InvFfnAkus on YouTube

For further similar videos, visit YouTube.

Simulation of a Self-Organizing Neural Network using Axonal Growth Rules

This simulation shows randomly arranged neurons (in 2D) making synaptic contacts with each other by using axon retraction and arborization. The purple cells are inhibitory neurons which (like certain basket-cell types) have denser and more spatially restricted arborizations than the excitatory cells shown in red.

Video 9InvFfnAkus on YouTube

Documentation & Published Papers

> Tutorial
> 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 above paper
> A comparison of Cx3D and another simulation tool, called NETMORPH, was published by an independent 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
> Article: Zubler, F., Hauri, A., Pfister, S., Whatley, A. M., Cook, M. and Douglas, R. (2011) An instruction language for self-construction in the context of neural networks. Front. Comput. Neurosci. 5:57. doi:10.3389/fncom.2011.00057
> Article: Bauer, R., Zubler, F., Hauri, A., Muir, D. R. and Douglas, R. J. (2012) Developmental Origin of Patchy Axonal Connectivity in the Neocortex: A Computational Model. Cerebral Cortex. doi:10.1093/cercor/bhs327
> Article: Zubler, F., Hauri, A., Pfister, S., Bauer, R., Anderson, J. C., Whatley, A. M. and Douglas, R. J. (2013) Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects. PLoS Computational Biology. 9(8):e1003173. doi:10.1371/journal.pcbi.1003173


> Cx3Dp (parallel version): The latest code can be checked out from our public read-only Subversion repository at
> - 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: GPLv3 Free Software

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.


The following people have contributed to Cx3D and/or Cx3Dp:

>Rodney J. Douglas *
>Andreas Hauri
>Frederic Zubler *
>Sabina Pfister *
>Gabriela Michel *
>Roman Bauer
>Adrian M. Whatley *
>Toby Weston

* NB. These contributors contributed to Cx3D or Cx3Dp while employed by the University of Zurich and/or ETH Zurich. The copyright in their contributions thus rests with those institutions and for this reason their names do not appear in the copyright notice.


All enquiries about Cx3D should be directed to Gabriela Michel.


Cx3D has been developed with the support of the SECO EU Project (EU grant 216593).
SECO project logo

Last modified: Tue 7 May 15:05 CEST 2019

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