The NETMORPH Core

The publication Koene, R.A., et al. (2009). NETMORPH: A Framework for the Stochastic Generation of Large Scale Neuronal Networks With Realistic Neuron Morphologies, Neuroinformatics, 7(3), pp.195-210, doi: 10.1007/s12021-009-9052-3 (PDF) describes the core framework and its validation, and includes a number of static representations of example results.

Please note that the NETMORPH source code is now maintained on GitHub at https://github.com/randalkoene/netmorph.

Alternatively, you can download a compressed archive of the source code and accompanying materials here: netmorph-pub1.0.tar.gz

The files in the GitHub repository contain the base code needed to build the netmorph and netmorph2D generator programs, and a curated minimum set of scripts and tools to get going. Additional example scripts are available from the development version of the NETMORPH source tree. Please contact the author for more information.

NETMORPH is a simulation environment for the developmental generation of 3D large-scale neuronal networks with realistic neuron morphologies. In NETMORPH, neuronal morphogenesis is simulated from the perspective of the individual growth cone. For each growth cone in a growing axonal or dendritic tree, its actions of elongation, branching and turning are described in a stochastic, phenomenological manner. In this way, neurons with realistic axonal and dendritic morphologies, including neurite curvature, can be generated. Synapses are formed as neurons grow out and axonal and dendritic branches come in close proximity of each other. NETMORPH is a flexible tool that can be applied to a wide variety of research questions regarding morphology and connectivity. Research applications include the formation of synaptic connectivity during development and the complex relationship between neuronal morphology and global patterns of synaptic connectivity.

NETMORPH is the result of the joint efforts of Randal A. Koene, Betty Tijms, Peter van Hees, Frank Postma, Sander de Ridder, Sacha Hoedemaker, Jaap van Pelt and Arjen van Ooyen of the Neuroinformatics Group at the Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, Amsterdam, the Netherlands. This work was made possible by grants from NL NWO-CLS2003 CASPAN (635.100.005), EU MC-RTN NEURoVERS-it (019247) and EU BIO-ICT SECO (216593) to Jaap van Pelt and Arjen van Ooyen.

Animated output from NETMORPH is demonstrated in the example files provided in the Examples folder of this site. Please note: Due to restrictions on the file size the quality of the movies is quite low and does not reflect the accuracy of results achieved with NETMORPH.

To use NETMORPH, obtain the NETMORPH Core package and follow the installation guidelines within. The latest version of the packaged NETMORPH Core Files are obtained through on the GitHub page at https://github.com/randalkoene/netmorph.

Additional sample scripts to use with the NETMORPH simulation environment are available from the development tree.

Contact: