NETMORPH simulator

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 Koene, Betty Tijms, Peter van Hees, Frank Postma, Sander de Ridder, Sacha Hoedemaker, Jaap van Pelt and Arjen van Ooyen from the Neuroinformatics Group at the Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, the Netherlands The work was/is supported 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.

Literature (at 2011):
Randal A. Koene, Betty Tijms, Peter van Hees, Frank Postma, Sander de Ridder, Ger Ramakers, Jaap van Pelt, Arjen van Ooyen. NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7 (2009) 195-210.

Ac'imovic' J, Mäki-Marttunen T, Havela R, Teppola H, Linne ML. 2011. Modeling of Neuronal Growth In Vitro: Comparison of Simulation Tools NETMORPH and CX3D. J. Bioinform Syst Biol. 2011:616382. doi:10.1155/2011/616382

Jaap van Pelt, Andrew Carnell, Sander de Ridder, Huibert D. Mansvelder, Arjen van Ooyen (2010). An algorithm for finding candidate synaptic sites in computer generated networks of neurons with realistic morphologies. Frontiers in Computational Neuroscience, doi:10.3389/fncom.2010.00148.

Versions NETMORPH code:



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NETMORPH manual:

NETMORPH scripts:


NETMORPH in Scholarpedia

Last Modified:
June 1, 2015