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NETMORPH: A Framework for the Stochastic Generation of Large Scale Neuronal Networks With Realistic Neuron Morphologies

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Abstract

We present a simulation framework, called NETMORPH, 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 studying the complex relationship between neuronal morphology and global patterns of synaptic connectivity. Possible future developments of NETMORPH are discussed.

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Acknowledgment

The development of the NETMORPH code by Dr. Randal Koene was supported by the Netherlands Organization for Scientific Research (Nederlandse Organisatie voor Wetenschappelijk Onderzoek) through the Program Computational Life Sciences grant CLS2003 (635.100.005) to Dr. Jaap van Pelt and Dr. Arjen van Ooyen, and by the EC Marie Curie Research and Training Network (RTN) NEURoVERS-it 019247. The validation of NETMORPH was additionally supported by the EU BIO-ICT Project SECO (grant 216593). The authors thank Nikos Green for contributing data sets of cultured neurons.

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Authors and Affiliations

  1. Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research, VU University Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, the Netherlands

    Randal A. Koene, Betty Tijms, Peter van Hees, Frank Postma, Alexander de Ridder, Jaap van Pelt & Arjen van Ooyen

  2. Netherlands Institute for Neuroscience, Meibergdreef 47, 1105, BA, Amsterdam, the Netherlands

    Ger J. A. Ramakers

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  1. Randal A. Koene
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  2. Betty Tijms
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  3. Peter van Hees
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  4. Frank Postma
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  6. Ger J. A. Ramakers
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  7. Jaap van Pelt
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  8. Arjen van Ooyen
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Correspondence to Arjen van Ooyen.

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Koene, R.A., Tijms, B., van Hees, P. et al. NETMORPH: A Framework for the Stochastic Generation of Large Scale Neuronal Networks With Realistic Neuron Morphologies. Neuroinform 7, 195–210 (2009). https://doi.org/10.1007/s12021-009-9052-3

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