The NETMORPH Core

Please note

Unfortunately, the previous authoritative pages for the project at neurodynamics.nl were lost in a recent update of servers. Luckily, safe backups of the NETMORPH code and documentation were preserved by Dr. Koene.

These pages will be redesigned to become the new authoritative site for the project code.

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



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.

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.

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 the project page at the Neuroinformatics Group at the Department of Integrative Neurophysiology of CNCR at the VU University Amsterdam: www.neurodynamics.nl/netmorph.html.

Sample scripts to use with the NETMORPH simulation environment: www.neurodynamics.nl/NETMORPH/netmorph_scripts.html. (Please see note at top with link to materials.)




Additional development of the NETMORPH Core was carried out at the Neural Engineering Corporation (Massachusetts): Neural-Engineering.Org.

Contact:


Subpages (1): Examples
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netmorph-pub1.0.tar.gz
(643k)
Randal Koene,
May 26, 2020, 10:04 PM