NeuroMaC’s documentation

NeuroMaC is a phenomenological, computational framework to generate large numbers of virtual neuronal morphologies (and resultant microcircuits) simultaneously according to growth-rules expressed in terms of interactions with the environment.

  • NeuroMaC: Neuronal Morphologies & Circuits
  • Computational framework: a suite of software tools built around a central concept
  • Virtual neuronal morphologies: 3D digital descriptions of neuronal shape (both axons and dendrites)
  • Microcircuits: Morphologies are generated together in a simulated volume. With the addition of connections rules circuits emerge.
  • Interactions: Growth-cones branch, terminate and elongate. Each of these steps can be influenced by environmental cues. Most obvious is guidance through repulsion and attraction to simulated cues.
  • Phenomenological: Neither biochemical pathways nor physics are simulated. As such, growth is purely phenomenological. NeuroMaC is not a simulator of actual neuronal development.

Warning

Currenly, a prototype of NeuroMaC is implemented in Python. This version is a proof-of-principle and nothing beyond that. This prototype has many limitations and we are working towards a non-prototype version, which should be released in the next year. The current prototype code is freely available.

Reference

When using NeuroMaC, please refer to the following paper:

Benjamin Torben-Nielsen & Erik De Schutter. Context-aware modelling of neuronal morphologies. Frontiers in Neuroanatomy, 8:92. doi: 10.3389/fnana.2014.00092.

License

NeuroMac - Neuronal Morphologies and Circuits

Copyright (C) 2014 Ben Torben-Nielsen & Okinawa Institute of Science and Technology, Japan.,

NeuroMac 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.

NeuroMaC 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.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

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