cns-oist/neuromac

NeuroMaC: simulator of the development of Neuronal Morphologies & Circuits

NeuroMaC: Neuronal Morphologies & Circuits

We think that to fully understand neuronal morphologies, circuits and their variance we have to look at the substrate at large. That is, how neurons developed and interactions between a developing neuron and the substrate (e.g., toher neurons, boundaries, capillaries,...) influence their morphology. For this purpose we developed NeuroMaC

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: this is a prototype version of NeuroMaC completely implemented in Python.

The current prototype code is freely available.

Reference: Torben-Nielsen, B., & De Schutter, E. (2014) Context-aware modeling of

neuronal morphologies. Frontiers in Neuroanatomy, 8, 92. http://doi.org/10.3389/fnana.2014.00092/abstract

neuromac's Issues

pip install

Hi, I stumbled upon your paper, and it looks interesting. There are a few things that are holding me back from using your code in my own projects:

• I don't think I can pip install it? So version/dependency management becomes tricky
• It doesn't look like the code has a public and documented API? eg, can I do something like this:

from neuromac import grow

grow("neuronA", 10000)

to "grow 10000 neurons", obviously entirely fictitious, but do such library functions exist to use neuromac in a programmatic way from Python? And is it documented?