FEM simulator for realistic neuron models and probes

Docker based installation installation (recommended)

We recommend using our docker container which has all the dependencies preinstalled.

You can pull the docker container with:

docker pull mirok/neuronmi

And run the container with a shared folder in the current directory with:

docker run -ti -v $(pwd):/home/fenics/shared mirok/neuronmi

Manual installation

The following are dependencies of neuronmi and how they can be obtained

1. Generating meshes for neuron simulations with EMI models

We rely on Gmsh for both mesh generation and geometry defition. All is done via python API of Gmsh. The gmsh module has to be on python path. For the current shell session this can be accomplised by running

export PYTHONPATH=`pwd`:"$PYTHONPATH"

in the directory where gmsh.py resides (e.g. /usr/local/lib/).

2. Partial differential equation part of EMI

The solver requires FEniCS version 2017.2.0. In our experience the simplest way of installation that also plays along nicely with Gmsh is by using the dedicated Ubuntu package.

3. Ordinary differential equation part of EMI

Membrane physics is solved for using cbc.beat (which depends on dolfin-adjoint).

Testing

Run from current directory

python -m unittest discover ./test/mesh
python -m unittest discover ./test/simulators/solver

Running the demo scripts

We provide two demo scripts to:

1. Simulate ephaptic effects between a pair of neurons

2. Simulate the effect of neural probes on extracellular action potentials

To run the demo scripts, go into the demo folder and run:

python ephaptic_effect.py

python probe_effect.py