mirok/neuronmi repository overview

⁠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