MembranePotentialMapping

UG4 plugin providing functionality to map membrane potential values calculated with the NEURON simulator to 3D plasma membrane surfaces for simulations with ug4.

Installation

Enable the plugin by cmake -DMembranePotentialMapping=ON during ug4 configuration and provide NEURON installation directory by -DMPMNEURON=/path/to/your/local/neuron/installation.

The user can decide which version to use, for compability reasons a stable version (v7.3) which works for all platforms is used, but the user can specify also to use the HEAD revision of the NEURON development branch by -DMPMNEURON_REVISION=ON or the v7.3 branch by -DMPMNEURON_REVISION=OFF (default).

Enable the Boost testsuite

To enable the Boost testsuite issue the following command: cmake -D MPMTestsuite=ON.

Issues

Static builds will prevent NEURON's .mod files from being loaded, thus use a dynamic build by -DSTATIC_BUILD=OFF.

How to use

There are two ways to do this:

1. Running Neuron in advance and writing the membrane potential values to file. They can then be read by the Vm2uGMPM class.
2. Running Neuron at the same time as the 3D simulation. The membrane potential values can then be mapped using the NeuronMPM class.