Neuron recipes

The diffusion MRI signal arising from neurons can be numerically simulated by solving the Bloch-Torrey partial differential equation. In order to facilitate the diffusion MRI simulation of realistic neurons by the research community, we constructed finite element meshes for a group of 36 pyramidal neurons and a group of 29 spindle neurons whose morphological descriptions were found in the publicly available neuron repository NeuroMopho.org Chengran Fang, Van-Dang Nguyen, Demian Wassermann, Jing-Rebecca Li (2020). These finite elements meshes range from having 15163 nodes to 622553 nodes. We also broke the neurons into the soma and dendrite branches and created finite elements meshes for these cell components. Through the Neuron Module, these neuron and components finite element meshes can be seamlessly coupled with the functionalities of SpinDoctor to provide the diffusion MRI signal that can be attributed to spins inside neurons.

The neuron models and the measurement data are from Giorgio A. Ascoli, Duncan E. Donohue, Maryam Halavi (2007) and Karli K Watson, Todd K Jones, John M Allman (2006).

The neuron mesh files are available at https://github.com/SpinDoctorMRI/RealNeuronMeshes.

The table below lists the names and the finite element mesh sizes of the group of 36 pyramidal neurons and the group of 29 spindle neurons.

The following table shows the morphological characteristics for the neurons.