NeMo-TMS Toolbox

Neuron Modeling for TMS (NeMo-TMS) toolbox is for multi-scale modeling of the effects of Transcranial Magnetic Stimulation on single neuron activity. The instructions and open-source codes provided here enable users with a different levels of expertese to investigate the neuronal behavior under TMS.

Refer to the following article for more details: Shirinpour et al., 2020. Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation. bioRxiv, https://doi.org/10.1101/2020.09.23.310219

Overview

This paradigm incorporates modeling at three scales:

• TMS-induced electric field calculation at the macroscopic scale
• Simulation of neuronal activity under the external electric field from the previous step
• Simulation of subcellular calcium concentrations based on the membrane voltages calculated in the previous step.

The procedures for running simulations at each scale and the intermediate steps are given in the instructions. This pipeline can run on Windows, and Linux (macOS not fully tested). However, the codes are developed to run on the native operating system's configurations and possibly not work if there are any modifications (for example, using other forms of shell).

Note: throughout this repository, neuron refers to the biological neural cells, while NEURON refers to the NEURON simulation environment used for the computational modeling of neurons.

Instructions

To run a full multi-scale model, follow the documentations in each directory in the given order. Make sure to set up the software requirements (described in the documentation in each folder) before running each step.

1. NEURON-Model-Generation generates neuron models from the morphological reconstructions of neurons (samples in Neuron_Reconstructions)
2. Export_NEURON_Segments exports the coordinates of the NEURON model segments to be used in later steps
3. Electric-Field-Modeling outlines the macroscopic electric field modeling
4. SimNIBS-NEURON-Coupling couples the electric fields in step 3 to the NEURON models generated in step 1
5. TMS_Waveform generates the TMS waveform that is used in the NEURON simulation
6. NEURON-Simulation simulates the activity of the neuron based on the data from previous steps (you can also run this step under the assumption of uniform electric field, in which case, you can skip steps 2 to 4)
7. NEURON_UG4_Interface exports the NEURON simulation data in the compatible format for calcium modeling
8. Calcium-Modeling runs the simulations for calcium concentration based on the data from step 7
9. Visualization outlines the procedure for visualizing the results

Reference

Please use the following reference to cite this toolbox: Shirinpour et al., 2020. Multi-scale Modeling Toolbox for Single Neuron and Subcellular Activity under (repetitive) Transcranial Magnetic Stimulation. bioRxiv, https://doi.org/10.1101/2020.09.23.310219

Correspondence

aopitz -at- umn.edu (Alex Opitz)