Characterization of peripheral nerve recordings

This is the repository for the article Biophysical characterization of the recording of unmyelinated and myelinated fiber activity with peripheral interfaces. iScience (2025). DOI: 10.1016/j.isci.2025.112495.

Authors: Claudio Verardo, Simone Romeni, Silvestro Micera

Code overview

• hm: Matlab classes to instatiate hybrid models and simulate SUAPs
• neuron: Python functions to generate the fiber excitation templates in Neuron
• run_simulations: Matlab scripts to simulate the data used in the paper
• run_analyses: Matlab scripts to reproduce the figures of the paper

Requirements

• Matlab R2023a
• Python 3.10.11
• Comsol Multiphysics 6.1 (with LiveLink for Matlab)
• Neuron 8.2.2

Installation

• Add Python dependencies (from terminal)

pip install -r requirements.txt

• Compile the Neuron mechanisms (from terminal)

nrnivmodl neuron/fibers/mod_mrg02
nrnivmodl neuron/fibers/mod_sundt15

• Add paths (from Matlab): run setup.m

Getting started

Generate fiber excitation templates

cd neuron
python excitation_template_fibers_parallel.py internode-CV DIR_DATA N_CORES

• DIR_DATA: path to the directory where to store the simulated data
• N_CORES: number of CPU cores to use for the simulations

Instantiate hybrid models and simulate SUAPs

Execute the following Matlab script(s) in run_simulations depending of the figure(s) data you want to reproduce. The figure panels related to each script are listed at the first lines of its code. DIR_DATA must be specified at the beginning of each script before executing it.

• sim1_SUAPs.m
• sim2_SUAPs_along_fiber.m
• sim3_SUAPs_along_fiber_perineurium.m
• sim4_SUAPs_along_fiber_cuff_coverage.m
• sim5_SUAPs_along_fiber_cuff_design.m
• sim6_SUAPs_along_fiber_chronic.m

NOTE: the Comsol LiveLink for Matlab must be active (mphstart command). Please, refer to the official documentation for further details.

Reproduce figures of the paper

Execute the following Matlab script(s) in run_analyses depending of the figure plot(s) you want to reproduce. The figure panels related to each script are listed at the first lines of the script. DIR_DATA must be specified at the beginning of each script before executing it.

• fig1_SUAPs_overview.m
• fig2_S1_SUAPs_spatial_maps.m
• fig3_4_S3_S4_SUAPs_fixed_distance.m
• fig3_4_S3_S4_SUAPs_overlap_win.m
• fig5_6_SUAPs_vs_distance_violin.m
• fig5_SUAPs_perineurium.m
• fig6_SUAPs_perineurium.m
• fig6_SUAPs_cuff_coverage.m
• fig6_SUAPs_cuff_design.m
• fig7_SUAPs_overlap_win_chronic.m

NOTE: the SUAPs data must be simulated beforehand (see previous section).