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ViNERS (Visceral Nerve Ensemble Recording & Stimulation) peripheral neural interface modeling environment

Calvin D Eiber, Ph.D.
,
James Fallon, Ph.D.
,
Peregrine Osborne, Ph.D.
,
Janet R Keast, Ph.D.

ViNERS (Visceral Nerve Ensemble Recording & Stimulation) is a MATLAB-based neural interface modeling pipeline for modeling peripheral neural interface stimulation and recording performance for individual axons and whole-nerve ensembles.

Updated on December 15, 2021 (Version 1)

Corresponding Contributor:

Janet Keast
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Dataset Overview

Study Purpose:ViNERS (Visceral Nerve Ensemble Recording & Stimulation) is a MATLAB-based peripheral neural interface model incorporating electrode array geometry, the nerve and fascicle geometry, and the distributions of axon ultrastructural and biophysical properties within the nerve. ViNERS is an automated, MATLAB+NEURON-based simulation pipeline which combines multidomain electro-anatomical electric field models and biophysical models of individual myelinated and unmyelinated visceral axons to compute nerve-electrode coupling, action potential firing, and single-fibre action potentials (SFAPs), which may then be combined to simulate electrically-evoked compound action potentials (ECAPs).

Data Collected: ViNERS uses GMSH to generate finite-element meshes, EIDORS to simulate electrical fields and sensitivity functions, and NEURON to simulate individual axons. A setup and installation script has been included which will walk you through the process of installing ViNERS and its dependencies on your system.

Usage Notes: Running a simulation in ViNERS can be broken into several steps, as demonstrated in the example script:

  1. Set up the array, nerve, and axon population to be simulated using models.electrode_array, mesh.insert_gmsh_fascicles, and models.axon_population.
  2. Generate a mesh and electric fields using models.nerve_anatomy
  3. Generate membrane current templates using models.membrane_currents
  4. (if needed) compute nerve stimulation responses using models.nerve_stimulation or models.axon_thresholds
  5. (if needed) compute ensemble or single-axon nerve recordings using models.nerve_recording or models.axon_sfap
  6. (if needed) combine axon responses to electrical stimulation into whole-nerve recording using models.ECAP_recording
  7. Visualise your results using the visualisations in the +plots package.

See Files for more details about the data files generated by each of these steps.


Curator's Notes

Experimental design: A computation model.

Completeness: This dataset is a part of a larger study: ViNERS (Visceral Nerve Ensemble Recording & Stimulation) peripheral neural interface modeling environment.

Subjects & Samples: N/A (computational modeling dataset)

Primary vs. derivative data: N/A (computational modeling dataset)

Code Availability: https://gitlab.unimelb.edu.au/lab-keast-osborne-release/ViNERS

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About this dataset

Publishing history

December 15, 2021
Originally Published
December 15, 2021 (Version 1)
Last Updated

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