ASCENT
v1.1.2
Contents:
Metadata required to model an in vivo experiment using the ASCENT pipeline
Installation
ASCENT data hierarchy
Your first run
Helper Scripts
Command-Line Arguments
Template for methods reporting
Enums
JSON configuration files
JSON file parameter guide
Python utility classes
Submitting NEURON jobs
Morphology Files
Python MockSample class for creating binary masks of nerve morphology
Python classes for representing nerve morphology (Sample)
Creating sample specific nerve morphologies in COMSOL
Micro Leads cuff measurements
Library of part primitives for electrode contacts and cuffs
Creating custom preset cuffs from instances of part primitives
Creating new part primitives
Cuff placement on nerve
Fiberset
Implementation of NEURON fiber models
Simulation Protocols
ModelWrapper Class
Making geometries in COMSOL (Part class)
Control of medium surrounding nerve and cuff electrode
Java utility classes
Defining and assigning materials in COMSOL
Definition of perineurium
Data interchange between COMSOL and NEURON
Python simulation class
NEURON launch.hoc
NEURON Wrapper.hoc
Data analysis tools
Convergence analysis example
Sim4Life validation
Comparison of MRG fit to Bucksot 2019
ASCENT Troubleshooting Guide
Paper References
ASCENT
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