Human auditory periphery model: cochlea, IHC-AN, auditory brainstem responses (Verhulst et al 2018)

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Accession:246535
The human auditory periphery model can simulate single-unit response of basilar-membrane vibration, IHC receptor potential, instantaneous AN/CN/IC firing rates, as well as population responses such as otoacoustic emissions, auditory brainstem responses. The neuron models (IHC, AN,CN,IC) can be run independently to relate their responses to electrophysiology, or be simulated as part of the human auditory periphery.
References:
1 . Verhulst S, Altoè A, Vasilkov V (2018) Computational modeling of the human auditory periphery: Auditory-nerve responses, evoked potentials and hearing loss. Hear Res 360:55-75 [PubMed]
2 . Altoè A, Pulkki V, Verhulst S (2018) The effects of the activation of the inner-hair-cell basolateral K+ channels on auditory nerve responses. Hear Res 364:68-80 [PubMed]
3 . Altoè A, Pulkki V, Verhulst S (2014) Transmission line cochlear models: improved accuracy and efficiency. J Acoust Soc Am 136:EL302-8 [PubMed]
4 . Verhulst S, Dau T, Shera CA (2012) Nonlinear time-domain cochlear model for transient stimulation and human otoacoustic emission. J Acoust Soc Am 132:3842-8 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism:
Cell Type(s): Cochlea hair inner GLU cell; Cochlear nucleus bushy GLU cell; Auditory nerve; Brainstem neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Python; MATLAB;
Model Concept(s):
Implementer(s): Verhulst, Sarah [s.verhulst at ugent.be]; Altoé, Alessandro ;
Search NeuronDB for information about:  Cochlear nucleus bushy GLU cell; Cochlea hair inner GLU cell;
close all;
clear all;

%this file runs an example simulation for a click stimulus of different
%stimulus levels

L=[0 10 20 30 40 50 60 70 80 90 100];
fs=100e3;
p0=2e-5;
dur=50e-3;
t=(0:1/fs:dur);
click_duration=10; % 100 us click
stim=zeros(numel(L),length(t)); %the simulation runs as long as the stimulus

%depending on the number of cores you have, you can run more or less stimuli in one simulation
%the dimensions are: conditions x duration (the code takes care of it in case you do the inverse)
for j=1:numel(L) 
    stim(j,10:10+click_duration)=p0*10^(L(j)/20)*sqrt(2)*2;
end
%to set the amplitude of the stimulus, the digital 1 is multiplied with a
%Pascal value:
%   for rms: make a stimulus with rms of 1: multiply with p0*10^(L_{SPLindB}/20);
%   for pure tone: multiply A with sqrt(2)*p0*10^(L_{SPLindB}/20)
%   for condensation click in peSPL: multiply with
%   2*sqrt(2)*p0*10^(L_{SPLindB}/20);

%% load the starting poles (alpha*,30) for NH or HI models
sheraP=load('StartingPoles.dat');
%for a hearing impaired model, load other startingpoles e.g.:
%sheraP=load('./Poles/Flat00_Slope30/StartingPoles.dat');

%% set synaptopathy and store the results
% decide how many channels you want to store in the simulations ('all','half','abr')
% decide how many fibers you want to include to compute the CN and IC responses
% default: 13 HSR (70 spikes/s), 3 MSR (10) and 3 LSR (1) fibers (across all CF-channels) , you want
% to set CF-dependent synaptopathy profiles, insert a vector of size:   
    %1000x1 for 'all'
    %500x1 for 'half'
    %401x1 for 'abr'
% the indices should correspond to the CFs simulated for that condition (output(1).cf)
% run the model ones using default settings to write out the CFs, and then
% determine your CF dependent synaptopathy profiles.

% decide which responses you want to store: 
    % e= emission 
    % v= velocity 
    % i=ihc 
    % h=hsr 
    % m=msr 
    % l=lsr 
    % b=summed AN responses for each CF as well as CN and IC responses 
    % w=population response waves I, III, V
    
% to store all channels (1000)
 output=model2018(stim,fs,'all',1,'evihmlbw',1,sheraP,0.05,'vel',13,3,3,1,[pwd(),'/']);
% to store half of the channels (500)
% output=model2018(stim,fs,'half',1,'evihmlbw',1,sheraP,0.05,'vel',13*ones(500,1),3,3,1,[pwd(),'/']);
%store only the ABR channels: CFs between 112 Hz and 12 kHz
%output=model2018(stim,fs,'abr',1,'evihmlbw',1,sheraP,0.05,'vel',13,3,3,1,[pwd(),'/']);

save('Simulations.mat','output','-v7.3')




%The model code and interface was written by Alessandro Altoè and Sarah Verhulst (copyright 2012,2014,2015,2016,2018) 
%and is licensed under the UGent acadamic license (see details in license file that is part of this repository). 
%The Verhulstetal2018Model consists of the following files: 
%tridiag.so, cochlea_utils.c, run_model2018.py, model2018.m, cochlear_model2017.py, inner_hair_cell2018.py, auditory_nerve2017.py, ic_cn2017.py, ExampleSimulation.m, ExampleAnalysis.m, the HI profiles in the Poles folder. 
 

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