Parameter estimation for Hodgkin-Huxley based models of cortical neurons (Lepora et al. 2011)

 Download zip file 
Help downloading and running models
Accession:136808
Simulation and fitting of two-compartment (active soma, passive dendrite) for different classes of cortical neurons. The fitting technique indirectly matches neuronal currents derived from somatic membrane potential data rather than fitting the voltage traces directly. The method uses an analytic solution for the somatic ion channel maximal conductances given approximate models of the channel kinetics, membrane dynamics and dendrite. This approach is tested on model-derived data for various cortical neurons.
Reference:
1 . Lepora NF, Overton PG, Gurney K (2012) Efficient fitting of conductance-based model neurons from somatic current clamp. J Comput Neurosci 32:1-24 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I Na,t; I L high threshold; I T low threshold; I K; I M;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Parameter Fitting; Simplified Models; Parameter sensitivity;
Implementer(s): Lepora, Nathan [n.lepora at shef.ac.uk];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; I Na,t; I L high threshold; I T low threshold; I K; I M;
%% ==============================
% load simulated Xk Yk parameters
%================================
function [t,X_k,Y_k,E_k,Gbar_k,p_k,q_k,chan] = load_XYk(dir_output,rt)

% read Ik simulation data 
data_Xk = load([dir_output,'/data_Xk.dat']);
data_Yk = load([dir_output,'/data_Yk.dat']);
nchan = size(data_Xk,2)-1; rchan = 1:nchan;

% read channel parameters
[ignore chan ignore E_k ignore Gbar_k ignore p_k ignore q_k] =...    
    textread([dir_output,'/data_Xk.dat',file_k],'%s %s %s %f %s %f %s %f %s %f',nchan); 

% extract data (vector format)
t1 = data_Xk(rt,1); Xchan1 = data_Xk(rt,1+rchan); clear data_Xk;
t1 = data_Yk(rt,1); Ychan1 = data_Yk(rt,1+rchan); clear data_Yk;

% change data to array format (recogise cols from diff(t)<0)
n = [1; find(diff(t1)<0)+1; length(t1)+1]; 
nt = min(diff(n))-1; t = t1(1:nt); clear t1; % be careful with nt here - can give error
nsim = length(n)-1; 

Xchan = zeros(nt,nsim,nchan);
Ychan = zeros(nt,nsim,nchan);
for j= 1:nsim
    X_k(:,j,:) = Xchan1(n(j):n(j)+nt-1,:);
    Y_k(:,j,:) = Ychan1(n(j):n(j)+nt-1,:);
end
clear Xchan1 Ychan1;

end

Loading data, please wait...