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

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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.
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:
Simulation Environment: GENESIS; MATLAB;
Model Concept(s): Parameter Fitting; Simplified Models; Parameter sensitivity;
Implementer(s): Lepora, Nathan [n.lepora at];
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;
function simChan(id, t,Vs, chan,chan_sc,Vhalf, dir_sim,dir_model)

% ensure names of appropriate format for genesis
wdir = cd; cd ~; hdir = cd; cd(wdir); 
if all(~strcmp(dir_sim(1),{'/','~'})); dir_sim = [wdir,'/',dir_sim]; end
if strcmp(dir_sim(1),'~'); dir_sim = [hdir,dir_sim(2:end)]; end

if all(~strcmp(dir_model(1),{'/','~'})); dir_model = [wdir,'/',dir_model]; end
if strcmp(dir_model(1),'~'); dir_model = [hdir,dir_model(2:end)]; end

if ~iscell(chan); chan = {chan}; end; nchan = length(chan); rchan = 1:nchan;
for k = rchan; if all(~strcmp(chan{k}(1),{'/','~'})); chan{k} = [wdir,'/',chan{k}]; end; end
for k = rchan; if strcmp(chan{k}(1),'~'); chan{k} = [hdir,chan{k}(2:end)]; end; end

% save voltage
if ~isdir(dir_sim); mkdir(dir_sim); end; cd(dir_sim);
if ~isdir([dir_sim,'/voltage']); mkdir([dir_sim,'/voltage']); end
for j = 1:size(Vs,2)
    file_voltage{j} = [dir_sim,'/voltage/voltage',num2str(j),'.dat ']; 
    tV = [t,Vs(:,j)]; save(file_voltage{j}(1:end-1),'tV','-ascii'); 

% channels
if ~iscell(chan); chan = {chan}; end; nchan = length(chan);

% genesis scales
v = chan_sc;
ox_Xinf = v(:,1)./v(:,2)-Vhalf(:,1).*(1-1./v(:,2)); ox_Xtau = v(:,1);
sx_Xinf = v(:,2); sx_Xtau = ones(nchan,1);
sy_Xtau = v(:,3); 
ox_Yinf = v(:,4)./v(:,5)-Vhalf(:,2).*(1-1./v(:,5)); ox_Ytau = v(:,4);
sx_Yinf = v(:,5); sx_Ytau = ones(nchan,1);
sy_Ytau = v(:,6);

%% write channels to genesis file

fid = fopen('runSim.g','w');
fprintf(fid,'str loc_chans="/channels"\n');
fprintf(fid,'create neutral {loc_chans}\n');

for i = 1:nchan
    fprintf(fid,'create neutral temp_chan\n');
    fprintf(fid,'pushe temp_chan\n');  
    fprintf(fid,['    str chan_dir="',fileparts(chan{i}),'" \n']);
    fprintf(fid,['    include ',chan{i},'\n']);
    fprintf(fid,['    scaletabchan {el #[CLASS=channel]} X minf ',num2str(sx_Xinf(i)),' 1 ',num2str(ox_Xinf(i)),' 0 \n']);
    fprintf(fid,['    scaletabchan {el #[CLASS=channel]} X tau ',num2str(sx_Ytau(i)),' ',num2str(sy_Xtau(i)),' ',num2str(ox_Xtau(i)),' 0 \n']);
    fprintf(fid,['    scaletabchan {el #[CLASS=channel]} Y minf ',num2str(sx_Yinf(i)),' 1 ',num2str(ox_Yinf(i)),' 0 \n']);
    fprintf(fid,['    scaletabchan {el #[CLASS=channel]} Y tau ',num2str(sx_Ytau(i)),' ',num2str(sy_Ytau(i)),' ',num2str(ox_Ytau(i)),' 0 \n']);
    fprintf(fid, '    move {el #[CLASS=channel]} {loc_chans}\n');
    fprintf(fid,'pope temp_chan\n');

fprintf(fid,['str files_voltage="',file_voltage{:},'"\n']);
fprintf(fid,['str dir_out="',dir_sim,'"\n']);
fprintf(fid,['include ',dir_model,'/simChan.g\n']);

%% run genesis 

[s,d] = system('genesis -nox -notty -batch runSim.g > dump.txt');

% report on settings
disp(['dir_sim = "',dir_sim,'"']);
disp(['dir_model = "',dir_model,'"']);
for k = rchan; disp(['channel_',num2str(k),' = "',chan{k},'"']); end
disp(' ');

%% HACK - delete final line of data_Ik (genesis IO problem)

% fid = fopen([dir_sim,'/data_Ik.dat'],'r+');
% fseek(fid,-1000,'eof'); i = find(fread(fid,1000)==10,1,'last');
% fseek(fid,i-1000,'eof'); fprintf(fid,repmat(' ',[1000-i 1]));
% fclose(fid);


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