LGNcircuit: Minimal LGN network model of temporal processing of visual input (Norheim et al. 2012)

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Accession:153092
The responses of relay cells in the lateral geniculate nucleus (LGN) are shaped by their diverse set of impinging inputs: feedforward synaptic inputs stemming from retina, and feedback inputs stemming from the visual cortex and the thalamic reticular nucleus. This MATLAB model, with an easy-to-use graphical user interface (GUI), explores possible roles of these feedforward and feedback inputs in shaping the temporal part of the receptive fields of LGN relay cells with, so called, ON symmetry. A minimal mechanistic firing-rate model tailored to elucidate salient feedforward and feedback effects is considered including, in particular, feedforward excitation and inhibition (via interneurons) from retinal ON cells and excitatory and inhibitory (via thalamic reticular nucleus cells and interneurons) feedback from cortical ON and OFF cells. Various types of visual stimuli can be explored: flashing spots, impulses, sinusoidal gratings.
Reference:
1 . Norheim ES, Wyller J, Nordlie E, Einevoll GT (2012) A minimal mechanistic model for temporal signal processing in the lateral geniculate nucleus. Cogn Neurodyn 6:259-81 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neural mass;
Brain Region(s)/Organism:
Cell Type(s): Thalamus geniculate nucleus/lateral principal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s): Tutorial/Teaching; Rate-coding model neurons; Vision;
Implementer(s): Norheim, Eivind [norheim.eivind at gmail.com];
Search NeuronDB for information about:  Thalamus geniculate nucleus/lateral principal GLU cell;
function LGNcircuit

% LGN_GUI Give input vector/function to the LGN relay cell and choose
% parameters. The GUI plots the resulting LGN response including separate
% components of the response, if requested.
    
    % including the data files and data file path
    file_reg = ['dataFiles' filesep '*.dat'];
    file_struct = dir(file_reg);
    filenames = cell(1, length(file_struct));
    for ifile = 1:length(file_struct)
        filenames(1,ifile)=cellstr(file_struct(ifile).name);
    end
    
    data_path = ['dataFiles' filesep];
    addpath(data_path);
    
    % Setting default parameter values    
    lgn_struct=struct('eta_ffi',0.7,'tau_rg',20,'tau_rig',50,'Delta_rig',0,...
        'l_rON',-1,'w_fbON',0,'w_fbOFFx',0,'tau_rc',20,'Delta_fb',10,...
        'l_cON',0.1,'l_cOFF',-0.1);
    in_struct=struct('form','vec',...
        'interpol_method','linear',...
        'data_file',' ','mode','gui');
    
    % Set properties for the parameters table
    rowname = {'eta_ffi', 'tau_rg', 'tau_rig', 'Delta_rig', 'l_rON' 'w_fbON',...
        'w_fbOFFx', 'tau_rc', 'Delta_fb', 'l_cON', 'l_cOFF'};
    rowname_tab = {'eta_ffi', 'tau_rg (ms)', 'tau_rig (ms)', 'Delta_rig (ms)',...
        'l_rON','w_fbON','w_fbOFFx', 'tau_rc (ms)', 'Delta_fb (ms)', 'l_cON',...
        'l_cOFF'};
    
    dat = {lgn_struct.eta_ffi;...
        lgn_struct.tau_rg;...
        lgn_struct.tau_rig;...
        lgn_struct.Delta_rig;...
        lgn_struct.l_rON;...
        lgn_struct.w_fbON;...
        lgn_struct.w_fbOFFx;...
        lgn_struct.tau_rc;...
        lgn_struct.Delta_fb;...
        lgn_struct.l_cON;...
        lgn_struct.l_cOFF};
    columnname = {'Value'};
    columnformat = {'numeric'};
    columneditable = true;
    columnwidth = {80};
    
    ih1 = 1;
    
    % Initialize and hide GUI at construction.
    f_width=900;
    f_height=900;
    f = figure('Visible','off','Tag','gui',...
        'Position',[0,100,f_width,f_height]);
    %    'BackgroundColor',[0.5 0.5 0.5],...
    % Define an axes that covers the whole figure
    %ax_root = axes('position', [0,0,1.0,1.0]); 
    
    % Construct the components
    bcgp = uipanel('Parent',f,'Units','pixels',...
        'BackgroundColor',[.7 .7 .7],...
        'Position',[0,0,f_width,f_height]); 
    mp = uipanel('Parent',f,'Title','LGNcircuit','Units','pixels',...
        'Position',[570,160,315,720]);
%     inputform_text = uicontrol(mp,'Units','pixels','Style','text',...
%         'String','Select input format','Position',[10,730,160,20]);
%     inputform_pop = uicontrol(mp,'Units','pixels','Style','popupmenu',...
%         'String',{'Data file'},...
%         'Position',[10,695,180,35],...
%         'BackgroundColor','w',...
%         'Callback',{@popup_callback});
%     ipf_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
%         'String','Help',...
%         'Position',[200,704,105,30],...
%         'Tag','ipf',...
%         'Callback',{@helpbutton_callback});
    inputdata_text = uicontrol(mp,'Units','pixels','Style','text',...
        'String','Data file',...
        'Position',[10,665,100,20]);
    inputdata_pop = uicontrol(mp,'Units','pixels',...
        'Style','popupmenu',...
        'String',filenames,...
        'BackgroundColor','w',...
        'Position',[10,630,180,30],...
        'Callback',{@datapop_callback});
    ipd_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
        'String','Help',...
        'Tag','ipd',...
        'Position',[200,640,105,30],...
        'Callback',{@helpbutton_callback});
%     interpolate_text = uicontrol(mp,'Units','pixels','Style','text',...
%         'String','Numerical interpolation method','Position',[10,295,160,40]);
%     interpolate_pop = uicontrol(mp,'Style','popupmenu',...
%         'String',{'linear','spline','pchip','nearest'},...
%         'Position',[10,270,180,30],'Tag','interpop',...
%         'BackgroundColor','w',...
%         'Callback',{@interpop_callback});
%     intp_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
%         'String','Help',...
%         'Tag','intp',...
%         'Position',[200,274,105,30],...
%         'Callback',{@helpbutton_callback});
    im_panel = uipanel('Parent',mp,...
        'Title','Model system',...
        'Units','pixels',...
        'BackgroundColor','w',...
        'Position',[10,325,295,291]);
    im_ax = axes('Parent',im_panel,...
        'Units','pixels','Position',[10,10,275,251]);
    im=image(imread('model6.jpg'),'Parent',im_ax);
        axis off;
        %set(hObject,'Color','white');
    param_panel = uipanel('Parent',mp,...
        'Title','Loop parameters',...
        'Units','pixels',...
        'Position',[10,40,240,260]);
    param_table = uitable(param_panel,...
        'Data',dat,...
        'ColumnName',columnname,...
        'ColumnFormat',columnformat,...
        'ColumnEditable',columneditable,...
        'ColumnWidth',columnwidth,...
        'RowName',rowname_tab,...
        'Units','pixels',...
        'Position',[5,5,230,230],...
        'CellEditCallback',{@table_callback});
    ptab_help = uicontrol(mp,'Units','pixels','Style','pushbutton',...
        'String','Help',...
        'Tag','ptab',...
        'Position',[260, 45, 45, 247],...
        'Callback',{@helpbutton_callback});
    hold_check = uicontrol(f,'Style','checkbox',...
        'String','Keep the current plot',...
        'Value',0,...%'BackgroundColor','w',...
        'Position',[640,110,180,30],...
        'Callback',{@holdcheck_callback});
    simulate = uicontrol(f,'Units','pixels','Style','pushbutton',...
        'String','Simulate',...
        'Position',[675,70,90,30],...
        'Callback',{@simulatebutton_callback});
    mailauthor = uicontrol(f,'Units','pixels','Style','pushbutton',...
        'String','Contact Authors',...
        'Position',[665,30,110,30],...
        'Callback',{@mailauthor_callback});
    messages = uicontrol(f,'Units','pixels','Style','text',...
        'String',' ',...
        'Position',[570,10,315,20]);
    
    a1 = axes('Units','pixels','Tag','a1','Position',[90,90,450,405]);
    grid on
    a2 = axes('Units','pixels','Tag','a2','Position',[90,585,450,270]);
    grid on
    %a3 = axes('Position',[0.1,0.1,0.5,0.15]);
    %grid on
    
    
    % Initialize the code
    % Change units of the figure, so it resizes automatically
    set([f, bcgp, mp, ...
        inputdata_text, inputdata_pop, ipd_help, ...    
        param_panel, param_table, ptab_help, ...
        hold_check, simulate, mailauthor, messages, ...
        a1, a2, im_panel,im_ax],'Units','normalized');
    %    inputform_text,inputform_pop,ipf_help,...
    %    interpolate_text,interpolate_pop,intp_help,...
    
    % Generate initial data
    set([a1,a2],'FontSize',20)
    xlabel(a1,'Time t (ms)')
    ylabel(a1,'LGN response')
    ylabel(a2,'Cortical response')
    %ylabel(a3,'Response')
    
    % Make the GUI visible
    set(f,'Visible','on')
    
    function popup_callback(source, eventdata) 
        % Determine the selected input form
        str = get(source, 'String');
        val = get(source, 'Value');
        % Set current input to the selected input
        switch str{val};
            case 'Data file'
                in_struct.form = 'vec';
                set(inputdata_text,'String','Data file');
                set(inputdata_edit,'String','Provide a data file')
            case 'Function'
                in_struct.form = 'fnc';
                set(inputdata_text,'String','Function name/path');
                set(inputdata_edit,'String','Provide a function name')
            case 'In-line'
                in_struct.form = 'ilfnc';
                set(inputdata_text,'String','In-line function');
                set(inputdata_edit,'String','Provide an in-line function (use t for time)')
        end
        
    end
    
    function helpbutton_callback(source,eventdata)
        % Opens the respective help file
        str = get(source, 'Tag');
        hfile = ['helpFiles/' str '_help.pdf'];
        open(hfile);            
    end

    function datapop_callback(source, eventdata) 
        % Set data parameters
        str = get(source, 'String');
        val = get(source, 'Value');
        switch in_struct.form
            case 'vec'
                data=load(str{val});
                in_struct.t_in=data(:,1);
                in_struct.r_in=data(:,2);
                in_struct.data_file = str{val};
                clear data
                plot(a1,in_struct.t_in,in_struct.r_in, 'k--',...
                    'LineWidth',2);
                set(a1,'FontSize',20)
                legend(a1,'r_g')        
                ylabel(a1,'LGN response')
                [y1max,y1min] = find_max(a1);
                axis(a1,[0,max(in_struct.t_in),1.2*y1min,1.2*y1max])
                set([a1,a2],'XGrid','on','YGrid','on')
            case 'fnc'
                in_struct.h=user_string;
            case 'ilfnc'
        end
    end
    
    function interpop_callback(source, eventdata)
        % Determines the selected interpolation method
        str = get(source,'String');
        val = get(source,'Value');
        in_struct.interpol_method = str{val};
    end

    function table_callback(source, eventdata) %#ok<INUSL>
        % Update the parameter struct
        i=eventdata.Indices(1);
        val=str2double(eventdata.EditData);
        parname=cell2mat(rowname(i));
        lgn_struct.(parname)=val;
    end

    function holdcheck_callback(source, eventdata)
        val = get(source,'Value');
        if val == 0
            set([a1,a2],'NextPlot','replace')
            set(messages,'String',' ')
            ih1=1;
        elseif val ==1
            set([a1,a2],'NextPlot','add')
        end
    end
        
    function simulatebutton_callback(source, eventdata) %#ok<INUSD>
        % Simulate and plot
        
        % Create the waitbar
        w = waitbar(0,'Computing','Position',[300,300,288,60]);
        
        % load the first data file if there is no other data set 
        if strcmp(in_struct.data_file,' ')
            str = get(inputdata_pop,'String');
            val = get(inputdata_pop,'Value');
            defaultf=str{val};
            data=load(defaultf);
            in_struct.t_in=data(:,1);
            in_struct.r_in=data(:,2);
            in_struct.data_file = defaultf;
            clear data
        end
        
        % convolution of input with feedforward kernel
        [in_struct.t_g,in_struct.r_g]=filterMyInput(lgn_struct, in_struct);
        
        % evaluate the ode/dde governing the dynamics
        if (lgn_struct.Delta_fb==0)
            [t_rtmp,r_rtmp] = evaluate_ode(lgn_struct, in_struct);
        else
            [t_rtmp,r_rtmp] = evaluate_dde(lgn_struct, in_struct);
        end
        
        % Unpacking some parameters
        l_rON = lgn_struct.l_rON;
        l_cON = lgn_struct.l_cON;
        l_cOFF = lgn_struct.l_cOFF;
        
        % Setting the time vector
        t_r=in_struct.t_g;
        
        % smoothing the solution by interpolation        
        r_rn=interp1(t_rtmp,r_rtmp,t_r,in_struct.interpol_method);
        r_cON = (r_rn - l_cON) .* (r_rn - l_cON >= 0);
        r_cOFF = (-r_rn + l_cOFF) .* (-r_rn + l_cOFF >= 0);
        r_r = (r_rn - l_rON) .* (r_rn - l_rON >=0) + l_rON;
        clear t_rtmp r_rtmp r_cONtmp r_cOFFtmp
        % set the time vector for the cortical solution, no delay in
        % feedforward connection at the time...
        t_c = t_r;      % + lgn_struct.Delta_fb;
        % pack the solution and time vectors into the 'in_struct'
        in_struct.t_r=t_r;
        in_struct.t_c=t_c;
        in_struct.r_r=r_r;
        in_struct.r_cON=r_cON;
        in_struct.r_cOFF=r_cOFF;
        
        % dump parameters and in/out data to file tmp.mat
        save tmp.mat lgn_struct in_struct
        
        % unpack input vectors
        t_in=in_struct.t_in;
        r_in=in_struct.r_in;
            
        % ploting the results
        pl1 = plot(a1,[t_in;t_r(end)],[r_in;r_in(end)], '--',t_r,r_r,'-',...
            'LineWidth',2);
        set(a1,'FontSize',20)
        legend(a1,'r_g','r_r')        
        xlabel(a1,'Time t (ms)')
        ylabel(a1,'LGN response')
        [y1max,y1min] = find_max(a1);
        axis(a1,[0,max(t_r)-120,1.2*y1min,1.2*y1max])
        
        pl2 = plot(a2,[0; t_c],[0; r_cON],'-',...
            [0;t_c],[0; r_cOFF],'--',...
            'LineWidth',2);
        set(a2,'FontSize',20)
        legend(a2,'r_c^{ON}','r_c^{OFF}')
        ylabel(a2,'Cortical response')

        [y2max,y2min] = find_max(a2);
        if y2max == y2min
            axis(a2,[0,max(t_r),0,0.2])
        else
            axis(a2,[0,max(t_r)-120,1.2*y2min,1.2*y2max])
        end
        
%         plot(a3,[0; t_c],[0; r_cOFF],'k-',...
%             'LineWidth',2)
%         set(a3,'FontSize',20)
%         legend(a3,'r_c^{OFF}')
%         xlabel(a3,'Time t (ms)')
%         ylabel(a3,'Response')
%         [y3max,y3min] = find_max(a3);        
%         axis(a3,[0,max(t_r),1.2*y3min,1.2*y3max])
        
        set([a1,a2],'XGrid','on','YGrid','on')
        
        % setting colors for successive plots        
        %h1=get(a1,'Children');
        %ih1=length(h1)/2;
        linecol = ['k','b','r','c','m','y'];      
        if get(hold_check,'Value') == 1
            if ih1<length(linecol)
                ih1=ih1+1;
                col = linecol(ih1);                
            else
                set(messages,'String','All colors chosen, black will be used')
                col = 'k';
            end
        else 
            col = 'k';
        end
        set([pl1,pl2],'Color',col)        
        set(pl1(1),'Color','k')
        
        close(w)
        %set(messages,'String','Done');        
    end
    
    function mailauthor_callback(source, eventdata)
        web mailto:gaute.einevoll@nmbu.no
    end
end

function [yxmax,yxmin] =  find_max(ax)
    % function to find the max point of the lines in a plot
    hx=get(ax,'Children');
    yxraw = get(hx,'YData');
    if iscell(yxraw)
        m = size(yxraw);
        yxmax=0;
        yxmin=0;
        for icell = 1:m
            yxdata = cell2mat(yxraw(icell));
            yxmax_tmp = max(yxdata);
            yxmin_tmp = min(yxdata);
            if yxmax_tmp > yxmax
                yxmax=yxmax_tmp;
            end
            if yxmin_tmp < yxmin
                yxmin = yxmin_tmp;
            end
        end
    else
        yxmax=max(max(yxraw,[],2));
        yxmin=min(min(yxraw,[],2));
    end
end

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