Impact of dendritic size and topology on pyramidal cell burst firing (van Elburg and van Ooyen 2010)

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Accession:114359
The code provided here was written to systematically investigate which of the physical parameters controlled by dendritic morphology underlies the differences in spiking behaviour observed in different realizations of the 'ping-pong'-model. Structurally varying dendritic topology and length in a simplified model allows us to separate out the physical parameters derived from morphology underlying burst firing. To perform the parameter scans we created a new NEURON tool the MultipleRunControl which can be used to easily set up a parameter scan and write the simulation results to file. Using this code we found that not input conductance but the arrival time of the return current, as measured provisionally by the average electrotonic path length, determines whether the pyramidal cell (with ping-pong model dynamics) will burst or fire single spikes.
Reference:
1 . van Elburg RA, van Ooyen A (2010) Impact of dendritic size and dendritic topology on burst firing in pyramidal cells. PLoS Comput Biol 6:e1000781 [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: Neocortex;
Cell Type(s): Neocortex V1 L6 pyramidal corticothalamic GLU cell;
Channel(s): I Na,t; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Activity Patterns; Bursting; Spatio-temporal Activity Patterns; Simplified Models; Active Dendrites; Influence of Dendritic Geometry; Detailed Neuronal Models; Methods;
Implementer(s): van Elburg, Ronald A.J. [R.van.Elburg at ai.rug.nl];
Search NeuronDB for information about:  Neocortex V1 L6 pyramidal corticothalamic GLU cell; I Na,t; I K; I M; I K,Ca; I Sodium; I Calcium; I Potassium;
% Filename: simplifiedTopologiesDConst.m
%
% Calculate burstmeasure for all 23 simplified toplogies over a range of
% lengths, with somatic stimulation.
%
%
% Author:   Ronald A.J. van Elburg ,(RonaldAJ at vanelburg eu)
% Affiliation:
%           Department of Artificial Intelligence
%           Groningen University
%
% Set path to location spike analysis script
clear all
close all


addpath(genpath('./../analysis'))

FilenameBase='SimplifiedTopologiesDConst/Results/Sim_';
FilenameBase2='SimplifiedTopologiesDConst/Results/IC';


Filename='';
ISI_Cutoff=3000;
Analysis_Start=1000;

% Specify endianness
machineformat='l';

% Morphological parameter ranges
bStim =1:1;

Length_step=25;
Length_start=500;
Length_end=2500;
Length_simrange=Length_start:Length_step:Length_end;
Length_plotrange=1:1:length(Length_simrange);

Topology_step=1;
Topology_start=1;
Topology_end=23;
Topology_simrange=Topology_start:Topology_step:Topology_end;
Topology_plotrange=1:1:length(Topology_simrange);

x_plotrange=Length_plotrange;
x_simrange=Length_simrange;
x_plot_size=length(x_plotrange);

y_plotrange=Topology_plotrange;
y_simrange=Topology_simrange;
y_plot_size=length(y_plotrange);

offset=-1;

f=zeros(bStim(end),x_plot_size,y_plot_size);
B2=zeros(bStim(end),x_plot_size,y_plot_size);
MeanISI=zeros(bStim(end),x_plot_size,y_plot_size);
IC=zeros(bStim(end),x_plot_size,y_plot_size);
MEP=zeros(bStim(end),x_plot_size,y_plot_size);

DendArea=zeros(bStim(end),x_plot_size,y_plot_size);

fMat=zeros(x_plot_size,y_plot_size);
ICMat=zeros(x_plot_size,y_plot_size);
B2Mat=zeros(x_plot_size,y_plot_size);
DendAreaMat=zeros(x_plot_size,y_plot_size);
MepMat=zeros(x_plot_size,y_plot_size);

for somaStimulus=bStim 
    for y_coord=1:1:y_plot_size     % Topology
        for x_coord=1:1:x_plot_size % Length

            Filename=[FilenameBase,'0_0_',num2str(somaStimulus+offset),'_',num2str(y_plotrange(y_coord)+offset),'_',num2str(x_plotrange(x_coord)+offset),'_spikes_spikes_soma.dat'];        
            j4a_spikes_soma=nrn_vread(Filename,machineformat);
            
            Filename=[FilenameBase2,'_',num2str(y_plotrange(y_coord)+offset),'_',num2str(x_plotrange(x_coord)+offset),'_ic.dat'];       
            [ic,dummy]=nrn_vread(Filename,machineformat);
            IC(somaStimulus,x_coord,y_coord)=ic;
                        
            Filename=[FilenameBase2,'_',num2str(y_plotrange(y_coord)+offset),'_',num2str(x_plotrange(x_coord)+offset),'_da.dat'];       
            da=nrn_vread(Filename,machineformat);
            DendArea(somaStimulus,x_coord,y_coord)=da;
  
            Filename=[FilenameBase2,'_',num2str(y_plotrange(y_coord)+offset),'_',num2str(x_plotrange(x_coord)+offset),'_mep.dat'];        
            mep=nrn_vread(Filename,machineformat);
            MEP(somaStimulus,x_coord,y_coord)=mep;
            
            [B2(somaStimulus,x_coord,y_coord),MeanISI(somaStimulus,x_coord,y_coord)] = burstMeasure(j4a_spikes_soma(j4a_spikes_soma > Analysis_Start),ISI_Cutoff);

            f(somaStimulus,x_coord,y_coord)=spikeFrequency(j4a_spikes_soma(j4a_spikes_soma > Analysis_Start));
            
        end
   end
end




%%
bStim=1;
figure(8)
clf

scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])

   
    
    subplot(3,3,3)
    yvalues=zeros(23,1);
    yvalues(:)=B2( bStim,31,:);
    plot(1:23,yvalues,'k.')
    xlim([0,24])
    ylim([-0.1,1.1])

    subplot(3,3,[1:2,4:5,7:8])
    hold on
    NoOfColors=23;
    vspace=0.05;
  
    for y_coord=1:1:y_plot_size;            
        ColorShift=mod(y_coord-1,NoOfColors)/(NoOfColors-1);
        plot(x_simrange(x_plotrange),B2( bStim,:,y_coord)+vspace*(23-y_simrange(y_plotrange(y_coord))),'-','Color',[1-ColorShift,ColorShift,ColorShift])

        set(gca,'Box','off')
        xlabel('Length')
        ylabel('Burstiness')
        ylim([-0.1,1.1+22*vspace])
    end





%%
figure(9)
clf

scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])

%orient landscape
FirstVarMeshParams=Topology_simrange;
SecondVarMeshParams=Length_simrange;

% Meshing things up ...
[FirstVarMesh,SecondVarMesh] = meshgrid(FirstVarMeshParams, SecondVarMeshParams);

somaStimulus=1;
fMat(:,:)=f( somaStimulus,:,:);
ICMat(:,:)=IC( somaStimulus,:,:);
B2Mat(:,:)=B2( somaStimulus,:,:);
DendAreaMat(:,:)=DendArea( somaStimulus,:,:);
MepMat(:,:)=MEP( somaStimulus,:,:);
        
subplot(1,8,1:3)
        cla
        hold on
        image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
        [C,h] =contour(FirstVarMesh,SecondVarMesh,ICMat*1000,0:1:8,'w','Linewidth',3);
        % Set the area to be plotted
        axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
        clabel(C,h,'Color','w')
        caxis auto
        caxis([0,1])
        title('Bursting and IC' )
        ylabel('Length \mum')
        xlabel('Topology')
    
subplot(1,8,4:6)
        cla
        hold on
        image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
        [C,h] =contour(FirstVarMesh,SecondVarMesh,MepMat,0.07:0.07:0.5,'w','Linewidth',3);
        clabel(C,h,'Color','w')
        % Set the area to be plotted
        axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
        clabel(C,h,'Color','w')
        caxis auto
        caxis([0,1])
        title('Bursting and MEP' )
        set(gca,'Ytick',[])
         xlabel('Topology')

subplot(2,8,7:8)
        cla
        hold on
        image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
        % Set the area to be plotted
        axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
        clabel(C,h,'Color','w')
        caxis auto
        caxis([0,1])
        colorbar('EastOutside','YTick',0:0.5:1,'YTicklabel',{'B=0.0','B=0.5','B=1.0'})
        set(gca,'Ytick',[],'Xtick',[])




%%
figure(901)
clf

scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])

%orient landscape
FirstVarMeshParams=Topology_simrange;
SecondVarMeshParams=Length_simrange;

% Meshing things up ...
[FirstVarMesh,SecondVarMesh] = meshgrid(FirstVarMeshParams, SecondVarMeshParams);

somaStimulus=1;
fMat(:,:)=f( somaStimulus,:,:);
ICMat(:,:)=IC( somaStimulus,:,:);
B2Mat(:,:)=B2( somaStimulus,:,:);
DendAreaMat(:,:)=DendArea( somaStimulus,:,:);
MepMat(:,:)=MEP( somaStimulus,:,:);



subplot(1,9,1:3)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,ICMat*1000,0:1:8,'w','Linewidth',3);

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    clabel(C,h,'Color','w')
    caxis auto
    caxis([0,1])
    title('Bursting and IC')
    ylabel('Length \mum')
    xlabel('Topology')

subplot(1,9,4:6)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,MepMat,0.07:0.07:0.5,'w','Linewidth',3);
    clabel(C,h,'Color','w')

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    clabel(C,h,'Color','w')
    caxis auto
    caxis([0,1])
    title('Bursting and MEP' )
    xlabel('Topology')

subplot(1,9,7:9)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,B2Mat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,DendAreaMat,'w','Linewidth',3);
    clabel(C,h,'Color','w')

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    clabel(C,h,'Color','w')
    caxis auto
    caxis([0,1])
    title('Bursting and DendArea' )
     xlabel('Topology')






%%
figure(902)
clf

scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])

%orient landscape
FirstVarMeshParams=Topology_simrange;
SecondVarMeshParams=Length_simrange;

% Meshing things up ...
[FirstVarMesh,SecondVarMesh] = meshgrid(FirstVarMeshParams, SecondVarMeshParams);

somaStimulus=1;
 
fMat(:,:)=f( somaStimulus,:,:);
ICMat(:,:)=IC( somaStimulus,:,:);
B2Mat(:,:)=B2( somaStimulus,:,:);
DendAreaMat(:,:)=DendArea( somaStimulus,:,:);
MepMat(:,:)=MEP( somaStimulus,:,:);

subplot(1,9,1:3)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,fMat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,ICMat*1000,0:1:8,'w','Linewidth',3);

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    clabel(C,h,'Color','w')
    caxis auto

    title('Frequency and IC' )
    ylabel('Length \mum')
    xlabel('Topology')

subplot(1,9,4:6)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,fMat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,MepMat,0.05:0.07:0.5,'w','Linewidth',3);
    clabel(C,h,'Color','w')

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    clabel(C,h,'Color','w')
    caxis auto

    title('Frequency  and MEP' )
    xlabel('Topology')


subplot(1,9,7:9)
    cla
    hold on

    image(FirstVarMeshParams,SecondVarMeshParams,fMat,'CDataMapping','scaled')
    [C,h] =contour(FirstVarMesh,SecondVarMesh,DendAreaMat/1000,4:2:30,'w','Linewidth',3); % Scaling of matrix fixes a matlab bug.
    %      [C,h] =contour(FirstVarMesh,SecondVarMesh,DendAreaMat,'w','Linewidth',3);
    clabel(C,h,'Color','w')

    % Set the area to be plotted
    axis( [FirstVarMesh(1),FirstVarMesh(end),SecondVarMeshParams(1),SecondVarMeshParams(end)] )
    caxis auto

    title('Frequency  and DendArea' )
    xlabel('Topology')



%%
figure(903)
clf
bStim=1;
scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])

for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,1)
        hold on
        plot(DendArea( somaStimulus,:,y_coord),B2( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        set(gca,'Box','off')
        xlabel('Dendritic Surface Area')
        ylabel('Burstiness')
        
    end
    xlim([min(DendArea(:)),max(DendArea(:))])
end

for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,2)
        hold on
        plot(IC( somaStimulus,:,y_coord),B2( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        set(gca,'Box','off')
        xlabel('Input Conductance')
        ylabel('Burstiness')
    end
     xlim([min(IC(:)),max(IC(:))])
end

for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,3)
        hold on
        plot(MEP( somaStimulus,:,y_coord),B2( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        
        set(gca,'Box','off')
        xlabel('MEP')
        ylabel('Burstiness') 
    end
     xlim([min(MEP(:)),max(MEP(:))])
end

%%
figure(904)
clf
bStim=1;
scrsz = get(0,'ScreenSize');
set(gcf,'Position',[1 scrsz(4) scrsz(3)/2 scrsz(4)])
for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,1)
        hold on
        plot(DendArea( somaStimulus,:,y_coord),f( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        set(gca,'Box','off')
        xlabel('Dendritic Surface Area')
        ylabel('Frequency')
        
    end
    xlim([min(DendArea(:)),max(DendArea(:))])
end

for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,2)
        hold on
        plot(IC( somaStimulus,:,y_coord),f( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        set(gca,'Box','off')
        xlabel('Input Conductance')
        ylabel('Frequency')
    end
     xlim([min(IC(:)),max(IC(:))])
end

for somaStimulus=bStim
    for y_coord=1:1:y_plot_size;
        
        subplot(3,1,3)
        hold on
        plot(MEP( somaStimulus,:,y_coord),f( somaStimulus,:,y_coord) ,'-','Color',[1-y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23,y_simrange(y_plotrange(y_coord))/23])
        
        set(gca,'Box','off')
        xlabel('MEP')
        ylabel('Frequency') 
    end
     xlim([min(MEP(:)),max(MEP(:))])
end


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