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noisy_OB_PC_network_2CG_modified.m
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noisy_OB_PC_network_2CG_modified.m
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function [Mitral GraProximal GraDistal Feedforward Pyramidal Feedback OSNsource param InputCurrent] = noisy_OB_PC_network_2CG_modified(inputFile,Delay,Wfrac)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is an adaption of two programs, bulbmain.m and piriformmain.m,
% originally developed by Licurgo de Almeida.
%
% description of the original model can be found in....
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% INPUTS:
% inputfile - txt file with parameters
% Delay - [LOTdelay OPdelay MitGABAdelay GraAMPAdelay GraGABAdelay PyrGABAdelay PyrAMPAdelay IntAMPAdelay]
% in ms
% Wfrac - a vector of length ntimepoints specifying how weights
% increase over time.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% OUTPUTS:
% Mitral, GraProximal, GraDistal, Feedforward, Pyramidal,
% Feedback - data structures including parameters and simulated neuronal activity
% OSNsource - odor matrix (simulates odor by stimulating subset of OSN)
% param - model parameters
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Starting program
tic;
if strcmpi(inputFile(end - 2:end),'txt') % if we use a txt as input, the
% program reads the txt file and create the variables, if we use a mat file,
% the program loads the variables.
% Set new rand seed.
% s = RandStream.create('mt19937ar','seed',sum(100*clock));
% RandStream.setDefaultStream(s);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Reading parameters from input file and creating neurons
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
param.inputFile = 'noisy_OB_PC_params_2CG.txt';
% Open the input file for reading
fid1 = fopen(param.inputFile,'r');
if fid1 == -1
msgbox('Could not open the input file! Make sure the filname and path are correct.','ERROR');
return;
end
str = fgetl(fid1);
% Get network parameters.
while ~strcmpi(str,'neurons')
switch lower(str)
case '' % It's possible to use blank lines to organize the
% network parameters
otherwise
param = SetNetworkParameters(param,str,Delay,Wfrac);
end
str = fgetl(fid1);
end
% Create cells
OSNfile = strcat(param.outputPath,param.OSNsource);
[param,OSNsource,Mitral,GraProximal,GraDistal,Feedforward,Pyramidal,Feedback] = CreateCells(param,OSNfile);
str = fgetl(fid1);
% Get cell parameters.
while ~strcmpi(str,'end')
switch lower(str)
case '' % It's possible to use blank lines to organize the
% neuronal parameters
case 'mitral'
celltype = 'mitral';
case 'graproximal'
celltype = 'graproximal';
case 'gradistal'
celltype = 'gradistal';
case 'feedforward'
celltype = 'feedforward';
case 'pyramidal'
celltype = 'pyramidal';
case 'feedback'
celltype = 'feedback';
otherwise
switch celltype
case 'mitral'
Mitral = SetNeuronParameters(Mitral,param.nMitral,str);
case 'graproximal'
GraProximal = SetNeuronParameters(GraProximal,param.nGraprox,str);
case 'gradistal'
GraDistal = SetNeuronParameters(GraDistal,param.nGradist,str);
case 'feedforward'
Feedforward = SetNeuronParameters(Feedforward,param.nPyramidal,str);
case 'pyramidal'
Pyramidal = SetNeuronParameters(Pyramidal,param.nPyramidal,str);
case 'feedback'
Feedback = SetNeuronParameters(Feedback,param.nFeedback,str);
end
end
str = fgetl(fid1);
end
fclose(fid1); % Close input file
fname = inputFile(1:end - 3);
fname = strcat(fname,'mat');
save(fname,'Mitral','GraProximal','GraDistal','Feedforward','Pyramidal','Feedback','OSNsource','param');
elseif strcmpi(inputFile(end - 2:end),'mat') %if the input file is .mat
% we have to
load(inputFile,'Mitral','GraProximal','GraDistal','OSNsource','param');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Neuronal activity
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[Mitral GraProximal GraDistal Feedforward Pyramidal Feedback param InputCurrent] = NeuroActivity(Mitral,GraProximal,GraDistal,Feedforward,Pyramidal,Feedback,param,OSNsource);
toc;
end
function param = SetNetworkParameters(param,str,Delay,Wfrac)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%-----------OB--------------OB----------------OB--------------------------
%
% This function sets the parameters for the different neurons
%
% Modified by Boleszek Osinski on 06/14/2013
%
% Licurgo de Almeida
% 12/20/2010
% Information not related with the parameters of different neuros.
% Path: path where we save input and output file
% dt: timestep (in ms)
% tsim: simulation time (in ms)
% tinit: stimulus begin (in ms)
% tfinal: stimulus end (in ms)
% nMitral: number of mitral cells
% nGradist: number of granule distal synapses
% nGraprox: number of granule cell soma
% GraGracon = if true, granule cells connect to each other
% DistalON = if true graded inhibitory distal Granule dendrites are present
% ProximalON = if true spiking inhibitory proximal Granule soma are present
% BulbH = Bulb height (in distance units)
% BulbW = Bulb width (in distance units)
% NoiseMit = Mitral cell noise std
% NoiseGraprox = Granule proximal dendrite noise std
% NoiseGradist = Granule distal dendrite noise std
% mFactor = multiplicative factor. number of granule cells = number of
% mitral cells * mFactor
% OSNsource = source of the OSN inputs.
% Odorant = odortant number.
% Grasource = source of the granule cells (used only for comparison
% (add the name of new parameters here)
% mitAHP = if true, mitral cells show AHP
% graAHP = if true, granule cells show AHP
% graLLD = if true, granule cells show LLD
% Respiration = if true, the input is modulated by an oscillation
% representing the respiration
% RespFreq = Respiratory frequency
% Iext = external current to OSNs
% Inoise = noise fraction of OSN input
% randfrac = fraction of uniform input to MCs
% SpikeV = Spike voltage
% CChanceGraMit = Chance of connection between Gra and Mit
% CChanceGraGra = Chance of connection between Gra
%
%
%-------------PC-------------PC-------------PC-------------PC-------------
%
%
% Modified by Boleszek Osinski on 06/14/2013
%
% Licurgo de Almeida
% 02/25/2011
% Information not related with the parameters of different neuros.
% * nPyramidal = number of pyramindal cells (and feedforward inhibitory neurons)
% * nFeedback = number of feedback inhibitory cells
% * CChancePyrPyr = Chance of connection between two different Pyramidal
% cells.
% * CChancePyrFba = Chance of connection between Pyramidal and Feedback
% cells.
% * CChanceFbaPyr = Chance of connection between Feedback and Pyramidal
% cells.
% * CChanceFfoPyr = Chance of connection between Feedforward cells and Pyramidal
% cells.
% * NoiseFfo = Feedforward neuron noise std
% * NoisePyr = Pyramidal cell noise std
% * NoiseFba = Feedback cell noise std
% * NoiseParam = true if we want a slighly variation on the parameters
% * Noiselevel = percetage of variation in each parameter
% * pyrAHP = if true, pyrAHP is ON
%
%
%-----------OBPC-----------OBPC-----------OBPC-----------OBPC-------------
%
% Boleszek Osinski 06/14/2013
%
% flagLOT = if true Mi-Pyr connection is in tact
% LOTvar = variability of LOT conduction delay (in ms)
% flagOP = if true then Pyr-Gr connection is in tact
% OPvar = variability of OP conduction delay (in ms)
% flagWLOTvar = if true mit-pyr weights are scaled at each timestep with Wfrac
% flagWOPvar = if true pyr-gra weights are scaled at each timestep with Wfrac
% flagWGRAMITvar = if true gra-mit weights are scaled at each timestep with Wfrac
% flagWMitGravar = if true mit-gra weights are scaled at each timestep with Wfrac
% CChancePyrGra = Chance of connection between Pyramidal and Granule cells
% CChanceMitPyr = Chance of connection between Mitral cells and Pyramidal cells
% CChanceMitFfo = Chance of connection between Mitral cells and Feedforward cells
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
param.Wfrac = Wfrac; % Weight fraction for scaling weights over time
param.Delay = Delay; % Synaptic latencies
str_aux = 1;
% Find parameter name
while str(str_aux) ~= ' '
str_aux = str_aux + 1;
end
ParName = str(1:str_aux - 1); % name of the parameter
ParValue = str(str_aux + 1:end); % value of the parameter
switch lower(ParName)
% OB parameters
case 'path'
param.outputPath = ParValue; %path
case 'dt'
param.dt = str2num(ParValue); %step
case 'tsim'
param.tsim = str2num(ParValue); %simulation time
case 'tinit'
param.tinit = str2num(ParValue); %stimulus begin
case 'tfinal'
param.tfinal = str2num(ParValue); %stimulus end
case 'nmitral'
param.nMitral = str2num(ParValue); %number of Mitral cells
case 'ngradist'
param.nGradist = str2num(ParValue); %number of granule distal synapses
case 'ngraprox'
param.nGraprox = str2num(ParValue); %number of Granule cell soma
case 'gragracon'
param.GraGracon = str2num(ParValue); %Gra-Gra connections
case 'distalon'
param.DistalON = str2num(ParValue); %flag distal gra dendrites
case 'proximalon'
param.ProximalON = str2num(ParValue); %flag proximal gra dendrites
case 'bulbh'
param.BulbH = str2num(ParValue); %Bulb height
case 'bulbw'
param.BulbW = str2num(ParValue); %Bulb width
case 'noisemit'
param.noisemit = str2num(ParValue); %noise Mitral
case 'noisegraprox'
param.noisegraprox = str2num(ParValue); %noise granule prox
case 'noisegradist'
param.noisegradist = str2num(ParValue); %noise granule dist
case 'preset'
param.flagpreset = str2num(ParValue); %flag preset positions
case 'mfactor'
param.mFactor = str2num(ParValue); % multiplicative factor
case 'osnsource'
param.OSNsource = ParValue; %name of the file source for OSN information
case 'odorant'
param.Odorant = str2num(ParValue); %odorant number
case 'grasource'
param.Grasource = ParValue; %name of the file source for granule cells information
case 'mitahp'
param.mitAHP = str2num(ParValue); %flag presence of mitral AHP
case 'graahp'
param.graAHP = str2num(ParValue); %flag presence of granule AHP
case 'gralld'
param.graLLD = str2num(ParValue); %flag presence of granule LLD
case 'respiration'
param.flagRespiration = str2num(ParValue); %flag respiratory modulation
case 'respfreq'
param.RespFreq = str2num(ParValue); %respiratory frequency
case 'iext'
param.Iext = str2num(ParValue); %External current to OSNs
case 'inoise'
param.Inoise = str2num(ParValue); %noise fraction of OSN input
case 'randfrac'
param.randfrac = str2num(ParValue); %fraction of uniform input (scaling input to MCs)
case 'spikev'
param.SpikeV = str2num(ParValue); %Spike voltage
case 'cchancegramit'
param.CChanceGraMit = str2num(ParValue); %chance of connection between Granule and Mitral cells
case 'cchancegragra'
param.CChanceGraGra = str2num(ParValue); %chance of connection between Granule cells
% PC parameters
case 'npyramidal'
param.nPyramidal = str2num(ParValue); %number of Pyramidal cells (and Feedforward)
case 'nfeedback'
param.nFeedback = str2num(ParValue); %number of Feedback cells
case 'cchancepyrpyr'
param.CChancePyrPyr = str2num(ParValue); %chance of connection between two Pyramidal cells
case 'cchancepyrfba'
param.CChancePyrFba = str2num(ParValue); %chance of connection between Pyramidal and Feedback cells
case 'cchancefbapyr'
param.CChanceFbaPyr = str2num(ParValue); %chance of connection between Feedback and Pyramidal cells
case 'cchanceffopyr'
param.CChanceFfoPyr = str2num(ParValue); %chance of connection between Feedforward and Pyramidal cells
case 'ffoneurons'
param.FfoNeurons = str2num(ParValue); %flag distal ffo neurons
case 'noiseffo'
param.noiseffo = str2num(ParValue); %noise Feedforward neurons
case 'noisepyr'
param.noisepyr = str2num(ParValue); %noise Pyramidal cells
case 'noisefba'
param.noisefba = str2num(ParValue); %noise Feedback neurons
case 'noiseparam'
param.NoiseParam = str2num(ParValue); %flag noise on the parameters
case 'noiselevel'
param.NoiseLevel = str2num(ParValue); %noise value
case 'pyrahp'
param.pyrAHP = str2num(ParValue); %flag use of pyrAHP
% OB-PC parameters...
case 'flaglot'
param.flagLOT = str2num(ParValue); %if true Mi-Pyr connections are in tact
case 'lotvar'
param.LOTvar = str2num(ParValue); %variability in LOT conduction delay
case 'flagop'
param.flagOP = str2num(ParValue); %if true Pyr-Gr connections are in tact
case 'opvar'
param.OPvar = str2num(ParValue); %variability in OP conduction delay
case 'flagwlotvar'
param.flagWLOTvar = str2num(ParValue); %if true mit-gra weights scale with time by Wfrac
case 'flagwopvar'
param.flagWOPvar = str2num(ParValue); %if true pyr-gra weights scale with time by Wfrac
case 'flagwgramitvar'
param.flagWGRAMITvar = str2num(ParValue); %if true gramit weights scale with time by Wfrac
case 'flagwmitgravar'
param.flagWMitGravar = str2num(ParValue); %if true mitgra weights scale with time by Wfrac
case 'cchancepyrgra'
param.CChancePyrGra = str2num(ParValue); %chance of connection between Pyramidal and Granule cells
case 'cchancemitpyr'
param.CChanceMitPyr = str2num(ParValue); %chance of connection between Mitral and Pyramidal cells
case 'cchancemitffo'
param.CChanceMitFfo = str2num(ParValue); %chance of connection between Mitral and Feedforward cells
otherwise
disp(['parameter ' ParName ' does not exist']);
end
end
function [param,OSNsource,Mitral,GraProximal,GraDistal,Feedforward,Pyramidal,Feedback] = CreateCells(param,OSNfile)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function creates neurons based on the OSN file source (excel file)
%
% Modified by Boleszek Osinski on 06/16/2013 and 08/13/2014
% Licurgo de Almeida
% 12/21/2010
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% input pattern to MCs
aux_inputs = load(OSNfile); %read file with OSN information
% OSNsource.inputs = ones(param.nMitral,1);
OSNsource.inputs = aux_inputs.inputmatrand(param.Odorant,:);
OSNsource.inputs(OSNsource.inputs<param.randfrac) = 1;
% OSNsource.inputs = aux_inputs.inputmat(param.Odorant,:);
%OSNsource.inputs = OSNsource.inputs / max(OSNsource.inputs); %%normalize data
Mitral = cell(param.nMitral,1);
for ii = 1:param.nMitral
Mitral{ii}.input = []; %no input for now
Mitral{ii}.label = 'Mitral';
end
GraProximal = cell(param.nGraprox,1);
GraDistal = cell(param.nGradist,1);
for ii = 1:param.nGraprox
GraProximal{ii}.input = [];
GraProximal{ii}.label = 'GraProximal';
end
for ii = 1:param.nGradist
GraDistal{ii}.input = [];
GraDistal{ii}.label = 'GraDistal';
end
Pyramidal = cell(param.nPyramidal,1);
Feedforward = cell(param.nPyramidal,1);
for ii = 1:param.nPyramidal
Pyramidal{ii}.input = []; %no input for now
Pyramidal{ii}.label = 'Pyramidal';
Feedforward{ii}.input = [];
Feedforward{ii}.label = 'Feedforward'; %the number of pyramidal and
% feedforward cells is always the same
end
Feedback = cell(param.nFeedback,1);
for ii = 1:param.nFeedback
Feedback{ii}.input = []; %no input for now
Feedback{ii}.label = 'Feedback';
end
end
function N = SetNeuronParameters(N,ncells,str)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function set the parameters for the different neurons
% Modified by Boleszek Osinski on 06/18/2013
%
%----------OB&PC-------------OB&PC----------OB&PC----------OB&PC----------
%
% OB and PC Neurons can present the following set of parameters:
% * tau = charging time constant of the neuron (ms). ms (not s) is the basic time unit in this program.
% * R = Membrane resistance (in ohms)
% * Fthresh = Average firing threshold (in V)
% * Vrest = resting potential
% * Vhyper = hyperpolarization potential
% * EAMPA = AMPA's Nernst potential.
% * EGABA = GABA's Nernst potential.
% * EAHP = AHP's Nernst potential.
% * ELLD = LLD's Nernst potential.
% * tauAMPA1 = AMPA's rising tau.
% * tauAMPA2 = AMPA's falling tau.
% * tauGABA1 = GABA's rising tau.
% * tauGABA2 = GABA's falling tau.
% * tauAHP = AHP time constant.
% * tauLLD = LLD time constant.
%
%
%-------------OB-------------OB-------------OB-------------OB-------------
%
% Licurgo de Almeida
% 11/02/2010
% OB Neurons can present the following set of parameters:
%
% * gmaxAMPA = AMPA's max conductance
% * gmaxGABA = GABA's max conductance
% * gmaxGABAP = Periglomerula GABA's max conductance (for Mitral cells
% only)
% * gmaxAHP = AHP's max conductance
% * IACh = Addition current when ACh is ON in non-spiking cells.
% * nGracon = number of granule cells connected to mitral or granule cells
% * CellRadius = radius of mitral and granule cells' dendrites
% * tauPROX1 = proximal Pyr-Gra synapse rising tau (Gra cell only)
% * tauPROX2 = proximal Pyr-Gra synapse falling tau (Gra cell only)
% * tauAMPA1 = distal Mit-Gra AMPA receptor rising tau (Gra cell only)
% * tauAMPA2 = distal Mit-Gra AMPA receptor falling tau (Gra cell only)
% * tauNMDA1 = distal Mit-Gra NMDA receptor rising tau (Gra cell only)
% * tauNMDA2 = distal Mit-Gra NMDA receptor falling tau (Gra cell only)
% * tauCA1 = distal Ca spike rising tau (Gra cell only)
% * tauCA2 = distal Ca spike falling (Gra cell only)
% * VCAthresh = distal Ca spike falling (Gra cell only)
% * wAMPAMI = excitatory synaptic weight from Mitral cell to Granule cell AMPA
% * wNMDAMI = excitatory synaptic weight from Mitral cell to Granule cell NMDA
% * wGABAGR = inhibitory synaptic weight from Granule cell to Gra or Mit
% * wAMPAGL = excitatory synaptic weight from Glomerulus cell to Mitral cell
%-------------PC-------------PC-------------PC-------------PC-------------
%
% Licurgo de Almeida
% 02/28/2011
% PC Neurons cah present the following set of parameters:
%
% * wAMPA = excitatory synaptic weight
% * wAMPAPY = excitatory synaptic weight for Pyramidal association fibers
% (for Pyramidal cells only)
% * wGABA = inhibitory synaptic weight
% * wGABAFF = inhibitory synaptic weight from Feedforward cells (for
% Pyramidal cells only)
% * wAHP = AHP synaptic weight used to calculate AHP activation curves.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
str_aux = 1;
% Find parameter name
while str(str_aux) ~= ' '
str_aux = str_aux + 1;
end
ParName = str(1:str_aux - 1); % name of the parameter
ParValue = str(str_aux + 1:end); % value of the parameter
switch lower(ParName)
% OB and PC
case 'tau'
for ii = 1:ncells
N{ii}.tau = str2num(ParValue); %time in ms
end
case 'r'
for ii = 1:ncells
N{ii}.R = str2num(ParValue); %resistance in ohms
end
case 'fthresh'
for ii = 1:ncells
N{ii}.FThresh = str2num(ParValue); %potential in volts
end
case 'vrest'
for ii = 1:ncells
N{ii}.Vrest = str2num(ParValue); %potential in volts
end
case 'vhyper'
for ii = 1:ncells
N{ii}.Vhyper = str2num(ParValue); %potential in volts
end
case 'noise'
for ii = 1:ncells
N{ii}.Noise = str2num(ParValue);
end
case 'eampa'
for ii = 1:ncells
N{ii}.EAMPA = str2num(ParValue); %potential in volts
end
case 'egaba'
for ii = 1:ncells
N{ii}.EGABA = str2num(ParValue); %potential in volts
end
case 'eahp'
for ii = 1:ncells
N{ii}.EAHP = str2num(ParValue); %potential in volts
end
case 'elld'
for ii = 1:ncells
N{ii}.ELLD = str2num(ParValue); %potential in volts
end
case 'tauampa1'
for ii = 1:ncells
N{ii}.tauAMPA1 = str2num(ParValue); %time in ms
end
case 'tauampa2'
for ii = 1:ncells
N{ii}.tauAMPA2 = str2num(ParValue); %time in ms
end
case 'taugaba1'
for ii = 1:ncells
N{ii}.tauGABA1 = str2num(ParValue); %time in ms
end
case 'taugaba2'
for ii = 1:ncells
N{ii}.tauGABA2 = str2num(ParValue); %time in ms
end
case 'tauahp'
for ii = 1:ncells
N{ii}.tauAHP = str2num(ParValue); %time in ms
end
case 'taulld'
for ii = 1:ncells
N{ii}.tauLLD = str2num(ParValue); %time in ms
end
% OB
case 'gmaxampa'
for ii = 1:ncells
N{ii}.gmaxAMPA = str2num(ParValue); %AMPA channel
% conductance in siemens
end
case 'gmaxgaba'
for ii = 1:ncells
N{ii}.gmaxGABA = str2num(ParValue); %GABA channel
% conductance in siemens
end
case 'gmaxahp'
for ii = 1:ncells
N{ii}.gmaxAHP = str2num(ParValue); %"AHP" channel (for the simulation)
% conductance in siemens
end
case 'iach'
for ii = 1:ncells
N{ii}.IACh = str2num(ParValue); %Additional current when ACh is ON
% in non-spiking neurons
end
case 'gmaxgabap'
for ii = 1:ncells
N{ii}.gmaxGABAP = str2num(ParValue); %GABA channel from PG cells
% conductance in siemens
end
case 'ngracon'
for ii = 1:ncells
N{ii}.NGraCon = str2num(ParValue); %number of granule cells
% connected to a mitral or granule cell
end
case 'cellradius'
for ii = 1:ncells
N{ii}.CellRadius = str2num(ParValue); % (in distance units) If
% param.conntype is 'spatial' the user must set the radius of
% mitral and granule cells
end
case 'tauprox1'
for ii = 1:ncells
N{ii}.tauPROX1 = str2num(ParValue); %time in ms
end
case 'tauprox2'
for ii = 1:ncells
N{ii}.tauPROX2 = str2num(ParValue); %time in ms
end
case 'taudist1'
for ii = 1:ncells
N{ii}.tauAMPA1 = str2num(ParValue); %time in ms
end
case 'taudist2'
for ii = 1:ncells
N{ii}.tauAMPA2 = str2num(ParValue); %time in ms
end
case 'taunmda1'
for ii = 1:ncells
N{ii}.tauNMDA1 = str2num(ParValue); %time in ms
end
case 'taunmda2'
for ii = 1:ncells
N{ii}.tauNMDA2 = str2num(ParValue); %time in ms
end
case 'tauca1'
for ii = 1:ncells
N{ii}.tauCA1 = str2num(ParValue); %time in ms
end
case 'tauca2'
for ii = 1:ncells
N{ii}.tauCA2 = str2num(ParValue); %time in ms
end
case 'vcathresh'
for ii = 1:ncells
N{ii}.VCAthresh = str2num(ParValue); %Ca spike threshold in V
end
case 'wampami'
for ii = 1:ncells
N{ii}.wAMPAMI = str2num(ParValue); % excitatory synaptic weight from Mitral to Granule AMPA
end
case 'wnmdami'
for ii = 1:ncells
N{ii}.wNMDAMI = str2num(ParValue); % excitatory synaptic weight from Mitral to Granule NMDA
end
case 'wgabagr'
for ii = 1:ncells
N{ii}.wGABAGR = str2num(ParValue); % inhibitory synaptic weight from Granule to Gra or Mit
end
case 'wampagl'
for ii = 1:ncells
N{ii}.wAMPAGL = str2num(ParValue); % excitatory synaptic weight from Glom to Mit
end
% PC
case 'wampa'
for ii = 1:ncells
N{ii}.wAMPA = str2num(ParValue); % excitatory synaptic weight
end
case 'wampapy'
for ii = 1:ncells
N{ii}.wAMPAPY = str2num(ParValue); % excitatory synaptic weight
% from associative connections (pyramidal cells only)
end
case 'wgaba'
for ii = 1:ncells
N{ii}.wGABA = str2num(ParValue); % inhibitory synaptic weight
end
case 'wgabaff'
for ii = 1:ncells
N{ii}.wGABAFF = str2num(ParValue); % inhibitory synaptic weight
% from feedforward cells (pyramidal cells only)
end
case 'wahp'
for ii = 1:ncells
N{ii}.wAHP = str2num(ParValue); % AHP amplitude
end
% New parameters must be added here...
otherwise
disp(['parameter ' ParName ' does not exist']);
end
end
function Cell = SetCellPosition(Cell,param)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function set the position on different neurons when no preset is
% presented.
% The main function of this program is neurogenesismain.m
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ncells = length(Cell);
auxposy = param.BulbH / floor(sqrt(ncells));
if sqrt(ncells) == floor(sqrt(ncells))
auxposx = param.BulbW / sqrt(ncells);
else
auxposx = param.BulbW / (sqrt(ncells) + 1);
end
countcell = 0;
x = 0;
y = 0;
while countcell < ncells
countcell = countcell + 1;
if y >= param.BulbH
y = 0;
x = x + auxposx;
end
Cell{countcell}.X = mean([x,(x + auxposx)]);
Cell{countcell}.Y = mean([y,(y + auxposy)]);
y = y + auxposy;
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MAIN FUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [Mitral GraProximal GraDistal Feedforward Pyramidal Feedback param InputCurrent] = NeuroActivity(Mitral,GraProximal,GraDistal,Feedforward,Pyramidal,Feedback,param,OSNsource)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% This function creates the neuronal activity
%
% Licurgo de Almeida
% 11/03/2010
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Create initial setup -- OB
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if param.flagRespiration == true
Respiration = CreateRespFreq(param);
else
Respiration = ones(1,round(param.tsim / param.dt));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set connections
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% OB %%%%%
nds = param.nGradist/param.nGraprox; % number of distal spines per granule cell
% random connectivity
MatGradistMit = SetConnections(param.nMitral,param.nGradist,param.CChanceGraMit);
MatMitGradist = MatGradistMit'; % reciprocal synapses
MatProxProx = SetConnections(param.nGraprox,param.nGraprox,param.CChanceGraGra);
% There are nds distal synapses to each granule cell soma. Note: nGradist must = nds*nGraprox
% (this is hard coded)
MatProxDist = zeros(param.nGradist,param.nGraprox);
for ii = 1:param.nGraprox
MatProxDist((nds*(ii-1)+1):nds*ii,ii) = 1;
end
%%%%% PC %%%%%
MatPyrFba = SetConnections(param.nFeedback,param.nPyramidal,param.CChancePyrFba);
MatFbaPyr = SetConnections(param.nPyramidal,param.nFeedback,param.CChanceFbaPyr);
MatFfoPyr = SetConnections(param.nPyramidal,param.nPyramidal,param.CChanceFfoPyr);
MatPyrPyr = SetConnections(param.nPyramidal,param.nPyramidal,param.CChancePyrPyr);
%%%%% OB-PC %%%%%
MatPyrGraprox = SetConnections(param.nGraprox,param.nPyramidal,param.CChancePyrGra);
MatMitPyr = SetConnections(param.nPyramidal,param.nMitral,param.CChanceMitPyr);
MatMitFfo = SetConnections(param.nPyramidal,param.nMitral,param.CChanceMitFfo);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set weights matrix -- PC
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% OB %%%%%
wGloMit = eye(param.nMitral)*Mitral{1}.wAMPAGL;
wPglMit = wGloMit;
wGABAMit = zeros(param.nMitral,1);
for ii = 1:param.nMitral
wGABAMit(ii) = Mitral{ii}.wGABAGR;
end
wGradistMit = SetWeights(MatGradistMit,wGABAMit,param);
wAMPAGradist = zeros(param.nGradist,1);
wNMDAGradist = zeros(param.nGradist,1);
wGABAGraProx = zeros(param.nGraprox,1);
for ii = 1:param.nGradist
wAMPAGradist(ii) = GraDistal{ii}.wAMPAMI;
wNMDAGradist(ii) = GraDistal{ii}.wNMDAMI;
end
for ii = 1:param.nGraprox
wGABAGraProx(ii) = GraProximal{ii}.wGABAGR;
end
wMitGradistAMPA = SetWeights(MatMitGradist,wAMPAGradist,param);
wMitGradistNMDA = SetWeights(MatMitGradist,wNMDAGradist,param);
wProxProx = SetWeights(MatProxProx,wGABAGraProx,param);
%%%%% PC %%%%%
wGABAPyr = zeros(param.nPyramidal,1);
wAMPAPYPyr = wGABAPyr;
wGABAFFPyr = wGABAPyr;
for ii = 1:param.nPyramidal
wGABAPyr(ii) = Pyramidal{ii}.wGABA;
wAMPAPYPyr(ii) = Pyramidal{ii}.wAMPAPY;
wGABAFFPyr(ii) = Pyramidal{ii}.wGABAFF;
end
wFbaPyr = SetWeights(MatFbaPyr,wGABAPyr,param);
wPyrPyr = SetWeights(MatPyrPyr,wAMPAPYPyr,param);
wFfoPyr = SetWeights(MatFfoPyr,wGABAFFPyr,param);
wAMPAFba = zeros(param.nFeedback,1);
for ii = 1:param.nFeedback
wAMPAFba(ii) = Feedback{ii}.wAMPA;
end
wPyrFba = SetWeights(MatPyrFba,wAMPAFba,param);
%%%%% OB-PC %%%%%
wAMPAPyr = zeros(param.nPyramidal,1);
wAMPAFfo = wAMPAPyr;
for ii = 1:param.nPyramidal
wAMPAPyr(ii) = Pyramidal{ii}.wAMPA;
wAMPAFfo(ii) = Feedforward{ii}.wAMPA;
end
wMitPyr = SetWeights(MatMitPyr,wAMPAPyr,param);
wMitFfo = SetWeights(MatMitFfo,wAMPAFfo,param);
wAMPAGraprox = zeros(param.nGraprox,1);
for ii = 1:param.nGraprox
wAMPAGraprox(ii) = GraProximal{ii}.wAMPAPY;
end
wPyrGraprox = SetWeights(MatPyrGraprox,wAMPAGraprox,param);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set OSN parameters and variables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% OSN external input
% Iextosn = SetExtInput(param,OSN);
Iextosn = zeros(param.nMitral,round(param.tsim / param.dt));
for ii = 1:param.nMitral
Iextosn(ii,round(param.tinit / param.dt) : round(param.tfinal / param.dt)) = param.Iext * OSNsource.inputs(ii);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set Mitral cells parameters and variables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Stores the voltage of each Mitral cell at a given time
Vmit = zeros(param.nMitral,round(param.tsim / param.dt));
% Binary matrix recording only the spikes
Smit = Vmit;
VAHPmit = Vmit;
refracmit = 3; % Refractory period after firing (ms)
Restmit = zeros(param.nMitral,1); % resting potential
Threshmit = Restmit; % current firing threshold
Hypermit = Restmit; % hyperpolarization potential
Rmit = Restmit; % membrane resistance
taumit = Restmit; % tau neuron
countrefracmit = Restmit; % Refractory period counter. This is assumed to
% be the same for all Mitral cells so we don't need to add it to the for
% below.
gmaxAMPAmit = Restmit; % Max AMPA conductance
tauAMPA1mit = Restmit; % AMPA's rising tau.
tauAMPA2mit = Restmit; % AMPA's falling tau.
EAMPAmit = Restmit; % AMPA's Nernst potential.
gmaxGABAmit = Restmit; % Max GABA conductance
tauGABA1mit = Restmit; % GABA's rising tau.
tauGABA2mit = Restmit; % GABA's falling tau.
EGABAmit = Restmit; % GABA's Nernst potential.
if param.mitAHP == true
gmaxAHPmit = Restmit; % Max AHP conductance
tauAHPmit = Restmit; % AHP tau.
EAHPmit = Restmit; % AHP's Nernst potential.
end
% ...New parameters should be added here and inside the 'for'...
for ii = 1:param.nMitral
Restmit(ii) = Mitral{ii}.Vrest;
Hypermit(ii) = Mitral{ii}.Vhyper;
Rmit(ii) = Mitral{ii}.R;
taumit(ii) = Mitral{ii}.tau;
gmaxAMPAmit(ii) = Mitral{ii}.gmaxAMPA;
tauAMPA1mit(ii) = Mitral{ii}.tauAMPA1;
tauAMPA2mit(ii) = Mitral{ii}.tauAMPA2;
EAMPAmit(ii) = Mitral{ii}.EAMPA;
gmaxGABAmit(ii) = Mitral{ii}.gmaxGABA;
tauGABA1mit(ii) = Mitral{ii}.tauGABA1;
tauGABA2mit(ii) = Mitral{ii}.tauGABA2;
EGABAmit(ii) = Mitral{ii}.EGABA;
if param.mitAHP == true
gmaxAHPmit(ii) = Mitral{ii}.gmaxAHP;
tauAHPmit(ii) = Mitral{ii}.tauAHP;
EAHPmit(ii) = Mitral{ii}.EAHP;
end
Threshmit(ii) = Mitral{ii}.FThresh;
Mitral{ii}.Connections = MatGradistMit(ii,:);
Mitral{ii}.ConWeights = wGradistMit(ii,:);
end
% Initialize Mitral cells potentials
Vmit(:,1) = Restmit;
Vmit_nospike = Vmit;
% AMPA time counter. This variable starts with a very negative value just
% to make sure that the currents will be = 0
tAMPA0mit = zeros(param.nMitral,1) - 10000000;
Iglomit = zeros(param.nMitral,1); % Input coming from Glo
Iglomit_matrix = zeros(param.nMitral,round(param.tsim / param.dt));
maxgAMPAmit = getmaxg(param.dt,tauAMPA1mit,tauAMPA2mit); % Get max conductance
% amplitude
% GABA time counter. This variable starts with a very negative value just
% to make sure that the currents will be = 0. Each Mitral cell can be
% connected to a varied number of granule cells
tGABA0mit = zeros(param.nGradist,round(param.tsim / param.dt)) - 10000000; %NOTE!!! for 2CG model tGABA0mit exists for each dendrite!
Igradistmit = zeros(param.nMitral,1); % Input coming from Granule cells
Igradistmit_matrix = zeros(param.nMitral,round(param.tsim / param.dt));
% only used when distal gra dendrites are removed
Igraproxmit = zeros(param.nMitral,1); % Input coming from Granule cells
Igraproxmit_matrix = zeros(param.nMitral,round(param.tsim / param.dt));
maxgGABAmit = getmaxg(param.dt,tauGABA1mit,tauGABA2mit); % Get max conductance
% amplitude
% AHP time counter. This variable starts with a very negative value just
% to make sure that the currents will be = 0.
if param.mitAHP == true
tAHP0mit = zeros(param.nMitral,1) - 10000000;
% maxgAHPmit = getmaxg(param.dt,tauAHP1mit,tauAHP2mit); % Get max conductance
% not using the rising and falling taus for AHP current
end