Striatal GABAergic microcircuit, spatial scales of dynamics (Humphries et al, 2010)

 Download zip file 
Help downloading and running models
Accession:137502
The main thrust of this paper was the development of the 3D anatomical network of the striatum's GABAergic microcircuit. We grew dendrite and axon models for the MSNs and FSIs and extracted probabilities for the presence of these neurites as a function of distance from the soma. From these, we found the probabilities of intersection between the neurites of two neurons given their inter-somatic distance, and used these to construct three-dimensional striatal networks. These networks were examined for their predictions for the distributions of the numbers and distances of connections for all the connections in the microcircuit. We then combined the neuron models from a previous model (Humphries et al, 2009; ModelDB ID: 128874) with the new anatomical model. We used this new complete striatal model to examine the impact of the anatomical network on the firing properties of the MSN and FSI populations, and to study the influence of all the inputs to one MSN within the network.
Reference:
1 . Humphries MD, Wood R, Gurney K (2010) Reconstructing the three-dimensional GABAergic microcircuit of the striatum. PLoS Comput Biol 6:e1001011 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Striatum;
Cell Type(s): Neostriatum fast spiking interneuron;
Channel(s):
Gap Junctions: Gap junctions;
Receptor(s): D1; D2; GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Dopamine; Gaba; Glutamate;
Simulation Environment: MATLAB;
Model Concept(s): Activity Patterns; Spatio-temporal Activity Patterns; Winner-take-all; Connectivity matrix;
Implementer(s): Humphries, Mark D [m.d.humphries at shef.ac.uk]; Wood, Ric [ric.wood at shef.ac.uk];
Search NeuronDB for information about:  D1; D2; GabaA; AMPA; NMDA; Dopamine; Gaba; Glutamate;
function net = GetNeuronPositions(net)
% set the minimum distance allowed between two cells
limit = 10; % um

% calculate the number of cells in the network
net.MS.N  = round(prod(net.PhysicalDimensions./1000) .* net.CellsPerMillimeterCube); % get the number of MS neurons in the slice
net.FS.N = round(net.MS.N .* (net.FSpercentage/100)); 
N = net.MS.N + net.FS.N;

% get the neuron positions
P = get_positions(net.PhysicalDimensions, N, limit);

% --------------------------------------------------------------
% randomly assign the cells to the MS and FS neuron populations.
x = randperm(N);
net.MS.Position = P(x(1:net.MS.N),:);
net.FS.Position = P(x(net.MS.N+1:end),:);

% randomly assign MSN's to the D1 and D2 class
x = randperm(net.MS.N);
net.MS.D1inds = sort(x(1:round(net.MS.N/2)));
net.MS.D2inds = sort(x((round(net.MS.N/2)+1):net.MS.N));

% -------------------------------------------------------------------------
% get the positions of the cells
function [P] = get_positions(dims, N, limit)
P = rand(N,3);
P(:,1) = P(:,1).*dims(1);
P(:,2) = P(:,2).*dims(2);
P(:,3) = P(:,3).*dims(3);

% move any cell that is closer to its nabours than the limit
P = check_dist(P, dims, limit); 

% -------------------------------------------------------------------------
% set the distance between cells so that it is never less than the limit
function P = check_dist(P, dims, limit)
i = 0;
while i < length(P)
    i = i+1;
    d = get_distance(P, P(i,:));
    inds = find(d<limit);

    selfind = find(inds==i);
    inds = inds([1:selfind-1 selfind+1:end]);
    
    if ~isempty(inds)   
        P(i,:) = rand(1,3) .* dims;
        i = i-1;
    end
end

% -------------------------------------------------------------------------
% calculate the distance between one cell, and all others in the network
function d = get_distance(targetcoords, sourcecoords)
[n,m] = size(targetcoords);
a = targetcoords(:,1) - sourcecoords(1);
b = targetcoords(:,2) - sourcecoords(2);
c = targetcoords(:,3) - sourcecoords(3);
d = sqrt(a.^2 + b.^2 + c.^2);

Loading data, please wait...