Generation of granule cell dendritic morphology (Schneider et al. 2014)

 Download zip file 
Help downloading and running models
Accession:167638
The following code was used to generate a complete population of 1.2 million granule cell dendritic morphologies within a realistic three-dimensional context. These generated dendritic morphologies match the known biological variability and context-dependence of morphological features.
Reference:
1 . Schneider CJ, Cuntz H, Soltesz I (2014) Linking macroscopic with microscopic neuroanatomy using synthetic neuronal populations. PLoS Comput Biol 10:e1003921 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Dentate gyrus granule GLU cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s): Detailed Neuronal Models;
Implementer(s):
Search NeuronDB for information about:  Dentate gyrus granule GLU cell;
%% Combines Parallel Soma Files

function dentate_3_s_combinesomata(directory)

% Combine Soma Position Files
% Determine number of files
files       = dir(sprintf('%s/Soma_Position/*.mat',directory));

% Concatenate positions of all somata and write to file
pos = cell(length(files),1);
for i = 1:length(files)
    file        = sprintf('%s/Soma_Position/%i.mat',directory,i);
    load(file);
    pos{i}      = Somata_pos;
end
Somata_pos = vertcat(pos{1:length(files)});
save('Outputs/Somata_pos.mat','Somata_pos','-v7.3');


% Combine Trimmed Soma Files
% Cycle through folder and determine number of files
files = dir(sprintf('%s/Soma_Trimmed/*.mat',directory));

% Concatenate all somata and write to file
trimmed = cell(length(files),1);
for i = 1:length(files)
    file        = sprintf('%s/Soma_Trimmed/%i.mat',directory,i);
    load(file);
    trimmed{i}  = Somata;
end
Somata = vertcat(trimmed{1:length(files)});
save('Outputs/Somata.mat','Somata','-v7.3');