Prob. Inference of Short-Term Synaptic Plasticity in Neocort. Microcircuits (Costa et al. 2013)

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" ... As a solution (for Short Term Plasticity (STP) inference), we introduce a Bayesian formulation, which yields the posterior distribution over the model parameters given the data. First, we show that common STP protocols yield broad distributions over some model parameters. Using our result we propose a experimental protocol to more accurately determine synaptic dynamics parameters. Next, we infer the model parameters using experimental data from three different neocortical excitatory connection types. This reveals connection-specific distributions, which we use to classify synaptic dynamics. Our approach to demarcate connection-specific synaptic dynamics is an important improvement on the state of the art and reveals novel features from existing data."
1 . Costa RP, Sjöström PJ, van Rossum MC (2013) Probabilistic inference of short-term synaptic plasticity in neocortical microcircuits. Front Comput Neurosci 7:75 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s):
Gap Junctions:
Simulation Environment: MATLAB;
Model Concept(s): Short-term Synaptic Plasticity;
Implementer(s): Costa, Rui Ponte [ruipontecosta at];
%EPS2PDF  Convert an eps file to pdf format using ghostscript
% Examples:
%   eps2pdf source dest
%   eps2pdf(source, dest, crop)
%   eps2pdf(source, dest, crop, append)
%   eps2pdf(source, dest, crop, append, gray)
%   eps2pdf(source, dest, crop, append, gray, quality)
% This function converts an eps file to pdf format. The output can be
% optionally cropped and also converted to grayscale. If the output pdf
% file already exists then the eps file can optionally be appended as a new
% page on the end of the eps file. The level of bitmap compression can also
% optionally be set.
% This function requires that you have ghostscript installed on your
% system. Ghostscript can be downloaded from:
%   source - filename of the source eps file to convert. The filename is
%            assumed to already have the extension ".eps".
%   dest - filename of the destination pdf file. The filename is assumed to
%          already have the extension ".pdf".
%   crop - boolean indicating whether to crop the borders off the pdf.
%          Default: true.
%   append - boolean indicating whether the eps should be appended to the
%            end of the pdf as a new page (if the pdf exists already).
%            Default: false.
%   gray - boolean indicating whether the output pdf should be grayscale or
%          not. Default: false.
%   quality - scalar indicating the level of image bitmap quality to
%             output. A larger value gives a higher quality. quality > 100
%             gives lossless output. Default: ghostscript prepress default.

% Copyright (C) Oliver Woodford 2009-2011

% Suggestion of appending pdf files provided by Matt C at:

% Thank you to Fabio Viola for pointing out compression artifacts, leading
% to the quality setting.
% Thank you to Scott for pointing out the subsampling of very small images,
% which was fixed for lossless compression settings.

% 9/12/2011 Pass font path to ghostscript.

function eps2pdf(source, dest, crop, append, gray, quality)
% Intialise the options string for ghostscript
options = ['-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress -sOutputFile="' dest '"'];
% Set crop option
if nargin < 3 || crop
    options = [options ' -dEPSCrop'];
% Set the font path
fp = font_path();
if ~isempty(fp)
    options = [options ' -sFONTPATH="' fp '"'];
% Set the grayscale option
if nargin > 4 && gray
    options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray'];
% Set the bitmap quality
if nargin > 5 && ~isempty(quality)
    options = [options ' -dAutoFilterColorImages=false -dAutoFilterGrayImages=false'];
    if quality > 100
        options = [options ' -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode -c ".setpdfwrite << /ColorImageDownsampleThreshold 10 /GrayImageDownsampleThreshold 10 >> setdistillerparams"'];
        options = [options ' -dColorImageFilter=/DCTEncode -dGrayImageFilter=/DCTEncode'];
        v = 1 + (quality < 80);
        quality = 1 - quality / 100;
        s = sprintf('<< /QFactor %.2f /Blend 1 /HSample [%d 1 1 %d] /VSample [%d 1 1 %d] >>', quality, v, v, v, v);
        options = sprintf('%s -c ".setpdfwrite << /ColorImageDict %s /GrayImageDict %s >> setdistillerparams"', options, s, s);
% Check if the output file exists
if nargin > 3 && append && exist(dest, 'file') == 2
    % File exists - append current figure to the end
    tmp_nam = tempname;
    % Copy the file
    copyfile(dest, tmp_nam);
    % Add the output file names
    options = [options ' -f "' tmp_nam '" "' source '"'];
        % Convert to pdf using ghostscript
        [status message] = ghostscript(options);
        % Delete the intermediate file
    % Delete the intermediate file
    % File doesn't exist or should be over-written
    % Add the output file names
    options = [options ' -f "' source '"'];
    % Convert to pdf using ghostscript
    [status message] = ghostscript(options);
% Check for error
if status
    % Report error
    if isempty(message)
        error('Unable to generate pdf. Check destination directory is writable.');

% Function to return (and create, where necessary) the font path
function fp = font_path()
fp = user_string('gs_font_path');
if ~isempty(fp)
% Create the path
% Start with the default path
fp = getenv('GS_FONTPATH');
% Add on the typical directories for a given OS
if ispc
    if ~isempty(fp)
        fp = [fp ';'];
    fp = [fp getenv('WINDIR') filesep 'Fonts'];
    if ~isempty(fp)
        fp = [fp ':'];
    fp = [fp '/usr/share/fonts:/usr/local/share/fonts:/usr/share/fonts/X11:/usr/local/share/fonts/X11:/usr/share/fonts/truetype:/usr/local/share/fonts/truetype'];
user_string('gs_font_path', fp);