Hotspots of dendritic spine turnover facilitates new spines and NN sparsity (Frank et al 2018)

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Accession:227087
Model for the following publication: Adam C. Frank, Shan Huang, Miou Zhou, Amos Gdalyahu, George Kastellakis, Panayiota Poirazi, Tawnie K. Silva, Ximiao Wen, Joshua T. Trachtenberg, and Alcino J. Silva Hotspots of Dendritic Spine Turnover Facilitate Learning-related Clustered Spine Addition and Network Sparsity
Reference:
1 . Frank AC, Huang S, Zhou M, Gdalyahu A, Kastellakis G, Silva TK, Lu E, Wen X, Poirazi P, Trachtenberg JT, Silva AJ (2018) Hotspots of dendritic spine turnover facilitate clustered spine addition and learning and memory. Nat Commun 9:422 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Connectionist Network;
Brain Region(s)/Organism:
Cell Type(s): Abstract integrate-and-fire leaky neuron with dendritic subunits;
Channel(s):
Gap Junctions:
Receptor(s): NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Active Dendrites; Synaptic Plasticity;
Implementer(s): Kastellakis, George [gkastel at gmail.com];
Search NeuronDB for information about:  NMDA;
/
tomodel
exportfig
.ignore
README.md *
.gitignore *
append_pdfs.m *
copyfig.m *
crop_borders.m *
eps2pdf.m *
export_fig.m *
fix_lines.m *
ghostscript.m *
im2gif.m *
isolate_axes.m *
LICENSE *
pdf2eps.m *
pdftops.m *
print2array.m *
print2eps.m *
read_write_entire_textfile.m *
user_string.m *
using_hg2.m *
                            
%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: http://www.ghostscript.com
%
%IN:
%   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:
% http://www.mathworks.com/matlabcentral/fileexchange/23629

% 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'];
end
% Set the font path
fp = font_path();
if ~isempty(fp)
    options = [options ' -sFONTPATH="' fp '"'];
end
% Set the grayscale option
if nargin > 4 && gray
    options = [options ' -sColorConversionStrategy=Gray -dProcessColorModel=/DeviceGray'];
end
% 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"'];
    else
        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);
    end
end
% 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 '"'];
    try
        % Convert to pdf using ghostscript
        [status, message] = ghostscript(options);
    catch me
        % Delete the intermediate file
        delete(tmp_nam);
        rethrow(me);
    end
    % Delete the intermediate file
    delete(tmp_nam);
else
    % 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);
end
% Check for error
if status
    % Report error
    if isempty(message)
        error('Unable to generate pdf. Check destination directory is writable.');
    else
        error(message);
    end
end
end

% Function to return (and create, where necessary) the font path
function fp = font_path()
fp = user_string('gs_font_path');
if ~isempty(fp)
    return
end
% 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 ';'];
    end
    fp = [fp getenv('WINDIR') filesep 'Fonts'];
else
    if ~isempty(fp)
        fp = [fp ':'];
    end
    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'];
end
user_string('gs_font_path', fp);
end

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