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 *
                            
%PRINT2ARRAY  Exports a figure to an image array
%
% Examples:
%   A = print2array
%   A = print2array(figure_handle)
%   A = print2array(figure_handle, resolution)
%   A = print2array(figure_handle, resolution, renderer)
%   [A bcol] = print2array(...)
%
% This function outputs a bitmap image of the given figure, at the desired
% resolution.
%
% If renderer is '-painters' then ghostcript needs to be installed. This
% can be downloaded from: http://www.ghostscript.com
%
% IN:
%   figure_handle - The handle of the figure to be exported. Default: gcf.
%   resolution - Resolution of the output, as a factor of screen
%                resolution. Default: 1.
%   renderer - string containing the renderer paramater to be passed to
%              print. Default: '-opengl'.
%
% OUT:
%   A - MxNx3 uint8 image of the figure.
%   bcol - 1x3 uint8 vector of the background color

% Copyright (C) Oliver Woodford 2008-2012

% 05/09/11: Set EraseModes to normal when using opengl or zbuffer
%           renderers. Thanks to Pawel Kocieniewski for reporting the
%           issue.
% 21/09/11: Bug fix: unit8 -> uint8! Thanks to Tobias Lamour for reporting
%           the issue.
% 14/11/11: Bug fix: stop using hardcopy(), as it interfered with figure
%           size and erasemode settings. Makes it a bit slower, but more
%           reliable. Thanks to Phil Trinh and Meelis Lootus for reporting
%           the issues.
% 09/12/11: Pass font path to ghostscript.
% 27/01/12: Bug fix affecting painters rendering tall figures. Thanks to
%           Ken Campbell for reporting it.
% 03/04/12: Bug fix to median input. Thanks to Andy Matthews for reporting
%           it.
% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for
%           reporting the issue.

function [A, bcol] = print2array(fig, res, renderer)
% Generate default input arguments, if needed
if nargin < 2
    res = 1;
    if nargin < 1
        fig = gcf;
    end
end
% Warn if output is large
old_mode = get(fig, 'Units');
set(fig, 'Units', 'pixels');
px = get(fig, 'Position');
set(fig, 'Units', old_mode);
npx = prod(px(3:4)*res)/1e6;
if npx > 30
    % 30M pixels or larger!
    warning('MATLAB:LargeImage', 'print2array generating a %.1fM pixel image. This could be slow and might also cause memory problems.', npx);
end
% Retrieve the background colour
bcol = get(fig, 'Color');
% Set the resolution parameter
res_str = ['-r' num2str(ceil(get(0, 'ScreenPixelsPerInch')*res))];
% Generate temporary file name
tmp_nam = [tempname '.tif'];
if nargin > 2 && strcmp(renderer, '-painters')
    % Print to eps file
    tmp_eps = [tempname '.eps'];
    print2eps(tmp_eps, fig, 0, renderer, '-loose');
    try
        % Initialize the command to export to tiff using ghostscript
        cmd_str = ['-dEPSCrop -q -dNOPAUSE -dBATCH ' res_str ' -sDEVICE=tiff24nc'];
        % Set the font path
        fp = font_path();
        if ~isempty(fp)
            cmd_str = [cmd_str ' -sFONTPATH="' fp '"'];
        end
        % Add the filenames
        cmd_str = [cmd_str ' -sOutputFile="' tmp_nam '" "' tmp_eps '"'];
        % Execute the ghostscript command
        ghostscript(cmd_str);
    catch me
        % Delete the intermediate file
        delete(tmp_eps);
        rethrow(me);
    end
    % Delete the intermediate file
    delete(tmp_eps);
    % Read in the generated bitmap
    A = imread(tmp_nam);
    % Delete the temporary bitmap file
    delete(tmp_nam);
    % Set border pixels to the correct colour
    if isequal(bcol, 'none')
        bcol = [];
    elseif isequal(bcol, [1 1 1])
        bcol = uint8([255 255 255]);
    else
        for l = 1:size(A, 2)
            if ~all(reshape(A(:,l,:) == 255, [], 1))
                break;
            end
        end
        for r = size(A, 2):-1:l
            if ~all(reshape(A(:,r,:) == 255, [], 1))
                break;
            end
        end
        for t = 1:size(A, 1)
            if ~all(reshape(A(t,:,:) == 255, [], 1))
                break;
            end
        end
        for b = size(A, 1):-1:t
            if ~all(reshape(A(b,:,:) == 255, [], 1))
                break;
            end
        end
        bcol = uint8(median(single([reshape(A(:,[l r],:), [], size(A, 3)); reshape(A([t b],:,:), [], size(A, 3))]), 1));
        for c = 1:size(A, 3)
            A(:,[1:l-1, r+1:end],c) = bcol(c);
            A([1:t-1, b+1:end],:,c) = bcol(c);
        end
    end
else
    if nargin < 3
        renderer = '-opengl';
    end
    err = false;
    % Set paper size
    old_pos_mode = get(fig, 'PaperPositionMode');
    old_orientation = get(fig, 'PaperOrientation');
    set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait');
    try
        % Print to tiff file
        print(fig, renderer, res_str, '-dtiff', tmp_nam);
        % Read in the printed file
        A = imread(tmp_nam);
        % Delete the temporary file
        delete(tmp_nam);
    catch ex
        err = true;
    end
    % Reset paper size
    set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation);
    % Throw any error that occurred
    if err
        rethrow(ex);
    end
    % Set the background color
    if isequal(bcol, 'none')
        bcol = [];
    else
        bcol = bcol * 255;
        if isequal(bcol, round(bcol))
            bcol = uint8(bcol);
        else
            bcol = squeeze(A(1,1,:));
        end
    end
end
% Check the output size is correct
if isequal(res, round(res))
    px = [px([4 3])*res 3];
    if ~isequal(size(A), px)
        % Correct the output size
        A = A(1:min(end,px(1)),1:min(end,px(2)),:);
    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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