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 *
                            
%PRINT2EPS  Prints figures to eps with improved line styles
%
% Examples:
%   print2eps filename
%   print2eps(filename, fig_handle)
%   print2eps(filename, fig_handle, bb_padding)
%   print2eps(filename, fig_handle, bb_padding, options)
%
% This function saves a figure as an eps file, with two improvements over
% MATLAB's print command. First, it improves the line style, making dashed
% lines more like those on screen and giving grid lines their own dotted
% style. Secondly, it substitutes original font names back into the eps
% file, where these have been changed by MATLAB, for up to 11 different
% fonts.
%
%IN:
%   filename - string containing the name (optionally including full or
%              relative path) of the file the figure is to be saved as. A
%              ".eps" extension is added if not there already. If a path is
%              not specified, the figure is saved in the current directory.
%   fig_handle - The handle of the figure to be saved. Default: gcf().
%   bb_padding - Scalar value of amount of padding to add to border around
%                the figure, in points. Can be negative as well as
%                positive. Default: 0.
%   options - Additional parameter strings to be passed to print.

% Copyright (C) Oliver Woodford 2008-2014

% The idea of editing the EPS file to change line styles comes from Jiro
% Doke's FIXPSLINESTYLE (fex id: 17928)
% The idea of changing dash length with line width came from comments on
% fex id: 5743, but the implementation is mine :)

% 14/11/2011: Fix a MATLAB bug rendering black or white text incorrectly.
%             Thanks to Mathieu Morlighem for reporting the issue and
%             obtaining a fix from TMW.
% 08/12/11: Added ability to correct fonts. Several people have requested
%           this at one time or another, and also pointed me to printeps
%           (fex id: 7501), so thank you to them. My implementation (which
%           was not inspired by printeps - I'd already had the idea for my
%           approach) goes slightly further in that it allows multiple
%           fonts to be swapped.
% 14/12/11: Fix bug affecting font names containing spaces. Thanks to David
%           Szwer for reporting the issue.
% 25/01/12: Add a font not to be swapped. Thanks to Anna Rafferty and Adam
%           Jackson for reporting the issue. Also fix a bug whereby using a
%           font alias can lead to another font being swapped in.
% 10/04/12: Make the font swapping case insensitive.
% 26/10/12: Set PaperOrientation to portrait. Thanks to Michael Watts for
%           reporting the issue.
% 26/10/12: Fix issue to do with swapping fonts changing other fonts and
%           sizes we don't want, due to listeners. Thanks to Malcolm Hudson
%           for reporting the issue.
% 22/03/13: Extend font swapping to axes labels. Thanks to Rasmus Ischebeck
%           for reporting the issue.
% 23/07/13: Bug fix to font swapping. Thanks to George for reporting the
%           issue.
% 13/08/13: Fix MATLAB feature of not exporting white lines correctly.
%           Thanks to Sebastian Heßlinger for reporting it.

function print2eps(name, fig, bb_padding, varargin)
options = {'-depsc2'};
if nargin > 3
    options = [options varargin];
elseif nargin < 3
    bb_padding = 0;
    if nargin < 2
        fig = gcf();
    end
end
% Construct the filename
if numel(name) < 5 || ~strcmpi(name(end-3:end), '.eps')
    name = [name '.eps']; % Add the missing extension
end
% Set paper size
old_pos_mode = get(fig, 'PaperPositionMode');
old_orientation = get(fig, 'PaperOrientation');
set(fig, 'PaperPositionMode', 'auto', 'PaperOrientation', 'portrait');
% Find all the used fonts in the figure
font_handles = findall(fig, '-property', 'FontName');
fonts = get(font_handles, 'FontName');
if ~iscell(fonts)
    fonts = {fonts};
end
% Map supported font aliases onto the correct name
fontsl = lower(fonts);
for a = 1:numel(fonts)
    f = fontsl{a};
    f(f==' ') = [];
    switch f
        case {'times', 'timesnewroman', 'times-roman'}
            fontsl{a} = 'times-roman';
        case {'arial', 'helvetica'}
            fontsl{a} = 'helvetica';
        case {'newcenturyschoolbook', 'newcenturyschlbk'}
            fontsl{a} = 'newcenturyschlbk';
        otherwise
    end
end
fontslu = unique(fontsl);
% Determine the font swap table
matlab_fonts = {'Helvetica', 'Times-Roman', 'Palatino', 'Bookman', 'Helvetica-Narrow', 'Symbol', ...
                'AvantGarde', 'NewCenturySchlbk', 'Courier', 'ZapfChancery', 'ZapfDingbats'};
matlab_fontsl = lower(matlab_fonts);
require_swap = find(~ismember(fontslu, matlab_fontsl));
unused_fonts = find(~ismember(matlab_fontsl, fontslu));
font_swap = cell(3, min(numel(require_swap), numel(unused_fonts)));
fonts_new = fonts;
for a = 1:size(font_swap, 2)
    font_swap{1,a} = find(strcmp(fontslu{require_swap(a)}, fontsl));
    font_swap{2,a} = matlab_fonts{unused_fonts(a)};
    font_swap{3,a} = fonts{font_swap{1,a}(1)};
    fonts_new(font_swap{1,a}) = {font_swap{2,a}};
end
% Swap the fonts
if ~isempty(font_swap)
    fonts_size = get(font_handles, 'FontSize');
    if iscell(fonts_size)
        fonts_size = cell2mat(fonts_size);
    end
    M = false(size(font_handles));
    % Loop because some changes may not stick first time, due to listeners
    c = 0;
    update = zeros(1000, 1);
    for b = 1:10 % Limit number of loops to avoid infinite loop case
        for a = 1:numel(M)
            M(a) = ~isequal(get(font_handles(a), 'FontName'), fonts_new{a}) || ~isequal(get(font_handles(a), 'FontSize'), fonts_size(a));
            if M(a)
                set(font_handles(a), 'FontName', fonts_new{a}, 'FontSize', fonts_size(a));
                c = c + 1;
                update(c) = a;
            end
        end
        if ~any(M)
            break;
        end
    end
    % Compute the order to revert fonts later, without the need of a loop
    [update, M] = unique(update(1:c));
    [M, M] = sort(M);
    update = reshape(update(M), 1, []);
end
% MATLAB bug fix - black and white text can come out inverted sometimes
% Find the white and black text
white_text_handles = findobj(fig, 'Type', 'text');
M = get(white_text_handles, 'Color');
if iscell(M)
    M = cell2mat(M);
end
M = sum(M, 2);
black_text_handles = white_text_handles(M == 0);
white_text_handles = white_text_handles(M == 3);
% Set the font colors slightly off their correct values
set(black_text_handles, 'Color', [0 0 0] + eps);
set(white_text_handles, 'Color', [1 1 1] - eps);
% MATLAB bug fix - white lines can come out funny sometimes
% Find the white lines
white_line_handles = findobj(fig, 'Type', 'line');
M = get(white_line_handles, 'Color');
if iscell(M)
    M = cell2mat(M);
end
white_line_handles = white_line_handles(sum(M, 2) == 3);
% Set the line color slightly off white
set(white_line_handles, 'Color', [1 1 1] - 0.00001);
% Print to eps file
print(fig, options{:}, name);
% Reset the font and line colors
set(black_text_handles, 'Color', [0 0 0]);
set(white_text_handles, 'Color', [1 1 1]);
set(white_line_handles, 'Color', [1 1 1]);
% Reset paper size
set(fig, 'PaperPositionMode', old_pos_mode, 'PaperOrientation', old_orientation);
% Reset the font names in the figure
if ~isempty(font_swap)
    for a = update
        set(font_handles(a), 'FontName', fonts{a}, 'FontSize', fonts_size(a));
    end
end
% Do post-processing on the eps file
try
    fstrm = read_write_entire_textfile(name);
catch
    warning('Loading EPS file failed, so unable to perform post-processing. This is usually because the figure contains a large number of patch objects. Consider exporting to a bitmap format in this case.');
    return
end
% Replace the font names
if ~isempty(font_swap)
    for a = 1:size(font_swap, 2)
        %fstrm = regexprep(fstrm, [font_swap{1,a} '-?[a-zA-Z]*\>'], font_swap{3,a}(~isspace(font_swap{3,a})));
        fstrm = regexprep(fstrm, font_swap{2,a}, font_swap{3,a}(~isspace(font_swap{3,a})));
    end
end
if using_hg2(fig)
    % Convert miter joins to line joins
    fstrm = regexprep(fstrm, '10.0 ML\n', '1 LJ\n');
    % Move the bounding box to the top of the file
    [s, e] = regexp(fstrm, '%%BoundingBox: [\w\s()]*%%');
    if numel(s) == 2
        fstrm = fstrm([1:s(1)-1 s(2):e(2)-2 e(1)-1:s(2)-1 e(2)-1:end]);
    end
else
    % Fix the line styles
    fstrm = fix_lines(fstrm);
end
% Apply the bounding box padding
if bb_padding
    add_padding = @(n1, n2, n3, n4) sprintf(' %d', str2double({n1, n2, n3, n4}) + [-bb_padding -bb_padding bb_padding bb_padding]);
    fstrm = regexprep(fstrm, '%%BoundingBox:[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)[ ]+([-]?\d+)', '%%BoundingBox:${add_padding($1, $2, $3, $4)}');
end
% Write out the fixed eps file
read_write_entire_textfile(name, fstrm);
end

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