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 *
                            
%IM2GIF Convert a multiframe image to an animated GIF file
%
% Examples:
%   im2gif infile
%   im2gif infile outfile
%   im2gif(A, outfile)
%   im2gif(..., '-nocrop')
%   im2gif(..., '-nodither')
%   im2gif(..., '-ncolors', n)
%   im2gif(..., '-loops', n)
%   im2gif(..., '-delay', n) 
%   
% This function converts a multiframe image to an animated GIF.
%
% To create an animation from a series of figures, export to a multiframe
% TIFF file using export_fig, then convert to a GIF, as follows:
%
%    for a = 2 .^ (3:6)
%       peaks(a);
%       export_fig test.tif -nocrop -append
%    end
%    im2gif('test.tif', '-delay', 0.5);
%
%IN:
%   infile - string containing the name of the input image.
%   outfile - string containing the name of the output image (must have the
%             .gif extension). Default: infile, with .gif extension.
%   A - HxWxCxN array of input images, stacked along fourth dimension, to
%       be converted to gif.
%   -nocrop - option indicating that the borders of the output are not to
%             be cropped.
%   -nodither - option indicating that dithering is not to be used when
%               converting the image.
%   -ncolors - option pair, the value of which indicates the maximum number
%              of colors the GIF can have. This can also be a quantization
%              tolerance, between 0 and 1. Default/maximum: 256.
%   -loops - option pair, the value of which gives the number of times the
%            animation is to be looped. Default: 65535.
%   -delay - option pair, the value of which gives the time, in seconds,
%            between frames. Default: 1/15.

% Copyright (C) Oliver Woodford 2011

function im2gif(A, varargin)

% Parse the input arguments
[A, options] = parse_args(A, varargin{:});

if options.crop ~= 0
    % Crop
    A = crop_borders(A, A(ceil(end/2),1,:,1));
end

% Convert to indexed image
[h, w, c, n] = size(A);
A = reshape(permute(A, [1 2 4 3]), h, w*n, c);
map = unique(reshape(A, h*w*n, c), 'rows');
if size(map, 1) > 256
    dither_str = {'dither', 'nodither'};
    dither_str = dither_str{1+(options.dither==0)};
    if options.ncolors <= 1
        [B, map] = rgb2ind(A, options.ncolors, dither_str);
        if size(map, 1) > 256
            [B, map] = rgb2ind(A, 256, dither_str);
        end
    else
        [B, map] = rgb2ind(A, min(round(options.ncolors), 256), dither_str);
    end
else
    if max(map(:)) > 1
        map = double(map) / 255;
        A = double(A) / 255;
    end
    B = rgb2ind(im2double(A), map);
end
B = reshape(B, h, w, 1, n);

% Bug fix to rgb2ind
map(B(1)+1,:) = im2double(A(1,1,:));

% Save as a gif
imwrite(B, map, options.outfile, 'LoopCount', round(options.loops(1)), 'DelayTime', options.delay);
end

%% Parse the input arguments
function [A, options] = parse_args(A, varargin)
% Set the defaults
options = struct('outfile', '', ...
                 'dither', true, ...
                 'crop', true, ...
                 'ncolors', 256, ...
                 'loops', 65535, ...
                 'delay', 1/15);

% Go through the arguments
a = 0;
n = numel(varargin);
while a < n
    a = a + 1;
    if ischar(varargin{a}) && ~isempty(varargin{a})
        if varargin{a}(1) == '-'
            opt = lower(varargin{a}(2:end));
            switch opt
                case 'nocrop'
                    options.crop = false;
                case 'nodither'
                    options.dither = false;
                otherwise
                    if ~isfield(options, opt)
                        error('Option %s not recognized', varargin{a});
                    end
                    a = a + 1;
                    if ischar(varargin{a}) && ~ischar(options.(opt))
                        options.(opt) = str2double(varargin{a});
                    else
                        options.(opt) = varargin{a};
                    end
            end
        else
            options.outfile = varargin{a};
        end
    end
end

if isempty(options.outfile)
    if ~ischar(A)
        error('No output filename given.');
    end
    % Generate the output filename from the input filename
    [path, outfile] = fileparts(A);
    options.outfile = fullfile(path, [outfile '.gif']);
end

if ischar(A)
    % Read in the image
    A = imread_rgb(A);
end
end

%% Read image to uint8 rgb array
function [A, alpha] = imread_rgb(name)
% Get file info
info = imfinfo(name);
% Special case formats
switch lower(info(1).Format)
    case 'gif'
        [A, map] = imread(name, 'frames', 'all');
        if ~isempty(map)
            map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
            A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
            A = permute(A, [1 2 5 4 3]);
        end
    case {'tif', 'tiff'}
        A = cell(numel(info), 1);
        for a = 1:numel(A)
            [A{a}, map] = imread(name, 'Index', a, 'Info', info);
            if ~isempty(map)
                map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
                A{a} = reshape(map(uint32(A{a})+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
            end
            if size(A{a}, 3) == 4
                % TIFF in CMYK colourspace - convert to RGB
                if isfloat(A{a})
                    A{a} = A{a} * 255;
                else
                    A{a} = single(A{a});
                end
                A{a} = 255 - A{a};
                A{a}(:,:,4) = A{a}(:,:,4) / 255;
                A{a} = uint8(A(:,:,1:3) .* A{a}(:,:,[4 4 4]));
            end
        end
        A = cat(4, A{:});
    otherwise
        [A, map, alpha] = imread(name);
        A = A(:,:,:,1); % Keep only first frame of multi-frame files
        if ~isempty(map)
            map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
            A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
        elseif size(A, 3) == 4
            % Assume 4th channel is an alpha matte
            alpha = A(:,:,4);
            A = A(:,:,1:3);
        end
end
end

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