Purkinje neuron network (Zang et al. 2020)

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Accession:266799
Both spike rate and timing can transmit information in the brain. Phase response curves (PRCs) quantify how a neuron transforms input to output by spike timing. PRCs exhibit strong firing-rate adaptation, but its mechanism and relevance for network output are poorly understood. Using our Purkinje cell (PC) model we demonstrate that the rate adaptation is caused by rate-dependent subthreshold membrane potentials efficiently regulating the activation of Na+ channels. Then we use a realistic PC network model to examine how rate-dependent responses synchronize spikes in the scenario of reciprocal inhibition-caused high-frequency oscillations. The changes in PRC cause oscillations and spike correlations only at high firing rates. The causal role of the PRC is confirmed using a simpler coupled oscillator network model. This mechanism enables transient oscillations between fast-spiking neurons that thereby form PC assemblies. Our work demonstrates that rate adaptation of PRCs can spatio-temporally organize the PC input to cerebellar nuclei.
Reference:
1 . Zang Y, Hong S, De Schutter E (2020) Firing rate-dependent phase responses of Purkinje cells support transient oscillations. Elife [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Realistic Network;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum Purkinje GABA cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; MATLAB;
Model Concept(s): Phase Response Curves; Action Potentials; Spatio-temporal Activity Patterns; Synchronization; Action Potential Initiation; Oscillations;
Implementer(s): Zang, Yunliang ; Hong, Sungho [shhong at oist.jp];
Search NeuronDB for information about:  Cerebellum Purkinje GABA cell;
function eps2pdf(source, dest, crop, append, gray, quality, gs_options)
%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)
%   eps2pdf(source, dest, crop, append, gray, quality, gs_options)
%
% 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
%
% Inputs:
%   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.
%   gs_options - optional ghostscript options (e.g.: '-dNoOutputFonts'). If
%                multiple options are needed, enclose in call array: {'-a','-b'}

% Copyright (C) Oliver Woodford 2009-2014, Yair Altman 2015-

% 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.

% 09/12/11: Pass font path to ghostscript
% 26/02/15: If temp dir is not writable, use the dest folder for temp
%           destination files (Javier Paredes)
% 28/02/15: Enable users to specify optional ghostscript options (issue #36)
% 01/03/15: Upon GS error, retry without the -sFONTPATH= option (this might solve
%           some /findfont errors according to James Rankin, FEX Comment 23/01/15)
% 23/06/15: Added extra debug info in case of ghostscript error; code indentation
% 04/10/15: Suggest a workaround for issue #41 (missing font path; thanks Mariia Fedotenkova)
% 22/02/16: Bug fix from latest release of this file (workaround for issue #41)
% 20/03/17: Added informational message in case of GS croak (issue #186)
% 16/01/18: Improved appending of multiple EPS files into single PDF (issue #233; thanks @shartjen)

    % 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
    % Enable users to specify optional ghostscript options (issue #36)
    if nargin > 6 && ~isempty(gs_options)
        if iscell(gs_options)
            gs_options = sprintf(' %s',gs_options{:});
        elseif ~ischar(gs_options)
            error('gs_options input argument must be a string or cell-array of strings');
        else
            gs_options = [' ' gs_options];
        end
        options = [options gs_options];
    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 '.pdf'];
        [fpath,fname,fext] = fileparts(tmp_nam);
        try
            % Ensure that the temp dir is writable (Javier Paredes 26/2/15)
            fid = fopen(tmp_nam,'w');
            fwrite(fid,1);
            fclose(fid);
            delete(tmp_nam);
        catch
            % Temp dir is not writable, so use the dest folder
            fpath = fileparts(dest);
            tmp_nam = fullfile(fpath,[fname fext]);
        end
        % Copy the existing (dest) pdf file to temporary folder
        copyfile(dest, tmp_nam);
        % Produce an interim pdf of the source eps, rather than adding the eps directly (issue #233)
        ghostscript([options ' -f "' source '"']);
        [~,fname] = fileparts(tempname);
        tmp_nam2 = fullfile(fpath,[fname fext]); % ensure using a writable folder (not necessarily tempdir)
        copyfile(dest, tmp_nam2);
        % Add the existing pdf and interim pdf as inputs to ghostscript
        %options = [options ' -f "' tmp_nam '" "' source '"'];  % append the source eps to dest pdf
        options = [options ' -f "' tmp_nam '" "' tmp_nam2 '"']; % append the interim pdf to dest pdf
        try
            % Convert to pdf using ghostscript
            [status, message] = ghostscript(options);
        catch me
            % Delete the intermediate files and rethrow the error
            delete(tmp_nam);
            delete(tmp_nam2);
            rethrow(me);
        end
        % Delete the intermediate (temporary) files
        delete(tmp_nam);
        delete(tmp_nam2);
    else
        % File doesn't exist or should be over-written
        % Add the source eps file as input to ghostscript
        options = [options ' -f "' source '"'];
        % Convert to pdf using ghostscript
        [status, message] = ghostscript(options);
    end
    % Check for error
    if status
        % Retry without the -sFONTPATH= option (this might solve some GS
        % /findfont errors according to James Rankin, FEX Comment 23/01/15)
        orig_options = options;
        if ~isempty(fp)
            options = regexprep(options, ' -sFONTPATH=[^ ]+ ',' ');
            status = ghostscript(options);
            if ~status, return; end  % hurray! (no error)
        end
        % Report error
        if isempty(message)
            error('Unable to generate pdf. Check destination directory is writable.');
        elseif ~isempty(strfind(message,'/typecheck in /findfont'))
            % Suggest a workaround for issue #41 (missing font path)
            font_name = strtrim(regexprep(message,'.*Operand stack:\s*(.*)\s*Execution.*','$1'));
            fprintf(2, 'Ghostscript error: could not find the following font(s): %s\n', font_name);
            fpath = fileparts(mfilename('fullpath'));
            gs_fonts_file = fullfile(fpath, '.ignore', 'gs_font_path.txt');
            fprintf(2, '  try to add the font''s folder to your %s file\n\n', gs_fonts_file);
            error('export_fig error');
        else
            fprintf(2, '\nGhostscript error: perhaps %s is open by another application\n', dest);
            if ~isempty(gs_options)
                fprintf(2, '  or maybe the%s option(s) are not accepted by your GS version\n', gs_options);
            end
            fprintf(2, '  or maybe you have another gs executable in your system''s path\n');
            fprintf(2, 'Ghostscript options: %s\n\n', orig_options);
            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