Robust transmission in the inhibitory Purkinje Cell to Cerebellar Nuclei pathway (Abbasi et al 2017)

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Accession:229279

References:
1 . Abbasi S, Hudson AE, Maran SK, Cao Y, Abbasi A, Heck DH, Jaeger D (2017) Robust Transmission of Rate Coding in the Inhibitory Purkinje Cell to Cerebellar Nuclei Pathway in Awake Mice PLOS Computational Biology
2 . Steuber V, Schultheiss NW, Silver RA, De Schutter E, Jaeger D (2011) Determinants of synaptic integration and heterogeneity in rebound firing explored with data-driven models of deep cerebellar nucleus cells. J Comput Neurosci 30:633-58 [PubMed]
3 . Steuber V, Jaeger D (2013) Modeling the generation of output by the cerebellar nuclei. Neural Netw 47:112-9 [PubMed]
4 . Steuber V, De Schutter E, Jaeger D (2004) Passive models of neurons in the deep cerebellar nuclei: the effect of reconstruction errors Neurocomputing 58-60:563-568
5 . Luthman J, Hoebeek FE, Maex R, Davey N, Adams R, De Zeeuw CI, Steuber V (2011) STD-dependent and independent encoding of input irregularity as spike rate in a computational model of a cerebellar nucleus neuron. Cerebellum 10:667-82 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum deep nucleus neuron;
Channel(s): I h; I T low threshold; I L high threshold; I Na,p; I Na,t; I K,Ca; I K;
Gap Junctions:
Receptor(s): AMPA; NMDA; GabaA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS;
Model Concept(s): Synaptic Integration;
Implementer(s): Jaeger, Dieter [djaeger at emory.edu];
Search NeuronDB for information about:  GabaA; AMPA; NMDA; I Na,p; I Na,t; I L high threshold; I T low threshold; I K; I h; I K,Ca; Gaba; Glutamate;
function a_plot = plotRowSpontSpikeAnal(prof, title_str)

% plotRowSpontSpikeAnal - Creates a row of plots that show spontaneous spikes, starting from the whole trace, zooming into the individual spike.
%
% Usage: 
% a_plot = plotRowSpontSpikeAnal(prof, title_str)
%
% Description:
%
%   Parameters:
%	prof: A cip_trace_allspikes_profile object.
%	title_str: (Optional) String to append to plot title.
%
%   Returns:
%	a_plot: A plot_abstract object that can be visualized.
%
% See also: trace, cip_trace, spike_shape/plotCompareMethodsSimple, plot_abstract
%
% $Id$
%
% Author: Cengiz Gunay <cgunay@emory.edu>, 2005/05/23

% Copyright (c) 2007 Cengiz Gunay <cengique@users.sf.net>.
% This work is licensed under the Academic Free License ("AFL")
% v. 3.0. To view a copy of this license, please look at the COPYING
% file distributed with this software or visit
% http://opensource.org/licenses/afl-3.0.php.

if ~ exist('title_str', 'var')
  title_str = '';
end

% If input is an array, then return array of plots
num_dbs = length(prof);
if num_dbs > 1 
  % Create array of plots
  [a_plot(1:num_dbs)] = deal(plot_stack);
  for plot_num = 1:num_dbs
    a_plot(plot_num) = plotRowSpontSpikeAnal(prof(plot_num), title_str);
  end
  return;
end

% Remove all '_' characters, because they interfere with TeX interpretation
class_name = strrep(class(prof), '_', ' ');

quiet_trace = setProp(prof.trace, 'quiet', 1);

% Analyze a spontaneous spike
try 
  a_spike = getSpike(quiet_trace, prof.spikes, 2);
  comparison_plots = plotCompareMethodsSimple(a_spike, title_str);
catch
  err = lasterror;
  if strcmp(err.identifier, 'spike_shape:not_a_spike')
    % Feeble attempt to get next spike 
    % TODO: not-a-spikes should've been removed by this time!
    a_spike = getSpike(quiet_trace, prof.spikes, 3);
    comparison_plots = plotCompareMethodsSimple(a_spike, title_str);
  else
    rethrow(err);
  end
end
top_row = comparison_plots.plots{2};

a_plot = plot_stack({plotData(quiet_trace), ...
		     plotData(withinPeriod(quiet_trace, period(1, 100*1e-3/prof.trace.dt))), ...
		     plotResults(a_spike), ...
		     top_row.plots{1} }, [NaN NaN -80 50], 'x', ...
		    [ sprintf('%s: %s', class_name, get(prof, 'id')) title_str ], ...
		    struct('yLabelsPos', 'left'));

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