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

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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]
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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;
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS;
Model Concept(s): Synaptic Integration;
Implementer(s): Jaeger, Dieter [djaeger at];
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 [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
% Multi-taper time-frequency coherence,cross-spectrum and individual spectra - two binned point processes
% Usage:
% [C,phi,S12,S1,S2,t,f,zerosp,confC,phistd,Cerr]=cohgrampb(data1,data2,movingwin,params,fscorr)
% Input: 
% Note units have to be consistent. Thus, if movingwin is in seconds, Fs
% has to be in Hz. see chronux.m for more information.
%       data1 (binned point process data in form samples x trials) -- required
%       data2 (binned point process data in form samples x trials) -- required
%       movingwin (in the form [window winstep] -- required
%       params: structure with fields tapers, pad, Fs, fpass, err, trialave
%       - optional
%           tapers : precalculated tapers from dpss or in the one of the following
%                    forms: 
%                   (1) A numeric vector [TW K] where TW is the
%                       time-bandwidth product and K is the number of
%                       tapers to be used (less than or equal to
%                       2TW-1). 
%                   (2) A numeric vector [W T p] where W is the
%                       bandwidth, T is the duration of the data and p 
%                       is an integer such that 2TW-p tapers are used. In
%                       this form there is no default i.e. to specify
%                       the bandwidth, you have to specify T and p as
%                       well. Note that the units of W and T have to be
%                       consistent: if W is in Hz, T must be in seconds
%                       and vice versa. Note that these units must also
%                       be consistent with the units of params.Fs: W can
%                       be in Hz if and only if params.Fs is in Hz.
%                       The default is to use form 1 with TW=3 and K=5
%                   Note that T has to be equal to movingwin(1).
%	        pad		    (padding factor for the FFT) - optional (can take values -1,0,1,2...). 
%                    -1 corresponds to no padding, 0 corresponds to padding
%                    to the next highest power of 2 etc.
%			      	 e.g. For N = 500, if PAD = -1, we do not pad; if PAD = 0, we pad the FFT
%			      	 to 512 points, if pad=1, we pad to 1024 points etc.
%			      	 Defaults to 0.
%           Fs   (sampling frequency) - optional. Default 1.
%           fpass    (frequency band to be used in the calculation in the form
%                                   [fmin fmax])- optional. 
%                                   Default all frequencies between 0 and Fs/2
%           err  (error calculation [1 p] - Theoretical error bars; [2 p] - Jackknife error bars
%                                   [0 p] or 0 - no error bars) - optional. Default 0.
%           trialave (average over trials when 1, don't average when 0) -
%           optional. Default 0
%       fscorr   (finite size corrections, 0 (don't use finite size corrections) or 
%                 1 (use finite size corrections) - optional
%                (available only for spikes). Defaults 0.
% Output:
%       C (magnitude of coherency time x frequencies x trials for trialave=0; 
%              time x frequency for trialave=1)
%       phi (phase of coherency time x frequencies x trials for no trial averaging; 
%              time x frequency for trialave=1)
%       S12 (cross spectrum - time x frequencies x trials for no trial averaging; 
%              time x frequency for trialave=1)
%       S1 (spectrum 1 - time x frequencies x trials for no trial averaging; 
%              time x frequency for trialave=1)
%       S2 (spectrum 2 - time x frequencies x trials for no trial averaging; 
%              time x frequency for trialave=1)
%       t (time)
%       f (frequencies)
%       zerosp (1 for windows and trials where spikes were absent (in either channel),zero otherwise)
%       confC (confidence level for C at 1-p %) - only for err(1)>=1
%       phistd - jackknife/theoretical standard deviation for phi - Note that 
%                phi + 2 phistd and phi -2 phistd will give 95% confidence bands for phi
%                 - only for err(1)>=1
%       Cerr  (Jackknife error bars for C - use only for Jackknife - err(1)=2)

if nargin < 3; error('Need data1 and data2 and window parameters'); end;
if nargin < 4; params=[]; end;

if length(params.tapers)==3 & movingwin(1)~=params.tapers(2);
    error('Duration of data in params.tapers is inconsistent with movingwin(1), modify params.tapers(2) to proceed')

if nargin < 5 || isempty(fscorr); fscorr=0; end;

if nargout > 8 && err(1)==0;
    error('When errors are desired, err(1) has to be non-zero.');
if nargout > 10 && err(1)~=2; 
    error('Cerr computed only for Jackknife. Correct inputs and run again');

Nwin=round(Fs*movingwin(1)); % number of samples in window
Nstep=round(movingwin(2)*Fs); % number of samples to step through
params.tapers=dpsschk(tapers,Nwin,Fs); % check tapers

if trialave;
%   phierr=zeros(2,nw,Nf);
%   phierr=zeros(2,nw,Nf,Ch);

for n=1:nw;
   if nargout==11;
%      phierr(1,n,:,:)=squeeze(phie(1,:,:));
%      phierr(2,n,:,:)=squeeze(phie(2,:,:));
   elseif nargout==10;
%      phierr(1,n,:,:)=squeeze(phie(1,:,:));
%      phierr(2,n,:,:)=squeeze(phie(2,:,:));      
C=squeeze(C); phi=squeeze(phi);S12=squeeze(S12); S1=squeeze(S1); S2=squeeze(S2);zerosp=squeeze(zerosp);
if nargout > 9; confC=confc; end;
if nargout==11;Cerr=squeeze(Cerr);end;
% if nargout==10; phierr=squeeze(phierr);end
if nargout==10; phistd=squeeze(phistd);end