FiringCurve - Compute firing curve (e.g. for a head direction cell).
Compute firing curve (e.g. for a head direction cell, or a place or grid cell
on a linear track), as well as occupancy and spike count curves. Optionnally,
curve statistics can also be computed, including in-field peak and mean firing
rates, firing field width, etc.
USAGE
[curve,stats] = FiringCurve(samples,spikes,<options>)
samples angular or linear <a href="matlab:help samples">samples</a>
spikes spike timestamps
<options> optional list of property-value pairs (see table below)
=========================================================================
Properties Values
-------------------------------------------------------------------------
'smooth' smoothing size in bins (0 = no smoothing, default = 2)
'nBins' number of bins (default = 50)
'minTime' minimum time spent in each bin (in s, default = 0)
'maxGap' z values recorded during time gaps between successive (x,y)
samples exceeding this threshold (e.g. undetects) will not
be interpolated; also, such long gaps in (x,y) sampling
will be clipped to 'maxGap' to compute the occupancy map
(default = 0.100 s)
'type' 'linear' for linear data, 'circular' for angular data
(default 'linear')
'threshold' values above threshold*peak belong to the field
(default = 0.2)
'minSize' fields smaller than this size are considered spurious
and ignored (default = 10)
'minPeak' peaks smaller than this size are considered spurious
and ignored (default = 1)
'mode' 'interpolate' to interpolate missing points (< minTime),
or 'discard' to discard them (default)
'maxDistance' maximal distance for interpolation (default = 5)
'verbose' display processing information (default = 'off')
=========================================================================
OUTPUT
curve.x x bins
curve.rate average firing rate curve (in Hz)
curve.count spike count curve
curve.time occupancy curve (in s)
stats.x location of the peak rate (in bins)
stats.peak in-field peak rate
stats.mean in-field mean value
stats.size field size (in bins)
stats.field field (1 = bin in field, 0 = bin not in field)
stats.fieldX field x boundaries (in bins)
stats.specificity spatial specificity (Skaggs et al., 1993)
For circular data:
stats.m mean angle
stats.mode distribution mode, prefered angle
stats.r mean resultant length
stats.k von Mises concentration
NOTE
This function is provided for convenience. It simply calls <a href="matlab:help Map">Map</a> and <a href="matlab:help MapStats">MapStats</a>
using the same parameters. The outputs are the same except for curve.z which
is replaced by curve.rate.
SEE
See also Map, MapStats, FiringMap, PlotXY.0001 function [curve,stats] = FiringCurve(samples,spikes,varargin) 0002 0003 %FiringCurve - Compute firing curve (e.g. for a head direction cell). 0004 % 0005 % Compute firing curve (e.g. for a head direction cell, or a place or grid cell 0006 % on a linear track), as well as occupancy and spike count curves. Optionnally, 0007 % curve statistics can also be computed, including in-field peak and mean firing 0008 % rates, firing field width, etc. 0009 % 0010 % USAGE 0011 % 0012 % [curve,stats] = FiringCurve(samples,spikes,<options>) 0013 % 0014 % samples angular or linear <a href="matlab:help samples">samples</a> 0015 % spikes spike timestamps 0016 % <options> optional list of property-value pairs (see table below) 0017 % 0018 % ========================================================================= 0019 % Properties Values 0020 % ------------------------------------------------------------------------- 0021 % 'smooth' smoothing size in bins (0 = no smoothing, default = 2) 0022 % 'nBins' number of bins (default = 50) 0023 % 'minTime' minimum time spent in each bin (in s, default = 0) 0024 % 'maxGap' z values recorded during time gaps between successive (x,y) 0025 % samples exceeding this threshold (e.g. undetects) will not 0026 % be interpolated; also, such long gaps in (x,y) sampling 0027 % will be clipped to 'maxGap' to compute the occupancy map 0028 % (default = 0.100 s) 0029 % 'type' 'linear' for linear data, 'circular' for angular data 0030 % (default 'linear') 0031 % 'threshold' values above threshold*peak belong to the field 0032 % (default = 0.2) 0033 % 'minSize' fields smaller than this size are considered spurious 0034 % and ignored (default = 10) 0035 % 'minPeak' peaks smaller than this size are considered spurious 0036 % and ignored (default = 1) 0037 % 'mode' 'interpolate' to interpolate missing points (< minTime), 0038 % or 'discard' to discard them (default) 0039 % 'maxDistance' maximal distance for interpolation (default = 5) 0040 % 'verbose' display processing information (default = 'off') 0041 % ========================================================================= 0042 % 0043 % OUTPUT 0044 % 0045 % curve.x x bins 0046 % curve.rate average firing rate curve (in Hz) 0047 % curve.count spike count curve 0048 % curve.time occupancy curve (in s) 0049 % 0050 % stats.x location of the peak rate (in bins) 0051 % stats.peak in-field peak rate 0052 % stats.mean in-field mean value 0053 % stats.size field size (in bins) 0054 % stats.field field (1 = bin in field, 0 = bin not in field) 0055 % stats.fieldX field x boundaries (in bins) 0056 % stats.specificity spatial specificity (Skaggs et al., 1993) 0057 % 0058 % For circular data: 0059 % 0060 % stats.m mean angle 0061 % stats.mode distribution mode, prefered angle 0062 % stats.r mean resultant length 0063 % stats.k von Mises concentration 0064 % 0065 % NOTE 0066 % 0067 % This function is provided for convenience. It simply calls <a href="matlab:help Map">Map</a> and <a href="matlab:help MapStats">MapStats</a> 0068 % using the same parameters. The outputs are the same except for curve.z which 0069 % is replaced by curve.rate. 0070 % 0071 % SEE 0072 % 0073 % See also Map, MapStats, FiringMap, PlotXY. 0074 0075 % Copyright (C) 2005-2016 by Michaël Zugaro 0076 % 0077 % This program is free software; you can redistribute it and/or modify 0078 % it under the terms of the GNU General Public License as published by 0079 % the Free Software Foundation; either version 3 of the License, or 0080 % (at your option) any later version. 0081 0082 % Default values 0083 type = 'linear'; 0084 0085 % Check number of parameters 0086 if nargin < 2, 0087 error('Incorrect number of parameters (type ''help <a href="matlab:help FiringCurve">FiringCurve</a>'' for details).'); 0088 end 0089 0090 if size(samples,2) ~= 2, 0091 error('Parameter ''samples'' is not a Nx2 matrix (type ''help <a href="matlab:help FiringCurve">FiringCurve</a>'' for details).'); 0092 end 0093 0094 im = 1;argsm = {}; 0095 is = 1;argss = {}; 0096 % Parse parameter list 0097 for i = 1:2:length(varargin), 0098 if ~ischar(varargin{i}), 0099 error(['Parameter ' num2str(i+2) ' is not a property (type ''help <a href="matlab:help FiringCurve">FiringCurve</a>'' for details).']); 0100 end 0101 switch(lower(varargin{i})), 0102 case 'type', 0103 argss{is} = 'type'; 0104 argss{is+1} = varargin{i+1}(1); 0105 is = is+2; 0106 argsm{im} = 'type'; 0107 argsm{im+1} = [varargin{i+1}(1) 'l']; 0108 im = im+2; 0109 case {'threshold','minsize','minpeak','verbose','debug'}, 0110 argss{is} = varargin{i}; 0111 argss{is+1} = varargin{i+1}; 0112 is = is+2; 0113 otherwise, 0114 argsm{im} = varargin{i}; 0115 argsm{im+1} = varargin{i+1}; 0116 im = im+2; 0117 end 0118 end 0119 0120 curve = Map(samples,spikes,argsm{:}); 0121 if nargout == 2, 0122 stats = MapStats(curve,argss{:}); 0123 end 0124 curve.rate = curve.z; 0125 curve = rmfield(curve,'z');