new project on serial correlations

projects/project_serialcorrelation/solution/firingrate.m

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+function rate = firingrate(spikes, tmin, tmax)
+% mean firing rate between tmin and tmax.
+rates = zeros(length(spikes), 1);
+for i = 1:length(spikes)
+	times= spikes{i};
+	rates(i) = length(times((times>=tmin)&(times<=tmax)))/(tmax-tmin);
+end
+rate = mean(rates);
+end

projects/project_serialcorrelation/solution/isiserialcorr.m

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+function isicorr = isiserialcorr(spikes, maxlag)
+% serial correlation of interspike intervals
+%
+% isicorr = isiserialcorr(spikes, maxlag)
+%
+% Arguments:
+%   spikes: spike times in seconds
+%   maxlag: the maximum lag
+%
+% Returns:
+%   isicorr: vector with the serial correlations for lag 0 to maxlag
+
+isivec = [];
+for k = 1:length(spikes)
+	times = spikes{k};
+	isivec = [isivec; diff(times(:))];
+end
+
+lags = 0:maxlag;
+isicorr = zeros(size(lags));
+for k = 1:length(lags)
+	lag = lags(k);
+	if length(isivec) > lag+10        % ensure "enough" data
+		isicorr(k) = corr(isivec(1:end-lag), isivec(lag+1:end));
+	end
+end

projects/project_serialcorrelation/solution/isiserialcorrbootstrap.m

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+function [isicorr, lowerbound, upperbound] = isiserialcorrbootstrap(spikes, maxlag)
+% serial correlation of interspike intervals
+%
+% isicorr = isiserialcorrbootstrap(spikes, maxlag)
+%
+% Arguments:
+%   spikes: spike times in seconds
+%   maxlag: the maximum lag
+%
+% Returns:
+%   isicorr: vector with the serial correlations for lag 0 to maxlag
+
+isivec = [];
+for k = 1:length(spikes)
+	times = spikes{k};
+	isivec = [isivec; diff(times(:))];
+end
+
+lags = 0:maxlag;
+
+isicorr = zeros(size(lags));
+for k = 1:length(lags)
+	lag = lags(k);
+	if length(isivec) > lag+10        % ensure "enough" data
+		isicorr(k) = corr(isivec(1:end-lag), isivec(lag+1:end));
+	end
+end
+
+repeats = 1000;
+isicorrshuffled = zeros(repeats, length(lags));
+for i = 1:repeats
+	isishuffled = isivec(randperm(length(isivec)));
+	for k = 1:length(lags)
+		lag = lags(k);
+		if length(isivec) > lag+10        % ensure "enough" data
+			isicorrshuffled(i, k) = corr(isishuffled(1:end-lag), isishuffled(lag+1:end));
+		end
+	end
+end
+bounds = prctile(isicorrshuffled, [1.0 99], 1);
+lowerbound = bounds(1, :);
+upperbound = bounds(2, :);
+end
+
+
+

projects/project_serialcorrelation/solution/serialcorrelation.m

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+%% load data:
+data = load('baselinespikes.mat');
+spikes = data.spikes;
+cells = data.cells;
+
+%% print raster:
+maxn = length(spikes);
+if maxn > 5
+	maxn = 5;
+end
+figure()
+for k = 1:maxn
+	subplot(maxn, 1, k);
+	spikeraster(spikes(k), 0.0, 1.0)
+	title(cells{k})
+end
+
+%% firing rates:
+rates = zeros(length(spikes), 1);
+for k = 1:length(spikes)
+	rates(k) = firingrate(spikes(k), 0.0, 9.0);
+end
+figure();
+subplot(1, 2, 1);
+boxplot(rates);
+subplot(1, 2, 2);
+hist(rates, 20)
+
+
+%% serial correlations:
+maxlag = 10;
+lags = 0:maxlag;
+corrs = zeros(length(spikes), 1);
+figure();
+for k = 1:length(spikes)
+	isicorrs = isiserialcorr(spikes(k), maxlag);
+	corrs(k) = isicorrs(2);
+	plot(lags, isicorrs);
+	hold on;
+end
+hold off;
+figure();
+plot(rates, corrs, 'o');
+ylim([-0.7 0])
+
+
+%% bootstrap serial correlations:
+maxlag = 10;
+lags = 0:maxlag;
+figure();
+for k = 1:maxn
+	[isicorr, lowerbound, upperbound] = isiserialcorrbootstrap(spikes(k), maxlag);
+	subplot(maxn, 1, k);
+	plot(lags, isicorr, 'b', 'linewidth', 2)
+	hold on;
+	plot(lags, lowerbound, 'r', 'linewidth', 1)
+	plot(lags, upperbound, 'r', 'linewidth', 1)
+	hold off;
+end
+
+
+
+
+

projects/project_serialcorrelation/solution/spikeraster.m

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+function spikeraster(spikes, tmin, tmax)
+% Display a spike raster of the spike times given in spikes.
+%
+% spikeraster(spikes, tmax)
+%   spikes: a cell array of vectors of spike times in seconds
+%   tmin: plot spike raster starting at tmin seconds
+%   tmax: plot spike raster upto tmax seconds
+
+ntrials = length(spikes);
+for k = 1:ntrials
+    times = spikes{k};
+    times = times((times>=tmin) & (times<=tmax));
+    if tmax < 1.5
+        times = 1000.0*times; % conversion to ms
+    end
+    for i = 1:length( times )
+      line([times(i) times(i)],[k-0.4 k+0.4], 'Color', 'k'); 
+    end
+end
+if (tmax-tmin) < 1.5
+    xlabel('Time [ms]');
+    xlim([1000.0*tmin 1000.0*tmax]);
+else
+    xlabel('Time [s]');
+    xlim([tmin tmax]);
+end
+ylabel('Trials');
+ylim([0.3 ntrials+0.7 ]);
+end
+