101 lines
2.6 KiB
Matlab
101 lines
2.6 KiB
Matlab
load('ampullary.mat')
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load('electroreceptor_stimulus.mat')
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sample_rate = 20000; % Hz
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max_time = 10;
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%% create instantaneous firing rate on the basis of the interspike intervals
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t = times{1};
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firing_rate = [0 1./diff(t)];
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start = 1;
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response = zeros(1, round(max_time * sample_rate));
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for i = 1:length(t)
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response(1,start:round(t(i) * sample_rate)) = firing_rate(i);
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start = round(t(i) * sample_rate);
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end
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fig = figure();
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set(gcf, 'PaperUnits', 'centimeters');
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set(gcf, 'PaperSize', [11.7 9.0]);
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set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
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set(gcf,'Color', 'white')
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plot((1/sample_rate:1/sample_rate:max_time), response)
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xlabel('time [s]')
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ylabel('firing rate [Hz]')
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ylim([0 300])
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xlim([0 1])
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title('instanataneous firing rate')
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saveas(fig, 'isi.pdf','pdf')
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%% create PSTH using the binning method
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bin_width = 0.0125; % s
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edges = 0:bin_width:max_time;
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firing_rate = [];
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for i = 1:size(times,2)
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t = times{i};
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[n, time] = hist(t, edges);
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if isempty(firing_rate)
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firing_rate = n / bin_width / size(times,2);
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else
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firing_rate = firing_rate + (n / bin_width / size(times,2));
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end
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end
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response = zeros(1, round(max_time * sample_rate));
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start_index = 1;
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for i = 1:length(edges)
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end_index = round(edges(i) * sample_rate);
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response(start_index:end_index) = firing_rate(i);
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start_index = end_index +1;
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end
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fig = figure();
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set(gcf, 'PaperUnits', 'centimeters');
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set(gcf, 'PaperSize', [11.7 9.0]);
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set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
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set(gcf,'Color', 'white')
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plot(0:1/sample_rate:max_time-1/sample_rate, response)
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ylim([0 300])
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xlim([0 1])
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xlabel('time [s]')
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ylabel('firing rate [Hz]')
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title('binning method')
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saveas(fig, 'binning.pdf', 'pdf')
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%% create PSTH using the kernel-convolution method
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kernel_width = 0.0125; %s
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binary_spikes = zeros(size(times,2), round(max_time*sample_rate));
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responses = zeros(size(binary_spikes));
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window = hann(kernel_width*sample_rate,'symmetric');
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window = window/sum(window);
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for i = 1:size(times,2)
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t = times{i};
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temp = round(t*sample_rate);
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if temp(1) <= 0
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temp(1) = 1;
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end
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binary_spikes(i, temp) = 1;
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responses(i,:) = conv(binary_spikes(i,:), window, 'same')*sample_rate;
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end
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fig = figure();
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set(gcf, 'PaperUnits', 'centimeters');
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set(gcf, 'PaperSize', [11.7 9.0]);
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set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0]);
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set(gcf,'Color', 'white')
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subplot(2,1,1)
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plot((1/sample_rate:1/sample_rate:max_time), mean(responses,1))
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ylim([0 300])
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xlim([0 1])
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xlabel('time [s]')
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ylabel('firing rate [Hz]')
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title('convolution method')
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subplot(2,1,2)
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plot(stimulus_strong(:,1), stimulus_strong(:,2))
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ylim([-1 1])
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xlim([0 1])
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xlabel('time [s]')
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ylabel('stimulus intensity [arb. units]')
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