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+function [uniformSpot_output]=BC_uniformSpot(loadData,filename,filename2,spotDuration,grayDuration,spotVersion,pathStimSignal)
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+%[uniformSpot_output]=BC_uniformSpot(loadData,filename,filename2,spotDuration,grayDuration,spotVersion,pathStimSignal)
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+%this function shows the example analysis for the uniform spot stimulus with
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+%different spot sizes for both preferred and non-preferred contrasts. It is
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+%used for cells that were recorded with stimulus version 1 and 2.
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+%Inputs:
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+% loadData = the folder path of the patterned spot files
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+% filename = the filename of the BC of interest for black
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+% contrast
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+% filename2 = the filename of the BC of interest for white
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+% contrast
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+% spotDuration = duration of spot in ms, found in
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+% the excel file LogInfo_UniformSpot.xlsx
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+% grayDuration = duration of gray screen in ms, found in
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+% the excel file LogInfo_UniformSpot.xlsx
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+% spotVersion = spot version used, found in
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+% the excel file LogInfo_UniformSpot.xlsx
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+% pathStimSignal = folder path to load the sequence of spot
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+% sizes shown
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+%
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+%Outpus: uniformSpot_output = structure containing the output
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+% average membrane potential per spot size of the uniform
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+% spot for the black and white spot
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+%
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+% code by HS last modiefied March 2021
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+
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+%% Constants
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+mircoMeter_proPixel=2.5; %one monitor pixel is 2.5 micrometers
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+
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+%-------------------------------------------------------------------------------
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+%% 1. load the spot sizes
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+if spotVersion ==1
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+ npatterns=13; %13 spot sizes were shown
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+ micro_meter=[2,4,5,6,8,10,16,24,32,50,100,200,240]'*2*mircoMeter_proPixel; %spot diameter size in micro meters
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+elseif spotVersion==2
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+ npatterns=11; %11 spot sizes were shown
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+ micro_meter=[2,4,6,8,10,16,24,32,50,100,200]'*2*mircoMeter_proPixel; %spot diameter size in micro meters
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+end
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+%for plotting add the mircometer label
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+micrometer_label=repmat(' \mum',size(micro_meter,1),1);
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+micro_meter_withLabel=strcat (num2str(micro_meter),micrometer_label);
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+
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+load(pathStimSignal); %load the order of the presentation of the diameter sizes. See Documentation_Data_BCRecordings. It contains values from 0-12 and the numbers refer to the spot size presented, where 0=smallest spot size and 12=largest spot size. It contains the pulses for a 15 minute recording
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+
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+%------------------------------------------------------------------------------------------
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+%% 2. extract the membrane potential data for each spot size of the black spot and build the average
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+data=load([loadData,filename]); %load the file for the black spot
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+%only get the frames where the gray screen was shown (that you have one
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+%frame per trial)
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+ttls_ms_forCond=data.ttls_ms(1:2:end);
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+%correct stimulus signal for the amount of ttls pulses you showed the
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+%spot -> usually less than 15minutes
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+stimulus_corr=stimulus(1:size(ttls_ms_forCond,1),:);
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+
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+%extract the membrane potential per spot
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+membPot_perTrialBlackSpot=cell(1,npatterns);
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+for j=0:npatterns-1 %loop over spot sizes
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+ spot_cond=find(stimulus_corr==j);%get all the spots with same size
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+ ttls_forCond=ttls_ms_forCond(spot_cond);%get the ttls signals for this circle size
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+ if ~isempty(ttls_forCond)
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+ %get the membrane potenial for this ttls signal (start gray screen) and go until
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+ %the next spot (grayScreen 1000ms+500msSpot+1000gray)
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+ for jj=1:length(ttls_forCond)
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+ if length(data.membPot)>=(ttls_forCond(jj)+spotDuration-1+grayDuration*2)==1 %only if you have enought data, when you end the recording it can happen that you end it during a trial -> those trials you dont consider here
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+ membPot_perTrialBlackSpot{j+1}(jj,:)=data.membPot(ttls_forCond(jj): ...
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+ (ttls_forCond(jj)+spotDuration-1+2*grayDuration)); %duration-1 -> because the next trial would start there
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+ end
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+ end
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+ end
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+ clear spot_cond ttls_forCond
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+end
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+
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+
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+% baseline on trial by trial bases -> substract from the time series of each trial
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+% the mean value of the 200 ms before the spot arrives
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+membPot_trBasMeanBlackSpot=cell(1,npatterns);
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+basValue=-200;%amount of baseline ->200ms
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+for ww=1:length(membPot_perTrialBlackSpot)%nbr of spot sizes
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+ val_before=membPot_perTrialBlackSpot{ww}(:,grayDuration+basValue:grayDuration-1);
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+ byTrBas_perSpot=(mean(val_before,2));
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+ trBas_repMAt=repmat(byTrBas_perSpot,1, ...
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+ size(membPot_perTrialBlackSpot{ww}(:,grayDuration+1:end),2)); %directly take the signal after gray screen
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+ membPot_trBasMeanBlackSpot{ww}=mean(membPot_perTrialBlackSpot{ww}(:,grayDuration+1:end)- ...
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+ trBas_repMAt,1);%mean for each trial, directly take the signal after gray screen
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+ clear trBas_perSpotrepMAt
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+end
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+
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+
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+%------------------------------------------------------------------------------------------
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+%% 3. extract the membrane potential data for each spot size of the white spot and build the average
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+data=load([loadData,filename2]); %load the file for the white spot
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+%only get the frames where the gray screen was shown (that you have one
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+%frame per trial)
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+ttls_ms_forCond=data.ttls_ms(1:2:end);
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+%correct stimulus signal for the amount of ttls pulses you showed the
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+%spot -> usually less than 15minutes
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+stimulus_corr=stimulus(1:size(ttls_ms_forCond,1),:);
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+clear stimulus
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+
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+%extract the membrane potential per spot
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+membPot_perTrialWhiteSpot=cell(1,npatterns);
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+for j=0:npatterns-1 %loop over spot sizes
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+ spot_cond=find(stimulus_corr==j);%get all the spots with same size
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+ ttls_forCond=ttls_ms_forCond(spot_cond);%get the ttls signals for this circle size
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+ if ~isempty(ttls_forCond)
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+ %get the membrane potenial for this ttls signal (start gray screen) and go until
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+ %the next spot (grayScreen 1000ms+500msSpot+1000gray)
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+ for jj=1:length(ttls_forCond)
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+ if length(data.membPot)>=(ttls_forCond(jj)+spotDuration-1+grayDuration*2)==1 %only if you have enought data, when you end the recording it can happen that you end it during a trial -> those trials you dont consider here
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+ membPot_perTrialWhiteSpot{j+1}(jj,:)=data.membPot(ttls_forCond(jj): ...
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+ (ttls_forCond(jj)+spotDuration-1+2*grayDuration)); %duration-1 -> because the next trial would start there
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+ end
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+ end
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+ end
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+ clear spot_cond ttls_forCond
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+end
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+
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+
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+% baseline on trial by trial bases -> substract from the time series of each trial
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+% the mean value of the 200 ms before the spot arrives
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+membPot_trBasMeanWhiteSpot=cell(1,npatterns);
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+basValue=-200;%amount of baseline ->200ms
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+for ww=1:length(membPot_perTrialWhiteSpot)%nbr of spot sizes
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+ val_before=membPot_perTrialWhiteSpot{ww}(:,grayDuration+basValue:grayDuration-1);
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+ byTrBas_perSpot=(mean(val_before,2));
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+ trBas_repMAt=repmat(byTrBas_perSpot,1, ...
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+ size(membPot_perTrialWhiteSpot{ww}(:,grayDuration+1:end),2)); %directly take the signal after gray screen
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+ membPot_trBasMeanWhiteSpot{ww}=mean(membPot_perTrialWhiteSpot{ww}(:,grayDuration+1:end)- ...
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+ trBas_repMAt,1);%mean for each trial, directly take the signal after gray screen
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+ clear trBas_perSpotrepMAt
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+end
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+
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+
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+%------------------------------------------------------------------------------------------
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+%% 4. Plot the data
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+figure;
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+subplot(1,2,1)
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+%black spot with different sizes If you use earlier MATLAB versions you
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+%might have to choose for each spot size a different color
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+%50um
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+micro50=find(micro_meter==50);
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+plot(membPot_trBasMeanBlackSpot{micro50},'linewidth',3)
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+hold on
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+%80um
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+micro80=find(micro_meter==80);
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+plot(membPot_trBasMeanBlackSpot{micro80},'linewidth',3)
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+%120um
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+micro120=find(micro_meter==120);
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+plot(membPot_trBasMeanBlackSpot{micro120},'linewidth',3)
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+%legend
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+legend({micro_meter_withLabel([micro50,micro80,micro120],:)})
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+title('black spot')
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+xlabel('time(ms)')
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+ylabel('voltage(mV)')
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+YLIM=ylim;
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+
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+subplot(1,2,2)
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+%white spot with different sizes
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+%50um
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+plot(membPot_trBasMeanWhiteSpot{micro50},'linewidth',3)
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+hold on
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+%80um
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+plot(membPot_trBasMeanWhiteSpot{micro80},'linewidth',3)
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+%120um
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+plot(membPot_trBasMeanWhiteSpot{micro120},'linewidth',3)
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+%legend
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+legend({micro_meter_withLabel([micro50,micro80,micro120],:)})
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+title('white spot')
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+xlabel('time(ms)')
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+ylabel('voltage(mV)')
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+YLIM2=ylim;
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+
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+%find max of the two ylims and adapt ylims to compare the two plots so that
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+%they have the same ylims
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+minY=min([YLIM,YLIM2])-0.5;
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+maxY=max([YLIM,YLIM2])+0.5;
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+subplot(1,2,1)
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+ylim([minY maxY])
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+subplot(1,2,2)
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+ylim([minY maxY])
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+
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+%-------------------------------------------------------------------------------
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+%% 5. add variables into the output
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+uniformSpot_output.membPot_trBasMeanBlackSpot=membPot_trBasMeanBlackSpot;
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+uniformSpot_output.membPot_trBasMeanWhiteSpot=membPot_trBasMeanWhiteSpot;
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+uniformSpot_output.micro_meter=micro_meter;
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+end
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