Schreyer_and_Gollisch_2021_salamander_retinal_bipolar_cell_recordings/Spot/code uniform spot/BC_uniformSpot3.m

function [uniformSpot_output]=BC_uniformSpot3(loadData,filename,spotDuration,grayDuration,inputFrames,pathStimSignal)
%[uniformSpot_output]=BC_uniformSpot3(loadData,filename,spotDuration,grayDuration,contrast)
%this function shows the example analysis for the uniform spot stimulus with
%different spot sizes for stimulus version 3. Here the black and white spot
%are recorded in the same file
%Inputs:
%               loadData = the folder path of the patterned spot files
%               filename = the filename of the BC of interest
%               spotDuration = duration of spot in ms, found in 
%               the excel file LogInfo_PatternedSpot.xlsx   
%               grayDuration = duration of gray screen in ms, found in 
%               the excel file LogInfo_PatternedSpot.xlsx 
%               inputFrames = start and end frames of the different
%               contrast spots, found in the excel file 
%               LogInfo_PatternedSpot.xlsx 
%               pathStimSignal = folder path to load the sequence of spot
%               sizes shown
%               
%
%Outpus:        uniformSpot_output = structure containing the output
%               average membrane potential per spot size of the uniform
%               spot for both black and white contrast.
%
% code by HS last modiefied March 2021

%% Constants
mircoMeter_proPixel=2.5; %one monitor pixel is 2.5 micrometers

%-------------------------------------------------------------------------------
%% 1. load the patterned spot file
data=load([loadData,filename]); %load the file

%-------------------------------------------------------------------------------
%% 2. load the spot sizes
%same as spot version 2
npatterns=11; %11 spot sizes were shown
micro_meter=[2, 6, 8, 10, 12, 16, 24, 32, 50, 100, 200 ]'*2*mircoMeter_proPixel; 
%for plotting add the mircometer label
micrometer_label=repmat(' \mum',size(micro_meter,1),1);
micro_meter_withLabel=strcat (num2str(micro_meter),micrometer_label);

load(pathStimSignal); %load the order of the presentation of the diameter sizes. See Documentation_Data_BCRecordings. It contains values from 10-1000 and the numbers refer to the spot size in micrometers. The same order was used for black and white spots

%------------------------------------------------------------------------------------------
%% 3. extract the membrane potential data for the black spot, for each spot size and build the average
%start of black spot
start_blackSpot=inputFrames(1);
%end of black spot
end_blackSpot=inputFrames(2);
%only get the frames where the gray screen was shown (that you have one
%frame per trial)
ttls_ms_forCond=data.ttls_ms(1:2:end_blackSpot);

%extract the membrane potential per spot
membPot_perTrialBlackSpot=cell(1,npatterns);
for j=1:npatterns %loop over spot sizes
    spot_cond=find(stimulus==micro_meter(j));%get all the spots with same size
    ttls_forCond=ttls_ms_forCond(spot_cond);%get the ttls signals for this circle size
    if ~isempty(ttls_forCond)
        %get the membrane potenial for this ttls signal (start gray screen) and go until
        %the next spot (grayScreen 1000ms+500msSpot+1000gray)
        for jj=1:length(ttls_forCond)
            if length(data.membPot)>=(ttls_forCond(jj)+spotDuration-1+grayDuration*2)==1 %only if you have enought data
                membPot_perTrialBlackSpot{j}(jj,:)=data.membPot(ttls_forCond(jj): ...
                    (ttls_forCond(jj)+spotDuration-1+2*grayDuration)); %duration-1 -> because the next trial would start there
            end
        end
    end
    clear spot_cond ttls_forCond
end


% baseline on trial by trial bases -> substract from the time series of each trial
% the mean value of the 200 ms before the spot arrives
membPot_trBasMeanBlackSpot=cell(1,npatterns);
basValue=-200;%amount of baseline ->200ms
for ww=1:length(membPot_perTrialBlackSpot)%nbr of spot sizes
    val_before=membPot_perTrialBlackSpot{ww}(:,grayDuration+basValue:grayDuration-1);
    byTrBas_perSpot=(mean(val_before,2));
    trBas_repMAt=repmat(byTrBas_perSpot,1, ...
        size(membPot_perTrialBlackSpot{ww}(:,grayDuration+1:end),2)); %directly take the signal after gray screen
    membPot_trBasMeanBlackSpot{ww}=mean(membPot_perTrialBlackSpot{ww}(:,grayDuration+1:end)- ...
        trBas_repMAt,1);%mean for each trial, directly take the signal after gray screen
    clear trBas_perSpotrepMAt
end

%------------------------------------------------------------------------------------------
%% 3. extract the membrane potential data for the white spot, for each spot size and build the average
%start of black spot
start_whiteSpot=inputFrames(3);
%end of black spot
end_whiteSpot=inputFrames(4);
%only get the frames where the gray screen was shown (that you have one
%frame per trial)
ttls_ms_forCond=data.ttls_ms(start_whiteSpot:2:end_whiteSpot); 

%extract the membrane potential per spot
membPot_perTrialWhiteSpot=cell(1,npatterns);
for j=1:npatterns %loop over spot sizes
    spot_cond=find(stimulus==micro_meter(j));%get all the spots with same size
    ttls_forCond=ttls_ms_forCond(spot_cond);%get the ttls signals for this circle size
    if ~isempty(ttls_forCond)
        %get the membrane potenial for this ttls signal (start gray screen) and go until
        %the next spot (grayScreen 1000ms+500msSpot+1000gray)
        for jj=1:length(ttls_forCond)
            if length(data.membPot)>=(ttls_forCond(jj)+spotDuration-1+grayDuration*2)==1 %only if you have enought data
                membPot_perTrialWhiteSpot{j}(jj,:)=data.membPot(ttls_forCond(jj): ...
                    (ttls_forCond(jj)+spotDuration-1+2*grayDuration)); %duration-1 -> because the next trial would start there
            end
        end
    end
    clear spot_cond ttls_forCond
end


% baseline on trial by trial bases -> substract from the time series of each trial
% the mean value of the 200 ms before the spot arrives
membPot_trBasMeanWhiteSpot=cell(1,npatterns);
basValue=-200;%amount of baseline ->200ms
for ww=1:length(membPot_perTrialWhiteSpot)%nbr of spot sizes
    val_before=membPot_perTrialWhiteSpot{ww}(:,grayDuration+basValue:grayDuration-1);
    byTrBas_perSpot=(mean(val_before,2));
    trBas_repMAt=repmat(byTrBas_perSpot,1, ...
        size(membPot_perTrialWhiteSpot{ww}(:,grayDuration+1:end),2)); %directly take the signal after gray screen
    membPot_trBasMeanWhiteSpot{ww}=mean(membPot_perTrialWhiteSpot{ww}(:,grayDuration+1:end)- ...
        trBas_repMAt,1);%mean for each trial, directly take the signal after gray screen
    clear trBas_perSpotrepMAt
end


%------------------------------------------------------------------------------------------
%% 4. Plot the data
figure;
%black spot
subplot(1,2,1)
%uniform spot, different sizes If you use earlier MATLAB versions you
%might have to choose for each spot size a different color
%50um
micro50=find(micro_meter==50);
plot(membPot_trBasMeanBlackSpot{micro50},'linewidth',3)
hold on
%80um
micro80=find(micro_meter==80);
plot(membPot_trBasMeanBlackSpot{micro80},'linewidth',3)
%120um
micro120=find(micro_meter==120);
plot(membPot_trBasMeanBlackSpot{micro120},'linewidth',3)
xlabel('time(ms)')
ylabel('voltage(mV)')
%legend
legend({micro_meter_withLabel([micro50,micro80,micro120],:)})
title('black spot')
YLIM=ylim;

%white spot
subplot(1,2,2)
%uniform spot, different sizes
%50um
micro50=find(micro_meter==50);
plot(membPot_trBasMeanWhiteSpot{micro50},'linewidth',3)
hold on
%80um
micro80=find(micro_meter==80);
plot(membPot_trBasMeanWhiteSpot{micro80},'linewidth',3)
%120um
micro120=find(micro_meter==120);
plot(membPot_trBasMeanWhiteSpot{micro120},'linewidth',3)
%legend
legend({micro_meter_withLabel([micro50,micro80,micro120],:)})
title('white spot')  
xlabel('time(ms)')
ylabel('voltage(mV)')
YLIM2=ylim;

%find max of the two ylims and adapt ylims to compare the two plots so that
%they have the same ylims
minY=min([YLIM,YLIM2])-0.5;
maxY=max([YLIM,YLIM2])+0.5;
subplot(1,2,1)
ylim([minY maxY])
subplot(1,2,2)
ylim([minY maxY])

%-------------------------------------------------------------------------------
%% 5. add variables into the output
uniformSpot_output.membPot_trBasMean=membPot_trBasMeanBlackSpot;
uniformSpot_output.membPot_trBasMeanWhiteSpot=membPot_trBasMeanWhiteSpot;
uniformSpot_output.micro_meter=micro_meter;
end