Schreyer_and_Gollisch_2021_salamander_retinal_bipolar_cell_recordings/Spot/code patterned spot/BC_patternedSpot.m

function [patternedSpot_output]=BC_patternedSpot(loadData,filename,Hz,inputFrames)
%[patternedSpot_output]=BC_patternedSpot(loadData,filename,Hz,inputFrames)
%this function shows the analysis for the patterned spot stimulus. The
%baseline average response per patterned spot stimulus is computed.
%Inputs:
%               loadData = the folder path of the patterned spot files
%               filename = the filename of the BC of interest
%               Hz = reversing frequency of the patterned spot
%               inputFrames = the starting and ending frame times of the 
%               patterned spots from the excel file LogInfo_PatternedSpot.xlsx   
%
%Outpus:        patternedSpot_output = structure containing the output
%               average membrane potential per patterned spot and fourier output
%
% code by HS last modiefied March 2021

%% Constants
%starting and end frame for the split-spot
start_halfSpot=inputFrames(1);
end_halfSpot=inputFrames(2);
%starting and end frame for the spot divided into 4 quarters
start_quarterSpot=inputFrames(3);
end_quarterSpot=inputFrames(4);
%starting and end frame for the spot with 25micron subfields
start_25microSpot=inputFrames(5);
end_25microSpot=inputFrames(6);
%start and end frame for the spots recorded with version 2 (see excel file)
if length(inputFrames) > 6
    %for 10 micron subfields
    start_10microSpot=inputFrames(7); end_10microSpot=inputFrames(8);
    %for the uniform spot
    start_UniformSpot=inputFrames(9); end_UniformSpot=inputFrames(10);
end

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

%------------------------------------------------------------------------------------------
%% 2. build average response to split spot
indx=start_halfSpot; %you start with the splitspot
basValue=200;%get baseline (200ms) before the stimulus.
%The index in the excel file gives
%the start of the 2 trial already, one trial is 1000ms, therefore you
%have to go 1200ms before the index to get the 200ms beseline
oneperiod=1000/Hz; %time in ms of one period of the stimulus

%get the average baselined response to the split spot
memPotAVG_splitSpot=getAVGResponse(data,basValue,oneperiod,indx);

%------------------------------------------------------------------------------------------
%% 3. build average response to quarter spot
indx=start_quarterSpot; %you start with the spot
%get the average baselined response to the quarter spot
memPotAVG_quarterSpot=getAVGResponse(data,basValue,oneperiod,indx);

%------------------------------------------------------------------------------------------
%% 4. build average response to 25micron spot
indx=start_25microSpot; %you start with the spot
%get the average baselined response to the 25micron spot
memPotAVG_25microSpot=getAVGResponse(data,basValue,oneperiod,indx);

%------------------------------------------------------------------------------------------
%% 5. only for stimulus version 2 build average for 10micron spot and uniform spot
if length(inputFrames) > 6
    %------------------------------------------------------------------------------------------
    %% 5.1 build average response to 15micron spot
    indx=start_10microSpot; %you start with the spot
    %get the average baselined response to the 10micron spot
    memPotAVG_10microSpot=getAVGResponse(data,basValue,oneperiod,indx);
    
    %------------------------------------------------------------------------------------------
    %% 5.2 build average response to uniform spot
    indx=start_UniformSpot; %you start with the spot
    %get the average baselined response to the uniform spot
    memPotAVG_uniformSpot=getAVGResponse(data,basValue,oneperiod,indx);
    
else
    %get the response to the uniform spot from the loaded file
    memPotAVG_uniformSpot=data.uniformTraceAVG;
end

%------------------------------------------------------------------------------------------
%% 6. Plot the data
figure;
%uniform spot
subplot(2,2,1)
%get max and min to set same axis for all the patterned
%spot
YLIM=[min([memPotAVG_uniformSpot,memPotAVG_splitSpot,memPotAVG_quarterSpot,memPotAVG_25microSpot])-0.5,...
    max([memPotAVG_uniformSpot,memPotAVG_splitSpot,memPotAVG_quarterSpot,memPotAVG_25microSpot])+0.5];
plot(memPotAVG_uniformSpot,'k','linewidth',3) %original membrane potential
title('uniform spot')
xlabel('time(ms)')
ylabel('voltage (mV)')
ylim(YLIM);
%split spot
subplot(2,2,2)
plot(memPotAVG_splitSpot,'k','linewidth',3) %original membrane potential
title('split spot')
xlabel('time(ms)')
ylabel('voltage (mV)')
ylim(YLIM);
%1/4 spot
subplot(2,2,3)
plot(memPotAVG_quarterSpot,'k','linewidth',3) %original membrane potential
title('quarter spot')
xlabel('time(ms)')
ylabel('voltage (mV)')
ylim(YLIM);
%25micron subfield spot
subplot(2,2,4)
plot(memPotAVG_25microSpot,'k','linewidth',3) %original membrane potential
title('25micron subfields spot')
xlabel('time(ms)')
ylabel('voltage (mV)')
ylim(YLIM);

%-------------------------------------------------------------------------------
%% 5. add variables into the output
patternedSpot_output.memPotAVG_uniformSpot=memPotAVG_uniformSpot;
patternedSpot_output.memPotAVG_splitSpot=memPotAVG_splitSpot;
patternedSpot_output.memPotAVG_quarterSpot=memPotAVG_quarterSpot;
patternedSpot_output.memPotAVG_25microSpot=memPotAVG_25microSpot;
if length(inputFrames) > 6
    patternedSpot_output.memPotAVG_10microSpot=memPotAVG_10microSpot;
end
end

function membPotAVG_trBas=getAVGResponse(data,basValue,oneperiod,indx)
memPot_basTemp=data.membPot(data.ttls_ms(indx)-oneperiod-basValue: ...
    data.ttls_ms(indx)-oneperiod-1); %baseline 200ms before
for jj=1:3 %amount of black spot start per size ->only analyse 3!
    membPot_perTrial(jj,:)=data.membPot(data.ttls_ms(indx): ...
        data.ttls_ms(indx)+oneperiod-1); %duration 1000 ms for black and white together
    indx=indx+2;
end
memPotAVG= mean(membPot_perTrial);
membPotAVG_trBas= memPotAVG-mean(memPot_basTemp);
end