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sammykattasammykatta
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Mini analysis of speed-controlled steps
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‎Analysis/SK/AnnotatedScripts/Velocity_VoltageAtt_180913.m‎

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for iVel = 1:length(eachVel)
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stepVel = eachVel(iVel);
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whichVel = abs(thisCell(:,1) - stepVel) < 12; %find closest velocity
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whichVel = abs(thisCell(:,1) - stepVel) < tol; %find closest velocity
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if any(whichVel)
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if any(hasAtt) && thisAtt{hasAtt,2} %if attenuation calc exists and not omitCell
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if noCorr == 0 && strcmp(dType,'peak') || strcmp(dType,'charge') %attenuation correction for current/charge but not taus

‎Analysis/SK/Scripts-in-progress/SpeedControlledSteps.m‎

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% SpeedControlledSteps.m
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%%Import data and metadata
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ephysData = ImportPatchData('incl',1);
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projects = {'FAT';'SYM'};
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%fix a couple messed up names
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ephysData.FAT029 = ephysData.FAT029s;
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ephysData.FAT017 = ephysData.FAT017e001;
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ephysData.FAT164 = ephysData.FAT164001;
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ephysData = rmfield(ephysData,{'FAT017e001';'FAT029s';'FAT164001'});
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ephysData = FilterProjectData(ephysData, projects);
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clear projects;
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ephysMetaData = ImportMetaData(); %Recording Database.xlsx
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attenuationData = ImportMetaData(); %AttenuationCalcs.xlsx
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%% Select recordings that match parameters based on metadata
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strainList = {'TU2769'};
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internalList = {'IC2'};
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stimPosition = {'anterior'};
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wormPrep = {'dissected'};
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cellDist = [40 200]; % stimulus/cell distance in um
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resistCutoff = '<250'; % Rs < 250 MOhm
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extFilterFreq = 2.5; % frequency of low-pass filter for stimulus command
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includeFlag = 1;
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anteriorControlCells = FilterRecordings(ephysData, ephysMetaData,...
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'strain', strainList, 'internal', internalList, ...
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'stimLocation', stimPosition, 'wormPrep', wormPrep, ...
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'cellStimDistUm',cellDist, 'RsM', resistCutoff, ...
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'stimFilterFrequencykHz', extFilterFreq, 'included', includeFlag);
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clear cellDist strainList internalList cellTypeList stimPosition resistCutoff ans wormPrep excludeCells;
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% This results in a file with three columns: cell ID, series, and sweeps
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% that have been approved for analysis use.
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%% Visual/manual exclusion of bad sweeps
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% This is mainly based on excluding sweeps with leak > 10pA, but also
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% sweeps where the recording was lost partway through or some unexpected
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% source of noise was clearly at play.
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% If you have already made a list of sweeps, skip this section and load the
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% list in the next section.
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protList ={'Control'};
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matchType = 'first';
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ExcludeSweeps(ephysData, protList, anteriorControlCells, 'matchType', matchType);
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%% Find MRCs
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% Lists: antAllSteps.xlsx and postAllSteps.xlsx from 180810 should contain
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% all relevant steps for anterior and posterior stimulation, respectively.
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protList ={'Control'};
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matchType = 'first';
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sortSweeps = {'magnitude','magnitude','magnitude','magnitude'};
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[anteriorMRCs, antStim] = IdAnalysis(ephysData,protList,anteriorControlCells,'num','matchType',matchType, ...
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'tauType','thalfmax', 'sortSweepsBy', sortSweeps, 'integrateCurrent',1 , ...
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'recParameters', ephysMetaData,'sepByStimDistance',1,'subZeroCharge',1);
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clear protList sortSweeps matchType
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%% Average and plot
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% Set the filename
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fname = 'PatchData/controlSpeed_attCorrected(190729).xls';
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eachSize = [4 8 12]';
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distLimits = [40 200]; % limit to same average distance for anterior and posterior
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distCol = 12;
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whichStim = 1; %on or off
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noCorr = 0; % 1 to skip space clamp voltage attenuation correction
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Vc = -0.06; %in V
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Ena = 0.094; % in V
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% Manually change dType to 'curr', 'char', 'act', or 'decay' depending on
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% which analysis you would like to do.
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whichMRCs = anteriorMRCs;
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dType = 'curr';
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switch dType
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case 'curr'
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peakCol = 6; % peak current
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case 'char'
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peakCol = 11; % integrated current/charge
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case 'act'
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peakCol = 8; % activation time constant
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case 'decay'
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peakCol = 9; % decay time constant
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end
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if whichStim == 2
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eachSize = -eachSize;
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end
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thisAtt = attenuationData(:,[2 8 10]);
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thisName = cell(0);
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ant_Out = cell(length(eachSize)+1,size(whichMRCs,1));
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for iCell = 1:size(whichMRCs,1)
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thisCell = whichMRCs{iCell,whichStim+2};
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thisDist = mean(thisCell(:,distCol)); % check if cell distance is in range
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if thisDist <= distLimits(2) && thisDist >= distLimits(1)
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thisName{iCell,1} = whichMRCs{iCell,1}; %name
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thisName{iCell,2} = thisDist;
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ant_Out{1,iCell} = [dType '_' thisName{iCell,1}];
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hasAtt = strcmp(thisName{iCell,1},thisAtt(:,1));
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Iact = [];
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for iSize = 1:length(eachSize)
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stepSize = eachSize(iSize);
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whichStep = round(thisCell(:,1)*2)/2 == stepSize; %round to nearest 0.5
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if any(whichStep)
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if any(hasAtt) && thisAtt{hasAtt,2} %if attenuation calc exists and not omitCell
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if noCorr == 0 || strcmp(dType,'peak') || strcmp(dType,'charge') %attenuation correction for current/charge but not taus
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Vm = Vc * thisAtt{hasAtt,3};
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Im = thisCell(whichStep,peakCol);
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Iact(iSize,1) = (Im * (Vc-Ena)) ./ (Vm-Ena);
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else
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Im = thisCell(whichStep,peakCol);
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Iact(iSize,1) = Im;
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end
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else
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Iact(iSize,1) = nan;
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end
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else
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Iact(iSize,1) = nan;
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end
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end
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ant_Out(2:length(eachSize)+1,iCell) = num2cell(Iact);
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end
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end
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ant_Name = [{'Anterior', 'Ant_Dist'}; thisName];
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ant_Out = ant_Out(:,~cellfun(@isempty, ant_Out(1,:))); % clear out empty waves (where dist didn't match)
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ant_Name = ant_Name(~cellfun(@isempty, ant_Name(:,1)),:);
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ant_Out = [[{'stepSize'};num2cell(eachSize)] ant_Out]; % append stepSize wave
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xlswrite(fname,ant_Out,['ant_' dType]);
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xlswrite(fname,ant_Name,'antStats');
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clear iCell thisCell Iact whichMRCs whichStep hasAtt thisAtt Vc Ena thisName
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%% Normalize based on current/charge at given step size and write to xls
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% Normalizes within each condition
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stepSize = 12; % must be negative for off
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%Anterior
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which_Out = ant_Out;
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norm_Out = cell(size(which_Out));
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currMat = cell2mat(which_Out(2:end,2:end));
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whichRow = find(cellfun(@(x) abs(x - stepSize) < 0.5, which_Out(2:end,1)));
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normRow = currMat(whichRow,:);
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normMat = bsxfun(@rdivide,currMat,normRow);
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norm_Out(2:end,2:end) = num2cell(normMat);
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norm_Out(:,1) = which_Out(:,1);
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norm_Out(1,2:end) = cellfun(@(x) ['norm_' x],which_Out(1,2:end),'un',0);
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ant_Norm = norm_Out;
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xlswrite(fname,ant_Norm,['ant_' dType '_Norm']);
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clear currMat which Row normRow normMat norm_Out
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