Velocity: added photodiode stimulus traces using calibration for representative traces, Sine: added shorter simulated linker tau to summary plots, Calib: testing calibration usefulness for non-step protocols, Charge: new script for exploring charge asymmetry

Author: sammykatta

Analysis/SK/AnnotatedScripts/Velocity_VoltageAtt_180913.m

@@ -16,7 +16,7 @@
 clear projects;
 
 ephysMetaData = ImportMetaData();  %Recording Database.xlsx
-attenuationData = ImportMetaData(); %AttenuationCalcs.xlsx
+attenuationData = ImportMetaData(); %AttenuationCalcs_IC2_180810.xlsx
 
 %% Analyze capacity transient for C, Rs, and tau
 
@@ -69,7 +69,7 @@
 
 [velocityMRCs, velocityStim] = IdAnalysis(ephysData,protList,velocityCells,'num','matchType',matchType, ...
     'tauType','thalfmax', 'sortSweepsBy', sortSweeps, 'integrateCurrent',1 , ...
-    'recParameters', ephysMetaData,'sepByStimDistance',1);
+    'recParameters', ephysMetaData,'sepByStimDistance',1,'pdCompare',1);
 
 clear protList sortSweeps matchType
 
@@ -100,20 +100,46 @@
 figure();
 plot(velocityMRCs{1,2}');
 cmapline('ax',gca,'colormap','copper');
+
 %% Plot selected representative traces and stimuli
 % FAT214 with on ramps for 106, 785, 1560, 7230, 39740 um/s
 whichTraces = [3 5 6 10 12];
 
 % Grab stimuli based on velocityStim (second output from IdAnalysis)
-% Just example stim from one trace 
-% Should this be photodiode trace? (if so don't forget to zero it)
+% Just example stim from one single trace, not averaged
 stimTrace = cell(0);
 stimTrace{1} = ephysData.FAT214.data{2,18}(:,2);
 stimTrace{2} = ephysData.FAT214.data{2,11}(:,2);
 stimTrace{3} = ephysData.FAT214.data{2,12}(:,3);
 stimTrace{4} = ephysData.FAT214.data{2,12}(:,4);
 stimTrace{5} = ephysData.FAT214.data{2,17}(:,5);
 
+% Plot calibrated photodiode trace as alternative
+a = ephysData.FAT214.data{3,24}; % probe steps
+a = a-mean(a(1:3000));
+b = ephysData.FAT214.data{3,25}-ephysData.FAT214.data{3,26}; %pd steps minus worm only pd steps
+b = b-mean(b(1:3000));
+c = [0 2.5 5 7.5 10 12.5];
+
+% calibCells = {'FAT214'};
+% calibData = cell(0);
+% calibData{1} = b;
+% 
+% clear handles;
+% plotData = calibData{:,1};
+% handles = selectCalibSteps(plotData,calibCells{1});
+% stepIdx = handles.cursorPoints(:,1);
+% stepIdx = reshape(stepIdx,2,[])';
+% for j = 1:size(stepIdx,1)
+%     stepValues(1,j) = mean(plotData(stepIdx(j,1):stepIdx(j,2)))';
+% end
+% close;      
+% d = stepValues(1:6);
+d = [0.000254495420305394,-0.0837948030556295,-0.321306248450060,-0.664159366423493,-1.04265743523145,-1.44646508446994];
+e = velocityStim{1,3};
+f = interp1(-d,c,-e,'pchip');
+pdTrace = f(whichTraces,:);
+
 %pad to same length
 sweepLengths = cellfun('length',stimTrace);
 maxLength = max(sweepLengths);
@@ -126,7 +152,7 @@
 
 figure();
 axh(1)=subplot(2,1,1);
-plot(tVec,stimTrace);
+plot(tVec,pdTrace);
 cmapline('ax',gca,'colormap','copper');
 chH = get(gca,'children');
 set(gca,'children',flipud(chH));
@@ -156,7 +182,7 @@
 offH{2} = vline(offBox(:,2),'b:');
 cmapline('lines',offH{1}','colormap','bone');
 cmapline('lines',offH{2}','colormap','bone');
- 
+
 %% Plot representative trace expansions
 figure();
 axh(1)=subplot(2,1,1);

Analysis/SK/PDCalibTest.m

@@ -33,15 +33,15 @@
 %% Select ranges from calibration protocol
 for iCell = 1:length(calibCells)
     clear handles;
-    plotData = calibData(:,iCell);
+    plotData = calibData{:,iCell};
 
     % Run GUI for selecting ranges (hit Begin Selection, then place data
     % cursors in pairs around your ranges. shift-Click for each new data
     % cursor, and click to move the most recently active cursor, or move
     % any cursor at a later time, but be sure to keep them paired with the
     % same start/end cursor).
     %TODO: Fix the datatip labels.
-    handles = selectCalibSteps(plotData);
+    handles = selectCalibSteps(plotData,calibCells{iCell});
 
     % Pull out the mean value of the signal between the indices set by the
     % user's cursor placement. Store in stepValues with [recordings, steps]

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

@@ -0,0 +1,22 @@
+% ChargeExploration.m
+% 
+% 
+% Exploring asymmetry in charge with multi-rep noise analysis traces.
+% Variation in charge asymmetry with small steps, and whether charge
+% actually returns to zero by the end of the on step even if there is no
+% current detectable above noise.
+
+strainList = {'TU2769'};
+internalList = {'IC6'};
+stimPosition = {'anterior'};
+
+wormPrep = {'dissected'};
+cellDist = [40 200];
+resistCutoff = '<250';
+extFilterFreq = [2.5 5];
+
+noiseTrapCells = FilterRecordings(ephysData, ephysMetaData,...
+    'strain', strainList, 'internal', internalList, ...
+    'stimLocation', stimPosition, 'wormPrep', wormPrep, ...
+    'cellStimDistUm',cellDist, 'RsM', resistCutoff, ...
+    'stimFilterFrequencykHz', extFilterFreq, 'included', 1);

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

@@ -6,7 +6,7 @@
 stimPosition = {'posterior'};
 
 wormPrep = {'dissected'};
-cellDist = [40 100];
+cellDist = [40 90];
 resistCutoff = '<250';
 extFilterFreq = [2.5 5];
 
@@ -32,6 +32,9 @@
 %as new file.
 
 %% Running analysis
+protList ={'WC_Probe8','WC_Probe4','WC_Probe3','WC_Probe12'};
+
+matchType = 'first';
 
 noisePre = NonStatNoiseAnalysis(ephysData,protList,noisePreCells,...
     'matchType',matchType,'recParameters',ephysMetaData);

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

@@ -78,10 +78,6 @@
 
 % sine_allExt_ant_PDfiltered(180923).xls for all
 
-% okay we're just going to plot the power spectrum in the morning and
-% ignore the bode plot because I don't know what a "system" object really
-% is in matlab or if my data can be one, or what a linear time-invariant
-% system is or why a Bode plot is useful
 %% Calculate PSD
 figure();
 eachFreq = [0 10 30 100 200 500 1000];
@@ -156,21 +152,31 @@
 meanPSDByFreqI = meanPSDByFreq;
 
 %% Read in simulated power spectra and steady-state/rms
-sim_path = 'C:\Users\Sammy\Dropbox\Goodman Lab\Posters Papers Proposals\2018-Katta-SpatiotemporalDynamics\source-data\temporal-frequency\figure_4c_stimulus.txt';
+freqSim_path = 'C:\Users\Sammy\Dropbox\Goodman Lab\Posters Papers Proposals\2018-Katta-SpatiotemporalDynamics\source-data\temporal-frequency\';
+
+sim_path = fullfile(freqSim_path,'figure_4c_stimulus.txt');
 sim_stim = dlmread(sim_path,'\t',1,0);
 sim_f = sim_stim(:,1);
 sim_stim = sim_stim(:,2:end);
 
-sim_path = 'C:\Users\Sammy\Dropbox\Goodman Lab\Posters Papers Proposals\2018-Katta-SpatiotemporalDynamics\source-data\temporal-frequency\figure_4c_response.txt';
+sim_path = fullfile(freqSim_path,'figure_4c_response.txt');
 sim_resp = dlmread(sim_path,'\t',1,1);
 
-sim_path = 'C:\Users\Sammy\Dropbox\Goodman Lab\Posters Papers Proposals\2018-Katta-SpatiotemporalDynamics\source-data\temporal-frequency\figure_4d.txt';
-sim_steady = dlmread(sim_path,'\t',1,0);
-sim_sum_f = sim_steady(:,1);
-sim_steady = sim_steady(:,2:end);
+sim_path = fullfile(freqSim_path, 'figure_4d.txt');
+sim_steady_t2p9 = dlmread(sim_path,'\t',1,0);
+sim_sum_f = sim_steady_t2p9(:,1);
+sim_steady_t2p9 = sim_steady_t2p9(:,2:end);
+
+sim_path = fullfile(freqSim_path, 'figure_4e.txt');
+sim_rms_t2p9 = dlmread(sim_path,'\t',1,1);
+
+sim_path = fullfile(freqSim_path, 'figure_7d.txt');
+sim_steady_t0p6 = dlmread(sim_path,'\t',1,0);
+sim_sum_f_t0p6 = sim_steady_t0p6(:,1);
+sim_steady_t0p6 = sim_steady_t0p6(:,2:end);
 
-sim_path = 'C:\Users\Sammy\Dropbox\Goodman Lab\Posters Papers Proposals\2018-Katta-SpatiotemporalDynamics\source-data\temporal-frequency\figure_4e.txt';
-sim_rms = dlmread(sim_path,'\t',1,1);
+sim_path = fullfile(freqSim_path, 'figure_7e.txt');
+sim_rms_t0p6 = dlmread(sim_path,'\t',1,1);
 
 %% Plot stacked power spectra for sim and experimental
 
@@ -287,10 +293,12 @@
 figure(); clear axh;
 yyh = cell(0);
 
-yyh = plotyy(eachFreq,meanSteadyByFreq(:,1),sim_sum_f,sim_steady,@semilogx);
+yyh = plotyy(eachFreq,meanSteadyByFreq(:,1),sim_sum_f,sim_steady_t2p9,@semilogx);
 set(yyh(1),'YLim',[0 60],'YTick',(0:20:60));
 hold(yyh(1),'on');
 errorbar(yyh(1),eachFreq,meanSteadyByFreq(:,1),meanSteadyByFreq(:,3),'bo');
+hold(yyh(2),'on');
+plot(yyh(2),sim_sum_f_t0p6,sim_steady_t0p6);
 set(yyh,'box','off');
 xlabel('Frequency (Hz)')
 ylabel(yyh(1),'Steady-state current (pA)');
@@ -299,10 +307,12 @@
 figure(); clear axh;
 yyh = cell(0);
 
-yyh = plotyy(eachFreq,meanRMSByFreq(:,1),sim_sum_f,sim_rms,@semilogx);
+yyh = plotyy(eachFreq,meanRMSByFreq(:,1),sim_sum_f,sim_rms_t2p9,@semilogx);
 set(yyh(1),'YLim',[0 8],'YTick',(0:2:8));
 hold(yyh(1),'on');
 errorbar(yyh(1),eachFreq,meanRMSByFreq(:,1),meanRMSByFreq(:,3),'bo');
+hold(yyh(2),'on');
+plot(yyh(2),sim_sum_f_t0p6,sim_rms_t0p6);
 set(yyh, 'box','off');
 xlabel('Frequency (Hz)')
 ylabel(yyh(1),'Steady-state RMS (pA)');