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analyzeTraces.m
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function analyzeTraces
% author: Bryce Grier
% last updated 2020.03.03
% contact: bdgrier@gmail.com
%% introduction
% This program can be used to analyze whole-cell electrophysiology data. It currently accepts
% '.txt' files. Files should be formatted as a column vector of current values in pA. Currently,
% only negative current can be analyzed. The ability to analyze positive current will be added
% in the future.
% As events are selected, they can be sorted into 1 of 3 analysis groups:
% full event = rise and decay of event are measured
% amplitude = rise of event is measured
% frequency = event in included only in measurement of frequency
% All events labeled for full analysis are added to the average event trace. Specific events
% can be removed from the average trace by selecting them on either the raw events plot or on
% the scaled events plot.
% Keyboard functionality requires the main panel of the GUI to have focus. Clicking in certain
% areas moves focus to a child component of the main panel. To return focus to the main panel,
% simply click anywhere where there is not a child component.
% The delete button has two functions:
% when an event is selected, it deletes the selected event
% when no event is selected, it clears all events from the current view window
%% initialize shared variables
% analysis parameters
RMS = 2; % default value for root mean square noise of trace
noiseThreshold = 3*RMS; % default threshold for event detection
decayStartPercent = 90; % default percentage of decay to measure from
decayEndPercent = 37; % default percentage of decay to measure to
riseStartPercent = 10; % default percentage of rise to measure from
riseEndPercent = 90; % default percentage of rise to measure to
samplesPerMilliSecond = 10; % sampling rate/1000
% diretory and cell strings
cellName = ""; % string containing experiment cell name
% fileType = ""; % string containing experiment file type
fileName = ""; % string containing experiment file name
matliststrings = string(); % string of matlab files present in experiment folder
traceliststrings = string(); % string of traces present in experiment folder
% display variables
yMax = 10; % default maximum y axis value of plotted trace
yMin = -50; % default minimum y axis value of plotted trace
yOffset = 0; % default y offset of plotted trace
sortedColumn = 1; % column number on which data table is sorted
ascendLogical = 1; % logical value indicating direction of sorting
windowScope = 800; % default width of viewing window in sample points
currentWindow = []; % array of sample points currently in view
autoZoom = 1; % logical value for auto zoon on event selection
traceAlignment = 'Align By Threshold'; % value for how to align traces
% trace variables
traceSamples = []; % imported whole cell trace
trace_first_der = []; % first derivative of whole cell trace
traceValueCol = 1; % membrane current values
traceTimeCol = 2; % sample points
eventPlotLogicalCol = 3; % logical values for presence of event threshold
eventPlotEndCol = 4; % sample points of event peaks
% data table column values
fullEventLogicalCol = 1; % logical value for inclusion of event in full event measurement
amplitudeLogicalCol = 2; % logical value for inclusion of event in amplitude measurement
frequencyLogicalCol = 3; % logical value for inclusion of event in frequency measurement
amplitudeValueCol = 4; % measurement of event amplitude
riseTimeValueCol = 5; % measurement of event 10-90 rise time
riseSlopeValueCol = 6; % measurement of event 10-90 slope
rise50TimeCol = 7; % sample point at which event rise 50 occurs
decay50TimeCol = 8; % sample point at which event decay 50 occurs
halfWidthValueCol = 9; % measurement of event half width
decayValueCol = 10; % measurement of decay time to desired percentage of peak value
aucValueCol = 11; % measurement of area to desired percentage of peak value
eventTimeCol = 12; % when event occurs
averageTraceLogicalCol = 13; % logical value for inclusion of event in average trace
% selection variables
eventCurrentlySelected = false; % logical value for whether event is selected
eventIndex = 0; % row of selectedEvents current being modified
selectedEvents = nan(500,15); % matrix containing measurements of events
eventPeakTime = []; % time of peak of currently selected event
eventThresholdTime = []; % time of threshold of currently selected event
eventPeakValue = []; % value of peak of currently selected event
eventThresholdValue = []; % value of threshold of currently selected event
eventDecayAUC = []; % area of decay portion of currently selected event
eventRiseAUC = []; % area of rise portion of currently selected event
% average trace variables
preEventSamples = 10; % # of samples before threshold in average trace
postEventSamples = 150; % # of samples after threshold in average trace
totalSamples = preEventSamples + postEventSamples; % total # of samples in average trace
allTraces = []; % totalSamples x n event matrix of event traces
averageTrace = []; % column vector with mean of each row of allTraces
eventPlots = gobjects(1,size(selectedEvents,1)); %place holders for trace plot objects
eventPlotsScaled = gobjects(1,size(selectedEvents,1)); %place holders for trace plot objects
% misc
updatingLogical = false;
averageTraceUpdate = false;
savePath = '';
%% set root directory
% the root directory should contain experiments separated into folders
% specific experiment folders can be navigated to within the GUI
rootDir = pwd;
%% get screen dimensions
% obtain information to assist in dynamically creating the GUI
% obtain information on screen sizes
screenDims = get(0,'ScreenSize');
screenOffset = [0 0];
% setting dimension variables for later use in generating the GUI layout
screenWidth = screenDims(3);
screenHeight = screenDims(4);
%% set working directory
% populate the list of experiment folders that you are able to choose from
% get list of items in the root directory
dirlist = dir();
dirliststrings = string();
for dirIndex = 3:size(dirlist,1)
dirliststrings(dirIndex-1) = convertCharsToStrings(dirlist(dirIndex).name);
end
% remove non-folder items from the list of strings and add a blank string to the beginning
dirliststrings = dirliststrings(isfolder(dirliststrings));
% dirliststrings = dirliststrings(~strncmp('exc',dirliststrings,3));
dirliststrings = [string() dirliststrings];
%% initialize main panel
% create the main GUI panel and add elements to it
% intialize and position main panel
mainPanel = uifigure('Position',[screenOffset(1) screenOffset(2) 100 100]);
% mainPanel.Position = [screenOffset(1) screenOffset(2) 100 100];
set(mainPanel,'WindowState','maximized');
% data table that will contain measurements
dataTable = table();
uit = uitable('Parent',mainPanel,...
'Data',dataTable,...
'Position',[20 20 screenWidth/2-(30) screenHeight/2-(100)],...
'CellSelectionCallback',@navigateToEvent,...
'ColumnSortable',true,...
'DisplayDataChangedFcn',@sortCallback);
% tab group that will contain tabs with buttons for interacting with the recording
buttonTabGroup = uitabgroup('Parent',mainPanel,...
'Position',[screenWidth/2+(10) 20 screenWidth/2-(30) screenHeight/2-(80)]);
% tab group that will contain plots of the main recording and of individual events
plotTabGroup = uitabgroup('Parent',mainPanel,...
'Position',[20 screenHeight/2-50 screenWidth-40 screenHeight/2-30],...
'SelectionChangedFcn',@evaluateCurrentPlotTab);
% counters for number of events sorted into each analysis group
avgCount = uilabel('Parent',mainPanel,...
'HorizontalAlignment','Center',...
'Text',sprintf('%s%i','# in Average Trace: ',nansum(selectedEvents(:,averageTraceLogicalCol))),...
'Position',[screenWidth*0.10-75 screenHeight/2-75 150 20],...
'fontweight', 'bold');
fullCount = uilabel('Parent',mainPanel,...
'HorizontalAlignment','Center',...
'Text',sprintf('%s%i','# in Full Event: ',nansum(selectedEvents(:,fullEventLogicalCol))),...
'Position',[screenWidth*0.20-75 screenHeight/2-75 150 20],...
'fontweight', 'bold');
ampCount = uilabel('Parent',mainPanel,...
'HorizontalAlignment','Center',...
'Text',sprintf('%s%i','# in Amplitude: ',nansum(selectedEvents(:,amplitudeLogicalCol))),...
'Position',[screenWidth*0.30-75 screenHeight/2-75 150 20],...
'fontweight', 'bold');
freqCount = uilabel('Parent',mainPanel,...
'HorizontalAlignment','Center',...
'Text',sprintf('%s%i','# in Frequency: ',nansum(selectedEvents(:,frequencyLogicalCol))),...
'Position',[screenWidth*0.40-75 screenHeight/2-75 150 20],...
'fontweight', 'bold');
%% create tabs for plots
% populate the tabs that will contain plots
% get dimensions of plot tab group for later use
plotTabGroupDims = plotTabGroup.Position;
plotTabGroupWidth = plotTabGroupDims(3);
plotTabGroupHeight = plotTabGroupDims(4);
% tab and plot that will display the main recording trace
traceTab = uitab('Parent',plotTabGroup,'Title','Trace');
tracePlot = uiaxes('Parent',traceTab,...
'Position',[20 20 plotTabGroupWidth-30 plotTabGroupHeight-50],...
'XTick',[]);
tracePlot.Toolbar.Visible = 'off';
% sliders that allow adjustment of view within a given window
ySlider = uislider('Parent',traceTab,...
'Orientation','vertical',...
'Position',[10 25 3 plotTabGroupHeight-60],...
'MajorTicks',[],...
'MinorTicks',[],...
'Limits',[-40 40],...
'Value',0,...
'ValueChangingFcn',@ySliderFunc);
xSlider = uislider('Parent',traceTab,...
'Orientation','horizontal',...
'Position',[40 10 plotTabGroupWidth-55 3],...
'MajorTicks',[],...
'MinorTicks',[],...
'Limits',[-windowScope windowScope],...
'Value',0,...
'ValueChangedFcn',@xSliderFunc);
% tab and plots that will display overlaid events and the average event trace
averageTraceTab = uitab('Parent',plotTabGroup,...
'Title','Average Event');
allTracePlot = uiaxes('Parent',averageTraceTab,...
'XTick',[],...
'Position',[5 10 plotTabGroupWidth/3-10 plotTabGroupHeight-40]);
allTracePlot.Title.String = 'All Traces';
allTracePlot.Toolbar.Visible = 'off';
scaledTracePlot = uiaxes('Parent',averageTraceTab,...
'XTick',[],...
'Position',[plotTabGroupWidth*(1/3)+5 10 plotTabGroupWidth/3-10 plotTabGroupHeight-40]);
scaledTracePlot.Title.String = 'Scaled Traces';
scaledTracePlot.Toolbar.Visible = 'off';
averageTracePlot = uiaxes('Parent',averageTraceTab,...
'XTick',[],...
'Position',[plotTabGroupWidth*(2/3)+5 10 plotTabGroupWidth/3-10 plotTabGroupHeight-40]);
averageTracePlot.Title.String = 'Average Trace';
averageTracePlot.Toolbar.Visible = 'off';
%% create navigation tab
% create and populate the tab that initializes analysis
% create tab and store dimensions for later use
navigationTab = uitab('Parent',buttonTabGroup,...
'Title','Navigation');
navigationTabDims = navigationTab.Position;
navigationTabWidth = navigationTabDims(3);
navigationTabHeight = navigationTabDims(4);
% list boxes containing experiments, recording files, and existing analysis files
uilabel('Parent',navigationTab,...
'Text','Choose an experiment',...
'HorizontalAlignment','Center',...
'Position',[navigationTabWidth*0.15-(175/2) navigationTabHeight*0.775 175 40],...
'fontweight', 'bold');
directoryControl = uilistbox('Parent',navigationTab,...
'Items',dirliststrings,...
'ValueChangedFcn',@populateLists,...
'Position',[navigationTabWidth*0.15-(150/2) navigationTabHeight*0.55-(125/2) 150 125]);
uilabel('Parent',navigationTab,...
'Text',sprintf('%s\n%s','Choose a trace',' to begin analysis'),...
'HorizontalAlignment','Center',...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.5-(175/2) navigationTabHeight*0.775 175 40]);
mainTraceControl = uilistbox('Parent',navigationTab,...
'Items',traceliststrings,...
'Position',[navigationTabWidth*0.5-(150/2) navigationTabHeight*0.55-(125/2) 150 125]);
uilabel('Parent',navigationTab,...
'Text',sprintf('%s\n%s','Choose an existing','file to resume analysis'),...
'HorizontalAlignment','Center',...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.85-(200/2) navigationTabHeight*0.775 200 40]);
analysisList = uilistbox('Parent',navigationTab,...
'Items',matliststrings,...
'Position',[navigationTabWidth*0.85-(150/2) navigationTabHeight*0.55-(125/2) 150 125]);
% buttons to initialize, save, and end analysis
uibutton('Parent',navigationTab,...
'Text',sprintf('%s\n%s','Begin','New Analysis'),...
'ButtonPushedFcn',@beginAnalysis,...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.2-(100/2) navigationTabHeight*0.1 100 40]);
uibutton('Parent',navigationTab,...
'Text',sprintf('%s\n%s','Load Existing','Analysis'),...
'ButtonPushedFcn',@resumeAnalysis,...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.4-(100/2) navigationTabHeight*0.1 100 40]);
uibutton('Parent',navigationTab,...
'Text',sprintf('%s\n%s','Save','Analysis'),...
'ButtonPushedFcn',@saveAnalysis,...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.6-(100/2) navigationTabHeight*0.1 100 40]);
uibutton('Parent',navigationTab,...
'Text','Exit',...
'ButtonPushedFcn',@exitAnalysis,...
'fontweight', 'bold',...
'Position',[navigationTabWidth*0.8-(100/2) navigationTabHeight*0.1 100 40]);
%% create settings tab
% create and populate the tab that contains analysis settings
% create tab and store dimensions for later use
settingsTab = uitab('Parent',buttonTabGroup,...
'Title','Settings');
settingsTabDims = settingsTab.Position;
settingsTabWidth = settingsTabDims(3);
settingsTabHeight = settingsTabDims(4);
% radio buttons for average trace alignment preference
traceButtonWidth = settingsTabWidth*0.25;
traceButtonHeight = settingsTabHeight*0.225;
traceAlignButton = uibuttongroup('Parent',settingsTab,...
'Title','Average Trace Alignment',...
'fontweight','bold',...
'SelectionChangedFcn',@alignmentChange,...
'Position',[settingsTabWidth*0.2-(traceButtonWidth/2) settingsTabHeight*0.75-(traceButtonHeight/2) traceButtonWidth traceButtonHeight]);
uiradiobutton('Parent',traceAlignButton,...
'Text','Align By Threshold',...
'fontweight', 'bold',...
'Position',[traceButtonWidth*0.5-(150/2) traceButtonHeight*0.5-(20/2) 150 20]);
uiradiobutton('Parent',traceAlignButton,...
'Text','Align By Peak',...
'fontweight', 'bold',...
'Position',[traceButtonWidth*.5-(150/2) traceButtonHeight*0.2-(20/2) 150 20]);
% checkbox for auto-zoom on event selection
zoomCheck = uicheckbox('Parent',settingsTab,...
'Text','Auto-zoom on event selection',...
'fontweight','bold',...
'Value',autoZoom,...
'ValueChangedFcn',@zoomChange,...
'Position',[settingsTabWidth*0.8-(200/2) settingsTabHeight*0.85-(40) 200 20]);
% controls for measuring and editing RMS/noise threshold
uibutton('Parent',settingsTab,...
'Text','Measure',...
'ButtonPushedFcn',@measureRMS,...
'fontweight', 'bold',...
'Position',[settingsTabWidth*0.08-(60/2) settingsTabHeight*0.505 60 20]);
uilabel('Parent',settingsTab,...
'Text','RMS =',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.16-(50/2) settingsTabHeight*0.5 50 20]);
rmsField = uieditfield(settingsTab,...
'numeric',...
'Value',RMS,...
'ValueChangedFcn',@rmsUpdate,...
'Position',[settingsTabWidth*0.22-(30/2) settingsTabHeight*0.5 40 20],...
'HorizontalAlignment','Center');
cutoffText = uilabel('Parent',settingsTab,...
'Text',strcat("Noise Threshold: ",num2str(noiseThreshold)," pA"),...
'Position',[settingsTabWidth*0.15-(175/2) settingsTabHeight*0.425 175 20],...
'fontweight', 'bold',...
'HorizontalAlignment','Center');
% labels and fields dealing with how event rise time is measured
uilabel('Parent',settingsTab,...
'Text','Rise Time Measurement',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.35-(160/2) settingsTabHeight*0.25 160 20]);
riseStartField = uieditfield(settingsTab,...
'numeric',...
'Value',riseStartPercent,...
'ValueChangedFcn',@fieldUpdate,...
'Position',[settingsTabWidth*0.30-(30/2) settingsTabHeight*0.175 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','%',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.33-(20/2) settingsTabHeight*0.175 20 20]);
uilabel('Parent',settingsTab,...
'Text','to',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.35-(20/2) settingsTabHeight*0.175 20 20]);
riseEndField = uieditfield(settingsTab,...
'numeric',...
'Value',riseEndPercent,...
'ValueChangedFcn',@fieldUpdate,...
'Position',[settingsTabWidth*0.39-(30/2) settingsTabHeight*0.175 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','%',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.42-(20/2) settingsTabHeight*0.175 20 20]);
% labels and fields dealing with how event decay time is measured
uilabel('Parent',settingsTab,...
'Text','Decay Time Measurement',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.65-(160/2) settingsTabHeight*0.25 160 20]);
decayStartField = uieditfield(settingsTab,...
'numeric',...
'Value',decayStartPercent,...
'ValueChangedFcn',@fieldUpdate,...
'Position',[settingsTabWidth*0.60-(30/2) settingsTabHeight*0.175 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','%',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.63-(20/2) settingsTabHeight*0.175 20 20]);
uilabel('Parent',settingsTab,...
'Text','to',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.65-(20/2) settingsTabHeight*0.175 20 20]);
decayEndField = uieditfield(settingsTab,...
'numeric',...
'Value',decayEndPercent,...
'ValueChangedFcn',@fieldUpdate,...
'Position',[settingsTabWidth*0.69-(30/2) settingsTabHeight*0.175 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','%',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.72-(20/2) settingsTabHeight*0.175 20 20]);
% labels and fields associated with sampling rate
uilabel('Parent',settingsTab,...
'Text','Sampling Rate',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.50-(110/2) settingsTabHeight*0.5 110 20]);
samplingField = uieditfield(settingsTab,...
'numeric',...
'Value',samplesPerMilliSecond,...
'ValueChangedFcn',@fieldUpdate,...
'Position',[settingsTabWidth*0.475-(30/2) settingsTabHeight*0.425 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','kHz',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.525-(30/2) settingsTabHeight*0.425 30 20]);
% labels and fields associated with average trace display parameters
uilabel('Parent',settingsTab,...
'Text','Samples in Average Trace',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.81-(200/2) settingsTabHeight*0.5 200 20]);
preEventField = uieditfield(settingsTab,...
'numeric',...
'Value',preEventSamples,...
'ValueChangedFcn',@sampleNumberUpdate,...
'Position',[settingsTabWidth*0.80-(30/2) settingsTabHeight*0.425 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','Pre Event',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.72-(50/2) settingsTabHeight*0.425 60 20]);
postEventField = uieditfield(settingsTab,...
'numeric',...
'Value',postEventSamples,...
'ValueChangedFcn',@sampleNumberUpdate,...
'Position',[settingsTabWidth*0.92-(30/2) settingsTabHeight*0.425 30 20],...
'HorizontalAlignment','Center');
uilabel('Parent',settingsTab,...
'Text','Decay',...
'fontweight', 'bold',...
'HorizontalAlignment','Center',...
'Position',[settingsTabWidth*0.865-(50/2) settingsTabHeight*0.425 50 20]);
%% create analysis tab
% create and populate the tab that contains buttons for analysis
% create the tab
analysisTab = uitab('Parent',buttonTabGroup,'Title','Analysis');
%buttons for zooming in and out
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Zoom Out','X [1]'),...
'ButtonPushedFcn',@expandXView,...
'Position',[navigationTabWidth*0.2-(100/2) navigationTabHeight*0.8-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Zoom In','X [2]'),...
'ButtonPushedFcn',@shrinkXView,...
'Position',[navigationTabWidth*0.4-(100/2) navigationTabHeight*0.8-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Zoom Out','Y [3]'),...
'ButtonPushedFcn',@expandYView,...
'Position',[navigationTabWidth*0.6-(100/2) navigationTabHeight*0.8-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Zoom In','Y [4]'),...
'ButtonPushedFcn',@shrinkYView,...
'Position',[navigationTabWidth*0.8-(100/2) navigationTabHeight*0.8-(40) 100 40],...
'fontweight', 'bold');
% buttons for shifting the position of the threshold and peak of a selected event
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Threshold Shift','Back [q]'),...
'ButtonPushedFcn',@backThreshold,...
'Position',[navigationTabWidth*0.2-(100/2) navigationTabHeight*0.6-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Threshold Shift','Forward [w]'),...
'ButtonPushedFcn',@forwardThreshold,...
'Position',[navigationTabWidth*0.4-(100/2) navigationTabHeight*0.6-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Peak Shift','Back [e]'),...
'ButtonPushedFcn',@backPeak,...
'Position',[navigationTabWidth*0.6-(100/2) navigationTabHeight*0.6-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Peak Shift','Forward [r]'),...
'ButtonPushedFcn',@forwardPeak,...
'Position',[navigationTabWidth*0.8-(100/2) navigationTabHeight*0.6-(40) 100 40],...
'fontweight', 'bold');
% buttons for adding a selected event to a specific analysis group
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Full Event','Sort [a]'),...
'ButtonPushedFcn',@addToFullDecayGroup,...
'Position',[navigationTabWidth*0.2-(100/2) navigationTabHeight*0.4-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Amplitude','Sort [s]'),...
'ButtonPushedFcn',@addToAmplitudeGroup,...
'Position',[navigationTabWidth*0.4-(100/2) navigationTabHeight*0.4-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Frequency','Sort [d]'),...
'ButtonPushedFcn',@addToFrequencyGroup,...
'Position',[navigationTabWidth*0.6-(100/2) navigationTabHeight*0.4-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Delete Event','[f]'),...
'ButtonPushedFcn',@deleteEvent,...
'Position',[navigationTabWidth*0.8-(100/2) navigationTabHeight*0.4-(40) 100 40],...
'fontweight', 'bold');
% buttons for moving through viewing windows
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Prev. Window','[z]'),...
'ButtonPushedFcn',@previousWindow,...
'Position',[navigationTabWidth*0.2-(100/2) navigationTabHeight*0.2-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Next Window','[x]'),...
'ButtonPushedFcn',@nextWindow,...
'Position',[navigationTabWidth*0.4-(100/2) navigationTabHeight*0.2-(40) 100 40],...
'fontweight', 'bold');
% misc. buttons
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Add Freq.','to Amp.'),...
'ButtonPushedFcn',@addFreqToAmp,...
'Position',[navigationTabWidth*0.6-(100/2) navigationTabHeight*0.2-(40) 100 40],...
'fontweight', 'bold');
uibutton('Parent',analysisTab,...
'Text',sprintf('%s\n%s','Add Amp.','to Full'),...
'ButtonPushedFcn',@addAmpToFull,...
'Position',[navigationTabWidth*0.8-(100/2) navigationTabHeight*0.2-(40) 100 40],...
'fontweight', 'bold');
%% wait for user input
% pause program execution to allow for interaction with GUI
uiwait(mainPanel);
%% initialization functions
function beginAnalysis(~,~)
% begin analysis on a new experiment
% ignore button click if an event is currently selected
if (eventCurrentlySelected == true)
uialert(mainPanel, 'Please sort or delete the selected event.','');
return;
end
if sum(~isnan(selectedEvents(:))) > 0
decisionSave = uiconfirm(mainPanel,...
'Save before opening a new experiment?','',...
'Options',{'Yes','No'});
if strcmp(decisionSave,'Yes')
saveAnalysis;
matlist = dir('*.mat');
matliststrings = string();
for matIndex = 1:size(matlist,1)
matliststrings(matIndex) = convertCharsToStrings(matlist(matIndex).name);
end
set(analysisList, 'Items', matliststrings);
end
end
% clear plots and reset certain parameters to their default values
cla(averageTracePlot);
cla(allTracePlot);
cla(scaledTracePlot);
RMS = 2;
windowScope = 800;
xSlider.Limits = [-windowScope windowScope];
ySlider.Limits = [-50 10];
currentWindow = 1:windowScope;
selectedEvents = NaN(500,15);
eventCurrentlySelected = false;
% turn on keyboard and click functions
set(mainPanel, 'KeyPressFcn', @keyPressListener);
set(mainPanel, 'WindowButtonDownFcn', @selectEvent);
% import and plot recording trace
fileName = mainTraceControl.Value;
if fileName ~= ""
cellName = convertCharsToStrings(split(fileName,"."));
% fileType = cellName(2);
cellName = cellName(1);
importTrace;
trace_first_der = diff(traceSamples(:,traceValueCol));
trace_first_der = cat(1,trace_first_der,0);
plotLocation;
displayEventData;
else
uialert(mainPanel, 'Please choose a trace for analysis.','');
return;
end
savePath = pwd;
end
function resumeAnalysis(~,~)
% resume analysis that has been previously worked on and saved
% ignore button click if an event is currently selected
if (eventCurrentlySelected == true)
uialert(mainPanel, 'Please sort or delete the selected event.','');
return;
end
if sum(~isnan(selectedEvents(:))) > 0
decisionSave = uiconfirm(mainPanel,...
'Save before opening a new experiment?','',...
'Options',{'Yes','No'});
if strcmp(decisionSave,'Yes')
saveAnalysis;
matlist = dir('*.mat');
matliststrings = string();
for matIndex = 1:size(matlist,1)
matliststrings(matIndex) = convertCharsToStrings(matlist(matIndex).name);
end
set(analysisList, 'Items', matliststrings);
end
end
% turn on keyboard and click functions
set(mainPanel, 'KeyPressFcn', @keyPressListener);
set(mainPanel, 'WindowButtonDownFcn', @selectEvent);
% clear plots
cla(averageTracePlot);
cla(allTracePlot);
cla(scaledTracePlot);
% check for experiment and analysis file being selected
if isempty(directoryControl.Value)
uialert(mainPanel, 'Please choose a folder first.','');
return;
end
if isempty(analysisList.Value)
uialert(mainPanel, 'Please choose an analysis file.','');
return;
end
% load relevant workspace variables from saved analysis
fileName = analysisList.Value;
cellName = convertCharsToStrings(split(fileName,"."));
cellName = cellName(1);
warning('off','MATLAB:load:variableNotFound');
load(analysisList.Value, 'dataTable', 'currentWindow', 'selectedEvents', 'traceSamples',...
'decayStartPercent','decayEndPercent','riseStartPercent','riseEndPercent',...
'RMS','samplesPerMilliSecond','preEventSamples','postEventSamples','autoZoom');
warning('on','MATLAB:load:variableNotFound');
% set view parameters to those of saved experiment
windowScope = length(currentWindow);
if (isempty(currentWindow)) || (size(currentWindow,2) == 1)
windowScope = 500;
currentWindow = 1:windowScope;
end
xSlider.Limits = [-windowScope windowScope];
ySlider.Limits = [-50 10];
% update displayed parameters with loaded values
rmsField.Value = RMS;
noiseThreshold = 3*RMS;
cutoffText.Text = strcat("Noise Threshold: ",num2str(noiseThreshold)," pA");
riseStartField.Value = riseStartPercent;
riseEndField.Value = riseEndPercent;
decayStartField.Value = decayStartPercent;
decayEndField.Value = decayEndPercent;
samplingField.Value = samplesPerMilliSecond;
preEventField.Value = preEventSamples;
postEventField.Value = postEventSamples;
zoomCheck.Value = autoZoom;
% misc. housekeeping before analysis begins
trace_first_der = diff(traceSamples(:,traceValueCol));
trace_first_der = cat(1,trace_first_der,0);
selectedEvents = sortrows(selectedEvents,eventTimeCol,'MissingPlacement','last');
selectedEvents = selectedEvents(:,1:15);
displayEventData;
plotLocation;
plotOverlaidEvents;
updateSortCounts;
savePath = pwd;
end
function importTrace
% import a recording trace for analysis
delimiter = {''};
startRow = 2;
formatSpec = '%f%[^\n\r]';
fileID = fopen(fileName,'r');
dataArray = textscan(fileID, formatSpec, 'Delimiter', delimiter,...
'TextType', 'string','EmptyValue', NaN, 'HeaderLines' ,startRow-1,...
'ReturnOnError', false, 'EndOfLine', '\r\n');
fclose(fileID);
traceSamples = [dataArray{1:end-1}];
% add auxiliary columns to recording trace to keep track of event locations
for i = 1:size(traceSamples,traceValueCol)
traceSamples(i,traceTimeCol) = i;
traceSamples(i,eventPlotLogicalCol) = 0;
traceSamples(i,eventPlotEndCol) = nan;
end
end
%% selection functions
function selectEvent(~,~)
% allows user to select events for analysis
% determine click location within the GUI
mainPoint = mainPanel.CurrentPoint;
% reacquire plot tab group dimensions in case GUI has been moved to new window
plotTabGroupDims = plotTabGroup.Position;
plotTabGroupHorz = plotTabGroupDims(1)+plotTabGroupDims(3);
plotTabGroupVert = plotTabGroupDims(2)+plotTabGroupDims(4);
% check to see if click was within the trace plot
% ignore the click if it was outside of the trace plot
if (sum(ismember(mainPoint(1),plotTabGroupDims(1)+20:plotTabGroupHorz-10)) == 0)...
|| (sum(ismember(mainPoint(2),plotTabGroupDims(2)+20:plotTabGroupVert-30)) == 0)
return;
end
% if the click was inside the trace plot, check for whether an event is already selected
if (eventCurrentlySelected == true)
uialert(mainPanel, 'Please sort or delete the currently selected event.','');
return;
end
eventCurrentlySelected = true;
% find location of click in trace plot and determine nearest sample point
pointLoc = tracePlot.CurrentPoint;
traceIndex = dsearchn(currentWindow',pointLoc(1));
% determine location of events that are already within the viewing window
eventsInViewLogical = traceSamples(currentWindow,eventPlotLogicalCol) == 1;
currentWindowEvents = currentWindow(eventsInViewLogical);
eventsInView = traceSamples(currentWindowEvents,:);
% check to see if mouse click location is on an event that has already been analyzed
% if so, highlight the selected event
if ~isempty(eventsInView)
for viewedEvent = 1:size(eventsInView,1)
tempThresholdTime = eventsInView(viewedEvent,traceTimeCol);
tempPeakTime = eventsInView(viewedEvent,eventPlotEndCol);
if currentWindow(traceIndex) >= tempThresholdTime...
&& currentWindow(traceIndex) <= tempPeakTime
eventThresholdTime = tempThresholdTime;
eventPeakTime = tempPeakTime;
highlightEvent(eventThresholdTime);
return;
end
end
end
% set initial values for the event threshold and peak
eventThresholdTime = currentWindow(traceIndex);
eventPeakTime = eventThresholdTime;
% determine the likely event threshold
while ((trace_first_der(eventThresholdTime-1,traceValueCol) < -1.5) ||...
(trace_first_der(eventThresholdTime-2,traceValueCol) < -1))
eventThresholdTime = eventThresholdTime - 1;
end
traceSamples(eventThresholdTime,eventPlotLogicalCol) = 1;
% determine the likely event peak
while ((traceSamples(eventPeakTime,traceValueCol) > traceSamples(eventPeakTime+1,traceValueCol))...
|| (traceSamples(eventPeakTime,traceValueCol) > traceSamples(eventPeakTime+2,traceValueCol))...
|| (traceSamples(eventPeakTime,traceValueCol) > traceSamples(eventPeakTime+3,traceValueCol))...
|| (traceSamples(eventPeakTime,traceValueCol) > traceSamples(eventPeakTime+4,traceValueCol)))
eventPeakTime = eventPeakTime + 1;
end
traceSamples(eventThresholdTime,eventPlotEndCol) = eventPeakTime;
% create a location for the event in selectedEvents and plot the event
eventIndex = length(selectedEvents);
plotEvent(eventThresholdTime);
end
function navigateToEvent(~,event)
% allows user to click on event in the data table and move to that event
if (eventCurrentlySelected == true)
uialert(mainPanel, 'Please sort or delete the selected event.','');
return;
end
% determine which event was selected
eventSelected = event.Indices;
if ~(eventSelected(1) > 0)
return;
end
eventIndex = table2array(event.Source.Data(eventSelected(1),1));
eventThresholdTime = selectedEvents(eventIndex,eventTimeCol);
% move view window and center it on selected event
newCurrentWindowBegin = eventThresholdTime-floor(windowScope/2)+1;
newCurrentWindowEnd = eventThresholdTime+floor(windowScope/2);
currentWindow = newCurrentWindowBegin:newCurrentWindowEnd;
if (currentWindow(end) > size(traceSamples,1))
currentWindow = traceSamples(end-windowScope+1:end,traceTimeCol)';
elseif (currentWindow(1) < 1)
currentWindow = 1:ceil(windowScope);
end
plotLocation;
end
function keyPressListener(~,eventdata)
% determine the key that was pressed and call the approptiate functiob
keyPressed = eventdata.Key;
if strcmpi(keyPressed,'a')
addToFullDecayGroup;
elseif strcmpi(keyPressed,'s')
addToAmplitudeGroup;
elseif strcmpi(keyPressed,'d')
addToFrequencyGroup;
elseif strcmpi(keyPressed,'z')
previousWindow;
elseif strcmpi(keyPressed,'x')
nextWindow;
elseif strcmpi(keyPressed,'q')
backThreshold;
elseif strcmpi(keyPressed,'w')
forwardThreshold;
elseif strcmpi(keyPressed,'e')
backPeak;
elseif strcmpi(keyPressed,'r')
forwardPeak;
elseif strcmpi(keyPressed,'f')
deleteEvent;
elseif strcmpi(keyPressed,'1')
expandXView;
elseif strcmpi(keyPressed,'2')
shrinkXView;
elseif strcmpi(keyPressed,'3')
expandYView;
elseif strcmpi(keyPressed,'4')
shrinkYView;
end
end
%% plotting functions
function plotEvent(eventTime)
% plot the rise and decay phases of the selected event
% determine values needed to plot rise and decay
tempThresholdTime = traceSamples(eventTime,traceTimeCol);
tempThresholdValue = traceSamples(tempThresholdTime,traceValueCol);
tempPeakTime = traceSamples(eventTime,eventPlotEndCol);
tempPeakValue = traceSamples(tempPeakTime,traceValueCol);
valueAtDesiredDecay = tempPeakValue...
+abs((1-(decayEndPercent/100))*(tempPeakValue-tempThresholdValue));
decayTime = tempPeakTime+1;
valueAtDecayTime = traceSamples(decayTime,traceValueCol);
while valueAtDecayTime < valueAtDesiredDecay
decayTime = decayTime + 1;
valueAtDecayTime = traceSamples(decayTime,traceValueCol);
end
% generate and plot X and Y values for rise and decay
meanWindowY = mean(traceSamples(currentWindow,traceValueCol));
riseX = traceSamples(tempThresholdTime:tempPeakTime,traceTimeCol);
riseY = traceSamples(tempThresholdTime:tempPeakTime,traceValueCol);
riseYoffset = riseY - meanWindowY;
decayX = traceSamples(tempPeakTime:decayTime,traceTimeCol);
decayY = traceSamples(tempPeakTime:decayTime,traceValueCol);
decayYoffset = decayY - meanWindowY;
hold(tracePlot, 'on');
plot(tracePlot,riseX,riseYoffset,'Color',[1 0 1]);
plot(tracePlot,decayX,decayYoffset,'Color',[0 1 0]);
hold(tracePlot, 'off');
% auto zoom to event if desired by user
if (autoZoom == 1) && (eventCurrentlySelected == true)
try
yRangeLims = traceSamples(eventTime-50:eventTime+50,traceValueCol) - meanWindowY;
yRange = range(traceSamples(eventTime-50:eventTime+50,traceValueCol));
catch
yRangeLims = traceSamples(eventTime-10:eventTime+10,traceValueCol) - meanWindowY;
yRange = range(traceSamples(eventTime-10:eventTime+10,traceValueCol));
end
ylim(tracePlot,[min(yRangeLims)-0.25*yRange max(yRangeLims)+0.25*yRange]);
yTemp = ylim(tracePlot);
if yTemp(2)-yTemp(1) < 25
ylim(tracePlot, ylim(tracePlot)*2);
end
xlim(tracePlot,[eventTime-200 eventTime+200]);
end
end
function highlightEvent(eventTime)
% hightlight an analyzed event that the user has selected
% clear measured values for highlighted event
[~,indexLoc] = ismember(eventTime,selectedEvents(:,eventTimeCol));
selectedEvents(indexLoc,:) = NaN;
eventIndex = indexLoc;
% determine values needed to plot rise and decay
eventThresholdTime = traceSamples(eventTime,traceTimeCol);
eventThresholdValue = traceSamples(eventThresholdTime,traceValueCol);
eventPeakTime = traceSamples(eventTime,eventPlotEndCol);
eventPeakValue = traceSamples(eventPeakTime,traceValueCol);
valueAtDesiredDecay = eventPeakValue...
+abs((1-(decayStartPercent/100))*(eventPeakValue-eventThresholdValue));
decayTime = eventPeakTime+1;
valueAtDecayTime = traceSamples(decayTime,traceValueCol);
while valueAtDecayTime < valueAtDesiredDecay
decayTime = decayTime + 1;
valueAtDecayTime = traceSamples(decayTime,traceValueCol);
end
% generate and plot X and Y values for rise and decay
meanWindowY = mean(traceSamples(currentWindow,traceValueCol));
riseX = traceSamples(eventThresholdTime:eventPeakTime,traceTimeCol);
riseY = traceSamples(eventThresholdTime:eventPeakTime,traceValueCol);
riseYoffset = riseY - meanWindowY;
decayX = traceSamples(eventPeakTime:decayTime,traceTimeCol);
decayY = traceSamples(eventPeakTime:decayTime,traceValueCol);
decayYoffset = decayY - meanWindowY;
hold(tracePlot, 'on');
plot(tracePlot,riseX,riseYoffset,'Color',[0 1 1]);
plot(tracePlot,decayX,decayYoffset,'Color',[0 1 1]);
hold(tracePlot, 'off');
% auto zoom to event if desired by user
if (autoZoom == 1) && (eventCurrentlySelected == true)
try
yRangeLims = traceSamples(eventTime-50:eventTime+50,traceValueCol) - meanWindowY;
yRange = range(traceSamples(eventTime-50:eventTime+50,traceValueCol));
catch
yRangeLims = traceSamples(eventTime-10:eventTime+10,traceValueCol) - meanWindowY;
yRange = range(traceSamples(eventTime-10:eventTime+10,traceValueCol));
end
ylim(tracePlot,[min(yRangeLims)-0.25*yRange max(yRangeLims)+0.25*yRange]);
yTemp = ylim(tracePlot);
if yTemp(2)-yTemp(1) < 25
ylim(tracePlot, ylim(tracePlot)*2);
end
xlim(tracePlot,[eventTime-200 eventTime+200]);
end
end
function plotLocation
% plot the current view window, as well as any analyzed events that reside within
% ignore call if no trace is present
if isempty(traceSamples)
return;
end
% generate and plot x and y values of trace
traceX = traceSamples(currentWindow,traceTimeCol);
traceY = traceSamples(currentWindow,traceValueCol);
meanWindowY = mean(traceSamples(currentWindow,traceValueCol));
traceYoffset = traceY - meanWindowY;
plot(tracePlot,traceX,traceYoffset,'Color','black');
axis(tracePlot,[currentWindow(1) currentWindow(end) yMin-yOffset yMax-yOffset]);
% plot scale bar
hold(tracePlot, 'on');
digits = ceil(log10(windowScope));
scaleNum = 10^(digits-2);
xBegin = currentWindow(end) - ceil(0.1*windowScope);
xVals = xBegin:xBegin+scaleNum;
yRange = abs(yMax-yMin);