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NeuroScope2.m
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NeuroScope2.m
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function NeuroScope2(varargin)
% % % % % % % % % % % % % % % % % % % % % % % % %
% NeuroScope2 (BETA) is a visualizer for electrophysiological recordings. It is inspired by the original Neuroscope (http://neurosuite.sourceforge.net/)
% and made to mimic its features, but built upon Matlab and the data structure of CellExplorer, making it much easier to hack/customize,
% and faster than the original NeuroScope. NeuroScope2 is part of CellExplorer - https://CellExplorer.org/
% https://cellexplorer.org/interface/neuroscope2/
%
% Major features:
% - Live trace filter with spike and event detection, single channel spectrogram
% - Plot multiple data streams together (ephys + analog + digital signals)
% - Plot CellExplorer/Buzcode structures: spikes, cell_metrics, events, timeseries, states, behavior, trials
%
% Example calls:
% NeuroScope2
% NeuroScope2('basepath',basepath)
% NeuroScope2('session',session)
%
% By Peter Petersen
% % % % % % % % % % % % % % % % % % % % % % % % %
% Global variables
UI = []; % Struct with UI elements and settings
data = []; % Contains all external data loaded like data.spikes, data.events, data.states, data.behavior
ephys = []; % Struct with ephys data for current shown time interval, e.g. ephys.raw (raw unprocessed data), ephys.traces (processed data)
ephys.traces = [];
ephys.sr = [];
t0 = 0; % Timestamp of the start of the current window (in seconds)
spikes_raster = []; % Spike raster (used for highlighting, to minimize computations)
epoch_plotElements.t0 = [];
epoch_plotElements.events = [];
score = [];
if isdeployed % Check for if NeuroScope2 is running as a deployed app (compiled .exe or .app for windows and mac respectively)
if ~isempty(varargin) % If a file name is provided it will load it.
[basepath,basename,ext] = fileparts(varargin{1});
if isequal(basepath,0)
UI.priority = ext;
return
end
else % Otherwise a file load dialog will be shown
[file1,basepath] = uigetfile('*.mat;*.dat;*.lfp;*.xml','Please select a file with the basename in it from the basepath');
if ~isequal(file1,0)
temp1 = strsplit(file1,'.');
basename = temp1{1};
UI.priority = temp1{2};
else
return
end
end
else
% Handling inputs if run from Matlab
p = inputParser;
addParameter(p,'basepath',pwd,@isstr);
addParameter(p,'basename',[],@isstr);
addParameter(p,'session',[],@isstruct);
addParameter(p,'spikes',[],@isstr);
addParameter(p,'events',[],@isstr);
addParameter(p,'states',[],@isstr);
addParameter(p,'behavior',[],@isstr);
addParameter(p,'cellinfo',[],@isstr);
addParameter(p,'channeltag',[],@isstr);
parse(p,varargin{:})
parameters = p.Results;
basepath = p.Results.basepath;
basename = p.Results.basename;
if isempty(basename)
basename = basenameFromBasepath(basepath);
end
if ~isempty(parameters.session)
basename = parameters.session.general.name;
basepath = parameters.session.general.basePath;
end
end
int_gt_0 = @(n,sr) (isempty(n)) || (n <= 0 ) || (n >= sr/2);
% % % % % % % % % % % % % % % % % % % % % %
% Initialization
% % % % % % % % % % % % % % % % % % % % % %
initUI
initData(basepath,basename);
initInputs
initTraces
% Maximazing figure to full screen
if ~verLessThan('matlab', '9.4')
set(UI.fig,'WindowState','maximize'), set(UI.fig,'visible','on')
else
warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame')
set(UI.fig,'visible','on')
drawnow nocallbacks; frame_h = get(UI.fig,'JavaFrame'); set(frame_h,'Maximized',1); drawnow nocallbacks;
end
% % % % % % % % % % % % % % % % % % % % % %
% Main while loop of the interface
% % % % % % % % % % % % % % % % % % % % % %
while t0>=0
% breaking if figure has been closed
if ~ishandle(UI.fig)
break
else
UI.selectedChannels = [];
UI.selectedUnits = [];
% Plotting data
plotData;
% Updating epoch axes
if ishandle(epoch_plotElements.t0)
delete(epoch_plotElements.t0)
end
epoch_plotElements.t0 = line(UI.epochAxes,[t0,t0],[0,1],'color','k', 'HitTest','off','linewidth',1);
% Update UI text and slider
UI.elements.lower.time.String = num2str(t0);
UI.elements.lower.slider.Value = min([t0/(UI.t_total-UI.settings.windowDuration)*100,100]);
if UI.settings.debug
drawnow
end
UI.elements.lower.performance.String = [' Processing: ' num2str(toc(UI.timerInterface),3) ' seconds (', num2str(numel(ephys.traces)*2/1024/1024,3) ' MB ephys data)'];
uiwait(UI.fig);
% Tracking viewed timestamps in file (can be used by pressing the backspace key)
UI.settings.stream = false;
t0 = max([0,min([t0,UI.t_total-UI.settings.windowDuration])]);
if UI.track && UI.t0_track(end) ~= t0
UI.t0_track = [UI.t0_track,t0];
end
UI.track = true;
end
UI.timerInterface = tic;
end
% % % % % % % % % % % % % % % % % % % % % %
% Closing
% % % % % % % % % % % % % % % % % % % % % %
% Closing all file readers
fclose('all');
% Closing main figure if open
if ishandle(UI.fig)
close(UI.fig);
end
% Using google analytics for anonymous tracking of usage
trackGoogleAnalytics('NeuroScope2',1);
% Saving session metadata
if UI.settings.saveMetadata
session = data.session;
try
saveStruct(session,'session','commandDisp',false);
catch
warning('Could not save session struct to basepath when closing NeuroScope2')
end
end
% % % % % % % % % % % % % % % % % % % % % %
% Embedded functions
% % % % % % % % % % % % % % % % % % % % % %
function initUI % Initialize the UI (settings, parameters, figure, menu, panels, axis)
% % % % % % % % % % % % % % % % % % % % % %
% Init settings
UI.forceNewData = true;
UI.timerInterface = tic;
UI.settings.colormap = 'hsv'; % any Matlab colormap, e.g. 'hsv' or 'lines'
UI.settings.windowDuration = 1; % in seconds
UI.settings.scalingFactor = 50;
UI.settings.plotStyle = 2;
UI.settings.plotSorting = 2;
UI.settings.plotColorGroups = 1;
UI.settings.saveMetadata = true;
UI.settings.fileRead = 'bof';
UI.settings.greyScaleTraces = 1;
UI.settings.columnTraces = false;
UI.settings.colorByChannels = false;
UI.settings.nColorGroups = 10;
UI.settings.displayMenu = 0;
UI.settings.channelTags.hide = [];
UI.settings.channelTags.filter = [];
UI.settings.channelTags.highlight = [];
UI.settings.showKilosort = false;
UI.settings.kilosortBelowTrace = false;
UI.settings.showKlusta = false;
UI.settings.klustaBelowTrace = false;
UI.settings.showSpykingcircus = false;
UI.settings.spykingcircusBelowTrace = false;
UI.settings.normalClick = true;
UI.settings.addEventonClick = false;
UI.settings.background = 'k';
UI.settings.textBackground = [0 0 0 0.7];
UI.settings.primaryColor = 'w';
UI.settings.showChannelNumbers = false;
UI.settings.channelList = [];
UI.settings.brainRegionsToHide = [];
UI.settings.removeDC = false;
UI.settings.showScalebar = false;
UI.settings.narrowPadding = false;
UI.settings.ephys_padding = 0.05; % Initial padding above and below ephys traces
UI.settings.text_spacing = 0.016;
UI.settings.detectedEventsBelowTrace = false;
UI.settings.detectedSpikesBelowTrace = false;
% Only Matlab 2020b and forward support vertical markers unfortunately
if verLessThan('matlab','9.9')
UI.settings.rasterMarker = 'o';
else
UI.settings.rasterMarker = '|';
end
UI.iLine = 1;
UI.colorLine = lines(256);
UI.freeText = '';
UI.selectedChannels = [];
UI.settings.debug = false; % For performance testing at this point
UI.settings.extraSpacing = true; % Adds spacing between the electrode groups traces
% Trace processing
UI.settings.plotEnergy = 0;
UI.settings.energyWindow = 0.030; % in seconds
UI.settings.detectEvents = false;
UI.settings.eventThreshold = 100; % in µV
UI.settings.filterTraces = false;
UI.settings.detectSpikes = false;
UI.settings.spikesDetectionThreshold = -100; % in µV
% Performance settings
UI.settings.plotStyleDynamicRange = true; % If true, in the range plot mode, all samples will be shown below a temporal threshold (default: 1.2 sec)
UI.settings.plotStyleDynamicThreshold = 1.2; % in seconds, threshold for switching between range and raw data presentation (Matlab plots linearly fast up to a certain number of points after which the performance drops and the range plotting style becomes faster)
UI.settings.plotStyleRangeSamples = 4; % average samples per second of data. Default: 4; Higher value will show less data points
% Spikes settings
UI.settings.showSpikes = false;
UI.settings.spikesBelowTrace = false;
UI.settings.useSpikesYData = false;
UI.settings.spikesYData = '';
UI.settings.spikesColormap = 'hsv';
UI.settings.spikesGroupColors = 1;
UI.settings.showPopulationRate = false;
UI.settings.populationRateBelowTrace = false;
UI.settings.populationRateWindow = 0.001; % in seconds
UI.settings.populationRateSmoothing = 35; % in seconds
UI.settings.spikeRasterLinewidth = 1.2;
% Cell metrics
UI.settings.useMetrics = false;
UI.params.cellTypes = [];
UI.params.cell_class_count = [];
UI.groupData1.groupsList = {'groups','tags','groundTruthClassification'};
UI.preferences.tags = {'Good','Bad','Noise','InverseSpike'};
UI.preferences.groundTruth = {'PV','NOS1','GAT1','SST','Axoaxonic','CellType_A'};
UI.tableData.Column1 = 'putativeCellType';
UI.tableData.Column2 = 'firingRate';
UI.params.subsetTable = [];
UI.params.subsetFilter = [];
UI.params.subsetCellType = [];
UI.params.subsetGroups = [];
UI.params.sortingMetric = 'putativeCellType';
UI.params.groupMetric = 'putativeCellType';
% Event settings
UI.settings.iEvent = 1;
UI.settings.showEvents = false;
UI.settings.eventData = [];
UI.settings.showEventsBelowTrace = false;
UI.settings.showEventsIntervals = false;
UI.settings.processing_steps = false;
% Timeseries settings
UI.settings.showTimeSeries = false;
UI.settings.timeseriesData = [];
UI.settings.timeseries.lowerBoundary = 34;
UI.settings.timeseries.upperBoundary = 38;
% States settings
UI.settings.showStates = false;
UI.settings.statesData = [];
% Behavior settings
UI.settings.showBehavior = false;
UI.settings.plotBehaviorLinearized = false;
UI.settings.showBehaviorBelowTrace = false;
UI.settings.behaviorData = [];
UI.settings.showTrials = false;
% Intan settings
UI.settings.intan_showAnalog = false;
UI.settings.intan_showAux = false;
UI.settings.intan_showDigital = false;
UI.settings.showTimeseriesBelowTrace = false;
% Spectrogram
UI.settings.spectrogram.show = false;
UI.settings.spectrogram.channel = 1;
UI.settings.spectrogram.window = 0.2;
UI.settings.spectrogram.freq_low = 4;
UI.settings.spectrogram.freq_high = 250;
UI.settings.spectrogram.freq_step_size = 2;
UI.settings.spectrogram.freq_range = [UI.settings.spectrogram.freq_low:UI.settings.spectrogram.freq_step_size:UI.settings.spectrogram.freq_high];
% CSD
UI.settings.CSD.show = false;
% % % % % % % % % % % % % % % % % % % % % %
% Creating figure
UI.fig = figure('Name','NeuroScope2','NumberTitle','off','renderer','opengl','KeyPressFcn', @keyPress,'KeyReleaseFcn',@keyRelease,'DefaultAxesLooseInset',[.01,.01,.01,.01],'visible','off','pos',[0,0,1600,800],'DefaultTextInterpreter', 'none', 'DefaultLegendInterpreter', 'none', 'MenuBar', 'None');
if ~verLessThan('matlab', '9.3')
menuLabel = 'Text';
menuSelectedFcn = 'MenuSelectedFcn';
else
menuLabel = 'Label';
menuSelectedFcn = 'Callback';
end
uix.tracking('off')
% % % % % % % % % % % % % % % % % % % % % %
% Creating menu
% NeuroScope2
UI.menu.cellExplorer.topMenu = uimenu(UI.fig,menuLabel,'NeuroScope2');
uimenu(UI.menu.cellExplorer.topMenu,menuLabel,'About NeuroScope2',menuSelectedFcn,@AboutDialog);
uimenu(UI.menu.cellExplorer.topMenu,menuLabel,'Quit',menuSelectedFcn,@exitNeuroScope2,'Separator','on','Accelerator','W');
% File
UI.menu.file.topMenu = uimenu(UI.fig,menuLabel,'File');
uimenu(UI.menu.file.topMenu,menuLabel,'Load session from folder',menuSelectedFcn,@loadFromFolder);
uimenu(UI.menu.file.topMenu,menuLabel,'Load session from file',menuSelectedFcn,@loadFromFile,'Accelerator','O');
UI.menu.file.recentSessions.main = uimenu(UI.menu.file.topMenu,menuLabel,'Recent sessions...','Separator','on');
uimenu(UI.menu.file.topMenu,menuLabel,'Export to .png file (image)',menuSelectedFcn,@exportPlotData,'Separator','on');
uimenu(UI.menu.file.topMenu,menuLabel,'Export to .pdf file (vector graphics)',menuSelectedFcn,@exportPlotData);
uimenu(UI.menu.file.topMenu,menuLabel,'Export figure via the export setup dialog',menuSelectedFcn,@exportPlotData,'Separator','on');
% Session
UI.menu.session.topMenu = uimenu(UI.fig,menuLabel,'Session');
uimenu(UI.menu.session.topMenu,menuLabel,'View metadata',menuSelectedFcn,@viewSessionMetaData);
uimenu(UI.menu.session.topMenu,menuLabel,'Save metadata',menuSelectedFcn,@saveSessionMetadata);
uimenu(UI.menu.session.topMenu,menuLabel,'Open basepath',menuSelectedFcn,@openSessionDirectory,'Separator','on');
% Cell metrics
UI.menu.cellExplorer.topMenu = uimenu(UI.fig,menuLabel,'Cell metrics');
UI.menu.cellExplorer.defineGroupData = uimenu(UI.menu.cellExplorer.topMenu,menuLabel,'Open group data dialog',menuSelectedFcn,@defineGroupData);
UI.menu.cellExplorer.saveCellMetrics = uimenu(UI.menu.cellExplorer.topMenu,menuLabel,'Save cell_metrics',menuSelectedFcn,@saveCellMetrics);
% uimenu(UI.menu.cellExplorer.topMenu,menuLabel,'View cell metrics in CellExplorer',menuSelectedFcn,@openCellExplorer);
% BuzLabDB
UI.menu.BuzLabDB.topMenu = uimenu(UI.fig,menuLabel,'BuzLabDB');
uimenu(UI.menu.BuzLabDB.topMenu,menuLabel,'Load session from BuzLabDB',menuSelectedFcn,@DatabaseSessionDialog,'Accelerator','D');
uimenu(UI.menu.BuzLabDB.topMenu,menuLabel,'Edit credentials',menuSelectedFcn,@editDBcredentials,'Separator','on');
uimenu(UI.menu.BuzLabDB.topMenu,menuLabel,'Edit repository paths',menuSelectedFcn,@editDBrepositories);
uimenu(UI.menu.BuzLabDB.topMenu,menuLabel,'View current session on website',menuSelectedFcn,@openSessionInWebDB,'Separator','on');
uimenu(UI.menu.BuzLabDB.topMenu,menuLabel,'View current animal subject on website',menuSelectedFcn,@showAnimalInWebDB);
% View
UI.menu.view.topMenu = uimenu(UI.fig,menuLabel,'View');
UI.menu.view.summaryFigure = uimenu(UI.menu.view.topMenu,menuLabel,'Summary figure',menuSelectedFcn,@summaryFigure);
UI.menu.view.channelRMS = uimenu(UI.menu.view.topMenu,menuLabel,'RMS noise across channels',menuSelectedFcn,@noiseFigure,'Separator','on');
UI.menu.view.channelSpectrum = uimenu(UI.menu.view.topMenu,menuLabel,'Power spectral density across channels',menuSelectedFcn,@powerSpectralFigure);
UI.menu.view.channelSpectrum2 = uimenu(UI.menu.view.topMenu,menuLabel,'Power spectral density across channels (log bins; slower)',menuSelectedFcn,@powerSpectralFigure2);
% Settings
UI.menu.display.topMenu = uimenu(UI.fig,menuLabel,'Settings');
UI.menu.display.ShowHideMenu = uimenu(UI.menu.display.topMenu,menuLabel,'Show full menu',menuSelectedFcn,@ShowHideMenu);
UI.menu.display.removeDC = uimenu(UI.menu.display.topMenu,menuLabel,'Remove DC from signal',menuSelectedFcn,@removeDC,'Separator','on');
UI.menu.display.ShowChannelNumbers = uimenu(UI.menu.display.topMenu,menuLabel,'Show channel numbers',menuSelectedFcn,@ShowChannelNumbers);
UI.menu.display.showScalebar = uimenu(UI.menu.display.topMenu,menuLabel,'Show scale bar',menuSelectedFcn,@showScalebar);
UI.menu.display.narrowPadding = uimenu(UI.menu.display.topMenu,menuLabel,'Narrow ephys padding',menuSelectedFcn,@narrowPadding);
UI.menu.display.plotStyleDynamicRange = uimenu(UI.menu.display.topMenu,menuLabel,'Dynamic ephys range plot',menuSelectedFcn,@plotStyleDynamicRange,'Checked','on');
%UI.menu.display.columnTraces = uimenu(UI.menu.display.topMenu,menuLabel,'Multiple columns',menuSelectedFcn,@columnTraces);
UI.menu.display.colorByChannels = uimenu(UI.menu.display.topMenu,menuLabel,'Color ephys traces by channel order',menuSelectedFcn,@colorByChannels);
UI.menu.display.changeColormap = uimenu(UI.menu.display.topMenu,menuLabel,'Change colormap of ephys traces',menuSelectedFcn,@changeColormap,'Separator','on');
UI.menu.display.changeSpikesColormap = uimenu(UI.menu.display.topMenu,menuLabel,'Change colormap of spikes',menuSelectedFcn,@changeSpikesColormap);
UI.menu.display.changeBackgroundColor = uimenu(UI.menu.display.topMenu,menuLabel,'Change background color & primary color (ticks, text and rasters)',menuSelectedFcn,@changeBackgroundColor);
UI.menu.display.detectedEventsBelowTrace = uimenu(UI.menu.display.topMenu,menuLabel,'Show detected events below traces',menuSelectedFcn,@detectedEventsBelowTrace,'Separator','on');
UI.menu.display.detectedSpikesBelowTrace = uimenu(UI.menu.display.topMenu,menuLabel,'Show detected spikes below traces',menuSelectedFcn,@detectedSpikesBelowTrace);
UI.menu.display.debug = uimenu(UI.menu.display.topMenu,menuLabel,'Debug','Separator','on',menuSelectedFcn,@toggleDebug);
% Help
UI.menu.help.topMenu = uimenu(UI.fig,menuLabel,'Help');
uimenu(UI.menu.help.topMenu,menuLabel,'Mouse and keyboard shortcuts',menuSelectedFcn,@HelpDialog);
uimenu(UI.menu.help.topMenu,menuLabel,'CellExplorer website',menuSelectedFcn,@openWebsite,'Separator','on');
uimenu(UI.menu.help.topMenu,menuLabel,'- About NeuroScope2',menuSelectedFcn,@openWebsite);
uimenu(UI.menu.help.topMenu,menuLabel,'- Tutorial on metadata',menuSelectedFcn,@openWebsite);
uimenu(UI.menu.help.topMenu,menuLabel,'- Documentation on session metadata',menuSelectedFcn,@openWebsite);
uimenu(UI.menu.help.topMenu,menuLabel,'Support',menuSelectedFcn,@openWebsite,'Separator','on');
uimenu(UI.menu.help.topMenu,menuLabel,'- Submit feature request',menuSelectedFcn,@openWebsite);
uimenu(UI.menu.help.topMenu,menuLabel,'- Report an issue',menuSelectedFcn,@openWebsite);
% % % % % % % % % % % % % % % % % % % % % %
% Creating UI/panels
UI.grid_panels = uix.GridFlex( 'Parent', UI.fig, 'Spacing', 5, 'Padding', 0); % Flexib grid box
UI.panel.left = uix.VBoxFlex('Parent',UI.grid_panels,'position',[0 0.66 0.26 0.31]); % Left panel
UI.panel.center = uix.VBox( 'Parent', UI.grid_panels, 'Spacing', 0, 'Padding', 0 ); % Center flex box
% UI.panel.right = uix.VBoxFlex('Parent',UI.grid_panels,'position',[0 0.66 0.26 0.31]); % Right panel
set(UI.grid_panels, 'Widths', [220 -1],'MinimumWidths',[220 1]); % set grid panel size
% Separation of the center box into three panels: title panel, plot panel and lower info panel
UI.panel.plots = uipanel('position',[0 0 1 1],'BorderType','none','Parent',UI.panel.center,'BackgroundColor','k'); % Main plot panel
UI.panel.info = uix.HBox('Parent',UI.panel.center, 'Padding', 1); % Lower info panel
set(UI.panel.center, 'Heights', [-1 20]); % set center panel size
% Left panel tabs
UI.uitabgroup = uiextras.TabPanel('Parent', UI.panel.left, 'Padding', 1,'FontSize',11 ,'TabSize',60);
UI.panel.general.main = uix.VBox('Parent',UI.uitabgroup, 'Padding', 1);
UI.panel.spikedata.main = uix.VBox('Parent',UI.uitabgroup, 'Padding', 1);
UI.panel.other.main = uix.VBox('Parent',UI.uitabgroup, 'Padding', 1);
UI.uitabgroup.TabNames = {'General', 'Spikes','Other'};
% % % % % % % % % % % % % % % % % % % % % %
% 1. PANEL: General elements
% Navigation
UI.panel.general.navigation = uipanel('Parent',UI.panel.general.main,'title','Navigation');
UI.buttons.play1 = uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.15 0.98],'String',char(9654),'Callback',@(~,~)streamDataButtons,'KeyPressFcn', @keyPress,'tooltip','Stream from current timepoint');
uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.17 0.01 0.15 0.98],'String',char(8592),'Callback',@(src,evnt)back,'KeyPressFcn', @keyPress,'tooltip','Go back in time');
uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.33 0.5 0.34 0.49],'String',char(8593),'Callback',@(src,evnt)increaseAmplitude,'KeyPressFcn', @keyPress,'tooltip','Increase amplitude of ephys data');
uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.33 0.01 0.34 0.49],'String',char(8595),'Callback',@(src,evnt)decreaseAmplitude,'KeyPressFcn', @keyPress,'tooltip','Decrease amplitude of ephys data');
uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.68 0.01 0.15 0.98],'String',char(8594),'Callback',@(src,evnt)advance,'KeyPressFcn', @keyPress,'tooltip','Forward in time');
UI.buttons.play2 = uicontrol('Parent',UI.panel.general.navigation,'Style','pushbutton','Units','normalized','Position',[0.84 0.01 0.15 0.98],'String',[char(9655) char(9654)],'Callback',@(~,~)streamDataButtons2,'KeyPressFcn', @keyPress,'tooltip','Stream from end of file');
% Electrophysiology
UI.panel.general.filter = uipanel('Parent',UI.panel.general.main,'title','Extracellular traces');
uicontrol('Parent',UI.panel.general.filter,'Style', 'text', 'String', 'Plot style', 'Units','normalized', 'Position', [0.01 0.87 0.3 0.1],'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.general.filter,'Style', 'text', 'String', 'Plot colors', 'Units','normalized', 'Position', [0.01 0.74 0.3 0.1],'HorizontalAlignment','left');
UI.panel.general.plotStyle = uicontrol('Parent',UI.panel.general.filter,'Style', 'popup','String',{'Downsampled','Range','Raw','LFP (*.lfp file)','Image'}, 'value', UI.settings.plotStyle, 'Units','normalized', 'Position', [0.3 0.86 0.69 0.12],'Callback',@changePlotStyle,'HorizontalAlignment','left');
UI.panel.general.colorScale = uicontrol('Parent',UI.panel.general.filter,'Style', 'popup','String',{'Colors','Colors 75%','Colors 50%','Colors 25%','Grey-scale','Grey-scale 75%','Grey-scale 50%','Grey-scale 25%'}, 'value', 1, 'Units','normalized', 'Position', [0.3 0.73 0.69 0.12],'Callback',@changeColorScale,'HorizontalAlignment','left');
UI.panel.general.filterToggle = uicontrol('Parent',UI.panel.general.filter,'Style', 'checkbox','String','Filter traces', 'value', 0, 'Units','normalized', 'Position', [0. 0.62 0.5 0.11],'Callback',@changeTraceFilter,'HorizontalAlignment','left');
UI.panel.general.extraSpacing = uicontrol('Parent',UI.panel.general.filter,'Style', 'checkbox','String','Group spacing', 'value', 0, 'Units','normalized', 'Position', [0.5 0.62 0.5 0.11],'Callback',@extraSpacing,'HorizontalAlignment','left');
if UI.settings.extraSpacing
UI.panel.general.extraSpacing.Value = 1;
end
uicontrol('Parent',UI.panel.general.filter,'Style', 'text', 'String', 'Lower filter (Hz)', 'Units','normalized', 'Position', [0.0 0.52 0.5 0.09],'HorizontalAlignment','center');
uicontrol('Parent',UI.panel.general.filter,'Style', 'text', 'String', 'Higher filter (Hz)', 'Units','normalized', 'Position', [0.5 0.52 0.5 0.09],'HorizontalAlignment','center');
UI.panel.general.lowerBand = uicontrol('Parent',UI.panel.general.filter,'Style', 'Edit', 'String', '400', 'Units','normalized', 'Position', [0.01 0.39 0.48 0.12],'Callback',@changeTraceFilter,'HorizontalAlignment','center','tooltip','Lower frequency boundary (Hz)');
UI.panel.general.higherBand = uicontrol('Parent',UI.panel.general.filter,'Style', 'Edit', 'String', '', 'Units','normalized', 'Position', [0.5 0.39 0.49 0.12],'Callback',@changeTraceFilter,'HorizontalAlignment','center','tooltip','Higher frequency band (Hz)');
UI.panel.general.plotEnergy = uicontrol('Parent',UI.panel.general.filter,'Style', 'checkbox','String','Absolute smoothing (sec)', 'value', 0, 'Units','normalized', 'Position', [0.01 0.26 0.68 0.12],'Callback',@plotEnergy,'HorizontalAlignment','left');
UI.panel.general.energyWindow = uicontrol('Parent',UI.panel.general.filter,'Style', 'Edit', 'String', num2str(UI.settings.energyWindow), 'Units','normalized', 'Position', [0.7 0.26 0.29 0.12],'Callback',@plotEnergy,'HorizontalAlignment','center','tooltip','Smoothing window (seconds)');
UI.panel.general.detectEvents = uicontrol('Parent',UI.panel.general.filter,'Style', 'checkbox','String',['Detect events (',char(181),'V)'], 'value', 0, 'Units','normalized', 'Position', [0.01 0.135 0.68 0.12],'Callback',@toogleDetectEvents,'HorizontalAlignment','left');
UI.panel.general.eventThreshold = uicontrol('Parent',UI.panel.general.filter,'Style', 'Edit', 'String', num2str(UI.settings.eventThreshold), 'Units','normalized', 'Position', [0.7 0.135 0.29 0.12],'Callback',@toogleDetectEvents,'HorizontalAlignment','center','tooltip',['Event detection threshold (',char(181),'V)']);
UI.panel.general.detectSpikes = uicontrol('Parent',UI.panel.general.filter,'Style', 'checkbox','String',['Detect spikes (',char(181),'V)'], 'value', 0, 'Units','normalized', 'Position', [0.01 0.01 0.68 0.12],'Callback',@toogleDetectSpikes,'HorizontalAlignment','left');
UI.panel.general.detectThreshold = uicontrol('Parent',UI.panel.general.filter,'Style', 'Edit', 'String', num2str(UI.settings.spikesDetectionThreshold), 'Units','normalized', 'Position', [0.7 0.01 0.29 0.12],'Callback',@toogleDetectSpikes,'HorizontalAlignment','center','tooltip',['Spike detection threshold (',char(181),'V)']);
% Electrode groups
UI.uitabgroup_channels = uiextras.TabPanel('Parent', UI.panel.general.main, 'Padding', 1,'FontSize',11 ,'TabSize',45);
UI.panel.electrodeGroups.main = uix.VBox('Parent',UI.uitabgroup_channels, 'Padding', 1);
UI.panel.chanelList.main = uix.VBox('Parent',UI.uitabgroup_channels, 'Padding', 1);
UI.panel.brainRegions.main = uix.VBox('Parent',UI.uitabgroup_channels, 'Padding', 1);
UI.panel.chanCoords.main = uix.VBox('Parent',UI.uitabgroup_channels, 'Padding', 1);
UI.uitabgroup_channels.TabNames = {'Groups', 'Channels','Regions','Layout'};
UI.table.electrodeGroups = uitable(UI.panel.electrodeGroups.main,'Data',{false,'','',''},'Units','normalized','Position',[0 0 1 1],'ColumnWidth',{20 20 45 150},'columnname',{'','','Group','Channels '},'RowName',[],'ColumnEditable',[true false false false],'CellEditCallback',@editElectrodeGroups,'CellSelectionCallback',@ClicktoSelectFromTable);
UI.panel.electrodeGroupsButtons = uipanel('Parent',UI.panel.general.main);
% Channel list
UI.listbox.channelList = uicontrol('Parent',UI.panel.chanelList.main,'Style','listbox','Position',[0 0 1 1],'Units','normalized','String',{'1'},'min',0,'Value',1,'fontweight', 'bold','Callback',@buttonChannelList,'KeyPressFcn', {@keyPress});
% Brain regions
UI.table.brainRegions = uitable(UI.panel.brainRegions.main,'Data',{false,'','',''},'Units','normalized','Position',[0 0 1 1],'ColumnWidth',{20 45 100 45},'columnname',{'','Region','Channels','Groups'},'RowName',[],'ColumnEditable',[true false false false],'CellEditCallback',@editBrainregionList);
% Channel coordinates
UI.chanCoordsAxes = axes('Parent',UI.panel.chanCoords.main,'Units','Normalize','Position',[0 0 1 1],'YLim',[0,1],'YTick',[],'XTick',[]); axis tight
% Group buttons
uicontrol('Parent',UI.panel.electrodeGroupsButtons,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.485 0.98],'String','Show all','Callback',@buttonsElectrodeGroups,'KeyPressFcn', @keyPress,'tooltip','Select all');
uicontrol('Parent',UI.panel.electrodeGroupsButtons,'Style','pushbutton','Units','normalized','Position',[0.505 0.01 0.485 0.98],'String','Show none','Callback',@buttonsElectrodeGroups,'KeyPressFcn', @keyPress,'tooltip','Deselect all');
% Channel tags
UI.panel.channelTagsList = uipanel('Parent',UI.panel.general.main,'title','Channel tags');
UI.table.channeltags = uitable(UI.panel.channelTagsList,'Data', {'','',false,false,false,'',''},'Units','normalized','Position',[0 0 1 1],'ColumnWidth',{20 60 20 20 20 55 55},'columnname',{'','Tags',char(8226),'+','-','Channels','Groups'},'RowName',[],'ColumnEditable',[false false true true true true false],'CellEditCallback',@editChannelTags,'CellSelectionCallback',@ClicktoSelectFromTable2);
UI.panel.channelTagsButtons = uipanel('Parent',UI.panel.general.main);
uicontrol('Parent',UI.panel.channelTagsButtons,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.485 0.98],'String','New tag','Callback',@buttonsChannelTags,'KeyPressFcn', @keyPress,'tooltip','Add channel tag');
uicontrol('Parent',UI.panel.channelTagsButtons,'Style','pushbutton','Units','normalized','Position',[0.505 0.01 0.485 0.98],'String','Delete tag(s)','Callback',@buttonsChannelTags,'KeyPressFcn', @keyPress,'tooltip','Delete channel tag');
% Notes
UI.panel.notes.main = uipanel('Parent',UI.panel.general.main,'title','Session notes');
UI.panel.notes.text = uicontrol('Parent',UI.panel.notes.main,'Style', 'Edit', 'String', '','Units' ,'normalized', 'Position', [0, 0, 1, 1],'HorizontalAlignment','left', 'Min', 0, 'Max', 200,'Callback',@getNotes);
% Epochs
UI.panel.epochs.main = uipanel('Parent',UI.panel.general.main,'title','Session epochs');
UI.epochAxes = axes('Parent',UI.panel.epochs.main,'Units','Normalize','Position',[0 0 1 1],'YLim',[0,1],'YTick',[],'ButtonDownFcn',@ClickEpochs,'XTick',[]); axis tight %,'Color',UI.settings.background,'XColor',UI.settings.primaryColor,'TickLength',[0.005, 0.001],'XMinorTick','on',,'Clipping','off');
% Time series data
UI.panel.timeseriesdata.main = uipanel('Title','Time series data','Position',[0 0.2 1 0.1],'Units','normalized','Parent',UI.panel.general.main);
UI.table.timeseriesdata = uitable(UI.panel.timeseriesdata.main,'Data',{false,'','',''},'Units','normalized','Position',[0 0.20 1 0.80],'ColumnWidth',{20 35 100 45},'columnname',{'','Tag','File name','nChan'},'RowName',[],'ColumnEditable',[true false false false],'CellEditCallback',@showIntan);
UI.panel.timeseriesdata.showTimeseriesBelowTrace = uicontrol('Parent',UI.panel.timeseriesdata.main,'Style','checkbox','Units','normalized','Position',[0 0 0.5 0.20], 'value', 0,'String','Below traces','Callback',@showTimeseriesBelowTrace,'KeyPressFcn', @keyPress,'tooltip','Show intan data below traces');
uicontrol('Parent',UI.panel.timeseriesdata.main,'Style','pushbutton','Units','normalized','Position',[0.5 0 0.49 0.19],'String','Metadata','Callback',@editIntanMeta,'KeyPressFcn', @keyPress,'tooltip','Edit input channels');
% Defining flexible panel heights
set(UI.panel.general.main, 'Heights', [65 210 -200 35 -100 35 100 40 150],'MinimumHeights',[65 210 100 35 100 35 50 30 150]);
% % % % % % % % % % % % % % % % % % % % % %
% 2. PANEL: Spikes related metrics
% Spikes
UI.panel.spikes.main = uipanel('Parent',UI.panel.spikedata.main,'title','Spikes (*.spikes.cellinfo.mat)');
UI.panel.spikes.showSpikes = uicontrol('Parent',UI.panel.spikes.main,'Style', 'checkbox','String','Show spikes', 'value', 0, 'Units','normalized', 'Position', [0.01 0.67 0.48 0.32],'Callback',@toggleSpikes,'HorizontalAlignment','left');
UI.panel.spikes.showSpikesBelowTrace = uicontrol('Parent',UI.panel.spikes.main,'Style', 'checkbox','String','Below traces', 'value', 0, 'Units','normalized', 'Position', [0.51 0.67 0.48 0.32],'Callback',@showSpikesBelowTrace,'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.spikes.main,'Style', 'text', 'String', ' Colors: ', 'Units','normalized', 'Position', [0 0.34 0.35 0.3],'HorizontalAlignment','left');
UI.panel.spikes.setSpikesGroupColors = uicontrol('Parent',UI.panel.spikes.main,'Style', 'popup', 'String', {'UID','Single color','Electrode groups'}, 'Units','normalized', 'Position', [0.35 0.34 0.64 0.32],'HorizontalAlignment','left','Enable','off','Callback',@setSpikesGroupColors);
uicontrol('Parent',UI.panel.spikes.main,'Style', 'text', 'String', ' Sorting/Ydata: ', 'Units','normalized', 'Position', [0.0 0.01 0.4 0.3],'HorizontalAlignment','left');
UI.panel.spikes.setSpikesYData = uicontrol('Parent',UI.panel.spikes.main,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.35 0.01 0.64 0.32],'HorizontalAlignment','left','Enable','off','Callback',@setSpikesYData);
% Cell metrics
UI.panel.cell_metrics.main = uipanel('Parent',UI.panel.spikedata.main,'title','Cell metrics (*.cell_metrics.cellinfo.mat)');
uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'text', 'String', ' Color groups', 'Units','normalized','Position', [0 0.74 0.5 0.13],'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'text', 'String', ' Sorting','Units','normalized','Position', [0 0.47 1 0.13],'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'text', 'String', ' Filter', 'Units','normalized','Position', [0 0.17 1 0.13], 'HorizontalAlignment','left');
UI.panel.cell_metrics.useMetrics = uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'checkbox','String','Use metrics', 'value', 0, 'Units','normalized','Position', [0 0.85 0.5 0.15], 'Callback',@toggleMetrics,'HorizontalAlignment','left');
UI.panel.cell_metrics.defineGroupData = uicontrol('Parent',UI.panel.cell_metrics.main,'Style','pushbutton','Units','normalized','Position',[0.5 0.82 0.49 0.18],'String','Group data','Callback',@defineGroupData,'KeyPressFcn', @keyPress,'tooltip','Filter and highlight by groups','Enable','off');
UI.panel.cell_metrics.groupMetric = uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'popup', 'String', {''}, 'Units','normalized','Position', [0.01 0.6 0.98 0.15],'HorizontalAlignment','left','Enable','off','Callback',@setGroupMetric);
UI.panel.cell_metrics.sortingMetric = uicontrol('Parent',UI.panel.cell_metrics.main,'Style', 'popup', 'String', {''}, 'Units','normalized','Position', [0.01 0.32 0.98 0.15],'HorizontalAlignment','left','Enable','off','Callback',@setSortingMetric);
UI.panel.cell_metrics.textFilter = uicontrol('Style','edit', 'Units','normalized','Position',[0.01 0.01 0.98 0.17],'String','','HorizontalAlignment','left','Parent',UI.panel.cell_metrics.main,'Callback',@filterCellsByText,'Enable','off','tooltip',sprintf('Search across cell metrics\nString fields: "CA1" or "Interneuro"\nNumeric fields: ".firingRate > 10" or ".cv2 < 0.5" (==,>,<,~=) \nCombine with AND // OR operators (&,|) \nEaxmple: ".firingRate > 10 & CA1"\nFilter by parent brain regions as well, fx: ".brainRegion HIP"\nMake sure to include spaces between fields and operators' ));
UI.panel.cellTypes.main = uipanel('Parent',UI.panel.spikedata.main,'title','Putative cell types');
UI.listbox.cellTypes = uicontrol('Parent',UI.panel.cellTypes.main,'Style','listbox', 'Units','normalized','Position',[0 0 1 1],'String',{''},'Enable','off','max',20,'min',0,'Value',[],'Callback',@setCellTypeSelectSubset,'KeyPressFcn', @keyPress,'tooltip','Filter putative cell types. Select to filter');
% Table with list of cells
UI.panel.cellTable.main = uipanel('Parent',UI.panel.spikedata.main,'title','List of cells');
UI.table.cells = uitable(UI.panel.cellTable.main,'Data', {false,'','',''},'Units','normalized','Position',[0 0 1 1],'ColumnWidth',{20 25 93 55},'columnname',{'','#','Cell type','Rate (Hz)'},'RowName',[],'ColumnEditable',[true false false false],'ColumnFormat',{'logical','char','char','numeric'},'CellEditCallback',@editCellTable,'Enable','off');
UI.panel.metricsButtons = uipanel('Parent',UI.panel.spikedata.main);
uicontrol('Parent',UI.panel.metricsButtons,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.32 0.98],'String','All','Callback',@metricsButtons,'KeyPressFcn', @keyPress,'tooltip','Show all cells');
uicontrol('Parent',UI.panel.metricsButtons,'Style','pushbutton','Units','normalized','Position',[0.34 0.01 0.32 0.98],'String','None','Callback',@metricsButtons,'KeyPressFcn', @keyPress,'tooltip','Hide all cells');
uicontrol('Parent',UI.panel.metricsButtons,'Style','pushbutton','Units','normalized','Position',[0.67 0.01 0.32 0.98],'String','Metrics','Callback',@metricsButtons,'KeyPressFcn', @keyPress,'tooltip','Show table with metrics');
% Population analysis
UI.panel.populationAnalysis.main = uipanel('Parent',UI.panel.spikedata.main,'title','Population dynamics');
UI.panel.spikes.populationRate = uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'checkbox','String','Show rate', 'value', 0, 'Units','normalized', 'Position', [0.01 0.68 0.485 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','left');
UI.panel.spikes.populationRateBelowTrace = uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'checkbox','String','Below traces', 'value', 0, 'Units','normalized', 'Position', [0.505 0.68 0.485 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'text','String','Binsize (in sec)', 'Units','normalized', 'Position', [0.01 0.33 0.68 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','left');
UI.panel.spikes.populationRateWindow = uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'Edit', 'String', num2str(UI.settings.populationRateWindow), 'Units','normalized', 'Position', [0.7 0.32 0.29 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','center','tooltip',['Binsize (seconds)']);
uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'text','String','Gaussian smoothing (bins)', 'Units','normalized', 'Position', [0.01 0.01 0.68 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','left');
UI.panel.spikes.populationRateSmoothing = uicontrol('Parent',UI.panel.populationAnalysis.main,'Style', 'Edit', 'String', num2str(UI.settings.populationRateSmoothing), 'Units','normalized', 'Position', [0.7 0.01 0.29 0.3],'Callback',@tooglePopulationRate,'HorizontalAlignment','center','tooltip',['Binsize (seconds)']);
% Spike sorting pipelines
UI.panel.spikesorting.main = uipanel('Title','Other spike sorting formats','Position',[0 0.2 1 0.1],'Units','normalized','Parent',UI.panel.spikedata.main);
UI.panel.spikesorting.showKilosort = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.01 0.66 0.485 0.32], 'value', 0,'String','Kilosort','Callback',@showKilosort,'KeyPressFcn', @keyPress,'tooltip','Open a KiloSort rez.mat data and show detected spikes');
UI.panel.spikesorting.kilosortBelowTrace = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.505 0.66 0.485 0.32], 'value', 0,'String','Below traces','Callback',@showKilosort,'KeyPressFcn', @keyPress,'tooltip','Show KiloSort spikes below trace');
UI.panel.spikesorting.showKlusta = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.01 0.33 0.485 0.32], 'value', 0,'String','Klustakwik','Callback',@showKlusta,'KeyPressFcn', @keyPress,'tooltip','Open Klustakwik clustered data files and show detected spikes');
UI.panel.spikesorting.klustaBelowTrace = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.505 0.33 0.485 0.32], 'value', 0,'String','Below traces','Callback',@showKlusta,'KeyPressFcn', @keyPress,'tooltip','Show Klustakwik spikes below trace');
UI.panel.spikesorting.showSpykingcircus = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.01 0 0.485 0.32], 'value', 0,'String','Spyking Circus','Callback',@showSpykingcircus,'KeyPressFcn', @keyPress,'tooltip','Open SpyKING CIRCUS clustered data and show detected spikes');
UI.panel.spikesorting.spykingcircusBelowTrace = uicontrol('Parent',UI.panel.spikesorting.main,'Style','checkbox','Units','normalized','Position',[0.505 0 0.485 0.32], 'value', 0,'String','Below traces','Callback',@showSpykingcircus,'KeyPressFcn', @keyPress,'tooltip','Show SpyKING CIRCUS spikes below trace');
% Defining flexible panel heights
set(UI.panel.spikedata.main, 'Heights', [95 170 100 -200 35 100 95],'MinimumHeights',[95 170 60 60 35 60 95]);
% % % % % % % % % % % % % % % % % % % % % %
% 3. PANEL: Other datatypes
% Events
UI.panel.events.navigation = uipanel('Parent',UI.panel.other.main,'title','Events (*.events.mat)');
UI.panel.events.files = uicontrol('Parent',UI.panel.events.navigation,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.01 0.85 0.98 0.13],'HorizontalAlignment','left','Callback',@setEventData);
UI.panel.events.showEvents = uicontrol('Parent',UI.panel.events.navigation,'Style','checkbox','Units','normalized','Position',[0.01 0.75 0.5 0.1], 'value', 0,'String','Show events','Callback',@showEvents,'KeyPressFcn', @keyPress,'tooltip','Show events');
UI.panel.events.showEventsBelowTrace = uicontrol('Parent',UI.panel.events.navigation,'Style','checkbox','Units','normalized','Position',[0.505 0.75 0.485 0.1], 'value', 0,'String','Below traces','Callback',@showEventsBelowTrace,'KeyPressFcn', @keyPress,'tooltip','Show events below traces');
UI.panel.events.showEventsIntervals = uicontrol('Parent',UI.panel.events.navigation,'Style','checkbox','Units','normalized','Position',[0.01 0.65 0.458 0.1], 'value', 0,'String','Intervals','Callback',@showEventsIntervals,'KeyPressFcn', @keyPress,'tooltip','Show events intervals');
UI.panel.events.processing_steps = uicontrol('Parent',UI.panel.events.navigation,'Style','checkbox','Units','normalized','Position',[0.505 0.65 0.458 0.1], 'value', 0,'String','Processing','Callback',@processing_steps,'KeyPressFcn', @keyPress,'tooltip','Show processing steps');
UI.panel.events.eventNumber = uicontrol('Parent',UI.panel.events.navigation,'Style', 'Edit', 'String', '', 'Units','normalized', 'Position', [0.01 0.485 0.485 0.14],'HorizontalAlignment','center','tooltip','Event number','Callback',@gotoEvents);
UI.panel.events.eventCount = uicontrol('Parent',UI.panel.events.navigation,'Style', 'Edit', 'String', 'nEvents', 'Units','normalized', 'Position', [0.505 0.485 0.485 0.14],'HorizontalAlignment','center','Enable','off');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.01 0.33 0.32 0.14],'String',char(8592),'Callback',@previousEvent,'KeyPressFcn', @keyPress,'tooltip','Previous event');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.34 0.33 0.32 0.14],'String','Random','Callback',@(src,evnt)randomEvent,'KeyPressFcn', @keyPress,'tooltip','Random event');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.67 0.33 0.32 0.14],'String',char(8594),'Callback',@nextEvent,'KeyPressFcn', @keyPress,'tooltip','Next event');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.01 0.17 0.485 0.14],'String','Flag event','Callback',@flagEvent,'KeyPressFcn', @keyPress,'tooltip','Flag selected event');
UI.panel.events.flagCount = uicontrol('Parent',UI.panel.events.navigation,'Style', 'Edit', 'String', 'nFlags', 'Units','normalized', 'Position', [0.505 0.17 0.485 0.14],'HorizontalAlignment','center','Enable','off');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.485 0.14],'String','Manual event','Callback',@addEvent,'KeyPressFcn', @keyPress,'tooltip','Add event');
uicontrol('Parent',UI.panel.events.navigation,'Style','pushbutton','Units','normalized','Position',[0.505 0.01 0.485 0.14],'String','Save events','Callback',@saveEvent,'KeyPressFcn', @keyPress,'tooltip','Save events');
% Time series
UI.panel.timeseries.main = uipanel('Parent',UI.panel.other.main,'title','Time series (*.timeseries.mat)');
UI.panel.timeseries.files = uicontrol('Parent',UI.panel.timeseries.main,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.01 0.67 0.98 0.31],'HorizontalAlignment','left','Callback',@setTimeseriesData);
UI.panel.timeseries.show = uicontrol('Parent',UI.panel.timeseries.main,'Style','checkbox','Units','normalized','Position',[0.01 0.34 0.485 0.33], 'value', 0,'String','Show','Callback',@showTimeSeries,'KeyPressFcn', @keyPress,'tooltip','Show timeseries data');
uicontrol('Parent',UI.panel.timeseries.main,'Style','pushbutton','Units','normalized','Position',[0.505 0.34 0.485 0.33],'String','Full trace','Callback',@plotTimeSeries,'KeyPressFcn', @keyPress,'tooltip','Show full trace in separate figure');
UI.panel.timeseries.lowerBoundary = uicontrol('Parent',UI.panel.timeseries.main,'Style', 'Edit', 'String', num2str(UI.settings.timeseries.lowerBoundary), 'Units','normalized', 'Position', [0.01 0 0.485 0.33],'HorizontalAlignment','center','tooltip','Lower bound','Callback',@setTimeSeriesBoundary);
UI.panel.timeseries.upperBoundary = uicontrol('Parent',UI.panel.timeseries.main,'Style', 'Edit', 'String', num2str(UI.settings.timeseries.upperBoundary), 'Units','normalized', 'Position', [0.505 0 0.485 0.33],'HorizontalAlignment','center','tooltip','Higher bound','Callback',@setTimeSeriesBoundary);
% States
UI.panel.states.main = uipanel('Parent',UI.panel.other.main,'title','States (*.states.mat)');
UI.panel.states.files = uicontrol('Parent',UI.panel.states.main,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.01 0.67 0.98 0.31],'HorizontalAlignment','left','Callback',@setStatesData);
UI.panel.states.showStates = uicontrol('Parent',UI.panel.states.main,'Style','checkbox','Units','normalized','Position',[0.01 0.35 1 0.33], 'value', 0,'String','Show states','Callback',@showStates,'KeyPressFcn', @keyPress,'tooltip','Show states data');
UI.panel.states.previousStates = uicontrol('Parent',UI.panel.states.main,'Style','pushbutton','Units','normalized','Position',[0.505 0.35 0.24 0.32],'String',char(8592),'Callback',@previousStates,'KeyPressFcn', @keyPress,'tooltip','Previous state');
UI.panel.states.nextStates = uicontrol('Parent',UI.panel.states.main,'Style','pushbutton','Units','normalized','Position',[0.755 0.35 0.235 0.32],'String',char(8594),'Callback',@nextStates,'KeyPressFcn', @keyPress,'tooltip','Next state');
UI.panel.states.statesNumber = uicontrol('Parent',UI.panel.states.main,'Style', 'Edit', 'String', '', 'Units','normalized', 'Position', [0.01 0.01 0.485 0.32],'HorizontalAlignment','center','tooltip','State number','Callback',@gotoState);
UI.panel.states.statesCount = uicontrol('Parent',UI.panel.states.main,'Style', 'Edit', 'String', 'nStates', 'Units','normalized', 'Position', [0.505 0.01 0.485 0.32],'HorizontalAlignment','center','Enable','off');
% Behavior
UI.panel.behavior.main = uipanel('Parent',UI.panel.other.main,'title','Behavior (*.behavior.mat)');
UI.panel.behavior.files = uicontrol('Parent',UI.panel.behavior.main,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.01 0.79 0.98 0.19],'HorizontalAlignment','left','Callback',@setBehaviorData);
UI.panel.behavior.showBehavior = uicontrol('Parent',UI.panel.behavior.main,'Style','checkbox','Units','normalized','Position',[0 0.60 1 0.19], 'value', 0,'String','Show behavior','Callback',@showBehavior,'KeyPressFcn', @keyPress,'tooltip','Show behavior');
UI.panel.behavior.previousBehavior = uicontrol('Parent',UI.panel.behavior.main,'Style','pushbutton','Units','normalized','Position',[0.505 0.60 0.24 0.19],'String',['| ' char(8592)],'Callback',@previousBehavior,'KeyPressFcn', @keyPress,'tooltip','Start of behavior');
UI.panel.behavior.nextBehavior = uicontrol('Parent',UI.panel.behavior.main,'Style','pushbutton','Units','normalized','Position',[0.755 0.60 0.235 0.19],'String',[char(8594) ' |'],'Callback',@nextBehavior,'KeyPressFcn', @keyPress,'tooltip','End of behavior','BusyAction','cancel');
UI.panel.behavior.showBehaviorBelowTrace = uicontrol('Parent',UI.panel.behavior.main,'Style','checkbox','Units','normalized','Position',[0.505 0.41 0.485 0.19], 'value', 0,'String','Below traces','Callback',@showBehaviorBelowTrace,'KeyPressFcn', @keyPress,'tooltip','Show behavior data below traces');
UI.panel.behavior.plotBehaviorLinearized = uicontrol('Parent',UI.panel.behavior.main,'Style','checkbox','Units','normalized','Position',[0.01 0.41 0.485 0.19], 'value', 0,'String','Linearize','Callback',@plotBehaviorLinearized,'KeyPressFcn', @keyPress,'tooltip','Show linearized behavior');
UI.panel.behavior.showTrials = uicontrol('Parent',UI.panel.behavior.main,'Style','checkbox','Units','normalized','Position',[0.01 0.22 0.99 0.19], 'value', 0,'String','Trials','Callback',@showTrials,'KeyPressFcn', @keyPress,'tooltip','Show trial data');
UI.panel.behavior.previousTrial = uicontrol('Parent',UI.panel.behavior.main,'Style','pushbutton','Units','normalized','Position',[0.505 0.22 0.24 0.19],'String',char(8592),'Callback',@previousTrial,'KeyPressFcn', @keyPress,'tooltip','Previous trial');
UI.panel.behavior.nextTrial = uicontrol('Parent',UI.panel.behavior.main,'Style','pushbutton','Units','normalized','Position',[0.755 0.22 0.235 0.19],'String',char(8594),'Callback',@nextTrial,'KeyPressFcn', @keyPress,'tooltip','Next trial');
UI.panel.behavior.trialNumber = uicontrol('Parent',UI.panel.behavior.main,'Style', 'Edit', 'String', '', 'Units','normalized', 'Position', [0.01 0.01 0.485 0.20],'HorizontalAlignment','center','tooltip','Trial number','Callback',@gotoTrial);
UI.panel.behavior.trialCount = uicontrol('Parent',UI.panel.behavior.main,'Style', 'Edit', 'String', 'nTrials', 'Units','normalized', 'Position', [0.505 0.01 0.485 0.20],'HorizontalAlignment','center','Enable','off');
% Spectrogram
UI.panel.spectrogram.main = uipanel('Parent',UI.panel.other.main,'title','Spectrogram');
UI.panel.spectrogram.showSpectrogram = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'checkbox','String','Show spectrogram', 'value', 0, 'Units','normalized', 'Position', [0.01 0.80 0.99 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','left');
uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'text','String','Channel', 'Units','normalized', 'Position', [0.01 0.60 0.49 0.19],'HorizontalAlignment','left');
UI.panel.spectrogram.spectrogramChannel = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'Edit', 'String', num2str(UI.settings.spectrogram.channel), 'Units','normalized', 'Position', [0.505 0.60 0.485 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','center');
uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'text','String','Window width (sec)', 'Units','normalized', 'Position', [0.01 0.40 0.49 0.19],'HorizontalAlignment','left');
UI.panel.spectrogram.spectrogramWindow = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'Edit', 'String', num2str(UI.settings.spectrogram.window), 'Units','normalized', 'Position', [0.505 0.40 0.485 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','center');
uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'text','String','Low freq (Hz)', 'Units','normalized', 'Position', [0.01 0.20 0.32 0.16],'HorizontalAlignment','left');
UI.panel.spectrogram.freq_low = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'Edit', 'String', num2str(UI.settings.spectrogram.freq_low), 'Units','normalized', 'Position', [0.01 0.01 0.32 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','center');
uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'text','String','Step size (Hz)', 'Units','normalized', 'Position', [0.34 0.20 0.32 0.16],'HorizontalAlignment','center');
UI.panel.spectrogram.freq_step_size = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'Edit', 'String', num2str(UI.settings.spectrogram.freq_step_size), 'Units','normalized', 'Position', [0.34 0.01 0.32 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','center');
uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'text','String','High freq (Hz)', 'Units','normalized', 'Position', [0.67 0.20 0.32 0.16],'HorizontalAlignment','right');
UI.panel.spectrogram.freq_high = uicontrol('Parent',UI.panel.spectrogram.main,'Style', 'Edit', 'String', num2str(UI.settings.spectrogram.freq_high), 'Units','normalized', 'Position', [0.67 0.01 0.32 0.19],'Callback',@toggleSpectrogram,'HorizontalAlignment','center');
% Current Source Density
UI.panel.csd.main = uipanel('Parent',UI.panel.other.main,'title','Current Source Density');
UI.panel.csd.showCSD = uicontrol('Parent',UI.panel.csd.main,'Style', 'checkbox','String','Show Current Source Density', 'value', 0, 'Units','normalized', 'Position', [0.01 0.01 0.98 0.98],'Callback',@show_CSD,'HorizontalAlignment','left');
% Defining flexible panel heights
set(UI.panel.other.main, 'Heights', [200 95 95 140 95 50],'MinimumHeights',[220 100 100 150 150 50]);
% % % % % % % % % % % % % % % % % % % % % %
% Lower info panel elements
uicontrol('Parent',UI.panel.info,'Style', 'text', 'String', ' Time (s)', 'Units','normalized', 'Position', [0.1 0 0.05 0.8],'HorizontalAlignment','center');
UI.elements.lower.time = uicontrol('Parent',UI.panel.info,'Style', 'Edit', 'String', '', 'Units','normalized', 'Position', [0.15 0 0.05 1],'HorizontalAlignment','right','tooltip','Current timestamp (seconds)','Callback',@setTime);
uicontrol('Parent',UI.panel.info,'Style', 'text', 'String', ' Window duration (s)', 'Units','normalized', 'Position', [0.25 0 0.05 0.8],'HorizontalAlignment','center');
UI.elements.lower.windowsSize = uicontrol('Parent',UI.panel.info,'Style', 'Edit', 'String', UI.settings.windowDuration, 'Units','normalized', 'Position', [0.3 0 0.05 1],'HorizontalAlignment','right','tooltip','Window size (seconds)','Callback',@setWindowsSize);
UI.elements.lower.scalingText = uicontrol('Parent',UI.panel.info,'Style', 'text', 'String', ' Scaling ', 'Units','normalized', 'Position', [0.0 0 0.05 0.8],'HorizontalAlignment','right');
UI.elements.lower.scaling = uicontrol('Parent',UI.panel.info,'Style', 'Edit', 'String', num2str(UI.settings.scalingFactor), 'Units','normalized', 'Position', [0.05 0 0.05 1],'HorizontalAlignment','right','tooltip','Ephys scaling','Callback',@setScaling);
UI.elements.lower.performance = uicontrol('Parent',UI.panel.info,'Style', 'text', 'String', 'Performance', 'Units','normalized', 'Position', [0.25 0 0.05 0.8],'HorizontalAlignment','center','KeyPressFcn', @keyPress);
UI.elements.lower.slider = uicontrol(UI.panel.info,'Style','slider','Units','normalized','Position',[0.5 0 0.5 1],'Value',0, 'SliderStep', [0.0001, 0.1], 'Min', 0, 'Max', 100,'Callback',@moveSlider);
set(UI.panel.info, 'Widths', [70 80 120 60 120 60 280 -1],'MinimumWidths',[70 80 120 60 60 60 250 1]); % set grid panel size
% % % % % % % % % % % % % % % % % % % % % %
% Creating plot axes
UI.plot_axis1 = axes('Parent',UI.panel.plots,'Units','Normalize','Position',[0 0 1 1],'ButtonDownFcn',@ClickPlot,'Color',UI.settings.background,'XColor',UI.settings.primaryColor,'TickLength',[0.005, 0.001],'XMinorTick','on','XLim',[0,UI.settings.windowDuration],'YLim',[0,1],'YTickLabel',[],'Clipping','off');
hold on
UI.plot_axis1.XAxis.MinorTick = 'on';
UI.plot_axis1.XAxis.MinorTickValues = 0:0.01:2;
set(0,'units','pixels');
ce_dragzoom(UI.plot_axis1,'on');
UI.Pix_SS = get(0,'screensize');
UI.Pix_SS = UI.Pix_SS(3)*2;
setScalingText
end
function plotData
% Generates all data plots
% Deletes existing plot data
delete(UI.plot_axis1.Children)
set(UI.fig,'CurrentAxes',UI.plot_axis1)
UI.settings.textOffset = 0;
if UI.settings.showChannelNumbers
set(UI.plot_axis1,'XLim',[-0.01*UI.settings.windowDuration,UI.settings.windowDuration],'YLim',[0,1])
else
set(UI.plot_axis1,'XLim',[0,UI.settings.windowDuration],'YLim',[0,1])
end
% Ephys traces
plot_ephys
% KiloSort data
if UI.settings.showKilosort
plotKilosortData(t0,t0+UI.settings.windowDuration,'c')
end
% Klusta data
if UI.settings.showKlusta
plotKlustaData(t0,t0+UI.settings.windowDuration,'g')
end
% Spyking circus data
if UI.settings.showSpykingcircus
plotSpykingcircusData(t0,t0+UI.settings.windowDuration,'m')
end
% Spike data
if UI.settings.showSpikes
plotSpikeData(t0,t0+UI.settings.windowDuration,UI.settings.primaryColor,UI.plot_axis1)
end
% Spectrogram
if UI.settings.spectrogram.show
plotSpectrogram
end
% States data
if UI.settings.showStates
plotTemporalStates(t0,t0+UI.settings.windowDuration)
end
% Event data
if UI.settings.showEvents
plotEventData(t0,t0+UI.settings.windowDuration,UI.settings.primaryColor,'m')
end
% Time series
if UI.settings.showTimeSeries
plotTimeSeriesData(t0,t0+UI.settings.windowDuration,'m')
end
% Intan analog
if UI.settings.intan_showAnalog
plotAnalog('adc')
end
% Intan aux
if UI.settings.intan_showAux
plotAnalog('aux')
end
% Intan digital
if UI.settings.intan_showDigital
plotDigital('dig')
end
% Behavior
if UI.settings.showBehavior
plotBehavior(t0,t0+UI.settings.windowDuration,[0.5 0.5 0.5])
end
% Trials
if UI.settings.showTrials
plotTrials(t0,t0+UI.settings.windowDuration,UI.settings.primaryColor)
end
% % PCA spike representation
% if UI.settings.detectSpikes && ~isempty(UI.channelOrder)
% raster = [];
% electrodeGroup = 10;
% for i = 1:numel(UI.channels{10})
% idx = find(diff(ephys.filt(:,UI.channels{10}(i)) < UI.settings.spikesDetectionThreshold)==1)+1;
% raster = [raster;idx];
% end
% if ~isempty(raster)
% raster = sort(raster);
% raster(diff(raster)<0.001/data.session.extracellular.sr)=[];
% wfWin_sec = 0.0008;
% raster(raster/data.session.extracellular.sr<wfWin_sec | raster/data.session.extracellular.sr>UI.settings.windowDuration-wfWin_sec)=[];
%
% nChannels = numel(UI.channels{electrodeGroup});
% sr = data.session.extracellular.sr;
% wfWin = round((wfWin_sec * sr)/2);
% startIndicies2 = (raster - wfWin)*nChannels+1;
% stopIndicies2 = (raster + wfWin)*nChannels;
% X2 = cumsum(accumarray(cumsum([1;stopIndicies2(:)-startIndicies2(:)+1]),[startIndicies2(:);0]-[0;stopIndicies2(:)]-1)+1);
% ephys_data = ephys.filt(:,UI.channels{electrodeGroup})';
% wf = reshape(double(ephys_data(X2(1:end-1))),nChannels,(wfWin*2),[]);
% wf2 = reshape(permute(wf,[2,1,3]),nChannels*(wfWin*2),[]);
% if isempty(score)
% [~,score] = pca(wf2,'NumComponents',3);
% end
% figure(5);
% temp = wf2'*score;
% plot3(temp(:,1),temp(:,2),temp(:,3),'.'), hold on, axis tight
% figure(UI.fig)
% % set(UI.fig,'CurrentAxes',UI.plot_axis1)
% end
% end
end
function text_center(message)
text(UI.plot_axis1,0.5,0.5,message,'Color',UI.settings.primaryColor,'FontSize',14,'Units','normalized','FontWeight', 'Bold','BackgroundColor',UI.settings.textBackground)
end
function plot_ephys
% Loading and plotting ephys data
% There are five plot styles, for optimized plotting performance
% 1. Downsampled: Shows every 16th sample of the raw data (no filter or averaging)
% 2. Range: Shows a sample count optimized for the screen resolution. For each sample the max and the min is plotted of data in the corresponding temporal range
% 3. Raw: Raw data at full sampling rate
% 4. LFP: .LFP file, typically the raw data has been downpass filtered and downsampled to 1250Hz before this. All samples are shown.
% 5. Image: Raw data displaued with the imagesc function
% Only data thas is not currently displayed will be loaded.
if UI.settings.greyScaleTraces < 5
colors = UI.colors/UI.settings.greyScaleTraces;
elseif UI.settings.greyScaleTraces >=5
colors = ones(size(UI.colors))/(UI.settings.greyScaleTraces-4);
colors(1:2:end,:) = colors(1:2:end,:)-0.08*(9-UI.settings.greyScaleTraces);
end
% Setting booean for validating ephys loading and plotting
ephys.loaded = false;
ephys.plotted = false;
if UI.settings.plotStyle == 4 % lfp file
if UI.fid.lfp == -1
UI.settings.stream = false;
ephys.loaded = false;
text_center('Failed to load LFP data')
return
end
sr = data.session.extracellular.srLfp;
ephys.sr = sr;
fileID = UI.fid.lfp;
else % dat file
if UI.fid.ephys == -1
UI.settings.stream = false;
ephys.loaded = false;
text_center('Failed to load raw data')
return
end
sr = data.session.extracellular.sr;
ephys.sr = sr;
fileID = UI.fid.ephys;
end
if strcmp(UI.settings.fileRead,'bof')
% Loading data
if t0>UI.t1 && t0 < UI.t1 + UI.settings.windowDuration && ~UI.forceNewData
t_offset = t0-UI.t1;
newSamples = round(UI.samplesToDisplay*t_offset/UI.settings.windowDuration);
existingSamples = UI.samplesToDisplay-newSamples;
% Keeping existing samples
ephys.raw(1:existingSamples,:) = ephys.raw(newSamples+1:UI.samplesToDisplay,:);
% Loading new samples
fseek(fileID,round((t0+UI.settings.windowDuration-t_offset)*sr)*data.session.extracellular.nChannels*2,'bof'); % bof: beginning of file
try
ephys.raw(existingSamples+1:UI.samplesToDisplay,:) = double(fread(fileID, [data.session.extracellular.nChannels, newSamples],UI.settings.precision))'*UI.settings.leastSignificantBit;
ephys.loaded = true;
catch
UI.settings.stream = false;
text_center('Failed to read file')
end
elseif t0 < UI.t1 && t0 > UI.t1 - UI.settings.windowDuration && ~UI.forceNewData
t_offset = UI.t1-t0;
newSamples = round(UI.samplesToDisplay*t_offset/UI.settings.windowDuration);
% Keeping existing samples
existingSamples = UI.samplesToDisplay-newSamples;
ephys.raw(newSamples+1:UI.samplesToDisplay,:) = ephys.raw(1:existingSamples,:);
% Loading new data
fseek(fileID,round(t0*sr)*data.session.extracellular.nChannels*2,'bof');
ephys.raw(1:newSamples,:) = double(fread(fileID, [data.session.extracellular.nChannels, newSamples],UI.settings.precision))'*UI.settings.leastSignificantBit;
ephys.loaded = true;
elseif t0==UI.t1 && ~UI.forceNewData
ephys.loaded = true;
else
fseek(fileID,round(t0*sr)*data.session.extracellular.nChannels*2,'bof');
ephys.raw = double(fread(fileID, [data.session.extracellular.nChannels, UI.samplesToDisplay],UI.settings.precision))'*UI.settings.leastSignificantBit;
ephys.loaded = true;
end
UI.forceNewData = false;
else
fseek(fileID,ceil(-UI.settings.windowDuration*sr)*data.session.extracellular.nChannels*2,'eof'); % eof: end of file
ephys.raw = double(fread(fileID, [data.session.extracellular.nChannels, UI.samplesToDisplay],UI.settings.precision))'*UI.settings.leastSignificantBit;
UI.forceNewData = true;
ephys.loaded = true;
end
UI.t1 = t0;
if ~ephys.loaded
return
end
% Removing DC
if UI.settings.removeDC
ephys.traces = ephys.raw-mean(ephys.raw);
else
ephys.traces = ephys.raw;
end
if UI.settings.filterTraces && UI.settings.plotStyle == 4
if int_gt_0(UI.settings.filter.lowerBand,sr) && ~int_gt_0(UI.settings.filter.higherBand,sr)
[b1, a1] = butter(3, UI.settings.filter.higherBand/sr*2, 'low');
elseif int_gt_0(UI.settings.filter.higherBand,sr) && ~int_gt_0(UI.settings.filter.lowerBand,sr)
[b1, a1] = butter(3, UI.settings.filter.lowerBand/sr*2, 'high');
else
[b1, a1] = butter(3, [UI.settings.filter.lowerBand,UI.settings.filter.higherBand]/sr*2, 'bandpass');
end
ephys.traces(:,UI.channelOrder) = filtfilt(b1, a1, ephys.traces(:,UI.channelOrder) * (UI.settings.scalingFactor)/1000000);
elseif UI.settings.filterTraces
ephys.traces(:,UI.channelOrder) = filtfilt(UI.settings.filter.b1, UI.settings.filter.a1, ephys.traces(:,UI.channelOrder) * (UI.settings.scalingFactor)/1000000);
else
ephys.traces(:,UI.channelOrder) = ephys.traces(:,UI.channelOrder) * (UI.settings.scalingFactor)/1000000;
end
if UI.settings.plotEnergy == 1
for i = UI.channelOrder
ephys.traces(:,i) = 2*smooth(abs(ephys.traces(:,i)),round(UI.settings.energyWindow*sr),'moving');
end
end
% CSD Background plot
if UI.settings.CSD.show & numel(UI.channelOrder)>1
plotCSD
end
if UI.settings.colorByChannels
channelsList2 = [UI.channels{UI.settings.electrodeGroupsToPlot}];
channelsList = {};
temp = rem(0:numel(channelsList2)-1,UI.settings.nColorGroups)+1;
for i = 1:max(temp)
channelsList{i} = channelsList2(find(temp==i));
end
colors = eval([UI.settings.colormap,'(',num2str(numel(channelsList)),')']);
electrodeGroupsToPlot = 1:max(temp);
if UI.settings.greyScaleTraces < 5
colors = colors/UI.settings.greyScaleTraces;
elseif UI.settings.greyScaleTraces >=5
colors = ones(size(colors))/(UI.settings.greyScaleTraces-4);
colors(1:2:end,:) = colors(1:2:end,:)-0.08*(9-UI.settings.greyScaleTraces);
end
colorsList = colors;
else
electrodeGroupsToPlot = UI.settings.electrodeGroupsToPlot;
channelsList = UI.channels;
colorsList = colors;
end
if UI.settings.plotStyle == 1
% Low sampled values (Faster plotting)
for iShanks = electrodeGroupsToPlot
channels = channelsList{iShanks};
[~,ia,~] = intersect(UI.channelOrder,channels,'stable');
line(UI.plot_axis1,[1:UI.nDispSamples]/UI.nDispSamples*UI.settings.windowDuration,ephys.traces(UI.dispSamples,channels)-UI.channelOffset(channels),'color',colorsList(iShanks,:), 'HitTest','off');
end
elseif UI.settings.plotStyle == 2 && (UI.settings.windowDuration>=UI.settings.plotStyleDynamicThreshold || ~UI.settings.plotStyleDynamicRange) % Range values per sample (ala Neuroscope1)
% Range data (low sampled values with min and max per interval)
excess_samples = rem(size(ephys.traces,1),ceil(UI.settings.plotStyleRangeSamples*UI.settings.windowDuration));
ephys_traces3 = ephys.traces(1:end-excess_samples,:);
ephys_traces2 = reshape(ephys_traces3,ceil(UI.settings.plotStyleRangeSamples*UI.settings.windowDuration),[]);
ephys.traces_min = reshape(min(ephys_traces2),[],size(ephys.traces,2));
ephys.traces_max = reshape(max(ephys_traces2),[],size(ephys.traces,2));
for iShanks = electrodeGroupsToPlot
tist = [];
timeLine = [];
channels = channelsList{iShanks};
[~,ia,~] = intersect(UI.channelOrder,channels,'stable');
tist(1,:,:) = ephys.traces_min(:,channels)-UI.channelOffset(channels);
tist(2,:,:) = ephys.traces_max(:,channels)-UI.channelOffset(channels);
tist(:,end+1,:) = nan;
timeLine1 = repmat([1:size(ephys.traces_min,1)]/size(ephys.traces_min,1)*UI.settings.windowDuration,numel(channels),1)';
timeLine(1,:,:) = timeLine1;
timeLine(2,:,:) = timeLine1;
timeLine(:,end+1,:) = timeLine(:,end,:);
line(UI.plot_axis1,timeLine(:)',tist(:)','color',colorsList(iShanks,:)','LineStyle','-', 'HitTest','off');
end
elseif UI.settings.plotStyle == 5
% Image representation
timeLine = [1:size(ephys.traces,1)]/size(ephys.traces,1)*UI.settings.windowDuration;
multiplier = [size(ephys.traces,1)-1:-1:0]/(size(ephys.traces,1)-1)*0.9+0.05;
imagesc(UI.plot_axis1,timeLine,multiplier,ephys.traces(:,UI.channelOrder)', 'HitTest','off')
else
% Raw data
timeLine = [1:size(ephys.traces,1)]/size(ephys.traces,1)*UI.settings.windowDuration;
for iShanks = electrodeGroupsToPlot
channels = channelsList{iShanks};
if ~isempty(channels)
line(UI.plot_axis1,timeLine,ephys.traces(:,channels)-UI.channelOffset(channels),'color',colorsList(iShanks,:),'LineStyle','-', 'HitTest','off');
end
end
end
if ~isempty(UI.settings.channelTags.highlight)
for i = 1:numel(UI.settings.channelTags.highlight)
channels = data.session.channelTags.(UI.channelTags{UI.settings.channelTags.highlight(i)}).channels;
if ~isempty(channels)
channels = UI.channelMap(channels); channels(channels==0) = [];
if ~isempty(channels) && any(ismember(channels,UI.channelOrder))
highlightTraces(channels,UI.colors_tags(UI.settings.channelTags.highlight(i),:));
end
end
end
end
% Detecting and plotting spikes
if UI.settings.detectSpikes && ~isempty(UI.channelOrder)
[UI.settings.filter.b2, UI.settings.filter.a2] = butter(3, 500/(ephys.sr/2), 'high');
if UI.settings.removeDC
ephys.filt = ephys.raw-mean(ephys.raw);
else
ephys.filt = ephys.raw;
end
ephys.filt(:,UI.channelOrder) = filtfilt(UI.settings.filter.b2, UI.settings.filter.a2, ephys.filt(:,UI.channelOrder));
raster = [];
raster.x = [];
raster.y = [];
for i = 1:size(ephys.filt,2)
idx = find(diff(ephys.filt(:,i) < UI.settings.spikesDetectionThreshold)==1)+1;
if ~isempty(idx)
raster.x = [raster.x;idx];
if UI.settings.plotStyle == 5
raster.y = [raster.y;-UI.channelScaling(idx,i)];
elseif UI.settings.detectedSpikesBelowTrace