Spring cleaning

Many new additions to the GUI, including global reference data and ground truth data
petersenpeter · Oct 31, 2019 · ca49624 · ca49624
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commit ca49624
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diff --git a/CellExplorer.m b/CellExplorer.m
diff --git a/CellExplorer_Preferences.m b/CellExplorer_Preferences.m
@@ -3,29 +3,32 @@
 
 % By Peter Petersen
 % petersen.peter@gmail.com
-% Last edited: 07-06-2019
+% Last edited: 16-08-2019
 
 % % % % % % % % % % % % % % % % % % % % % %
 % Cell Explorer Preferences  
 % % % % % % % % % % % % % % % % % % % % % %
 
-% Display settings - A incomplete list:
-%    'Single waveform','All waveforms','All waveforms (image)','Single raw waveform','All raw waveforms','Single ACG',
-%    'All ACGs','All ACGs (image)','CCGs (image)','Sharp wave-ripple','firingRateAcrossTime','firingRateMap',
-%    'firingRateMap_CoolingStates','firingRateMap_LeftRight','rippleCorrelogram','thetaPhaseResponse'
-UI.settings.customCellPlotIn1 = 'Single waveform';
+% Display settings - An incomplete list:
+% 'Single waveform','All waveforms','All waveforms (image)','Single raw waveform','All raw waveforms','Single ACG',
+% 'All ACGs','All ACGs (image)','CCGs (image)','Sharp wave-ripple'
+UI.settings.customCellPlotIn1 = 'All waveforms';
 UI.settings.customCellPlotIn2 = 'Single ACG'; 
-UI.settings.customCellPlotIn3 = 'firingRateAcrossTime';
+UI.settings.customCellPlotIn3 = 'responseCurves_firingRateAcrossTime';
 UI.settings.customCellPlotIn4 = 'All waveforms';
 UI.settings.customCellPlotIn5 = 'CCGs (image)';
 UI.settings.customCellPlotIn6 = 'firingRateMap';
 
-UI.settings.acgType = 'Normal';                 % Normal (100ms), Wide (1s), Narrow (30ms)
+UI.settings.acgType = 'Normal';                 % Normal (100ms), Wide (1s), Narrow (30ms), Log10
+UI.settings.isiNormalization = 'Rate';          % 'Rate', 'Occurance'
 UI.settings.monoSynDispIn = 'Selected';         % 'All', 'Upstream', 'Downstream', 'Up & downstream', 'Selected', 'None'
-UI.settings.metricsTableType = 'Cells';         % ['Metrics','Cells','None']
+UI.settings.metricsTableType = 'Metrics';         % ['Metrics','Cells','None']
 UI.settings.plotCountIn = 'GUI 3+3';            % ['GUI 1+3','GUI 2+3','GUI 3+3','GUI 3+4','GUI 3+5','GUI 3+6']
 UI.settings.dispLegend = 0;                     % [0,1] Display legend for scatter plots?
 UI.settings.plotWaveformMetrics = 0;            % show waveform metrics on the single waveform
+UI.settings.sortingMetric = 'burstIndex_Royer2012'; % metrics used for sorting image data
+UI.settings.referenceData = 'None';             % ['None','Image','Points']
+UI.settings.groundTruthData = 'None';             % ['None','Image','Points']
 
 % Autosave settings
 UI.settings.autoSaveFrequency = 6;              % How often you want to autosave (classifications steps). Put to 0 to turn autosave off
@@ -40,29 +43,39 @@
 UI.settings.cellTypes = {'Unknown','Pyramidal Cell','Narrow Interneuron','Wide Interneuron'};
 UI.settings.deepSuperficial = {'Unknown','Cortical','Deep','Superficial'};
 UI.settings.tags = {'Good','Bad','Mua','Noise','InverseSpike','Other'};
-UI.settings.groundTruth = {'PV+','NOS1+','GAT1+','SST+'}; 
-UI.settings.groundTruthMarkers = {'ok','db','sm','*k','+d','p'}; % Supports any Matlab marker symbols: https://www.mathworks.com/help/matlab/creating_plots/create-line-plot-with-markers.html
-
-% Cell type classification colors
+UI.settings.groundTruth = {'PV+','NOS1+','GAT1+','SST+','Axoaxonic','5HT3a'}; 
+UI.settings.groundTruthMarkers = {'om','dg','sm','*k','+k','+p'}; % Supports any Matlab marker symbols: https://www.mathworks.com/help/matlab/creating_plots/create-line-plot-with-markers.html
+UI.settings.groundTruthColors = [[.5,.5,.5];[.8,.2,.2];[.2,.2,.8];[0.2,0.8,0.8];[0.8,0.2,0.8];[.2,.8,.2]];
 UI.settings.cellTypeColors = [[.5,.5,.5];[.8,.2,.2];[.2,.2,.8];[0.2,0.8,0.8];[0.8,0.2,0.8];[.2,.8,.2]];
 
-% Fields used to define the tSNE represetation
+% tSNE representation
+UI.settings.tSNE_metrics = {'firingRate','thetaModulationIndex','burstIndex_Mizuseki2012','troughToPeak','ab_ratio','burstIndex_Royer2012','acg_tau_rise','acg_tau_burst','acg_h','acg_tau_decay','cv2','burstIndex_Doublets','troughtoPeakDerivative'};
+UI.settings.tSNE_dDistanceMetric = 'euclidean'; % default: 'euclidean'
+UI.settings.tSNE_exaggeration = 15;             % default: 15
+UI.settings.tSNE_standardize = false;           % boolean
+
 UI.settings.tSNE_calcWideAcg = false;           % boolean
 UI.settings.tSNE_calcNarrowAcg = false;         % boolean
+UI.settings.tSNE_calcLogAcg = false;            % boolean
+UI.settings.tSNE_calcLogIsi = false;            % boolean
 UI.settings.tSNE_calcFiltWaveform = false;      % boolean
 UI.settings.tSNE_calcRawWaveform = false;       % boolean
 
-% List of fields to use in the general tSNE representation
-UI.settings.tSNE_metrics = {'firingRate','thetaModulationIndex','burstIndex_Mizuseki2012','troughToPeak','ab_ratio','burstIndex_Royer2012','acg_tau_rise','acg_tau_burst','acg_h','acg_tau_decay','cv2','burstIndex_Doublets','derivative_TroughtoPeak','filtWaveform_zscored','acg2_zscored'}; % 'thetaPhaseTrough','thetaEntrainment'
-
 % Highlight excitatory / inhibitory cells
 UI.settings.displayInhibitory = false;          % boolean
 UI.settings.displayExcitatory = false;          % boolean
+UI.settings.displayExcitatoryPostsynapticCells = false; % boolean
+UI.settings.displayInhibitoryPostsynapticCells = false; % boolean
+
+% Firing rate map setting
+UI.settings.firingRateMap.showHeatmap = false;          % boolean
+UI.settings.firingRateMap.showLegend = false;           % boolean
+UI.settings.firingRateMap.showHeatmapColorbar = false;  % boolean
 
 % % % % % % % % % % % % % % % % % % % % % %
 % Spikes plot definitions
 %
-% Can be loaded by pressing S in the Cell Explorer
+% Can be loaded by pressing CTRL+A in the Cell Explorer
 % % % % % % % % % % % % % % % % % % % % % %
 
 plotName = 'spikes_pos_vs_phase';
@@ -75,6 +88,7 @@
 spikesPlots.(plotName).filterType = 'greater than';     % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 20;
 spikesPlots.(plotName).event = '';
+spikesPlots.(plotName).eventType = 'event';             % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'peak';         % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds
@@ -95,6 +109,7 @@
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = '';
+spikesPlots.(plotName).eventType = 'event';        % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'peak';         % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds
@@ -115,6 +130,7 @@
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = '';
+spikesPlots.(plotName).eventType = 'event';        % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'peak';         % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds
@@ -135,6 +151,7 @@
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = '';
+spikesPlots.(plotName).eventType = 'event';        % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'peak';         % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds
@@ -152,20 +169,21 @@
 spikesPlots.(plotName).y_label = 'Event';
 spikesPlots.(plotName).state = '';
 spikesPlots.(plotName).filter = '';
-spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
+spikesPlots.(plotName).filterType = '';            % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = 'ripples';
-spikesPlots.(plotName).eventAlignment = 'peak';         % [onset, offset, center, peak]
-spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
-spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds
-spikesPlots.(plotName).eventSecAfter = 0.2;             % in seconds
+spikesPlots.(plotName).eventType = 'event';        % [event,manipulation,state]
+spikesPlots.(plotName).eventAlignment = 'peak';    % [onset, offset, center, peak]
+spikesPlots.(plotName).eventSorting = 'amplitude'; % [none, time, amplitude, duration]
+spikesPlots.(plotName).eventSecBefore = 0.2;       % in seconds
+spikesPlots.(plotName).eventSecAfter = 0.2;        % in seconds
 spikesPlots.(plotName).plotRaster = 1; 
 spikesPlots.(plotName).plotAverage = 1;
 spikesPlots.(plotName).plotAmplitude = 1;
 spikesPlots.(plotName).plotDuration = 1;
 spikesPlots.(plotName).plotCount = 0;
 
-plotName = 'spikes_pvLightStimulation';
+plotName = 'spikes_optoStim';
 spikesPlots.(plotName).x = 'times';
 spikesPlots.(plotName).y = 'times';
 spikesPlots.(plotName).x_label = 'Time';
@@ -174,7 +192,8 @@
 spikesPlots.(plotName).filter = '';
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
-spikesPlots.(plotName).event = 'pvLightStimulation';
+spikesPlots.(plotName).event = 'optoStim';
+spikesPlots.(plotName).eventType = 'manipulation';      % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'onset';        % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'time';           % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.1;            % in seconds
@@ -195,6 +214,7 @@
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = 'stimulation';
+spikesPlots.(plotName).eventType = 'manipulation';      % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'onset';        % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'amplitude';      % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 2;              % in seconds
@@ -215,6 +235,7 @@
 spikesPlots.(plotName).filterType = '';                 % [none, equal to, less than, greater than]
 spikesPlots.(plotName).filterValue = 0;
 spikesPlots.(plotName).event = 'pulses';
+spikesPlots.(plotName).eventType = 'manipulation';      % [event,manipulation,state]
 spikesPlots.(plotName).eventAlignment = 'onset';        % [onset, offset, center, peak]
 spikesPlots.(plotName).eventSorting = 'none';           % [none, time, amplitude, duration]
 spikesPlots.(plotName).eventSecBefore = 0.2;            % in seconds