forked from petersenpeter/CellExplorer
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathNeuroScope2.m
4388 lines (4004 loc) · 236 KB
/
NeuroScope2.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
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, fully
% support Matlab mat-files, and faster than the original NeuroScope. NeuroScope2 is part of CellExplorer - https://CellExplorer.org/
%
% 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) (isempty(n)) || (n <= 0);
% Initialization
initUI
initData(basepath,basename);
initInputs
initTraces
% % % % % % % % % % % % % % % % % % % % % %
% Maximazing figure to full screen
if ~verLessThan('matlab', '9.4')
set(UI.fig,'WindowState','maximize','visible','on'), drawnow nocallbacks;
else
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 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;
saveStruct(session,'session','commandDisp',false);
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.displayMenu = 0;
UI.settings.channelTags.hide = [];
UI.settings.channelTags.filter = [];
UI.settings.channelTags.highlight = [];
UI.settings.showKilosort = false;
UI.settings.kilosortBelowTrace = false;
UI.settings.normalClick = true;
UI.settings.addEventonClick = false;
UI.settings.background = 'k';
UI.settings.xtickColor = 'w';
UI.settings.showChannelNumbers = false;
UI.settings.channelList = [];
UI.settings.brainRegionsToHide = [];
UI.settings.removeDC = 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;
% 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.showIntanBelowTrace = 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,'Accelerator','G');
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);
UI.menu.view.channelCSD = uimenu(UI.menu.view.topMenu,menuLabel,'Current Source density across channels',menuSelectedFcn,@csdFigure,'Separator','on');
% Settings
UI.menu.display.topMenu = uimenu(UI.fig,menuLabel,'Settings');
UI.menu.display.removeDC = uimenu(UI.menu.display.topMenu,menuLabel,'Remove DC from signal',menuSelectedFcn,@removeDC);
UI.menu.display.ShowChannelNumbers = uimenu(UI.menu.display.topMenu,menuLabel,'Show channel numbers',menuSelectedFcn,@ShowChannelNumbers);
%UI.menu.display.columnTraces = uimenu(UI.menu.display.topMenu,menuLabel,'Multiple columns',menuSelectedFcn,@columnTraces);
UI.menu.display.changeColormap = uimenu(UI.menu.display.topMenu,menuLabel,'Change colormap of ephys traces',menuSelectedFcn,@changeColormap,'Separator','on');
UI.menu.display.changeBackgroundColor = uimenu(UI.menu.display.topMenu,menuLabel,'Change background/xtick color',menuSelectedFcn,@changeBackgroundColor);
UI.menu.display.ShowHideMenu = uimenu(UI.menu.display.topMenu,menuLabel,'Show full menu','Separator','on',menuSelectedFcn,@ShowHideMenu);
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,'Accelerator','V','Separator','on');
uimenu(UI.menu.help.topMenu,menuLabel,'Tutorial on metadata',menuSelectedFcn,@openWebsite,'Separator','on');
uimenu(UI.menu.help.topMenu,menuLabel,'Documentation on session metadata',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',@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',@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','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',60);
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.uitabgroup_channels.TabNames = {'Groups', 'Channels','Regions'};
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);
% 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.xtickColor,'TickLength',[0.005, 0.001],'XMinorTick','on',,'Clipping','off');
UI.panel.channelTagsButtons = uipanel('Parent',UI.panel.general.main,'title','Session metadata');
uicontrol('Parent',UI.panel.channelTagsButtons,'Style','pushbutton','Units','normalized','Position',[0.01 0.01 0.485 0.98],'String','Save','Callback',@buttonsChannelTags,'KeyPressFcn', @keyPress,'tooltip','Save session metadata');
uicontrol('Parent',UI.panel.channelTagsButtons,'Style','pushbutton','Units','normalized','Position',[0.505 0.01 0.485 0.98],'String','View','Callback',@buttonsElectrodeGroups,'KeyPressFcn', @keyPress,'tooltip','View session metadata');
% Intan
UI.panel.intan.main = uipanel('Title','Intan data','Position',[0 0.2 1 0.1],'Units','normalized','Parent',UI.panel.general.main);
UI.panel.intan.showAnalog = uicontrol('Parent',UI.panel.intan.main,'Style','checkbox','Units','normalized','Position',[0 0.75 1 0.25], 'value', 0,'String','Show analog','Callback',@showIntan,'KeyPressFcn', @keyPress,'tooltip','Show analog data');
UI.panel.intan.filenameAnalog = uicontrol('Parent',UI.panel.intan.main,'Style', 'Edit', 'String', 'analogin.dat', 'Units','normalized', 'Position', [0.5 0.75 0.49 0.24],'Callback',@showIntan,'HorizontalAlignment','left','tooltip','Filename of analog file','Enable','off');
UI.panel.intan.showAux = uicontrol('Parent',UI.panel.intan.main,'Style','checkbox','Units','normalized','Position',[0 0.5 1 0.25], 'value', 0,'String','Show aux','Callback',@showIntan,'KeyPressFcn', @keyPress,'tooltip','Show aux data');
UI.panel.intan.filenameAux = uicontrol('Parent',UI.panel.intan.main,'Style', 'Edit', 'String', 'auxiliary.dat', 'Units','normalized', 'Position', [0.5 0.5 0.49 0.24],'Callback',@showIntan,'HorizontalAlignment','left','tooltip','Filename of analog file','Enable','off');
UI.panel.intan.showDigital = uicontrol('Parent',UI.panel.intan.main,'Style','checkbox','Units','normalized','Position',[0 0.25 1 0.25], 'value', 0,'String','Show digital','Callback',@showIntan,'KeyPressFcn', @keyPress,'tooltip','Show digital data');
UI.panel.intan.filenameDigital = uicontrol('Parent',UI.panel.intan.main,'Style', 'Edit', 'String', 'digitalin.dat', 'Units','normalized', 'Position', [0.5 0.25 0.49 0.24],'Callback',@showIntan,'HorizontalAlignment','left','tooltip','Filename of analog file','Enable','off');
UI.panel.intan.showIntanBelowTrace = uicontrol('Parent',UI.panel.intan.main,'Style','checkbox','Units','normalized','Position',[0 0 0.5 0.25], 'value', 0,'String','Below traces','Callback',@showIntanBelowTrace,'KeyPressFcn', @keyPress,'tooltip','Show intan data below traces');
uicontrol('Parent',UI.panel.intan.main,'Style','pushbutton','Units','normalized','Position',[0.5 0 0.49 0.24],'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 50 120],'MinimumHeights',[65 210 100 35 100 35 50 30 50 120]);
% % % % % % % % % % % % % % % % % % % % % %
% 2. PANEL: Spikes related metrics
% Spikes
UI.panel.spikes.main = uipanel('Parent',UI.panel.spikedata.main,'title','Spikes');
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 0.3 0.3],'HorizontalAlignment','left');
UI.panel.spikes.setSpikesGroupColors = uicontrol('Parent',UI.panel.spikes.main,'Style', 'popup', 'String', {'UID','White'}, 'Units','normalized', 'Position', [0.3 0.34 0.69 0.32],'HorizontalAlignment','left','Enable','off','Callback',@setSpikesGroupColors);
uicontrol('Parent',UI.panel.spikes.main,'Style', 'text', 'String', ' Y-data: ', 'Units','normalized', 'Position', [0.0 0.01 0.3 0.3],'HorizontalAlignment','left');
UI.panel.spikes.setSpikesYData = uicontrol('Parent',UI.panel.spikes.main,'Style', 'popup', 'String', {''}, 'Units','normalized', 'Position', [0.3 0.01 0.69 0.32],'HorizontalAlignment','left','Enable','off','Callback',@setSpikesYData);
% Cell metrics
UI.panel.cell_metrics.main = uipanel('Parent',UI.panel.spikedata.main,'title','Cell metrics');
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 (below traces)','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','Fast backward in time','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)']);
% KiloSort
UI.panel.kilosort.main = uipanel('Title','Kilosort','Position',[0 0.2 1 0.1],'Units','normalized','Parent',UI.panel.spikedata.main);
UI.panel.kilosort.showKilosort = uicontrol('Parent',UI.panel.kilosort.main,'Style','checkbox','Units','normalized','Position',[0.01 0 0.485 1], 'value', 0,'String','Show spikes','Callback',@showKilosort,'KeyPressFcn', @keyPress,'tooltip','Open a KiloSort rez.mat data and show detected spikes');
UI.panel.kilosort.kilosortBelowTrace = uicontrol('Parent',UI.panel.kilosort.main,'Style','checkbox','Units','normalized','Position',[0.505 0 0.485 1], 'value', 0,'String','Below traces','Callback',@showKilosort,'KeyPressFcn', @keyPress,'tooltip','Open a KiloSort rez.mat data and show detected spikes');
% Defining flexible panel heights
set(UI.panel.spikedata.main, 'Heights', [95 170 100 -200 35 100 45],'MinimumHeights',[95 170 60 60 35 60 45]);
% % % % % % % % % % % % % % % % % % % % % %
% 3. PANEL: Other datatypes
% Events
UI.panel.events.navigation = uipanel('Parent',UI.panel.other.main,'title','Events');
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');
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');
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');
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');
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','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');
% Defining flexible panel heights
set(UI.panel.other.main, 'Heights', [200 95 95 140 95],'MinimumHeights',[220 100 100 150 150]);
% % % % % % % % % % % % % % % % % % % % % %
% 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);
uicontrol('Parent',UI.panel.info,'Style', 'text', 'String', ' Scaling', 'Units','normalized', 'Position', [0.0 0 0.05 0.8],'HorizontalAlignment','center');
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 60 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.xtickColor,'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;
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
% Spike data
if UI.settings.showSpikes
plotSpikeData(t0,t0+UI.settings.windowDuration,'w')
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,'w','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',data.session.extracellular.sr)
end
% Intan aux
if UI.settings.intan_showAux
plotAnalog('aux',data.session.extracellular.sr)
end
% Intan digital
if UI.settings.intan_showDigital
plotDigital('dig',data.session.extracellular.sr)
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,'w')
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 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;
MsgLog('Failed to load LFP data',4);
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;
MsgLog('Failed to load raw data',4);
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],'int16'))'*UI.settings.leastSignificantBit;
ephys.loaded = true;
catch
UI.settings.stream = false;
warning('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],'int16'))'*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],'int16'))'*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],'int16'))'*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) && ~int_gt_0(UI.settings.filter.higherBand)
[b1, a1] = butter(3, UI.settings.filter.higherBand/sr*2, 'low');
elseif int_gt_0(UI.settings.filter.higherBand) && ~int_gt_0(UI.settings.filter.lowerBand)
[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.plotStyle == 1
% Low sampled values (Faster plotting)
for iShanks = UI.settings.electrodeGroupsToPlot
channels = UI.channels{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',colors(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 = UI.settings.electrodeGroupsToPlot
tist = [];
timeLine = [];
channels = UI.channels{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',colors(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 = UI.settings.electrodeGroupsToPlot
channels = UI.channels{iShanks};
if ~isempty(channels)
line(UI.plot_axis1,timeLine,ephys.traces(:,channels)-UI.channelOffset(channels),'color',colors(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)];
else
raster.y = [raster.y;ephys.traces(idx,i)-UI.channelScaling(idx,i)];
end
end
end
if UI.settings.showSpikes
markerType = 'o';
else
markerType = UI.settings.rasterMarker;
end
line(raster.x/size(ephys.traces,1)*UI.settings.windowDuration, raster.y,'Marker',markerType,'LineStyle','none','color','w', 'HitTest','off','linewidth',UI.settings.spikeRasterLinewidth);
end
% Detecting and plotting events
if UI.settings.detectEvents && ~isempty(UI.channelOrder)
raster = [];
raster.x = [];
raster.y = [];
for i = 1:size(ephys.traces,2)
if UI.settings.eventThreshold>0
idx = find(diff(ephys.traces(:,i)/(UI.settings.scalingFactor/1000000) > UI.settings.eventThreshold)==1);
else
idx = find(diff(ephys.traces(:,i)/(UI.settings.scalingFactor/1000000) < UI.settings.eventThreshold)==1);
end
if ~isempty(idx)
raster.x = [raster.x;idx];
raster.y = [raster.y;ephys.traces(idx,i)-UI.channelScaling(idx,i)];
end
end
[~,ia] = sort(UI.channelOrder);
ia = -0.9*((ia-1)/(numel(UI.channelOrder)-1))-0.05+1;
ia2 = 1:data.session.extracellular.nChannels;
isx = find(ismember(ia2,[UI.channels{UI.settings.electrodeGroupsToPlot}]));
ia2(isx) = ia;
line(raster.x/size(ephys.traces,1)*UI.settings.windowDuration, raster.y,'Marker',UI.settings.rasterMarker,'LineStyle','none','color','m', 'HitTest','off');
end
% Plotting channel numbers
if UI.settings.showChannelNumbers
if UI.settings.plotStyle < 5
text(-0.001*UI.settings.windowDuration*ones(1,numel(UI.channelOrder)),ephys.traces(1,UI.channelOrder)-UI.channelOffset(UI.channelOrder),cellstr(num2str(UI.channelOrder')),'color','w','VerticalAlignment', 'middle','HorizontalAlignment','right','HitTest','off')
else
text(-0.001*UI.settings.windowDuration*ones(1,numel(UI.channelOrder)),-UI.channelOffset(UI.channelOrder),cellstr(num2str(UI.channelOrder')),'color','w','VerticalAlignment', 'middle','HorizontalAlignment','right','HitTest','off')
end
end
ephys.plotted = true;
end
function plotAnalog(signal,sr)
% Plotting analog traces
if strcmp(UI.settings.fileRead,'bof')
fseek(UI.fid.timeSeries.(signal),round(t0*sr)*data.session.timeSeries.(signal).nChannels*2,'bof'); % eof: end of file
else
fseek(UI.fid.timeSeries.(signal),ceil(-UI.settings.windowDuration*sr)*data.session.timeSeries.(signal).nChannels*2,'eof'); % eof: end of file
end
traces_analog = fread(UI.fid.timeSeries.(signal), [data.session.timeSeries.(signal).nChannels, UI.samplesToDisplay],'uint16')';
if UI.settings.showIntanBelowTrace
line((1:UI.nDispSamples)/UI.nDispSamples*UI.settings.windowDuration,traces_analog(UI.dispSamples,:)./2^16*diff(UI.dataRange.intan)+UI.dataRange.intan(1), 'HitTest','off','Marker','none','LineStyle','-','linewidth',1);
else
line((1:UI.nDispSamples)/UI.nDispSamples*UI.settings.windowDuration,traces_analog(UI.dispSamples,:)./2^16, 'HitTest','off','Marker','none','LineStyle','-','linewidth',1.5);
end
for i = 1:data.session.timeSeries.(signal).nChannels
text(UI.settings.windowDuration*(1-1/400),0.005+(UI.settings.textOffset+i-1)*0.012+UI.dataRange.intan(1),UI.settings.traceLabels.(signal){i},'color',UI.colorLine(i,:),'FontWeight', 'Bold','BackgroundColor',[0 0 0 0.7],'VerticalAlignment', 'bottom','Units','normalized','HorizontalAlignment','right','HitTest','off')
end
UI.settings.textOffset = UI.settings.textOffset + data.session.timeSeries.(signal).nChannels;
end
function plotDigital(signal,sr)
% Plotting digital traces
if strcmp(UI.settings.fileRead,'bof')
fseek(UI.fid.timeSeries.(signal),round(t0*sr)*2,'bof');
else
fseek(UI.fid.timeSeries.(signal),ceil(-UI.settings.windowDuration*sr)*2,'eof');
end
traces_digital = fread(UI.fid.timeSeries.(signal), [UI.samplesToDisplay],'uint16')';
traces_digital2 = [];
for i = 1:data.session.timeSeries.dig.nChannels
traces_digital2(:,i) = bitget(traces_digital,i)+i*0.001;
end
if UI.settings.showIntanBelowTrace
line((1:UI.nDispSamples)/UI.nDispSamples*UI.settings.windowDuration,0.98*traces_digital2(UI.dispSamples,:)*diff(UI.dataRange.intan)+UI.dataRange.intan(1)+0.004, 'HitTest','off','Marker','none','LineStyle','-');
else
line((1:UI.nDispSamples)/UI.nDispSamples*UI.settings.windowDuration,0.98*traces_digital2(UI.dispSamples,:)+0.005, 'HitTest','off','Marker','none','LineStyle','-');
end
for i = 1:data.session.timeSeries.(signal).nChannels
text(UI.settings.windowDuration*(1-1/400),0.005+(UI.settings.textOffset+i-1)*0.012+UI.dataRange.intan(1),UI.settings.traceLabels.(signal){i},'color',UI.colorLine(i,:),'FontWeight', 'Bold','BackgroundColor',[0 0 0 0.7],'VerticalAlignment', 'bottom','Units','normalized','HorizontalAlignment','right','HitTest','off')