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NewImageAnalysis_MWLab.m
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NewImageAnalysis_MWLab.m
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function hIA = NewImageAnalysis_MWLab(varargin)
% hIA = ImageAnalysis_MWLab(varargin)
% GUI for Flourescence Microscopy Image Analysis
% hIA is the GUI figure handle, data is stored as hIA.UserData.IAdata
% if varargin is empty, just opens the GUI
% else, varargin{1} must be mwfile struct (see loadFile_MWLab.m for more info)
%
% EXAMPLE:
% ImageAnalysis_MWLab(mwfile)
%% -------------------------------------------------------------------------
% Created/ Last Edited by:
% Thomas Rust: March, 2019 (Updated to include deltaF movie options and odortrials selection)
% -------------------------------------------------------------------------
% Notes:
% -The current version is designed to load only 1 image stack (or average of selected images)
% in order to reduce the memory load due to some large(>5GB) data files
% -Global variables have been eliminated. Data is stored/updated as hIA.UserData.IAdata (hIA=gcf;)
% -Select multiple files after clicking TimeSeries data or MapsData, or use batch script
%
% Suggestions for future work:
% -update code to an object-oriented programming style
% -improve where to send mouse focus after <enter> or <tab> key press in uicontrols
% -add/move some features to the menubar (e.g. batch functions)
% -add back in an auto ROI feature (Scanbox method, CellSort1.0 or other)
% -create an hdf5 file type specific to our lab
%
% -------------------------------------------------------------------------
%%
% Close previous
tmppath=which('NewImageAnalysis_MWLab');
[guipath,guiname,~]=fileparts(tmppath);
pathparts=strsplit(guipath,filesep);
figurename = [pathparts{end} '/' guiname];
prev = findobj('Name',figurename);
if ~isempty(prev); close(prev); end
typestr = getdatatypes;
cmapstrings = getcmaps;
auxstr = [getauxtypes; 'none selected'];
%load previous settings file
try
load(fullfile(guipath,'newIAsettings.mat'),'-mat','IAsettings');
catch
end
if ~exist('IAsettings','var')
getDefaultSettings;
end
function getDefaultSettings
IAsettings.figpos = [0.1 0.05 0.8 0.85];
IAsettings.divXpos = 0.29;
IAsettings.pathstr = '.';
IAsettings.datatypeval = 1;
IAsettings.brightpct = 0.1;
IAsettings.lpf_radius = 0.75;
IAsettings.dispmodeval = 1;
IAsettings.cmapval = 1;
IAsettings.fstart = 0.0;
IAsettings.fstop = 3.0;
IAsettings.fmask = 50;
IAsettings.overlaypct = 10.0;
IAsettings.auxval = 1;
IAsettings.delay = 3.0;
IAsettings.duration = 3.0;
IAsettings.interval = 10.0;
IAsettings.trials = 1;
IAsettings.avgtrialsval = 1;
IAsettings.trial_prestimtime = 3.0;
IAsettings.trial_poststimtime = 3.0;
IAsettings.map_basetimes = [-3.0 0.0];
IAsettings.map_resptimes = [0.0 3.0];
IAsettings.map_fmask = 50;
end
% Read command line arguments
IAdata.file.type = '';
IAdata.file.dir = '';
IAdata.file.name = '';
if nargin; IAdata.file = varargin{1}; end
if nargin > 1
errordlg(sprintf('Incorrect number of input arguments;\nType <help %s> for more info!',guiname));
return;
end
%%
% GUI figure setup
BGCol = [204 255 255]/255; %GUI Background Color
hIA = figure('NumberTitle','off','Name',figurename,'Units','Normalized','Position',IAsettings.figpos,...
'Color',BGCol,'CloseRequestFcn',@CB_CloseFig);
hIA.UserData.IAdata = IAdata;
set(hIA, 'DefaultAxesLineWidth', 2, 'DefaultAxesFontSize', 12); %Used by axes objects with plots
hmenu = uimenu(hIA,'Text','GUI Settings');
uimenu(hmenu,'Text','Save Settings','Callback',@CBSaveSettings);
uimenu(hmenu,'Text','Load Settings','Callback',@CBLoadSettings);
uimenu(hmenu,'Text','Default Settings','Callback',@CBDefaultSettings);
%tcr -add restore original settings
%Divider Panel - left/right adjustable
uipanel(hIA,'Tag','divider','Units','Normalized','BackgroundColor',[0.5 0.5 0.5],...
'Position',[IAsettings.divXpos 0 0.01 1],'ButtonDownFcn',@CBdivider);
%Controls Panel
fsize = 10;
hpControls = uipanel(hIA,'Tag','ControlsPanel','Units','Normalized','BackgroundColor',BGCol,...
'Position',[0 0 IAsettings.divXpos 1]);
uicontrol(hpControls,'Style','pushbutton','Units','normalized','Position',[0.05 0.95 0.3 0.04],...
'String', 'Load File', 'FontWeight', 'Bold', 'Callback', @CBloadFile);
uicontrol(hpControls,'Style','pushbutton','Units','normalized','Position',[0.4 0.95 0.3 0.04],...
'String', 'File info','FontWeight','Bold', 'Callback',@CBgetFileInfo);
uicontrol(hpControls,'Tag','channel_list','Style', 'listbox', 'Units', 'normalized', 'Position', ...
[0.75 0.95 0.2 0.04], 'String', {'channel 1'; 'channel 2'}, 'Callback', ...
@CBselectStimulus, 'Min', 1, 'Max', 2, 'Value', 1, 'Visible', 'off');
uicontrol(hpControls,'Style', 'text', 'String', 'File: ','FontSize',fsize,'Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.05 .91 .1 .02],'HorizontalAlignment','Left');
uicontrol(hpControls,'Tag','file_text','Style', 'text', 'String', IAdata.file.name,'Units','normalized', ...
'BackgroundColor', [1 1 1],'Position',[0.12 .90 .58 .04],'HorizontalAlignment' ...
,'Left', 'FontSize', fsize);
if ismember(IAdata.file.type,typestr)
IAsettings.datatypeval = find(strcmp(IAdata.file.type,typestr));
end
uicontrol(hpControls,'Tag','dataType','Style', 'popupmenu', 'Units', 'normalized', 'Position', ...
[0.72 .91 .23 .02], 'String', typestr, 'Max', 0, 'Min', 0,'Value', IAsettings.datatypeval);
%alignment
uicontrol(hpControls,'Tag','align_checkbox','Style', 'checkbox', 'Value', 0,'Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.05 0.87 0.5 0.02], 'String', 'Align Time Frames:',...
'FontSize',fsize,'Enable','on', 'Callback', @CBalign,...
'TooltipString',sprintf(['Shift selected timeframes to align with last frame of image (see alignImage_MWLab.m)\n'...
'2-channel data is currently aligned using the first channel, then results are applied to both']));
uicontrol(hpControls,'Tag','alignStart','Style', 'edit', 'String', '1','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.42 0.865 0.12 0.03],'HorizontalAlignment','Right');
uicontrol(hpControls,'Style', 'text', 'String', 'to','Units','normalized', ...
'BackgroundColor',BGCol,'Position',[0.56 0.87 0.05 0.02],'HorizontalAlignment','Left');
uicontrol(hpControls,'Tag','alignEnd','Style', 'edit', 'String', '1','Units','normalized', ...
'BackgroundColor',[1 1 1],'Position',[0.61 0.865 0.12 0.03],'HorizontalAlignment','Right');
%suppress bright pixels
uicontrol(hpControls,'Tag','suppressbright','Style', 'checkbox', 'Value', 0,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.05 0.83 0.5 0.02],'FontSize', fsize, ...
'Callback', @CBupdateMovie, 'BackgroundColor', BGCol, 'String', 'Suppress bright pixels');
uicontrol(hpControls,'Tag','brightpct','Style', 'edit', 'String', IAsettings.brightpct,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.42 0.825 0.12 0.03],'HorizontalAlignment','Right', ...
'Callback', @CBupdateMovie);
uicontrol(hpControls,'Style', 'text', 'String', '%(replace w/ local median)','Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.56 0.83 0.4 0.02],'HorizontalAlignment','Left');
%spatial filter
uicontrol(hpControls,'Tag','lpf','Style', 'checkbox', 'Value', 0,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.05 0.79 0.5 0.02],'FontSize',fsize, ...
'Callback', @CBupdateMovie, 'BackgroundColor', BGCol, 'String', 'Gauss Spatial Filter @');
uicontrol(hpControls,'Tag','lpf_radius','Style', 'edit', 'String', IAsettings.lpf_radius,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.42 0.785 0.12 0.03],'HorizontalAlignment','Right', ...
'Callback', @CBupdateMovie);
uicontrol(hpControls,'Style', 'text', 'String', 'pixels','Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.56 0.79 0.35 0.02],'HorizontalAlignment','Left');
% Display Mode
dispstr{1} = 'Mean Fluorescence Image';
dispstr{2} = 'Fluorescence Movie';
dispstr{3} = 'DeltaF Image';
dispstr{4} = 'DeltaF Movie';
dispstr{5} = '%DeltaF/FO Image';
dispstr{6} = '%DeltaF/FO Movie';
dispstr{7} = 'Overlay %DeltaF/FO Movie';
uicontrol(hpControls,'Style', 'text', 'String', 'Display: ','Units','Normalized',...
'HorizontalAlignment','Right', 'BackgroundColor',BGCol,'Fontsize',fsize,...
'Position',[0.02 0.73 0.2 0.03]);
uicontrol(hpControls,'Tag','dispmode','Style', 'popupmenu', 'Units', 'normalized', 'Position', ...
[0.22 0.745 0.32 0.02], 'String', dispstr,'Callback', @CBchangemode, ...
'Value',IAsettings.dispmodeval, 'BackgroundColor', [1 1 1],'FontSize',fsize);
% F0 window
ftimevis = 'off';
uicontrol(hpControls,'Tag','fowindow','style','text','string','F0 window (sec):','Units','Normalized',...
'Position',[0.57 0.755 0.22 0.02],'BackgroundColor',BGCol,'HorizontalAlignment','left',...
'Visible',ftimevis);
uicontrol(hpControls,'Tag','fstart','Style', 'edit', 'String', num2str(IAsettings.fstart),'Units','Normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.78 0.757 0.06 0.02],'HorizontalAlignment','Right',...
'Visible',ftimevis,'Callback',@CBupdateMovie);
uicontrol(hpControls,'Tag','fto','Style','text','String','to','Units','Normalized','Position',[0.85 0.755 0.04 0.02],...
'BackgroundColor',BGCol,'Visible',ftimevis);
uicontrol(hpControls,'Tag','fstop','Style', 'edit', 'String', num2str(IAsettings.fstop),'Units','Normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.89 0.757 0.06 0.02],'HorizontalAlignment','Right',...
'Visible',ftimevis,'Callback',@CBupdateMovie);
% F mask
fmaskvis = 'off';
uicontrol(hpControls,'Tag','fmasklabel','style','text','string','F mask:','Units','Normalized',...
'Position',[0.57 0.726 0.1 0.02],'BackgroundColor',BGCol,'HorizontalAlignment','left',...
'Visible',fmaskvis);
uicontrol(hpControls,'Tag','fmaskslider','style','slider','Units','Normalized','Position',[0.66 0.728 0.22 0.02],...
'Visible',fmaskvis,'Value',IAsettings.fmask,'Max',IAsettings.fmask*2,'Callback',@CBsetFmask);
uicontrol(hpControls,'Tag','fmaskedit','Style', 'edit', 'String', num2str(IAsettings.fmask),'Units','Normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.89 0.728 0.06 0.02],'HorizontalAlignment','Right',...
'Visible',fmaskvis,'Callback',@CBsetFmask);
% colormap
uicontrol(hpControls,'Style', 'text', 'String', 'Colormap: ','Units','normalized','HorizontalAlignment','Right', ...
'BackgroundColor',BGCol,'Fontsize',fsize,'Position',[0.02 0.685 0.2 0.03]);
uicontrol(hpControls,'Tag','cmapval','Style', 'popupmenu', 'Units', 'normalized', 'Position', ...
[0.22 0.7 0.32 0.02], 'String', cmapstrings,'Callback', @CBcmap, ...
'Value',IAsettings.cmapval, 'BackgroundColor', [1 1 1],'FontSize',fsize);
% Cmin/Cmax Thresholding Options
uicontrol(hpControls,'Tag','stack_auto','Style', 'radiobutton', 'Units', 'normalized', 'Position', ...
[0.05 0.635 0.3 0.05], 'String','<html><center>Auto Caxis<br>(0.02-99.8%)','FontWeight','Bold', ...
'FontSize',fsize, 'BackgroundColor', BGCol, 'Value', 1, 'Callback', @CBdrawFrame);
uicontrol(hpControls,'Style', 'text', 'String', 'Cmin: ','Units','normalized','FontSize',fsize, ...
'BackgroundColor',BGCol,'Position',[0.3 0.66 0.12 0.02],'HorizontalAlignment','Right');
uicontrol(hpControls,'Tag','stack_blackpix','Style', 'edit', 'String', '0','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.42 0.66 0.12 0.02],'HorizontalAlignment','Right', ...
'Callback', @CBdrawFrame, 'Enable', 'Off');
uicontrol(hpControls,'Tag','stack_min','Style', 'text', 'String', '(0)','Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.55 0.657 0.1 0.02],'HorizontalAlignment','Left');
uicontrol(hpControls,'Style', 'text', 'String', 'Cmax: ','Units','normalized','FontSize',fsize, ...
'BackgroundColor',BGCol,'Position',[0.3 0.635 0.12 0.02],'HorizontalAlignment','Right');
uicontrol(hpControls,'Tag','stack_whitepix','Style', 'edit', 'String', '1','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.42 0.635 0.12 0.02],'HorizontalAlignment','Right', ...
'Callback', @CBdrawFrame, 'Enable', 'Off');
uicontrol(hpControls,'Tag','stack_max','Style', 'text', 'String', '(0)','Units','normalized' ...
,'BackgroundColor',BGCol,'Position',[0.55 0.633 0.1 0.02],'HorizontalAlignment','Left');
% Overlay
overlayvis = 'off';
hpOverlay = uipanel(hpControls,'Tag','overlaypanel','Units','Normalized','Position', [0.65 0.62 0.3 0.1],...
'Visible',overlayvis);
uicontrol(hpOverlay,'style','text','string','Overlay %','Units','Normalized','Position',[0 0.75 .5 0.2],...
'HorizontalAlignment','center');
uicontrol(hpOverlay,'Tag','overlaypct','Style', 'edit', 'String', num2str(IAsettings.overlaypct),'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.54 0.74 .4 0.2],'HorizontalAlignment','Right','Callback',@CBoverlay);
uicontrol(hpOverlay,'Style','text','String','(or Value)','Units','normalized','Position',[0 0.55 .5 0.2]);
uicontrol(hpOverlay,'Tag','overlayval','Style', 'edit', 'String', '','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.54 0.54 .4 0.2],'HorizontalAlignment','Right','Callback',@CBoverlay);
uicontrol(hpOverlay,'Style', 'text', 'String', 'bgCmin:','Units','normalized','Position',[0 0.26 0.4 0.2],...
'HorizontalAlignment','Right');
uicontrol(hpOverlay,'Tag','overlay_blackpix','Style', 'edit', 'String', '0','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.54 0.26 0.4 0.2],'HorizontalAlignment','Right', ...
'Callback', @CBdrawFrame, 'Enable', 'Off');
uicontrol(hpOverlay,'Style', 'text', 'String', 'bgCmax:','Units','normalized','Position',[0 0.06 0.4 0.2],...
'HorizontalAlignment','Right');
uicontrol(hpOverlay,'Tag','overlay_whitepix','Style', 'edit', 'String', '1','Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.54 0.06 0.4 0.2],'HorizontalAlignment','Right', ...
'Callback', @CBdrawFrame, 'Enable', 'Off');
annotation(hpControls,'Line',[0 1],[.61 .61]);
% stimulus signal
%Aux/Stimulus
auxpanel = uipanel(hpControls,'Tag','auxPanel','Units','Normalized','Position', [0.02 0.46 0.54 0.14]);
uicontrol(auxpanel, 'Style', 'text', 'String', 'Select Auxiliary Signal:','Units','Normalized',...
'Position',[0.1 0.85 .8 0.13]);
uicontrol(auxpanel,'Tag','Aux','Style', 'popupmenu', 'Value', IAsettings.auxval, 'Units', 'normalized', ...
'Position',[0.1 0.72 .8 0.12],'String',auxstr,'FontWeight','Bold',...
'Callback',@CBselectStimulus);
uicontrol(auxpanel,'Tag','delay','Style', 'edit', 'String', IAsettings.delay,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.2 0.48 0.18 0.12],'HorizontalAlignment','Right', ...
'Callback', @CBselectStimulus, 'Visible', 'off');
uicontrol(auxpanel,'Tag','delaylabel','Style', 'text', 'String', 'Initial Delay(sec)','Units','normalized' ...
,'Position',[0.41 0.48 0.7 0.12],'HorizontalAlignment','Left', 'Visible', 'off');
uicontrol(auxpanel,'Tag','duration','Style', 'edit', 'String', IAsettings.duration,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.2 0.33 0.18 0.12],'HorizontalAlignment','Right', ...
'Callback', @CBselectStimulus, 'Visible', 'off'); %tcrtcr: if used for scanbox - enable on and backgroundcolor green
uicontrol(auxpanel,'Tag','durationlabel','Style', 'text', 'String', 'Duration(sec)','Units','normalized' ...
,'Position',[0.41 0.33 0.7 0.12],'HorizontalAlignment','Left', 'Visible', 'off');
uicontrol(auxpanel,'Tag','interval','Style', 'edit', 'String', IAsettings.interval,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.2 0.18 0.18 0.12],'HorizontalAlignment','Right', ...
'Callback', @CBselectStimulus, 'Visible', 'off');
uicontrol(auxpanel,'Tag','intervallabel','Style', 'text', 'String', 'Interval(sec)','Units','normalized' ...
,'Position',[0.41 0.18 0.7 0.12],'HorizontalAlignment','Left', 'Visible', 'off');
uicontrol(auxpanel,'Tag','trials','Style', 'edit', 'String', IAsettings.trials,'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.2 0.03 0.18 0.12],'HorizontalAlignment','Right', ...
'Callback', @CBselectStimulus, 'Visible', 'off');
uicontrol(auxpanel,'Tag','trialslabel','Style', 'text', 'String', '# Trials','Units','normalized' ...
,'Position',[0.41 0.03 0.7 0.12],'HorizontalAlignment','Left', 'Visible', 'off');
uicontrol(hpControls,'Tag','avgtrials','Style','checkbox','String','Average Selected Odor Trials',...
'FontSize',fsize,'Units','Normalized','Position',[0.05 0.43 0.54 0.025],'BackgroundColor',BGCol,...
'Value',IAsettings.avgtrialsval,'Callback',@CBselectStimulus);
% trials settings panel
trialvis = 'off'; %show this when movie modes are selected
hp_trials = uipanel(hpControls,'Tag','trials_panel','Units','Normalized','Position',[0.02 0.36 0.54 0.065],'Visible',trialvis);
uicontrol(hp_trials,'Style','text','String','Pre-stimulus time (sec):','FontSize',fsize,...
'HorizontalAlignment','right','Units','Normalized','Position',[0.05 0.5 0.65 0.4]);
uicontrol(hp_trials,'Tag','trial_prestimtime','Style', 'edit', 'String', num2str(IAsettings.trial_prestimtime),'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.75 0.55 0.2 0.4],'HorizontalAlignment','Right','Callback',@CBselectStimulus);
uicontrol(hp_trials,'Style','text','String','Post-stimulus time (sec):','FontSize',fsize,...
'HorizontalAlignment','right','Units','Normalized','Position',[0.05 0.05 0.65 0.4]);
uicontrol(hp_trials,'Tag','trial_poststimtime','Style', 'edit', 'String', num2str(IAsettings.trial_poststimtime),'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.75 0.1 0.2 0.4],'HorizontalAlignment','Right','Callback',@CBselectStimulus);
% response maps settings panel
mapvis = 'off';%show this when df map modes are selected
hp_map = uipanel(hpControls,'Tag','maps_panel','Units','Normalized','Position',[0.02 0.36 0.54 0.065],'Visible',mapvis);
uicontrol(hp_map,'style','text','string','Base times (sec):','Units','Normalized',...
'Position',[0.01 0.65 0.47 0.3],'HorizontalAlignment','right');
uicontrol(hp_map,'Tag','map_basestart','Style', 'edit', 'String', num2str(IAsettings.map_basetimes(1)),...
'Units','Normalized','BackgroundColor',[1 1 1],'Position',[0.49 0.66 0.2 0.28],'HorizontalAlignment',...
'Right','Callback',@CBselectStimulus);
uicontrol(hp_map,'Style','text','String','to','Units','Normalized','Position',[0.71 0.65 0.06 0.3]);
uicontrol(hp_map,'Tag','map_basestop','Style', 'edit', 'String', num2str(IAsettings.map_basetimes(2)),...
'Units','Normalized','BackgroundColor',[1 1 1],'Position',[0.78 0.66 0.2 0.28],'HorizontalAlignment',...
'Right','Callback',@CBselectStimulus);
uicontrol(hp_map,'style','text','string','Resp. times (sec):','Units','Normalized',...
'Position',[0.01 0.33 0.47 0.3],'HorizontalAlignment','right');
uicontrol(hp_map,'Tag','map_respstart','Style', 'edit', 'String', num2str(IAsettings.map_resptimes(1)),...
'Units','Normalized','BackgroundColor',[1 1 1],'Position',[0.49 0.34 0.2 0.28],'HorizontalAlignment',...
'Right','Callback',@CBselectStimulus);
uicontrol(hp_map,'Style','text','String','to','Units','Normalized','Position',[0.71 0.33 0.06 0.3]);
uicontrol(hp_map,'Tag','map_respstop','Style', 'edit', 'String', num2str(IAsettings.map_resptimes(2)),...
'Units','Normalized','BackgroundColor',[1 1 1],'Position',[0.78 0.34 0.2 0.28],'HorizontalAlignment',...
'Right','Callback',@CBselectStimulus);
uicontrol(hp_map,'style','text','string','F mask:','Units','Normalized',...
'Position',[0.01 0.02 0.23 0.28],'HorizontalAlignment','Right');
uicontrol(hp_map,'Tag','map_fmaskslider','style','slider','Units','Normalized','Position',[0.26 0.04 0.51 0.28],...
'Value',IAsettings.map_fmask,'Max',IAsettings.map_fmask*2,'Callback',@CBsetMapFmask);
uicontrol(hp_map,'Tag','map_fmaskedit','Style', 'edit', 'String', num2str(IAsettings.map_fmask),...
'Units','Normalized','BackgroundColor',[1 1 1],'Position',[0.78 0.04 0.2 0.28],...
'HorizontalAlignment','Right','Callback',@CBsetMapFmask);
uicontrol(hpControls,'Tag','odortrialslist','style','listbox','Units','normalized',...
'Position',[0.58 0.36 0.4 0.24],'Callback',@CBupdateMovie);
annotation(hpControls,'Line',[0 1],[.35 .35]);
% ROIs
%ROIs Listbox & Tools
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.05 0.29 0.25 0.04],...
'String', 'Load ROIs','FontWeight','Bold', 'Callback', @CBloadROIs);
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.30 0.29 0.25 0.04],...
'String', 'Draw ROI', 'FontWeight', 'Bold', 'Callback', @CBdrawROI);
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.05 0.25 0.25 0.04],...
'String', 'Delete ROI(s)','FontWeight','Bold', 'Callback', @CBdeleteROIs);
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.30 0.25 0.25 0.04],...
'String', 'Shift ROI(s)', 'Fontweight', 'Bold', 'Callback', @CBshiftROIsButton_fcn);
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.05 0.21 0.25 0.04],...
'String', 'Save All ROIs','FontWeight','Bold', 'Callback', @CBsaveROI_button_fcn);
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.30 0.21 0.25 0.04],...
'String', 'Clear All ROIs','FontWeight','Bold', 'Callback', @CBclearROIs);
uicontrol(hpControls,'Tag','bgsubtract','Style','checkbox','String','Subtract Background ROI #',...
'FontSize',fsize,'Units','Normalized','Position',[0.05 0.17 0.45 0.02],'BackgroundColor',BGCol,...
'Callback',@CBupdateMovie);
uicontrol(hpControls,'Tag','bgroi','Style', 'edit', 'Units','normalized' ...
,'BackgroundColor',[1 1 1],'Position',[0.49 0.17 0.06 0.025],'HorizontalAlignment','Right',...
'Callback',@CBupdateMovie);
uicontrol(hpControls,'Tag','roisoverlay','Style','checkbox','String','Show ROI(s) Overlay',...
'FontSize',fsize,'Units','Normalized','Position',[0.05 0.14 0.45 0.02],'BackgroundColor',BGCol,...
'Callback',@CBoverlayROIs);
uicontrol(hpControls,'Tag','roisplot','Style','checkbox','String','Show ROI(s) Time Series',...
'FontSize',fsize,'Units','Normalized','Position',[0.05 0.11 0.5 0.02],'BackgroundColor',BGCol,...
'Callback',@CBchangemode);
uicontrol(hpControls,'Tag','roi_listbox','Style', 'listbox', 'Units', 'normalized', 'Position', ...
[0.58 0.1 0.4 0.24], 'Value', 1, 'BackgroundColor', [1 1 1], 'Max', 100,...
'Min', 0, 'FontSize',10,'Callback',@CBoverlayROIs);
annotation(hpControls,'Line',[0 1],[.09 .09]);
% MapsAnalysis
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.03 0.02 0.3 0.05],...
'String','<html><center>Maps Analysis', 'FontWeight','Bold','Callback', @CBmapsAnalysis, ...
'TooltipString',sprintf(['Creates Maps Data using current auxiliary signal, baseline, '...
'and response time windows and runs MapsAnalysis_MWLab.\n']));
% TimeSeriesAnalysis
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.35 0.02 0.3 0.05], ... %.585
'String','Time Series Analysis', 'FontWeight','Bold','Callback', @CBTimeSeriesAnalysis, ...
'TooltipString',sprintf('Creates TimeSeriesAnalysis_MWLab data. Image filters are not applied.'));
uicontrol(hpControls,'Style', 'pushbutton', 'Units', 'normalized', 'Position', [0.67 0.02 0.3 0.05], ...
'String','Save Image/Movie', 'FontWeight','Bold','Callback', @CBsaveImageMovie);
% Movie Panel - always show image; show movie controls when needed; show time series plot when needed.
hpMovie = uipanel(hIA,'Tag','MoviePanel','Units','Normalized','BackgroundColor',[0 0 0],...
'Position', [IAsettings.divXpos+.01 0 0.99-IAsettings.divXpos(1) 1]);
axes(hpMovie,'Tag','fPlotAx','Position',[0.01 0.82 .98 0.18],'Color',[0 0 0]); xticks([]);yticks([]);
axes(hpMovie,'Tag','MovieAx','Position',[0.0 0.1 1 0.7],'Color',[0 0 0]); xticks([]);yticks([]);
%Play movie controls
hpPlay = uipanel(hpMovie,'Tag','PlayPanel','Units','Normalized','BackgroundColor',[0 0 0],...
'Position',[0 0 1 .1]);
uicontrol(hpPlay,'Tag','play_button','Style', 'togglebutton', 'Units', 'normalized', 'Position', ...
[0.02 0.2 .1 0.6], 'String', 'Play','FontWeight','Bold', 'FontSize',14,'Callback', ...
@CBplayMovie, 'Min', 0, 'Max', 1, 'Value', 0);
uicontrol(hpPlay,'Tag','speedcontrol','Style', 'checkbox', 'String', 'Speed Control','Units','normalized' ...
,'ForegroundColor',[1 1 1],'BackgroundColor',[0 0 0],'Position',[0.14 0.6 .14 0.3],'HorizontalAlignment', ...
'Left', 'FontSize', 11, 'FontWeight', 'normal');
uicontrol(hpPlay,'Tag','speedslider','Style','slider','min',1,'max',100,'value',50,'sliderstep',[1/99 1/99],...
'Units','normalized','Position',[0.14 0.2 .14 0.3]);
uicontrol(hpPlay,'Tag','frame_slider','Style', 'Slider', 'Units', 'normalized', 'Position', ...
[0.3 0.55 .68 0.3], 'Min', 1, 'Max', 1.4, 'Value', 1, 'SliderStep', [1 1], ...
'Callback', @CBframeSlider, 'BackgroundColor', [1 1 1]);
uicontrol(hpPlay,'Tag','frame_text','Style', 'text', 'String', 'Frame #:','Units','normalized' ...
,'ForegroundColor',[1 1 1],'BackgroundColor',[0 0 0],'Position',[0.30 0.1 .23 .3],'HorizontalAlignment','Left','FontSize',fsize);
uicontrol(hpPlay,'Tag','frameRate_text','Style', 'text', 'String', 'FrameRate:','Units','normalized' ...
,'ForegroundColor',[1 1 1],'BackgroundColor',[0 0 0],'Position',[0.53 0.1 .23 .3],'HorizontalAlignment','Left','FontSize',fsize);
uicontrol(hpPlay,'Tag','duration_text','Style', 'text', 'String', 'Duration:','Units','normalized' ...
,'ForegroundColor',[1 1 1],'BackgroundColor',[0 0 0],'Position',[0.76 0.1 .23 .3],'HorizontalAlignment','Left','FontSize',fsize);
% Update GUI if data is loaded
CBchangemode;
%% Nested Callback functions
function CB_CloseFig(~,~)
%save settings file
getSettings;
save(fullfile(guipath,'newIAsettings.mat'),'IAsettings');
delete(hIA);
end
function CBSaveSettings(~, ~)
getSettings;
[setfile,setpath] = uiputfile(fullfile(guipath,'myIAsettings.mat'));
save(fullfile(setpath,setfile),'IAsettings');
end
function getSettings
IAsettings.figpos = hIA.Position;
divpos = get(findobj(hIA,'Tag','divider'),'Position');
IAsettings.divXpos = divpos(1);
IAsettings.pathstr = hIA.UserData.IAdata.file.dir;
IAsettings.datatypeval = get(findobj(hIA,'Tag','dataType'),'Value');
IAsettings.brightpct = str2double(get(findobj(hIA,'Tag','brightpct'),'string'));
IAsettings.lpf_radius = str2double(get(findobj(hIA,'Tag','lpf_radius'),'String'));
IAsettings.dispmodeval = get(findobj(hIA,'Tag','dispmode'), 'Value');
IAsettings.cmapval = get(findobj(hIA,'Tag','cmapval'), 'Value');
IAsettings.fstart = str2double(get(findobj(hIA,'Tag','fstart'),'String'));
IAsettings.fstop = str2double(get(findobj(hIA,'Tag','fstop'),'String'));
IAsettings.fmask = str2double(get(findobj(hIA,'Tag','fmaskedit'),'String'));
IAsettings.overlaypct = str2double(get(findobj(hIA,'Tag','overlaypct'),'String'));
IAsettings.auxval = get(findobj(hIA,'Tag','Aux'),'Value');
IAsettings.delay = str2double(get(findobj(hIA,'Tag','delay'),'String'));
IAsettings.duration = str2double(get(findobj(hIA,'Tag','duration'),'String'));
IAsettings.interval = str2double(get(findobj(hIA,'Tag','interval'),'String'));
IAsettings.trials = str2double(get(findobj(hIA,'Tag','trials'),'String'));
IAsettings.avgtrialsval = get(findobj(hIA,'Tag','avgtrials'),'Value');
IAsettings.trial_prestimtime = str2double(get(findobj(hIA,'Tag','trial_prestimtime'),'String'));
IAsettings.trial_poststimtime =str2double(get(findobj(hIA,'Tag','trial_poststimtime'),'String'));
IAsettings.map_basetimes(1) = str2double(get(findobj(hIA,'Tag','map_basestart'),'String'));
IAsettings.map_basetimes(2) = str2double(get(findobj(hIA,'Tag','map_basestop'),'String'));
IAsettings.map_resptimes(1) = str2double(get(findobj(hIA,'Tag','map_respstart'),'String'));
IAsettings.map_resptimes(2) = str2double(get(findobj(hIA,'Tag','map_respstop'),'String'));
IAsettings.map_fmask = str2double(get(findobj(hIA,'Tag','map_fmaskedit'),'String'));
end
function setSettings
hIA.Position = IAsettings.figpos;
divpos = get(findobj(hIA,'Tag','divider'),'Position'); divpos(1) = IAsettings.divXpos;
set(findobj(hIA,'Tag','divider'),'Position',divpos);
set(findobj(hIA,'Tag','dataType'),'Value',IAsettings.datatypeval);
set(findobj(hIA,'Tag','brightpct'),'string',num2str(IAsettings.brightpct));
set(findobj(hIA,'Tag','lpf_radius'),'String',num2str(IAsettings.lpf_radius));
set(findobj(hIA,'Tag','dispmode'), 'Value',IAsettings.dispmodeval);
set(findobj(hIA,'Tag','cmapval'), 'Value',IAsettings.cmapval);
set(findobj(hIA,'Tag','fstart'),'String',num2str(IAsettings.fstart));
set(findobj(hIA,'Tag','fstop'),'String',num2str(IAsettings.fstop));
set(findobj(hIA,'Tag','fmaskedit'),'String',num2str(IAsettings.fmask));
set(findobj(hIA,'Tag','overlaypct'),'String',num2str(IAsettings.overlaypct));
set(findobj(hIA,'Tag','Aux'),'Value',IAsettings.auxval);
set(findobj(hIA,'Tag','delay'),'String',num2str(IAsettings.delay));
set(findobj(hIA,'Tag','duration'),'String',num2str(IAsettings.duration));
set(findobj(hIA,'Tag','interval'),'String',num2str(IAsettings.interval));
set(findobj(hIA,'Tag','trials'),'String',num2str(IAsettings.trials));
set(findobj(hIA,'Tag','avgtrials'),'Value',IAsettings.avgtrialsval);
set(findobj(hIA,'Tag','trial_prestimtime'),'String',num2str(IAsettings.trial_prestimtime));
set(findobj(hIA,'Tag','trial_poststimtime'),'String',num2str(IAsettings.trial_poststimtime));
set(findobj(hIA,'Tag','map_basestart'),'String',num2str(IAsettings.map_basetimes(1)));
set(findobj(hIA,'Tag','map_basestop'),'String',num2str(IAsettings.map_basetimes(2)));
set(findobj(hIA,'Tag','map_respstart'),'String',num2str(IAsettings.map_resptimes(1)));
set(findobj(hIA,'Tag','map_respstop'),'String',num2str(IAsettings.map_resptimes(2)));
set(findobj(hIA,'Tag','map_fmaskedit'),'String',num2str(IAsettings.map_fmask));
set(findobj(hIA,'Tag','map_fmaskslider'),'Value',IAsettings.map_fmask);
CBselectStimulus;
end
function CBLoadSettings(~, ~)
[setfile,setpath] = uigetfile(fullfile(guipath,'*.mat'));
try
load(fullfile(setpath,setfile),'-mat','IAsettings');
if isempty(hIA.UserData.IAdata.file) || isempty(hIA.UserData.IAdata.file(1).dir)
set(findobj(hIA,'Tag','dataType'),'Value',IAsettings.datatypeval);
end
val = IAsettings.cmapval; set(findobj(hIA,'Tag','cmapval'), 'Value',val); CBcmap;
set(findobj(hIA,'Tag','fig_bright'),'String',num2str(IAsettings.brightpct));
setSettings;
catch
end
end
function CBDefaultSettings(~,~)
getDefaultSettings;
setSettings;
end
function CBdivider(~,~)
set(hIA,'WindowButtonMotionFcn',@paneldrag,'WindowButtonUpFcn',@paneldrop);
end
function paneldrag(~,~)
divpos = get(findobj(hIA,'Tag','divider'),'Position');
pt = get(hIA,{'CurrentPoint','Position'});
try
set(findobj(hIA,'Tag','divider'),'Position',[pt{1}(1) 0 0.01 1]);
set(hpControls,'Position',[0 0 divpos(1) 1]);
set(hpMovie,'Position',[divpos(1)+.01 0 0.99-divpos(1) 1]);
catch
end
IAsettings.divXpos = pt{1}(1);
end
function paneldrop(~,~)
divpos = get(findobj(hIA,'Tag','divider'),'Position');
IAsettings.divXpos = divpos(1);
set(hIA, 'WindowButtonMotionFcn', [], 'WindowButtonUpFcn', [])
end
function CBloadFile(~, ~) %load image(s), average if > 1
hIA.UserData.IAdata.file.type = ''; hIA.UserData.IAdata.file.dir = ''; hIA.UserData.IAdata.file.name = '';
hIA.UserData.IAdata.file.type = typestr{get(findobj(hIA,'Tag','dataType'),'Value')};
try
hIA.UserData.IAdata.file = loadFile_MWLab(hIA.UserData.IAdata.file.type,IAsettings.pathstr);
if iscell(hIA.UserData.IAdata.file.im) %image is a cell if 2-channels are present!
set(findobj(hIA,'Tag','channel_list'),'Visible','on');
set(findobj(hIA,'Tag','channel_list'),'Value',1);
else; set(findobj(hIA,'Tag','channel_list'),'Visible','off');
end
if ~isfield(hIA.UserData.IAdata.file,'aux1') || isempty(hIA.UserData.IAdata.file.aux1)
if max(get(findobj(hIA,'Tag','Aux'),'Value') == [1,3])
set(findobj(hIA,'Tag','Aux'),'Value', numel(get(findobj(hIA,'Tag','Aux'),'String')));
end
end
if ~isfield(hIA.UserData.IAdata.file,'aux2') && ~isempty(hIA.UserData.IAdata.file.aux2)
if max(get(findobj(hIA,'Tag','Aux'),'Value') == [2,3])
set(findobj(hIA,'Tag','Aux'),'Value', numel(get(findobj(hIA,'Tag','Aux'),'String')));
end
end
IAsettings.pathstr = hIA.UserData.IAdata.file.dir;
set(findobj(hIA,'Tag','alignStart'),'String','1');
set(findobj(hIA,'Tag','alignEnd'),'String',num2str(size(hIA.UserData.IAdata.file.im,3)));
if get(findobj(hpControls,'Tag','align_checkbox'),'Value'); CBalign; end
set(findobj(hpControls,'Tag','file_text'),'String',hIA.UserData.IAdata.file.name);
%auto-turn on avg trials for "large" datasets
if hIA.UserData.IAdata.file.frames>500; set(findobj(hpControls,'Tag','avgtrials'),'Value',1); end
if isfield(hIA.UserData.IAdata,'roi') && ~isempty(hIA.UserData.IAdata.roi)
if ~isequal(size(hIA.UserData.IAdata.roi(1).mask),hIA.UserData.IAdata.file.size)
CBclearROIs;
end
end
catch
return
end
CBselectStimulus;
end
function CBgetFileInfo(~,~) %calls external program to find image info from header and/or .txt files
if isempty(hIA.UserData.IAdata.file); return; end
getFileInfo(hIA.UserData.IAdata.file.type,hIA.UserData.IAdata.file.dir,hIA.UserData.IAdata.file.name);
end
function CBalign(~,~)
if ~isfield(hIA.UserData.IAdata,'file') || isempty(hIA.UserData.IAdata.file.im)
set(findobj(hIA,'Tag','align_checkbox'),'Value',0);
return;
end
if get(findobj(hIA,'Tag','align_checkbox'),'value')
startF = str2double(get(findobj(hIA,'Tag','alignStart'),'String'));
endF = str2double(get(findobj(hIA,'Tag','alignEnd'),'String'));
%compute alignment and save .align file... or use existing file
hIA.UserData.IAdata.file = alignImage_MWLab(hIA.UserData.IAdata.file,startF:endF);
else
hIA.UserData.IAdata.file = loadFile_MWLab(hIA.UserData.IAdata.file.type,...
hIA.UserData.IAdata.file.dir,hIA.UserData.IAdata.file.name);
set(findobj(hIA,'Tag','align_checkbox'),'Value',0);
end
CBselectStimulus;
end
function CBchangemode(~,~)
%set(findobj(hIA,'Tag','stack_auto'),'Value',1);
if ~isfield(hIA.UserData.IAdata,'roi') || isempty(hIA.UserData.IAdata.roi)
set(findobj(hpControls,'Tag','roisoverlay'),'Value',0);
set(findobj(hpControls,'Tag','roisplot'),'Value',0);
end
%set visibility and adjust size of Image Axes for Movie Panel
modeval = get(findobj(hpControls,'Tag','dispmode'),'Value');
if max(modeval == [2 4 6 7])
if get(findobj(hpControls,'Tag','roisplot'),'Value') %show movie controls, show tsplot
set(findobj(hpMovie,'Tag','fPlotAx'),'Visible','On');
set(findobj(hpMovie,'Tag','MovieAx'),'Position',[0.0 0.1 1 0.7]);
set(findobj(hpMovie,'Tag','PlayPanel'),'Visible','On');
else %show movie controls, no tsplot
cla(findobj(hIA,'Tag','fPlotAx'));
set(findobj(hpMovie,'Tag','fPlotAx'),'Visible','Off');
set(findobj(hpMovie,'Tag','MovieAx'),'Position',[0.0 0.1 1 0.9]);
set(findobj(hpMovie,'Tag','PlayPanel'),'Visible','On');
end
else %no movie controls, no tsplot
set(findobj(hpControls,'Tag','roisplot'),'Value',0);
cla(findobj(hIA,'Tag','fPlotAx'));
set(findobj(hpMovie,'Tag','fPlotAx'),'Visible','Off');
set(findobj(hpMovie,'Tag','MovieAx'),'Position',[0.0 0.0 1 1]);
set(findobj(hpMovie,'Tag','PlayPanel'),'Visible','Off');
end
CBselectStimulus;
end
function CBsetFmask(~,~) %applies to df movies
if ~isfield(hIA.UserData.IAdata,'current') || isempty(hIA.UserData.IAdata.current); return; end
hfmaskslider = findobj(hpControls,'Tag','fmaskslider');
hfmaskedit = findobj(hpControls,'Tag','fmaskedit');
clicked = hIA.CurrentObject;
if strcmp(clicked.Tag,'fmaskslider')
tmpval = round(clicked.Value);
else %edit box value
tmpval = round(str2double(clicked.String));
if tmpval<hfmaskslider.Min; tmpval=hfmaskslider.Min; end
if tmpval>hfmaskslider.Max; tmpval=hfmaskslider.Max; end
hfmaskslider.Value = tmpval;
end
hfmaskedit.String = num2str(tmpval);
CBupdateMovie;
end
function CBsetMapFmask(~,~) %applies to df map images
if ~isfield(hIA.UserData.IAdata,'current') || isempty(hIA.UserData.IAdata.current); return; end
hmapfmaskslider = findobj(hpControls,'Tag','map_fmaskslider');
hmapfmaskedit = findobj(hpControls,'Tag','map_fmaskedit');
clicked = hIA.CurrentObject;
if strcmp(clicked.Tag,'map_fmaskslider')
tmpval = round(clicked.Value);
if tmpval<hmapfmaskslider.Min; tmpval=hmapfmaskslider.Min; end
if tmpval>hmapfmaskslider.Max; tmpval=hmapfmaskslider.Max; end
else %edit box value
tmpval = round(str2double(clicked.String));
if tmpval<hmapfmaskslider.Min; tmpval=hmapfmaskslider.Min; end
if tmpval>hmapfmaskslider.Max; tmpval=hmapfmaskslider.Max; end
end
hmapfmaskslider.Value = tmpval;
hmapfmaskedit.String = num2str(tmpval);
CBupdateMovie;
end
function CBcmap(~, ~) %change colormap
if isempty(hIA.UserData.IAdata.file); return; end
val = get(findobj(hpControls,'Tag','cmapval'), 'Value');
hAx_Movie = findobj(hpMovie,'Tag','MovieAx'); %hAx_ax2 = findobj(hIA,'Tag','ax2');
if ~isempty(hAx_Movie); axes(hAx_Movie); colormap(hAx_Movie,[cmapstrings{val} '(256)']); end
end
function CBframeSlider(~, ~)
modeval = get(findobj(hpControls,'Tag','dispmode'),'Value');
if modeval == 1; return; end
ind = get(findobj(hIA,'Tag','frame_slider'), 'Value');
ind = round(ind);
set(findobj(hIA,'Tag','frame_slider')', 'Value', ind);
set(findobj(hIA,'Tag','frame_text'),'String', sprintf('Frame # %d/%d (%0.3f Sec)',...
ind,size(hIA.UserData.IAdata.current,3),(ind-1)/hIA.UserData.IAdata.file.frameRate));
CBdrawFrame;
tmptime = [(ind-1)/hIA.UserData.IAdata.file.frameRate (ind-1)/hIA.UserData.IAdata.file.frameRate];
set(findobj(hIA,'Tag','mark'),'Xdata',tmptime);%,'Ydata',tmp(ind));
end
function CBselectStimulus(~,~)
%check that stimulus is present
if ~isfield(hIA.UserData.IAdata,'file') || ~isfield(hIA.UserData.IAdata.file,'name') || ...
isempty(hIA.UserData.IAdata.file.name); return; end
if ~isfield(hIA.UserData.IAdata.file,'aux1') || isempty(hIA.UserData.IAdata.file.aux1) || ...
max(hIA.UserData.IAdata.file.aux1.signal)==0
if max(get(findobj(hIA,'Tag','Aux'),'Value') == [1,3])
set(findobj(hIA,'Tag','Aux'),'Value', numel(auxstr));
end
end
if ~isfield(hIA.UserData.IAdata.file,'aux2') || isempty(hIA.UserData.IAdata.file.aux2) || ...
max(hIA.UserData.IAdata.file.aux2.signal)==0
if max(get(findobj(hIA,'Tag','Aux'),'Value') == [2,3])
set(findobj(hIA,'Tag','Aux'),'Value', numel(auxstr));
end
end
if get(findobj(hIA,'Tag','Aux'),'Value')== numel(auxstr) && ...
max(get(findobj(hpControls,'Tag','dispmode'),'Value') == [3 5])
set(findobj(hpControls,'Tag','dispmode'),'Value',1);
%tcrtcrtcr might allow df w/out odortrial
disp('Select a valid stimulus signal before making maps!');
end
if get(findobj(hIA,'Tag','Aux'),'Value') == 3
odorDuration = str2double(get(findobj(hIA,'Tag','duration'),'String'));
if isnan(odorDuration) %empty string
hIA.UserData.IAdata.file.aux_combo = doAuxCombo(hIA.UserData.IAdata.file.aux1,...
hIA.UserData.IAdata.file.aux2);
else
hIA.UserData.IAdata.file.aux_combo = doAuxCombo(hIA.UserData.IAdata.file.aux1,...
hIA.UserData.IAdata.file.aux2,odorDuration);
end
elseif get(findobj(hIA,'Tag','Aux'),'Value') == 4; hIA.UserData.IAdata.file.def_stimulus = doDefineStimulus;
end
%set visibilities
if get(findobj(hIA,'Tag','Aux'),'Value') == 3 %&& get(findobj(hIA,'Tag','dataType'),'Value') == 1 %Aux_combo w/scanimage
set(findobj(hIA,'Tag','delay'),'Visible', 'off'); set(findobj(hIA,'Tag','delaylabel'),'Visible', 'off');
set(findobj(hIA,'Tag','duration'),'Visible', 'on'); set(findobj(hIA,'Tag','durationlabel'),'Visible', 'on');
set(findobj(hIA,'Tag','interval'),'Visible', 'off'); set(findobj(hIA,'Tag','intervallabel'),'Visible', 'off');
set(findobj(hIA,'Tag','trials'),'Visible', 'off'); set(findobj(hIA,'Tag','trialslabel'),'Visible', 'off');
elseif get(findobj(hIA,'Tag','Aux'),'Value') == 4 %Defined Stim
set(findobj(hIA,'Tag','delay'),'Visible', 'on'); set(findobj(hIA,'Tag','delaylabel'),'Visible', 'on');
set(findobj(hIA,'Tag','duration'),'Visible', 'on'); set(findobj(hIA,'Tag','durationlabel'),'Visible', 'on');
set(findobj(hIA,'Tag','interval'),'Visible', 'on'); set(findobj(hIA,'Tag','intervallabel'),'Visible', 'on');
set(findobj(hIA,'Tag','trials'),'Visible', 'on'); set(findobj(hIA,'Tag','trialslabel'),'Visible', 'on');
else
set(findobj(hIA,'Tag','delay'),'Visible', 'off'); set(findobj(hIA,'Tag','delaylabel'),'Visible', 'off');
set(findobj(hIA,'Tag','duration'),'Visible', 'off'); set(findobj(hIA,'Tag','durationlabel'),'Visible', 'off');
set(findobj(hIA,'Tag','interval'),'Visible', 'off'); set(findobj(hIA,'Tag','intervallabel'),'Visible', 'off');
set(findobj(hIA,'Tag','trials'),'Visible', 'off'); set(findobj(hIA,'Tag','trialslabel'),'Visible', 'off');
end
%get odortrials (timeframes/maps) and update odortrialslist
bavgtrials = get(findobj(hpControls,'Tag','avgtrials'),'Value');
modeval = get(findobj(hpControls,'Tag','dispmode'),'Value');
auxval = get(findobj(hIA,'Tag','Aux'),'Value');
if ismember(auxval, [1 2 3 4]) && max(modeval == [1 2 4 6 7]) && bavgtrials
set(findobj(hpControls,'Tag','trials_panel'),'Visible','on');
set(findobj(hpControls,'Tag','maps_panel'),'Visible','off');
% get odortrial timeframes and update odortrialslist
auxtype = auxstr{auxval};
trial_prestimtime = str2double(get(findobj(hIA,'Tag','trial_prestimtime'),'String'));
trial_poststimtime = str2double(get(findobj(hIA,'Tag','trial_poststimtime'),'String'));
hIA.UserData.IAdata.allOdorTrials = getAllOdorTrials(auxtype,trial_prestimtime,trial_poststimtime,hIA.UserData.IAdata.file);
cnt=0; trialstr = {};
odors = hIA.UserData.IAdata.allOdorTrials.odors;
for o = 1:length(odors)
trials = hIA.UserData.IAdata.allOdorTrials.odor(o).trials;
for t = trials
cnt=cnt+1;
trialstr{cnt} = ['Odor' num2str(odors(o)) 'Trial' num2str(t)];
end
end
if isempty(trialstr)
set(findobj(hpControls,'Tag','avgtrials'),'Value',0);%,'Enable','off');
set(findobj(hpControls,'Tag','odortrialslist'),'String','','Max',1);
else
set(findobj(hpControls,'Tag','odortrialslist'),'Value',1);
set(findobj(hpControls,'Tag','odortrialslist'),'String',trialstr,'Max',length(trialstr));
end
elseif ismember(auxval, [1 2 3 4]) && max(modeval == [3 5]) && bavgtrials
if isfield(hIA.UserData.IAdata,'maps'); hIA.UserData.IAdata = rmfield(hIA.UserData.IAdata,'maps'); end
set(findobj(hpControls,'Tag','trials_panel'),'Visible','off');
set(findobj(hpControls,'Tag','maps_panel'),'Visible','on');
% make maps and update odortrialslist
if iscell(hIA.UserData.IAdata.file.im)
channel = get(findobj(hIA,'Tag','channel_list'),'Value');
tmpdata = hIA.UserData.IAdata.file;
tmpdata = rmfield(tmpdata,'im');tmpdata.im = hIA.UserData.IAdata.file.im{channel};
else
tmpdata = hIA.UserData.IAdata.file;
end
auxtype = auxstr{auxval};
baseTimes(1) = str2double(get(findobj(hpControls,'Tag','map_basestart'),'String'));
baseTimes(2) = str2double(get(findobj(hpControls,'Tag','map_basestop'),'String'));
respTimes(1) = str2double(get(findobj(hpControls,'Tag','map_respstart'),'String'));
respTimes(2) = str2double(get(findobj(hpControls,'Tag','map_respstop'),'String'));
mapsdata = makeMaps(tmpdata,auxtype,baseTimes,respTimes);
clear tmpdata;
cnt=0; trialstr = {};
if ~isempty(mapsdata)
odors = mapsdata.file.odors;
for o = 1:length(mapsdata.file.odor)
for t = 1:length(mapsdata.file.odor(o).trial)
cnt=cnt+1;
trialstr{cnt} = ['Odor' num2str(odors(o)) 'Trial' num2str(t)];
end
end
hIA.UserData.IAdata.maps = mapsdata;
else
disp('error making maps... figure this out... try different settings'); %change display setting?
end
if isempty(trialstr)
set(findobj(hpControls,'Tag','avgtrials'),'Value',0);%,'Enable','off');
set(findobj(hpControls,'Tag','odortrialslist'),'String','','Max',1);
else
set(findobj(hpControls,'Tag','odortrialslist'),'Value',1);
set(findobj(hpControls,'Tag','odortrialslist'),'String',trialstr,'Max',length(trialstr));
end
else
set(findobj(hpControls,'Tag','trials_panel'),'Visible','off');
set(findobj(hpControls,'Tag','maps_panel'),'Visible','off');
set(findobj(hpControls,'Tag','avgtrials'),'Value',0);
set(findobj(hpControls,'Tag','odortrialslist'),'String','','Value',0,'Max',1);
if max(modeval == [3 5])
waitfor(errordlg('Click on <Average Selected Odor Trials> to display maps.'));
set(findobj(hpControls,'Tag','dispmode'),'Value',1);
end
end
CBupdateMovie;
end
function def_stimulus = doDefineStimulus %manually define a stimulus signal
if ~isfield(hIA.UserData.IAdata.file,'frameRate'); return; end
frames = size(hIA.UserData.IAdata.file.im,3);
delay = str2double(get(findobj(hIA,'Tag','delay'),'String')); % #frames delay
duration = str2double(get(findobj(hIA,'Tag','duration'),'String')); % #frames duration
interval = str2double(get(findobj(hIA,'Tag','interval'),'String')); % #frames interval
trials = str2double(get(findobj(hIA,'Tag','trials'),'String'));
trials = min(trials,floor((frames/hIA.UserData.IAdata.file.frameRate-delay+interval)/(duration+interval)));
set(findobj(hIA,'Tag','trials'),'String',trials);
endT = frames/hIA.UserData.IAdata.file.frameRate;
deltaT=1/150; %hardcoded: Stimulus sampling rate is set at 150Hz (lab standard)
def_stimulus = defineStimulus(0,endT,deltaT,delay,duration,interval,trials);
end
function CBupdateMovie(~,~)
IAdata = hIA.UserData.IAdata;
if ~isfield(IAdata.file,'im') || isempty(IAdata.file.im); return; end
if ~isfield(IAdata,'file') || ~isfield(IAdata.file,'im') || isempty(IAdata.file.im); return; end
if ~isfield(IAdata,'roi') || isempty(IAdata.roi)
set(findobj(hpControls,'Tag','bgsubtract'),'value',0)
end
if iscell(IAdata.file.im); channel = get(findobj(hIA,'Tag','channel_list'),'Value'); end
if get(findobj(hpControls,'Tag','bgsubtract'),'value') %background roi
RoiNum = str2double(get(findobj(hpControls,'Tag','bgroi'),'String'));
if isnan(RoiNum) || RoiNum>length(IAdata.roi)
fprintf('Background ROI # %d not found\n',RoiNum);
set(findobj(hpControls,'Tag','bgsubtract'),'Value',0);
else
BGroiIndex = IAdata.roi(RoiNum).mask>0.5;
end
end
%what to display...
modeval = get(findobj(hpControls,'Tag','dispmode'),'Value');
if max(modeval == [1 2 4 6 7])
%average selectedOdorTrials
if get(findobj(hpControls,'Tag','avgtrials'),'Value')
selected = get(findobj(hpControls,'Tag','odortrialslist'),'Value');
cnt = 0;
tmpbar = waitbar(0,'Averaging Trials');
for o = 1:length(IAdata.allOdorTrials.odor)
for t = 1:length(IAdata.allOdorTrials.odor(o).trial)
cnt = cnt+1;
if max(cnt==selected)
waitbar(cnt/length(selected),tmpbar);
tmpind = IAdata.allOdorTrials.odor(o).trial(t).imindex;
if iscell(IAdata.file.im)
tmptrial = single(IAdata.file.im{channel}(:,:,tmpind));
else
tmptrial = single(IAdata.file.im(:,:,tmpind));
end
%perform background roi subtraction (before averaging trials)
if get(findobj(hpControls,'Tag','bgsubtract'),'value') %background roi
bg=zeros(length(tmpind),1);
for i = 1:size(tmptrial,3)
tmp=tmptrial(:,:,i);
bg(i)=single(mean(tmp(BGroiIndex)));
clear tmp;
tmptrial(:,:,i) = tmptrial(:,:,i) - bg(i);
end
clear bg;
end
if cnt == selected(1)
tmpstack = tmptrial;
else
tmpstack = tmpstack + tmptrial;
end
clear tmptrial;
end
end
end
tmpstack = tmpstack./length(selected);
delete(tmpbar);
if modeval==1
tmpstack = single(mean(tmpstack,3)); %mean fluorescence of avgtrials
end
else %full length movie
%perform background roi subtraction (before averaging trials)
if get(findobj(hpControls,'Tag','bgsubtract'),'value') %compute background subtraction values
bg=zeros(IAdata.file.frames,1);
for i = 1:length(bg)
if iscell(IAdata.file.im); tmp = IAdata.file.im{channel}(:,:,i);
else; tmp = IAdata.file.im(:,:,i);
end
bg(i)=single(mean(tmp(BGroiIndex)));
end
end
if max(modeval == [ 2 4 6 7])
if iscell(IAdata.file.im)
if modeval==2
tmpstack = IAdata.file.im{channel};
else
tmpstack = single(IAdata.file.im{channel});
end
else
if modeval==2
tmpstack = IAdata.file.im;
else
tmpstack = single(IAdata.file.im);
end
end
%perform background roi subtraction (before averaging trials)
if get(findobj(hpControls,'Tag','bgsubtract'),'value') %background roi
if isa(tmpstack,'uint16'); tmpstack = single(tmpstack); end
for i = 1:size(tmpstack,3)
tmpstack(:,:,i) = tmpstack(:,:,i) - bg(i);
end
end
else %modeval == 1 %mean fluorescence - calculate line by row to limit memory usage
tmpstack = single(zeros(IAdata.file.size));
for r = 1:IAdata.file.size(1)
if iscell(IAdata.file.im)
tmprow = squeeze(IAdata.file.im{channel}(r,:,:));
else
tmprow = squeeze(IAdata.file.im(r,:,:));
end
if get(findobj(hpControls,'Tag','bgsubtract'),'value')
tmprow = single(tmprow) - repmat(bg',size(tmprow,1),1);
end
tmpstack(r,:) = single(mean(tmprow,2));
end
end
end
else %max(modeval == [3 5])df maps
if iscell(IAdata.file.im)
tmpstack = zeros(size(IAdata.file.im{1},1),size(IAdata.file.im{1},2));
else
tmpstack = zeros(size(IAdata.file.im,1),size(IAdata.file.im,2));
end
fmask = round(str2double(get(findobj(hIA,'Tag','map_fmaskedit'),'String')));
selected = get(findobj(hpControls,'Tag','odortrialslist'),'Value');
cnt = 0; fmaskmin = inf; fmaskmax = -inf;
tmpbar = waitbar(0,'Averaging Maps');
for o = 1:length(IAdata.maps.file.odor)
for t = 1:length(IAdata.maps.file.odor(o).trial)
cnt=cnt+1;
if ismember(cnt,selected)
waitbar(cnt/length(selected),tmpbar);
if get(findobj(hpControls,'Tag','bgsubtract'),'value')
respim = IAdata.maps.file.odor(o).trial(t).respim - ...
mean(IAdata.maps.file.odor(o).trial(t).respim(BGroiIndex));
baseim = IAdata.maps.file.odor(o).trial(t).baseim - ...
mean(IAdata.maps.file.odor(o).trial(t).baseim(BGroiIndex));
else
respim = IAdata.maps.file.odor(o).trial(t).respim;
baseim = IAdata.maps.file.odor(o).trial(t).baseim;
end
fmaskmin = min(fmaskmin,floor(min(baseim(:))));
fmaskmax = max(fmaskmax,round(mean(baseim(:))));
if modeval == 3 %df maps
tmpmap = respim-baseim;
tmpmap(baseim<fmask) = nan;
else %df/f maps
tmpmap = 100.*(respim-baseim)./baseim;
tmpmap(baseim<fmask) = nan;
end
tmpstack = tmpstack + tmpmap;
end
end
end
tmpstack = tmpstack./length(selected);
delete(tmpbar);
%reset fmask values
set(findobj(hIA,'tag','map_fmaskslider'),'Min',fmaskmin,'Max',fmaskmax);
if get(findobj(hIA,'tag','map_fmaskslider'),'Value')<fmaskmin
set(findobj(hIA,'tag','map_fmaskslider'),'Value',fmaskmin);
set(findobj(hIA,'tag','map_fmaskedit'),'String',num2str(fmaskmin));
end
if get(findobj(hIA,'tag','map_fmaskslider'),'Value')>fmaskmax
set(findobj(hIA,'tag','map_fmaskslider'),'Value',fmaskmax);
set(findobj(hIA,'tag','map_fmaskedit'),'String',num2str(fmaskmax));
end
end
%suppress bright pixels (this frame only)
if get(findobj(hIA,'Tag','suppressbright'), 'Value')
pct = 100 - str2double(get(findobj(hIA,'Tag','brightpct'),'string'));
tmpstack = imfilter_suppressBrightPixels(tmpstack,pct);
end
%spatial filter (this frame only)
if get(findobj(hIA,'Tag','lpf'), 'Value')
tmpbar = waitbar(0/size(tmpstack,3),'Gauss Spatial Filter');
sigma = str2double(get(findobj(hIA,'Tag','lpf_radius'), 'String'));
for f = 1:size(tmpstack,3)
if max(f==0:100:size(tmpstack,3)); waitbar(f/size(tmpstack,3),tmpbar);end
tmpstack(:,:,f) = imfilter_spatialLPF(tmpstack(:,:,f),sigma);
end
delete(tmpbar);
end
if isfield(IAdata,'currentbg'); IAdata.currentbg = rmfield(IAdata,'currentbg'); end
switch modeval
case 1 %mean fluorescence image
ftimevis = 'off'; fmaskvis = 'off'; overlayvis = 'off';
% IAdata.current = single(mean(tmpstack,3));
IAdata.current = tmpstack;
case 2 %fluorescence movie
ftimevis = 'off'; fmaskvis = 'off'; overlayvis = 'off';
IAdata.current = tmpstack;
case {3,5} %deltaf map
ftimevis = 'off'; fmaskvis = 'off'; overlayvis = 'off';
IAdata.current = single(tmpstack);
case {4,6,7} %deltaf movie and deltafoverf cases
IAdata.current = single(zeros(size(tmpstack)));
ftimevis = 'on'; fmaskvis = 'off'; overlayvis = 'off';
fstart = str2double(get(findobj(hpControls,'Tag','fstart'),'String'));
fstop = str2double(get(findobj(hpControls,'Tag','fstop'),'String'));
imtimes = (0:size(tmpstack,3)-1)./IAdata.file.frameRate;
ind1 = find(imtimes<=fstart,1,'first'); ind2 = find(imtimes<=fstop,1,'last');
baseim = single(mean(tmpstack(:,:,ind1:ind2),3));
if modeval == 4
IAdata.current = tmpstack-baseim;
elseif max(modeval == [6 7]) %deltaf over f cases
tmpF = tmpstack(~isnan(tmpstack(:)));
%check fmask and set slider min/max/value
set(findobj(hIA,'Tag','fmaskslider'),'Min', round(min(tmpF)));
set(findobj(hIA,'Tag','fmaskslider'),'Max', round(mean(tmpF)));
set(findobj(hIA,'Tag','fmaskslider'),'Value',round(str2double(get(findobj(hIA,'Tag','fmaskedit'),'String'))));
if get(findobj(hIA,'Tag','fmaskslider'),'Value')<round(min(tmpF))
set(findobj(hIA,'Tag','fmaskslider'),'Value',round(min(tmpF)));
set(findobj(hIA,'Tag','fmaskedit'),'String',num2str(round(min(tmpF))));
elseif get(findobj(hIA,'Tag','fmaskslider'),'Value')>round(mean(tmpF))
set(findobj(hIA,'Tag','fmaskslider'),'Value',round(mean(tmpF)));
set(findobj(hIA,'Tag','fmaskedit'),'String',num2str(round(mean(tmpF))));
end
ftimevis = 'on'; fmaskvis = 'on'; overlayvis = 'off';
Fmask = round(str2double(get(findobj(hIA,'Tag','fmaskedit'),'String')));
set(findobj(hIA,'Tag','fmaskedit'),'String',num2str(Fmask));
set(findobj(hIA,'Tag','dfmap_fmaskedit'),'String',num2str(Fmask));
for i = 1:size(tmpstack,3)
tmpim = tmpstack(:,:,i);
tmpim(baseim~=0) = 100*(tmpim(baseim~=0)-baseim(baseim~=0))./baseim(baseim~=0);
tmpim(baseim==0) = nan;
tmpim(tmpstack(:,:,i)<Fmask)=nan;
IAdata.current(:,:,i)=single(tmpim);
end
if modeval == 7 %overlay
ftimevis = 'on'; fmaskvis = 'on'; overlayvis = 'on';
IAdata.currentbg = single(tmpstack);
end
end
end
set(findobj(hpControls,'Tag','fowindow'),'Visible',ftimevis);
set(findobj(hpControls,'Tag','fstart'),'Visible',ftimevis);
set(findobj(hpControls,'Tag','fto'),'Visible',ftimevis);
set(findobj(hpControls,'Tag','fstop'),'Visible',ftimevis);
set(findobj(hpControls,'Tag','fmasklabel'),'Visible',fmaskvis);
set(findobj(hpControls,'Tag','fmaskslider'),'Visible',fmaskvis);
set(findobj(hpControls,'Tag','fmaskedit'),'Visible',fmaskvis);
set(findobj(hpControls,'Tag','overlaypanel'),'Visible',overlayvis);