function [ ] = dotQuant_GUI() if ishandle(findobj('tag', 'particleTrackingFigure')) == 1 close all; end guiHandle = figure('Position', [200, 100, 1200, 720],... 'tag','figure','color', 'w', 'MenuBar','none',... 'name','Main window','numbertitle','off', 'Visible', 'off'); particleTrackingFigureHandle = figure('Position', [50, 100, 400, 850],... 'tag','particleTrackingFigure','color', 'w', 'MenuBar','none',... 'name','Particle tracking','numbertitle','off','Visible', 'on'); statisticalAnalysisFigureHandle = figure('Position', [1200, 100, 225, 800],... 'tag','statisticalAnalysisFigure','color', 'w', 'MenuBar','none',... 'name','statistical analysis','numbertitle','off', 'Visible', 'off'); %-------------------------------------------------------------------------% %------------------------------- Axes handles ----------------------------% %-------------------------------------------------------------------------% axesHandle = subplot('position', [0.15 0.15 0.7 0.75], 'color', 'k',... 'parent', guiHandle, 'tag', 'mainAxes'); %[left,bottom,width,height] set(axesHandle,'XColor','w', 'xtick',[]); set(axesHandle,'YColor','w', 'ytick',[]); %-------------------------------------------------------------------------% %------------------------------- UI tables -------------------------------% %-------------------------------------------------------------------------% uitable('parent', guiHandle,... 'unit', 'norm',... 'position',[0.01 0.65 0.131 0.2],... %[left,bottom,width,height] 'Visible', 'off',... 'ColumnName', {'Track','Show'},... 'ColumnFormat', {'numeric','logical'},... 'ColumnWidth',{42},... 'tag', 'tracksTable1',... 'ColumnEditable', [false true],... 'Data', {}); uicontrol('Style','text',... 'parent', guiHandle,... 'String','Show tracks:',... 'HorizontalAlignment', 'left',... 'fontsize', 12,... 'Visible', 'off',... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.03 0.86 0.12 0.03],... %[left,bottom,width,height] 'tag','showTrack1Title'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'Visible', 'off',... 'Value', 1,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.01 0.87 0.02 0.02],... %[left,bottom,width,height] 'tag','showAllTracks1',... 'callback', {@showAll, 'tracksTable1'}); uitable('parent', guiHandle,... 'unit', 'norm',... 'position',[0.01 0.365 0.131 0.2],... %[left,bottom,width,height] 'Visible', 'off',... 'ColumnName', {'Track','Show'},... 'ColumnFormat', {'numeric','logical'},... 'ColumnWidth',{42},... 'tag', 'tracksTable2',... 'ColumnEditable', [false true],... 'Data', {}); uicontrol('Style','text',... 'parent', guiHandle,... 'String','Show tracks:',... 'HorizontalAlignment', 'left',... 'fontsize', 12,... 'Visible', 'off',... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.03 0.575 0.12 0.03],... %[left,bottom,width,height] 'tag','showTrack2Title'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'Visible', 'off',... 'Value', 1,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.01 0.585 0.02 0.02],... %[left,bottom,width,height] 'tag','showAllTracks2',... 'callback', {@showAll, 'tracksTable2'}); uitable('parent', guiHandle,... 'unit', 'norm',... 'position',[0.01 0.085 0.131 0.2],... %[left,bottom,width,height] 'Visible', 'off',... 'ColumnName', {'Track','Show'},... 'ColumnFormat', {'numeric','logical'},... 'ColumnWidth',{42},... 'tag', 'tracksTable3',... 'ColumnEditable', [false true],... 'Data', {}); uicontrol('Style','text',... 'parent', guiHandle,... 'String','Show tracks:',... 'HorizontalAlignment', 'left',... 'fontsize', 12,... 'Visible', 'off',... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.03 0.295 0.12 0.03],... %[left,bottom,width,height] 'tag','showTrack3Title'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'Visible', 'off',... 'Value', 1,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.01 0.305 0.02 0.02],... %[left,bottom,width,height] 'tag','showAllTracks3',... 'callback', {@showAll, 'tracksTable3'}); %-------------------------------------------------------------------------% %------------------------------- UI controls -----------------------------% %-------------------------------------------------------------------------% uicontrol('style' ,'slider',.... 'parent', guiHandle,... 'unit', 'norm',... 'position',[0.15 0.085 0.7 0.025],... %[left,bottom,width,height] 'Enable', 'off',... 'tag' ,'timePointSlider',... 'max' ,100,... %change values to fit number of time points 'min' ,1,... 'sliderstep',[0.01 0.1],... %change to 1 time point per minor step 'value' ,1,... 'callback', {@changeImage, axesHandle}); % Adds timepoint over slider uicontrol('Style','text',... 'parent', guiHandle,... 'String','Time point',... 'fontsize', 12,... 'HorizontalAlignment', 'left',... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.15 0.12 0.2 0.025],... %[left,bottom,width,height] 'tag','timePoint'); uicontrol('style' ,'popupmenu',... 'String', '3D time lapse|2D time lapse',... 'parent', particleTrackingFigureHandle,... 'unit', 'norm',... 'fontsize', 11,... 'position',[0.075 0.87 0.43 0.05],... %[left,bottom,width,height] 'tag','dataType'); % Adds title to pop up menu uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Data type',... 'fontsize', 14,... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.075 0.92 0.43 0.0375],... %[left,bottom,width,height] 'tag','dataTypeTitle'); %controls for user to enter pixel and step size uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '0.2',... 'value', 0.2,... 'fontsize', 10,... 'tag', 'pixelSize',... 'TooltipString', 'The pixel size (on the X and Y axes) in microns',... 'unit', 'norm',... 'position', [0.075 0.765 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Pixel size (microns)',... 'HorizontalAlignment', 'left',... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.795 0.43 0.025],... %[left,bottom,width,height] 'tag','pixelSizeTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '0.8',... 'value', 0.8,... 'fontsize', 10,... 'tag', 'stepSize',... 'TooltipString', 'The step size (or pixel size on the Z axis) in microns',... 'unit', 'norm',... 'position', [0.075 0.705 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Step size (microns)',... 'HorizontalAlignment', 'left',... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.735 0.43 0.025],... %[left,bottom,width,height] 'tag','stepSizeTitle'); % Adds title to text edit boxes uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Voxel size',... 'fontsize', 14,... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.075 0.825 0.43 0.0375],... %[left,bottom,width,height] 'tag','voxelSizeTitle'); %controls for user to adjust particle tracking uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Particles',... 'fontsize', 14,... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.075 0.645 0.43 0.0375],... %[left,bottom,width,height] 'tag','ParticleTrackingTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '140',... 'value', 140,... 'fontsize', 10,... 'tag', 'threshold',... 'TooltipString', ['The threshold value specifies the intensity value under which local maxima will', char(10),... 'be omitted, as a percentage of the mean intensity of the entire image.', char(10),... 'Insert a higher threshold to ignore all but the brightest dots.'],... 'unit', 'norm',... 'position', [0.075 0.575 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Threshold (percent of mean)',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.6 0.45 0.03],... %[left,bottom,width,height] 'tag','thresholdTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '250',... 'value', 250,... 'fontsize', 10,... 'tag', 'maxNoOfParticles',... 'TooltipString', ['The maximum number of particles expected per time point.', char(10),... 'For a maximum of 250 for example, the program will only find', char(10),... 'between 0 and 250 particles in each time point.'],... 'unit', 'norm',... 'position', [0.075 0.48 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Maximum number of particles in time point',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.51 0.43 0.05],... %[left,bottom,width,height] 'tag','maxNoOfParticlesTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '3',... 'value', 3,... 'fontsize', 10,... 'tag', 'maxLinkingDistance',... 'TooltipString', ['The maximum allowed distance between particles over time. The program will not link particles in successive time points', char(10),... 'if they are farther apart than the specified distance. Increase this value if the dots move around a lot in your data.', char(10),... 'Distance should be specified in microns.'],... 'unit', 'norm',... 'position', [0.075 0.385 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Maximum linking distance (microns)',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.415 0.43 0.05],... %[left,bottom,width,height] 'tag','maxLinkingDistanceTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '0',... 'value', 0,... 'fontsize', 10,... 'tag', 'maxLinkingGap',... 'TooltipString', ['The maximum gap that can be closed between two successive tracks. The program will not close', char(10),... 'gaps between tracks that are further apart than the specified value.', char(10),... 'Gap size should be specified in time points. Insert 0 to ignore this feature.'],... 'unit', 'norm',... 'position', [0.075 0.285 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Maximum linking gap (time points)',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.315 0.43 0.05],... %[left,bottom,width,height] 'tag','maxLinkingGapTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '45',... 'value', 45,... 'fontsize', 10,... 'tag', 'minTrackLength',... 'TooltipString', ['Insert the minimum acceptable particle track length. The program will omit tracks', char(10),... 'that are shorter than the specified length.', char(10),... 'Minimum size should be specified in time points. Insert 0 to ignore this feature.'],... 'unit', 'norm',... 'position', [0.075 0.195 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Minimum track length (time points)',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.225 0.43 0.05],... %[left,bottom,width,height] 'tag','minTrackLengthTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '10',... 'value', 10,... 'fontsize', 10,... 'tag', 'regionalMaximumRadiusXY',... 'TooltipString', ['Local maxima are detected as the brightest voxel in a cube of this size.', char(10),... 'The value specifies the X and Y radius of the cube in pixels.'],... 'unit', 'norm',... 'position', [0.31 0.095 0.23 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','XY radius',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.095 0.23 0.025],... %[left,bottom,width,height] 'tag','regionalMaximumRadiusXYTitle'); uicontrol('style' ,'edit',... 'parent', particleTrackingFigureHandle,... 'String', '4',... 'value', 4,... 'fontsize', 10,... 'tag', 'regionalMaximumRadiusZ',... 'TooltipString', ['Local maxima are detected as the brightest voxel in a cube of this size.', char(10),... 'The value specifies the Z radius of the cube in pixels.'],... 'unit', 'norm',... 'position', [0.31 0.06 0.23 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Z radius',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.06 0.23 0.025],... %[left,bottom,width,height] 'tag','regionalMaximaRadiusZTitle'); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Regional maximum area',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.12 0.43 0.05],... %[left,bottom,width,height] 'tag','regionalMaximumAreaTitle'); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'fontsize', 10,... 'backgroundColor','k',... 'foregroundColor','k',... 'unit', 'norm',... 'Position',[0.55 0.15 0.005 0.8]); %[left,bottom,width,height] %This part holds buttons for the user to choose a channel and its name uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Channels',... 'fontsize', 14,... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.575 0.92 0.43 0.0375],... %[left,bottom,width,height] 'tag','channelsTitle'); uicontrol('Style','text',... 'parent', particleTrackingFigureHandle,... 'String','Choose channels:',... 'HorizontalAlignment', 'left',... 'fontsize', 12,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.6 0.86 0.43 0.05],... %[left,bottom,width,height] 'tag','chooseChannelTitle'); %Check box and editable text box for first channel uicontrol('Style','checkbox',... 'parent', particleTrackingFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.6 0.835 0.2 0.02],... %[left,bottom,width,height] 'tag','chooseChannel1',... 'TooltipString', 'Tick to choose this channel',... 'callback', {@chooseChannel, 'Channel1'}); uicontrol('style','edit',... 'parent', particleTrackingFigureHandle,... 'TooltipString', 'Change name to match channel name',... 'String', 'c405',... 'Enable', 'off',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'position', [0.7 0.835 0.225 0.03],...%[left,bottom,width,height] 'tag','Channel1'); %Check box and editable text box for second channel uicontrol('Style','checkbox',... 'parent', particleTrackingFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.6 0.785 0.2 0.02],... %[left,bottom,width,height] 'tag','chooseChannel2',... 'TooltipString', 'Tick to choose this channel',... 'callback', {@chooseChannel, 'Channel2'}); uicontrol('style','edit',... 'parent', particleTrackingFigureHandle,... 'TooltipString', 'Change name to match channel name',... 'String', 'c488',... 'Enable', 'off',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'position', [0.7 0.785 0.225 0.03],...%[left,bottom,width,height] 'tag','Channel2'); %Check box and editable text box for third channel uicontrol('Style','checkbox',... 'parent', particleTrackingFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.6 0.735 0.2 0.02],... %[left,bottom,width,height] 'tag','chooseChannel3',... 'TooltipString', 'Tick to choose this channel',... 'callback', {@chooseChannel, 'Channel3'}); uicontrol('style','edit',... 'parent', particleTrackingFigureHandle,... 'TooltipString', 'Change name to match channel name',... 'String', 'c561',... 'Enable', 'off',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'position', [0.7 0.735 0.225 0.03],...%[left,bottom,width,height] 'tag','Channel3'); uicontrol('style','pushbutton',... 'parent', particleTrackingFigureHandle,... 'String', 'Align Tracks',... 'Enable', 'off',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'position', [0.6 0.55 0.35 0.03],...%[left,bottom,width,height] 'tag','alignTracks',... 'TooltipString', 'Correlate particles across channels. This will create additional tracks.',... 'callback', {@alignTracks}); uicontrol('Style','checkbox',... 'parent', particleTrackingFigureHandle,... 'String','Run parallel CPU',... 'value', 1,... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','k',... 'unit', 'norm',... 'Position',[0.6 0.68 0.45 0.02],... %[left,bottom,width,height] 'tag','multithread',... 'callback', {@setWarning, 'warning'}); uicontrol('style','text',... 'parent', particleTrackingFigureHandle,... 'String', 'Warning: may cause crashes if memory is insufficient',... 'Enable', 'on',... 'backgroundColor','w',... 'foregroundColor','r',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'position', [0.6 0.58 0.45 0.09],...%[left,bottom,width,height] 'tag','warning'); %This part holds buttons for the user to choose to show a channel and %its name uicontrol('Style','text',... 'parent', guiHandle,... 'String','Show channels:',... 'HorizontalAlignment', 'left',... 'fontsize', 12,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.87 0.85 0.1 0.03],... %[left,bottom,width,height] 'tag','showChannelTitle'); %Check box and editable text box for first channel uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.87 0.8 0.05 0.03],... %[left,bottom,width,height] 'tag','chooseShowChannel1',... 'TooltipString', 'Tick to show image of channel in current time point',... 'callback', {@changeImage, axesHandle}); uicontrol('style','edit',... 'parent', guiHandle,... 'String', 'c405',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'TooltipString', 'Change name to match channel name',... 'unit', 'norm',... 'position', [0.9 0.8 0.075 0.03],...%[left,bottom,width,height] 'tag','showChannel1'); uicontrol('style' ,'text',... 'parent', guiHandle,... 'backgroundColor','b',... 'foregroundColor','b',... 'unit', 'norm',... 'fontsize', 11,... 'position',[0.87 0.75 0.105 0.02],... %[left,bottom,width,height] 'tag','channel1Color'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','k',... 'String', 'Enhance contrast',... 'fontsize', 10,... 'unit', 'norm',... 'Position',[0.87 0.77 0.15 0.03],... %[left,bottom,width,height] 'tag','enhanceContrastChannel1',... 'TooltipString', 'Tick to enable image contrast enhancing'); %Check box and editable text box for second channel uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.87 0.7 0.05 0.03],... %[left,bottom,width,height] 'tag','chooseShowChannel2',... 'TooltipString', 'Tick to show image of channel in current time point',... 'callback', {@changeImage, axesHandle}); uicontrol('style','edit',... 'parent', guiHandle,... 'String', 'c488',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'TooltipString', 'Change name to match channel name',... 'unit', 'norm',... 'position', [0.9 0.7 0.075 0.03],...%[left,bottom,width,height] 'tag','showChannel2'); uicontrol('style' ,'text',... 'parent', guiHandle,... 'backgroundColor','g',... 'foregroundColor','g',... 'unit', 'norm',... 'fontsize', 11,... 'position',[0.87 0.65 0.105 0.02],... %[left,bottom,width,height] 'tag','channel2Color'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','k',... 'String', 'Enhance contrast',... 'fontsize', 10,... 'unit', 'norm',... 'Position',[0.87 0.67 0.15 0.03],... %[left,bottom,width,height] 'tag','enhanceContrastChannel2',... 'TooltipString', 'Tick to enable image contrast enhancing'); %Check box and editable text box for third channel uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.87 0.6 0.075 0.03],... %[left,bottom,width,height] 'tag','chooseShowChannel3',... 'TooltipString', 'Tick to show image of channel in current time point',... 'callback', {@changeImage, axesHandle}); uicontrol('style','edit',... 'parent', guiHandle,... 'String', 'c561',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'TooltipString', 'Change name to match channel name',... 'unit', 'norm',... 'position', [0.9 0.6 0.075 0.03],...%[left,bottom,width,height] 'tag','showChannel3'); uicontrol('style' ,'text',... 'parent', guiHandle,... 'backgroundColor','r',... 'foregroundColor','r',... 'unit', 'norm',... 'fontsize', 11,... 'position',[0.87 0.55 0.105 0.02],... %[left,bottom,width,height] 'tag','channel3Color'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','k',... 'String', 'Enhance contrast',... 'fontsize', 10,... 'unit', 'norm',... 'Position',[0.87 0.57 0.15 0.03],... %[left,bottom,width,height] 'tag','enhanceContrastChannel3',... 'TooltipString', 'Tick to enable image contrast enhancing'); %Check box and editable text box for forth channel uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.87 0.5 0.075 0.03],... %[left,bottom,width,height] 'tag','chooseShowChannel4',... 'TooltipString', 'Tick to show image of channel in current time point',... 'callback', {@changeImage, axesHandle}); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'foregroundColor','k',... 'String', 'Enhance contrast',... 'fontsize', 10,... 'unit', 'norm',... 'Position',[0.87 0.47 0.15 0.03],... %[left,bottom,width,height] 'tag','enhanceContrastChannel4',... 'TooltipString', 'Tick to enable image contrast enhancing'); uicontrol('style','edit',... 'parent', guiHandle,... 'String', 'cDIC',... 'fontsize', 11,... 'HorizontalAlignment', 'left',... 'TooltipString', 'Change name to match channel name',... 'unit', 'norm',... 'position', [0.9 0.5 0.075 0.03],...%[left,bottom,width,height] 'tag','showChannel4'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'unit', 'norm',... 'Position',[0.87 0.44 0.15 0.03],... %[left,bottom,width,height] 'tag','showSeparate',... 'TooltipString', ['Tick to show channel in a separate window. This is helpful', char(10),... 'for when this channel dims the general image.'],... 'callback', {@showSeparateFun, 'showChannel4'}); uicontrol('Style','text',... 'parent', guiHandle,... 'String','Show channel in separate window',... 'foregroundColor','k',... 'fontsize', 10,... 'backgroundColor','w',... 'HorizontalAlignment', 'left',... 'unit', 'norm',... 'Position',[0.885 0.4175 0.12 0.05],... %[left,bottom,width,height] 'tag','showDICSeparateTitle'); uicontrol('style' ,'text',... 'parent', guiHandle,... 'Enable', 'off',... 'unit', 'norm',... 'fontsize', 11,... 'position',[0.87 0.395 0.105 0.02],... %[left,bottom,width,height] 'tag','channel4Color'); uicontrol('Style','checkbox',... 'parent', guiHandle,... 'backgroundColor','w',... 'Value', 0,... 'foregroundColor','k',... 'fontsize', 12,... 'string', 'Zoom in',... 'unit', 'norm',... 'Position',[0.9 0.25 0.15 0.03],... %[left,bottom,width,height] 'tag','zoomIn',... 'TooltipString', ['Tick to zoom in on image.', char(10),... 'Draw an area or click to zoom in.', char(10),... 'Double click to reset view.'],... 'callback', {@Zoom, 'zoomIn', guiHandle, 'on'}); uicontrol('style' ,'pushbutton',... 'parent', guiHandle,... 'String','Reset view' ,... 'Enable', 'on',... 'unit', 'norm',... 'fontsize', 12,... 'position',[0.9 0.2 0.075 0.03],... %[left,bottom,width,height] 'tag','resetView',... 'TooltipString', 'Reset image view to original zoom factor',... 'callback', {@Zoom, 'zoomIn', guiHandle, 'out'}); uicontrol('style' ,'pushbutton',... 'parent', guiHandle,... 'String','Refresh' ,... 'Enable', 'on',... 'unit', 'norm',... 'fontsize', 12,... 'position',[0.9 0.15 0.075 0.03],... %[left,bottom,width,height] 'tag','refreshButton',... 'TooltipString', ['Refresh image to current time point.', char(10),... 'This is helpful when graphic processing is slow.'],... 'callback', {@refresh, axesHandle}); %------------------------------- data analysis ---------------------------% uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Data analysis',... 'fontsize', 14,... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.075 0.92 0.75 0.0375],... %[left,bottom,width,height] 'tag','dataAnalysisTitle'); %inserts title for section %sum according to a number of neighbors uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Sum object pixels:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.3 0.885 0.75 0.02],... %[left,bottom,width,height] 'tag','sumObjectPixelsTitle'); %Check box and editable text boxes for number of pixels to quantify around %local maxima uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.075 0.885 0.2 0.02],... %[left,bottom,width,height] 'tag','chooseSumPixels',... 'TooltipString', 'Tick to sum all voxels within range around local maxima',... 'callback', {@chooseSum}); %edit text boxes for user to input range for qunatifying sum uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '1',... 'value', 1,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'sumPixelsXY',... 'TooltipString', ['Choose radius in X and Y around local maxima to sum all voxels within cube.', char(10),... 'Radius value is specified in pixels.'],... 'unit', 'norm',... 'position', [0.5 0.835 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','XY pixels',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.835 0.4 0.025],... %[left,bottom,width,height] 'tag','sumPixelsXYTitle'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '0',... 'value', 0,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'sumPixelsZ',... 'TooltipString', ['Choose radius in Z around local maxima to sum all voxels within cube.', char(10),... 'Radius value is specified in pixels.'],... 'unit', 'norm',... 'position', [0.5 0.805 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Z pixels',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.805 0.4 0.025],... %[left,bottom,width,height] 'tag','sumPixelsZTitle'); %perform analysis within a selection cube uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Define selection cube',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.3 0.745 0.75 0.02],... %[left,bottom,width,height] 'tag','selectCubeTitle'); %Check box and editable text boxes to define a selection cube uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.075 0.745 0.2 0.02],... %[left,bottom,width,height] 'tag','selectCube',... 'TooltipString', 'Tick to define a selection cube around local maxima for further analysis',... 'callback', {@selectCube}); %edit text boxes for user to input range for selection cube uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '5',... 'value', 5,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'selectionPixelsXY',... 'TooltipString', 'Choose radius in X and Y around local maxima to define cube',... 'unit', 'norm',... 'position', [0.5 0.7 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','XY pixels',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.7 0.4 0.025],... %[left,bottom,width,height] 'tag','selectionPixelsXYTitle'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '2',... 'value', 2,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'selectionPixelsZ',... 'TooltipString', 'Choose radius in Z around local maxima to define cube',... 'unit', 'norm',... 'position', [0.5 0.67 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Z pixels',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.67 0.4 0.025],... %[left,bottom,width,height] 'tag','selectionPixelsZTitle'); %added checkboxes for user to decide how to quantify within selection cube %when needed, there's also an edit text box %quantify n brightest pixels uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Sum brightest pixels',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.3 0.64 0.75 0.02],... %[left,bottom,width,height] 'tag','sumBrightestPixelsTitle'); uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.64 0.2 0.02],... %[left,bottom,width,height] 'tag','sumBrightestPixels',... 'TooltipString', 'Tick to quantify box intensity by summing the #n brightest pixels within the cube',... 'callback', {@selectBrightestPixels}); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '12',... 'value', 12,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'numberOfBrightestPixels',... 'unit', 'norm',... 'TooltipString', 'Select number of brightest pixels to sum',... 'position', [0.5 0.6 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Pixels',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.6 0.4 0.025],... %[left,bottom,width,height] 'tag','numberOfBrightestPixelsTitle'); %sum pixels n% above median uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Sum pixels above median',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.3 0.56 0.75 0.02],... %[left,bottom,width,height] 'tag','sumPixelsAboveMedianTitle'); uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.56 0.2 0.02],... %[left,bottom,width,height] 'tag','sumPixelsAboveMedian',... 'TooltipString', ['Tick to quantify box intensity by summing all pixels', char(10),... 'that are #n percent above the cube median'],... 'callback', {@sumPixelsAboveMedian}); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '100',... 'value', 100,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'percentAboveMedian',... 'TooltipString', 'Select percent above median for intensity quantification',... 'unit', 'norm',... 'position', [0.5 0.52 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Percent above',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.52 0.4 0.025],... %[left,bottom,width,height] 'tag','percentAboveMedianTitle'); %sum pixels over n% of local maximum uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Sum pixels close to max',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.3 0.48 0.75 0.02],... %[left,bottom,width,height] 'tag','sumPixelsCloseToMaxTitle'); uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.48 0.2 0.02],... %[left,bottom,width,height] 'tag','sumPixelsCloseToMax',... 'TooltipString', ['Tick to quantify box intensity by summing all pixels that are', char(10),... 'between the cube median intensity and the maximum intensity'],... 'callback', {@sumPixelsCloseToMax}); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '50',... 'value', 50,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'percentOfMax',... 'TooltipString', ['Choose percent of the range between the cube median and the maximum value.', char(10),... 'For exemple, if the value is 50, then the sum will be that of all pixels above', char(10),... 'the intensity value that is at 50 percent between the cube median and maximum'],... 'unit', 'norm',... 'position', [0.5 0.44 0.4 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Percent of range',... 'HorizontalAlignment', 'left',... 'Enable', 'off',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'unit', 'norm',... 'Position',[0.075 0.44 0.42 0.025],... %[left,bottom,width,height] 'tag','percentOfMaxTitle'); %fit gaussian %uicontrol('Style','text',... %'parent', statisticalAnalysisFigureHandle,... % 'String','Fit to gaussian:',... % 'HorizontalAlignment', 'left',... % 'fontsize', 10,... % 'backgroundColor','w',... % 'foregroundColor','r',... % 'Enable', 'off',... % 'unit', 'norm',... % 'Position',[0.3 0.3 0.75 0.02],... %[left,bottom,width,height] % 'tag','fitGaussianTitle'); %Check box and editable text boxes for number of pixels to quantify around %local maxima %uicontrol('Style','checkbox',... % 'parent', statisticalAnalysisFigureHandle,... % 'backgroundColor','w',... % 'foregroundColor','r',... % 'Enable', 'off',... % 'unit', 'norm',... % 'Position',[0.075 0.3 0.2 0.02],... %[left,bottom,width,height] % 'tag','chooseFitGaussian',... % 'callback',{@chooseGaussian}); %edit text boxes for user to input range around maximum to fit gaussian %uicontrol('style' ,'edit',... %'parent', statisticalAnalysisFigureHandle,... %'String', '3',... %'value', 3,... %'fontsize', 10,... %'Enable', 'off',... %'tag', 'gaussianFitXY',... %'unit', 'norm',... %'position', [0.5 0.27 0.4 0.025],... %[left,bottom,width,height] %'callback', {@changeValue}); %uicontrol('Style','text',... %'parent', statisticalAnalysisFigureHandle,... % 'String','XY range',... %'HorizontalAlignment', 'left',... % 'Enable', 'off',... % 'fontsize', 10,... % 'backgroundColor','w',... % 'foregroundColor','r',... % 'unit', 'norm',... % 'Position',[0.075 0.27 0.4 0.025],... %[left,bottom,width,height] % 'tag','gaussianFitXYTitle'); %uicontrol('style' ,'edit',... %'parent', statisticalAnalysisFigureHandle,... %'String', '3',... %'value', 3,... %'fontsize', 10,... %'Enable', 'off',... % 'tag', 'gaussianFitZ',... % 'unit', 'norm',... % 'position', [0.5 0.24 0.4 0.025],... %[left,bottom,width,height] % 'callback', {@changeValue}); %uicontrol('Style','text',... %'parent', statisticalAnalysisFigureHandle,... %'String','Z range',... %'HorizontalAlignment', 'left',... %'Enable', 'off',... %'fontsize', 10,... %'backgroundColor','w',... %'foregroundColor','r',... %'unit', 'norm',... %'Position',[0.075 0.24 0.4 0.025],... %[left,bottom,width,height] %'tag','gaussianFitZTitle'); %noise subtraction uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Subtract background',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.3 0.38 0.75 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundTitle'); uicontrol('Style','checkbox',... 'parent', statisticalAnalysisFigureHandle,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'on',... 'unit', 'norm',... 'Position',[0.075 0.38 0.2 0.02],... %[left,bottom,width,height] 'tag','subtractBackground',... 'TooltipString', ['Tick to create a rectangle in image background to', char(10),... 'subtract noise from final intensity analysis'],... 'callback',{@subtractBackground, 'subtractBackgroundXMax', 'subtractBackgroundYMax',... 'subtractBackgroundXTitle1', 'subtractBackgroundXTitle2', 'subtractBackgroundXstart', 'subtractBackgroundXend',... 'subtractBackgroundYTitle1', 'subtractBackgroundYTitle2', 'subtractBackgroundYstart', 'subtractBackgroundYend'}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','X from:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.34 0.2 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundXTitle1'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '1',... 'value', 1,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'subtractBackgroundXstart',... 'unit', 'norm',... 'position', [0.275 0.34 0.2 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','to',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.5 0.34 0.1 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundXTitle2'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '',... 'value', 1,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'subtractBackgroundXend',... 'unit', 'norm',... 'position', [0.6 0.34 0.2 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'Visible', 'off',... 'unit', 'norm',... 'Position',[0.825 0.34 0.2 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundXMax'); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Y from:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.3 0.2 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundYTitle1'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '1',... 'value', 1,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'subtractBackgroundYstart',... 'unit', 'norm',... 'position', [0.275 0.3 0.2 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','to',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.5 0.3 0.1 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundYTitle2'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '',... 'value', 1,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'subtractBackgroundYend',... 'unit', 'norm',... 'position', [0.6 0.3 0.2 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'Visible', 'off',... 'unit', 'norm',... 'Position',[0.825 0.3 0.2 0.02],... %[left,bottom,width,height] 'tag','subtractBackgroundYMax'); uicontrol('style' ,'checkbox',.... 'parent', statisticalAnalysisFigureHandle,... 'unit', 'norm',... 'string','Analyze individual tracks',... 'Value', 1,... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','r',... 'position',[0.075 0.2375 0.9 0.022],... %[left,bottom,width,height] 'Enable', 'on',... 'tag','individualAnalysis',... 'TooltipString', 'Tick to perform analysis on separate unaligned tracks',... 'callback', {@toggle, 'individualAnalysis', 'alignedAnalysis', 'autoFitWindowTitle1', 'autoFitWindowTitle2',... 'autoFitWindowMin', 'autoFitWindowMax', 'autoFitDeltaTitle1', 'autoFitDeltaTitle2',... 'autoFitDeltaMin', 'autoFitDeltaMax'}); uicontrol('style' ,'checkbox',.... 'parent', statisticalAnalysisFigureHandle,... 'unit', 'norm',... 'string','Analyze aligned tracks',... 'Value', 0,... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','r',... 'position',[0.075 0.2 0.9 0.022],... %[left,bottom,width,height] 'Enable', 'off',... 'tag','alignedAnalysis',... 'TooltipString', 'Tick to perform analysis on aligned tracks',... 'callback', {@toggle, 'individualAnalysis', 'alignedAnalysis', 'autoFitWindowTitle1', 'autoFitWindowTitle2',... 'autoFitWindowMin', 'autoFitWindowMax', 'autoFitDeltaTitle1', 'autoFitDeltaTitle2',... 'autoFitDeltaMin', 'autoFitDeltaMax'}); uicontrol('style' ,'checkbox',.... 'parent', statisticalAnalysisFigureHandle,... 'unit', 'norm',... 'string','Auto fit sigmoid',... 'Value', 0,... 'fontsize', 11,... 'backgroundColor','w',... 'foregroundColor','r',... 'position',[0.075 0.1625 0.9 0.022],... %[left,bottom,width,height] 'Enable', 'off',... 'tag','autoFitSigmoid',... 'TooltipString', 'Tick to automatically fit sigmoid to data',... 'callback', {@autoFit, 'autoFitWindowTitle1', 'autoFitWindowTitle2',... 'autoFitWindowMin', 'autoFitWindowMax', 'autoFitDeltaTitle1', 'autoFitDeltaTitle2',... 'autoFitDeltaMin', 'autoFitDeltaMax'}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Window min:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.12 0.35 0.02],... %[left,bottom,width,height] 'tag','autoFitWindowTitle1'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '25',... 'value', 25,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'autoFitWindowMin',... 'unit', 'norm',... 'position', [0.425 0.12 0.15 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','max:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.6 0.12 0.15 0.02],... %[left,bottom,width,height] 'tag','autoFitWindowTitle2'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '90',... 'value', 90,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'autoFitWindowMax',... 'unit', 'norm',... 'position', [0.75 0.12 0.15 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','Delta T min:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.075 0.08 0.35 0.02],... %[left,bottom,width,height] 'tag','autoFitDeltaTitle1'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '7',... 'value', 7,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'autoFitDeltaMin',... 'unit', 'norm',... 'position', [0.425 0.08 0.15 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); uicontrol('Style','text',... 'parent', statisticalAnalysisFigureHandle,... 'String','max:',... 'HorizontalAlignment', 'left',... 'fontsize', 10,... 'backgroundColor','w',... 'foregroundColor','r',... 'Enable', 'off',... 'unit', 'norm',... 'Position',[0.6 0.08 0.15 0.02],... %[left,bottom,width,height] 'tag','autoFitDeltaTitle2'); uicontrol('style' ,'edit',... 'parent', statisticalAnalysisFigureHandle,... 'String', '30',... 'value', 30,... 'fontsize', 10,... 'Enable', 'off',... 'tag', 'autoFitDeltaMax',... 'unit', 'norm',... 'position', [0.75 0.08 0.15 0.025],... %[left,bottom,width,height] 'callback', {@changeValue}); %----------------------------- executing buttons -------------------------% uicontrol('style' ,'pushbutton',... 'parent', statisticalAnalysisFigureHandle,... 'string', 'Analyze',... 'unit', 'norm',... 'enable', 'on',... 'fontsize', 12,... 'position',[0.075, 0.02 0.4 0.03],... %[left,bottom,width,height] 'tag','analyze',... 'TooltipString', 'Execute analysis (one or more, simultaneously)',... 'callback', {@analyze}); uicontrol('style' ,'pushbutton',... 'parent', statisticalAnalysisFigureHandle,... 'string', 'Plot results',... 'unit', 'norm',... 'enable', 'off',... 'fontsize', 12,... 'position',[0.5, 0.02 0.45 0.03],... %[left,bottom,width,height] 'tag','plotAnalysisResults',... 'TooltipString', 'Plot graphs of all analyzed objects. Opens new window.',... 'callback', {@plotResults}); uicontrol('style' ,'pushbutton',... 'parent', particleTrackingFigureHandle,... 'string', 'Run',... 'unit', 'norm',... 'fontsize', 12,... 'position',[0.05, 0.01 0.4 0.03],... %[left,bottom,width,height] 'tag','run',... 'callback', {@run, guiHandle, axesHandle}); uicontrol('style' ,'pushbutton',... 'parent', particleTrackingFigureHandle,... 'string', 'Close all',... 'fontsize', 12,... 'unit', 'norm',... 'position',[0.5, 0.01 0.4 0.03],... %[left,bottom,width,height] 'tag','close',... 'callback', {@closepushbutton, guiHandle}); %-------------------------------------------------------------------------% %-------------------------------- call backs -----------------------------% %-------------------------------------------------------------------------% function [] = autoFit (calling_button, eventData, Handle1, Handle2, Handle3, Handle4, Handle5, Handle6, Handle7, Handle8) if get(calling_button, 'value') == 1 set(findobj('tag', Handle1), 'Enable', 'on'); set(findobj('tag', Handle2), 'Enable', 'on'); set(findobj('tag', Handle3), 'Enable', 'on'); set(findobj('tag', Handle4), 'Enable', 'on'); set(findobj('tag', Handle5), 'Enable', 'on'); set(findobj('tag', Handle6), 'Enable', 'on'); set(findobj('tag', Handle7), 'Enable', 'on'); set(findobj('tag', Handle8), 'Enable', 'on'); else set(findobj('tag', Handle1), 'Enable', 'off'); set(findobj('tag', Handle2), 'Enable', 'off'); set(findobj('tag', Handle3), 'Enable', 'off'); set(findobj('tag', Handle4), 'Enable', 'off'); set(findobj('tag', Handle5), 'Enable', 'off'); set(findobj('tag', Handle6), 'Enable', 'off'); set(findobj('tag', Handle7), 'Enable', 'off'); set(findobj('tag', Handle8), 'Enable', 'off'); end end function [] = setWarning (calling_button, eventData, warning) %sets a warning to red if checked if get(calling_button, 'value') == 1 set(findobj('tag', warning), 'Enable', 'on'); else set(findobj('tag', warning), 'Enable', 'off'); end end function [] = Zoom (calling_button, eventData, checkbox, fig, status) %allows the user to zoom in on axes if get(findobj('tag', checkbox), 'value') == 1 zoom(fig, status); else zoom(fig, 'out'); zoom(fig, 'off'); end end function [] = toggle (calling_button, eventData, individualTag, alignedTag, Handle1, Handle2, Handle3, Handle4, Handle5, Handle6, Handle7, Handle8) %sets the other checkbox to be checked or not depending the calling_button %checkbox alignedTagHandle = findobj('tag', alignedTag); individualTagHandle = findobj('tag', individualTag); enable = get(alignedTagHandle, 'Enable'); if strcmp(enable, 'on') == 1 if strcmp(get(calling_button, 'tag'),individualTag) == 1 if get(individualTagHandle, 'value') == 1 set(alignedTagHandle, 'value', 0); set(findobj('tag', 'autoFitSigmoid'), 'Enable', 'off', 'Value', 0); set(findobj('tag', Handle1), 'Enable', 'off'); set(findobj('tag', Handle2), 'Enable', 'off'); set(findobj('tag', Handle3), 'Enable', 'off'); set(findobj('tag', Handle4), 'Enable', 'off'); set(findobj('tag', Handle5), 'Enable', 'off'); set(findobj('tag', Handle6), 'Enable', 'off'); set(findobj('tag', Handle7), 'Enable', 'off'); set(findobj('tag', Handle8), 'Enable', 'off'); else set(alignedTagHandle, 'value', 1); set(findobj('tag', 'autoFitSigmoid'), 'Enable', 'on'); end elseif strcmp(get(calling_button, 'tag'),alignedTag) == 1 if get(alignedTagHandle, 'value') == 1 set(individualTagHandle, 'value', 0); set(findobj('tag', 'autoFitSigmoid'), 'Enable', 'on'); else set(individualTagHandle, 'value', 1); set(findobj('tag', 'autoFitSigmoid'), 'Enable', 'off', 'Value', 0); set(findobj('tag', Handle1), 'Enable', 'off'); set(findobj('tag', Handle2), 'Enable', 'off'); set(findobj('tag', Handle3), 'Enable', 'off'); set(findobj('tag', Handle4), 'Enable', 'off'); set(findobj('tag', Handle5), 'Enable', 'off'); set(findobj('tag', Handle6), 'Enable', 'off'); set(findobj('tag', Handle7), 'Enable', 'off'); set(findobj('tag', Handle8), 'Enable', 'off'); end end else set(individualTagHandle, 'value', 1); end end function [] = showAll (calling_button, eventData, table) %either shows all tracks or shows none tableHandle = findobj('tag', table); tableData = get(tableHandle, 'Data'); rows = size(tableData); rows = rows(1); if get(calling_button, 'value') == 1 tableData(:,2) = num2cell(true(rows, 1)); else tableData(:,2) = num2cell(false(rows, 1)); end set(tableHandle, 'Data', tableData); end function [] = changeImage (calling_button, eventData, axesHandle) %lets the user move slider and image time point sliderHandle = findobj('tag', 'timePointSlider'); sliderValue = get(sliderHandle, 'value'); %change text to show current time point timePointHandle = findobj('tag', 'timePoint'); sliderMax = get(sliderHandle, 'max'); set(timePointHandle, 'string', ['Time Point: ' num2str(round(sliderValue)) ' / ' num2str(sliderMax)]); %find which channels the user wants to present showChannel1Handle = findobj('tag','chooseShowChannel1'); showChannel1 = get(showChannel1Handle, 'value'); showChannel2Handle = findobj('tag','chooseShowChannel2'); showChannel2 = get(showChannel2Handle, 'value'); showChannel3Handle = findobj('tag','chooseShowChannel3'); showChannel3 = get(showChannel3Handle, 'value'); showChannel4Handle = findobj('tag','chooseShowChannel4'); showChannel4 = get(showChannel4Handle, 'value'); %if the user wants to show a channel find the image imageMatrixVector = cell(1,4); colorVector = cell(1,4); %create saver matrix with names to be used for plotTracks show = cell(1,3); %first find red, then green, then blue if showChannel3 == 1 Channel3Handle = findobj('tag','showChannel3'); imageMatrixName3 = get(Channel3Handle,'string'); show{3} = imageMatrixName3; color = 'r'; %find data set data = evalin('base',imageMatrixName3); %save data set imageMatrixVector{1} = data; colorVector{1} = color; end if showChannel2 == 1 Channel2Handle = findobj('tag','showChannel2'); imageMatrixName2 = get(Channel2Handle,'string'); show{2} = imageMatrixName2; color = 'g'; %find data set data = evalin('base',imageMatrixName2); %save data set imageMatrixVector{2} = data; colorVector{2} = color; end if showChannel1 == 1 Channel1Handle = findobj('tag','showChannel1'); imageMatrixName1 = get(Channel1Handle,'string'); show{1} = imageMatrixName1; color = 'b'; %find data set data = evalin('base',imageMatrixName1); %save data set imageMatrixVector{3} = data; colorVector{3} = color; end if showChannel4 == 1 Channel4Handle = findobj('tag','showChannel4'); imageMatrixName4 = get(Channel4Handle,'string'); color = 'w'; %find data set data = evalin('base',imageMatrixName4); %save data set imageMatrixVector{4} = data; colorVector{4} = color; end %find which channels the user tracked tracksVector = cell(2,3); chooseChannel1Handle = findobj('tag','chooseChannel1'); chooseChannel1 = get(chooseChannel1Handle, 'value'); chooseChannel2Handle = findobj('tag','chooseChannel2'); chooseChannel2 = get(chooseChannel2Handle, 'value'); chooseChannel3Handle = findobj('tag','chooseChannel3'); chooseChannel3 = get(chooseChannel3Handle, 'value'); if chooseChannel1 == 1 Channel1Handle = findobj('tag','Channel1'); imageMatrixName = get(Channel1Handle,'string'); imageMatrixName = ['finalTracks_' imageMatrixName]; %find data set data = evalin('base',imageMatrixName); %save data set tracksVector{1,1} = data; tracksVector{2,1} = imageMatrixName; end if chooseChannel2 == 1 Channel2Handle = findobj('tag','Channel2'); imageMatrixName = get(Channel2Handle,'string'); imageMatrixName = ['finalTracks_' imageMatrixName]; %find data set data = evalin('base',imageMatrixName); %save data set tracksVector{1,2} = data; tracksVector{2,2} = imageMatrixName; end if chooseChannel3 == 1 Channel3Handle = findobj('tag','Channel3'); imageMatrixName = get(Channel3Handle,'string'); imageMatrixName = ['finalTracks_' imageMatrixName]; %find data set data = evalin('base',imageMatrixName); %save data set tracksVector{1,3} = data; tracksVector{2,3} = imageMatrixName; end if isempty(find(~cellfun(@isempty,imageMatrixVector)) == 1) == 1 %this deals with unclicking a check box but still prompting a callback cla(axesHandle, 'reset'); set(axesHandle, 'color', 'k'); set(axesHandle,'XColor','w', 'xtick',[]); set(axesHandle,'YColor','w', 'ytick',[]); else showImage(imageMatrixVector, round(sliderValue), colorVector, axesHandle); %creates gray scale images of a time point and presents them color = 'm'; plotTracks(tracksVector, round(sliderValue), axesHandle, show, color); %plot tracks over image in axes alignTracksHandle = findobj('tag', 'toggleAlignedTracks'); clicked = get(alignTracksHandle, 'Value'); if clicked == 1 tracksVector = cell(2,1); finalAlignedTracks = evalin('base','finalAlignedTracks'); tracksVector{1,1} = finalAlignedTracks; tracksVector{2,1} = 'Aligned_tracks'; show = tracksVector(2,1); color = 'y'; plotTracks(tracksVector, round(sliderValue), axesHandle, show, color); end %plot aligned tracks over image in axes end end function [] = changeValue (calling_button, eventData) %Clears the sequence from edit text box and allows user input. userInput = get(calling_button, 'String'); if isempty(userInput) == 1 userInput = '0'; set(calling_button, 'String', userInput); end userValue = str2double(userInput); set(calling_button, 'value', userValue); end function [] = chooseChannel(calling_button, eventData, tag) %lets the user choose a channel and input its name checked = get(calling_button, 'value'); handle = findobj('tag', tag); if checked == 1 set(handle, 'Enable', 'on'); else set(handle, 'Enable', 'off'); end end %-------------------- statistical analysis call backs --------------------% function [] = chooseSum(calling_button, eventData) %lets the user choose to sum the pixels around the object handleXY = findobj('tag','sumPixelsXY'); handleXYTitle = findobj('tag','sumPixelsXYTitle'); handleZ = findobj('tag','sumPixelsZ'); handleZTitle = findobj('tag','sumPixelsZTitle'); checked = get(calling_button, 'value'); if checked == 1 set(handleXY, 'Enable', 'on'); set(handleXYTitle, 'Enable', 'on'); set(handleZ, 'Enable', 'on'); set(handleZTitle, 'Enable', 'on'); else set(handleXY, 'Enable', 'off'); set(handleXYTitle, 'Enable', 'off'); set(handleZ, 'Enable', 'off'); set(handleZTitle, 'Enable', 'off'); end end function [] = selectCube(calling_button, eventData) %lets the user analyze tracks within a selection cube selectionPixelsXYTitleHandle = findobj('tag', 'selectionPixelsXYTitle'); selectionPixelsXYHandle = findobj('tag', 'selectionPixelsXY'); selectionPixelsZTitleHandle = findobj('tag', 'selectionPixelsZTitle'); selectionPixelsZHandle = findobj('tag', 'selectionPixelsZ'); sumBrightestPixelsTitleHandle = findobj('tag', 'sumBrightestPixelsTitle'); sumBrightestPixelsHandle = findobj('tag', 'sumBrightestPixels'); numberOfBrightestPixelsTitleHandle = findobj('tag','numberOfBrightestPixelsTitle'); numberOfBrightestPixelsHandle = findobj('tag','numberOfBrightestPixels'); sumPixelsAboveMedianTitleHandle = findobj('tag', 'sumPixelsAboveMedianTitle'); sumPixelsAboveMedianHandle = findobj('tag', 'sumPixelsAboveMedian'); percentAboveMedianTitleHandle = findobj('tag','percentAboveMedianTitle'); percentAboveMedianHandle = findobj('tag','percentAboveMedian'); sumPixelsCloseToMaxTitleHandle = findobj('tag', 'sumPixelsCloseToMaxTitle'); sumPixelsCloseToMaxHandle = findobj('tag', 'sumPixelsCloseToMax'); percentOfMaxTitleHandle = findobj('tag','percentOfMaxTitle'); percentOfMaxHandle = findobj('tag','percentOfMax'); checked = get(calling_button, 'value'); if checked == 1 set(selectionPixelsXYTitleHandle, 'Enable', 'on'); set(selectionPixelsXYHandle, 'Enable', 'on'); set(selectionPixelsZTitleHandle, 'Enable', 'on'); set(selectionPixelsZHandle, 'Enable', 'on'); set(sumBrightestPixelsTitleHandle, 'Enable', 'on'); set(sumBrightestPixelsHandle, 'Enable', 'on'); set(sumPixelsAboveMedianTitleHandle, 'Enable', 'on'); set(sumPixelsAboveMedianHandle, 'Enable', 'on'); set(sumPixelsCloseToMaxTitleHandle, 'Enable', 'on'); set(sumPixelsCloseToMaxHandle, 'Enable', 'on'); else set(selectionPixelsXYTitleHandle, 'Enable', 'off'); set(selectionPixelsXYHandle, 'Enable', 'off'); set(selectionPixelsZTitleHandle, 'Enable', 'off'); set(selectionPixelsZHandle, 'Enable', 'off'); set(sumBrightestPixelsTitleHandle, 'Enable', 'off'); set(sumBrightestPixelsHandle, 'Enable', 'off', 'value', 0); set(numberOfBrightestPixelsTitleHandle, 'Enable', 'of'); set(numberOfBrightestPixelsHandle, 'Enable', 'of'); set(sumPixelsAboveMedianTitleHandle, 'Enable', 'off'); set(sumPixelsAboveMedianHandle, 'Enable', 'off', 'value', 0); set(percentAboveMedianTitleHandle, 'Enable', 'off'); set(percentAboveMedianHandle, 'Enable', 'off'); set(sumPixelsCloseToMaxTitleHandle, 'Enable', 'off'); set(sumPixelsCloseToMaxHandle, 'Enable', 'off', 'value', 0); set(percentOfMaxTitleHandle, 'Enable', 'off'); set(percentOfMaxHandle, 'Enable', 'off'); end end function [] = selectBrightestPixels(calling_button, eventData) %lets the user choose to sum a number of maximum intensity picels around %local maximum numberOfBrightestPixelsTitleHandle = findobj('tag','numberOfBrightestPixelsTitle'); numberOfBrightestPixelsHandle = findobj('tag','numberOfBrightestPixels'); checked = get(calling_button, 'value'); if checked == 1 set(numberOfBrightestPixelsTitleHandle, 'Enable', 'on'); set(numberOfBrightestPixelsHandle, 'Enable', 'on'); else set(numberOfBrightestPixelsTitleHandle, 'Enable', 'off'); set(numberOfBrightestPixelsHandle, 'Enable', 'off'); end end function [] = sumPixelsAboveMedian(calling_button, eventData) %lets user to choose to quantify all pixels that are above a certain %percent of the median intensity percentAboveMedianTitleHandle = findobj('tag','percentAboveMedianTitle'); percentAboveMedianHandle = findobj('tag','percentAboveMedian'); checked = get(calling_button, 'value'); if checked == 1 set(percentAboveMedianTitleHandle, 'Enable', 'on'); set(percentAboveMedianHandle, 'Enable', 'on'); else set(percentAboveMedianTitleHandle, 'Enable', 'off'); set(percentAboveMedianHandle, 'Enable', 'off'); end end function [] = sumPixelsCloseToMax(calling_button, eventData) %lets user to choose to quantify all pixels that are above a certain %percent of the max intensity percentOfMaxTitleHandle = findobj('tag','percentOfMaxTitle'); percentOfMaxHandle = findobj('tag','percentOfMax'); checked = get(calling_button, 'value'); if checked == 1 set(percentOfMaxTitleHandle, 'Enable', 'on'); set(percentOfMaxHandle, 'Enable', 'on'); else set(percentOfMaxTitleHandle, 'Enable', 'off'); set(percentOfMaxHandle, 'Enable', 'off'); end end function [] = subtractBackground(calling_button, eventData, maxX, maxY, xFrom, xTo, xStart, xEnd, yFrom, yTo, yStart, yEnd) %lets the user to choose an area in the image for background subtraction recAxes = findobj(findobj('tag', 'figure'),'type','axes'); if get(calling_button, 'Value') == 1 xLim = floor(get(recAxes, 'xlim')); xString = ['/ ' num2str(xLim(2))]; yLim = floor(get(recAxes, 'ylim')); yString = ['/ ' num2str(yLim(2))]; set(findobj('tag', maxX), 'Enable', 'on', 'Visible', 'on', 'string', xString) set(findobj('tag', maxY), 'Enable', 'on', 'Visible', 'on', 'string', yString) set(findobj('tag', xFrom), 'Enable', 'on') set(findobj('tag', xTo), 'Enable', 'on') set(findobj('tag', xStart), 'Enable', 'on') set(findobj('tag', xStart), 'Enable', 'on', 'string', num2str((xLim(2))/3), 'value', (xLim(2))/3); set(findobj('tag', xEnd), 'Enable', 'on', 'string', num2str((xLim(2)*2)/3), 'value', ((xLim(2)*2)/3)) width = get(findobj('tag', xEnd), 'Value'); set(findobj('tag', yFrom), 'Enable', 'on') set(findobj('tag', yTo), 'Enable', 'on') set(findobj('tag', yStart), 'Enable', 'on', 'string', num2str((yLim(2))/3), 'value', (yLim(2))/3); set(findobj('tag', yEnd), 'Enable', 'on', 'string', num2str((yLim(2)*2)/3), 'value', ((yLim(2)*2)/3)) height = get(findobj('tag', yEnd), 'Value'); axes(recAxes); %change current axis. Couldn't force rectangle into recAxes by playing %with properties rectangle('Position', [width/2 height/2 width/2 height/2], 'EdgeColor', 'w'); else set(findobj('tag', maxX), 'Enable', 'off', 'Visible', 'off') set(findobj('tag', maxY), 'Enable', 'off', 'Visible', 'off') set(findobj('tag', xFrom), 'Enable', 'off') set(findobj('tag', xTo), 'Enable', 'off') set(findobj('tag', xStart), 'Enable', 'off') set(findobj('tag', xEnd), 'Enable', 'off') set(findobj('tag', yFrom), 'Enable', 'off') set(findobj('tag', yTo), 'Enable', 'off') set(findobj('tag', yStart), 'Enable', 'off') set(findobj('tag', yEnd), 'Enable', 'off') refresh (calling_button, eventData, recAxes); delete(findobj(findobj('tag', 'statisticalAnalysisFigure'),'type','axes')); end end function [] = chooseGaussian(calling_button, eventData) %lets the user choose to sum the pixels around the object handleXY = findobj('tag','gaussianFitXY'); handleXYTitle = findobj('tag','gaussianFitXYTitle'); handleZ = findobj('tag','gaussianFitZ'); handleZTitle = findobj('tag','gaussianFitZTitle'); checked = get(calling_button, 'value'); if checked == 1 set(handleXY, 'Enable', 'on'); set(handleXYTitle, 'Enable', 'on'); set(handleZ, 'Enable', 'on'); set(handleZTitle, 'Enable', 'on'); else set(handleXY, 'Enable', 'off'); set(handleXYTitle, 'Enable', 'off'); set(handleZ, 'Enable', 'off'); set(handleZTitle, 'Enable', 'off'); end end %-------------------------- executing call backs -------------------------% function [] = refresh (calling_button, eventData, axesHandle) cla(axesHandle); changeImage(calling_button, eventData, axesHandle); end function [] = run (calling_button, eventData, guiHandle, axesHandle) %Runs the program. %profile on (shows amount of time take, if activated); waitBar = msgbox('You can go make yourself some coffee. I will do the work. Alone. In the dark.','Program is running'); %notify the user the program is running %find all user inputs for particle tracking xyRadiusHandle = findobj('tag','regionalMaximumRadiusXY'); maskXY = get(xyRadiusHandle,'value'); if maskXY < 1 || mod(maskXY,1) ~= 0 close(waitBar); errordlg('XY radius has to be a positive integer', 'False initial parametres'); error('XY radius has to be a positive integer'); end %look up user input for x and y radius for local maximum zRadiusHandle = findobj('tag','regionalMaximumRadiusZ'); maskZ = get(zRadiusHandle,'value'); if maskZ < 0 || mod(maskZ,1) ~= 0 close(waitBar); errordlg('Z radius has to be an integer greater than or equal to 0', 'False initial parametres'); error('Z radius has to be an integer greater than or equal to 0'); end %look up user input for z radius for local maximum thresholdHandle = findobj('tag','threshold'); threshold = get(thresholdHandle,'value'); if threshold < 0 close(waitBar); errordlg('Threshold has to be greater than or equal to 0', 'False initial parametres'); error('Threshold has to be greater than or equal to 0'); end %look up user input for intensity threshold useChannel1Handle = findobj('tag','chooseChannel1'); useChannel1 = get(useChannel1Handle, 'value'); useChannel2Handle = findobj('tag','chooseChannel2'); useChannel2 = get(useChannel2Handle, 'value'); useChannel3Handle = findobj('tag','chooseChannel3'); useChannel3 = get(useChannel3Handle, 'value'); %look up input image channles from user maxLinkingDistanceHandle = findobj('tag','maxLinkingDistance'); maxLinkingDistance = get(maxLinkingDistanceHandle, 'value'); if maxLinkingDistance < 0 || mod(maxLinkingDistance,1) ~= 0 close(waitBar); errordlg('Max linking distance has to be an integer greater than or equal to 0', 'False initial parametres'); error('Max linking distance has to be an integer greater than or equal to 0'); end %look up user input for maximum linking distance for two particles maxGapHandle = findobj('tag','maxLinkingGap'); maxGap = get(maxGapHandle, 'value'); if maxGap < 0 || mod(maxGap,1) ~= 0 close(waitBar); errordlg('Max gap has to be an integer greater than or equal to 0', 'False initial parametres'); error('Max gap has to be an integer greater than or equal to 0'); end %look up user input for max acceptable time gap minimumTrackLengthHandle = findobj('tag','minTrackLength'); minimumTrackLength = get(minimumTrackLengthHandle, 'value'); if minimumTrackLength < 0 || mod(minimumTrackLength,1) ~= 0 close(waitBar); errordlg('Minimal track length has to be an integer greater than or equal to 0', 'False initial parametres'); error('Minimal track length has to be an integer greater than or equal to 0'); end %look up user input for minimum acceptable track length pixelSizeHandle = findobj('tag','pixelSize'); pixelSize = get(pixelSizeHandle, 'value'); if (pixelSize > 0) == 0 close(waitBar); errordlg('Pixel size has to be greater than 0', 'False initial parametres'); error('Pixel size has to be greater than 0'); end %look up user input for pixel size stepSizeHandle = findobj('tag','stepSize'); stepSize = get(stepSizeHandle, 'value'); if (stepSize > 0) == 0 close(waitBar); errordlg('Step size has to be greater than 0', 'False initial parametres'); error('Step size has to be greater than 0'); end %look up user input for step size maxNoOfParticlesHandle = findobj('tag','maxNoOfParticles'); maxNoOfParticles = get(maxNoOfParticlesHandle, 'value'); if maxNoOfParticles < 1 || mod(maxNoOfParticles,1) ~= 0 close(waitBar); errordlg('Max number of particles has to be a positive integer', 'False initial parametres'); error('Max number of particles has to be a positive integer'); end %look up user input for maximum number of particles in a single time point %find input channels imageMatrixVector = cell(1,3); if useChannel1 == 1 Channel1Handle = findobj('tag','Channel1'); imageMatrixName = get(Channel1Handle,'string'); if any(strcmp(evalin('base','who'),imageMatrixName)) == 0 close(waitBar); errordlg('Channel not found. Please match channel name to an existing file or variable', 'Channel selection error'); error('Channel not found. Please match channel name to an existing file or variable'); end imageMatrixVector{1} = imageMatrixName; end if useChannel2 == 1 Channel2Handle = findobj('tag','Channel2'); imageMatrixName = get(Channel2Handle,'string'); if any(strcmp(evalin('base','who'),imageMatrixName)) == 0 close(waitBar); errordlg('Channel not found. Please match channel name to an existing file or variable', 'Channel selection error'); error('Channel not found. Please match channel name to an existing file or variable'); end imageMatrixVector{2} = imageMatrixName; end if useChannel3 == 1 Channel3Handle = findobj('tag','Channel3'); imageMatrixName = get(Channel3Handle,'string'); if any(strcmp(evalin('base','who'),imageMatrixName)) == 0 close(waitBar); errordlg('Channel not found. Please match channel name to an existing file or variable', 'Channel selection error'); error('Channel not found. Please match channel name to an existing file or variable'); end imageMatrixVector{3} = imageMatrixName; end channels2use = find(~cellfun(@isempty,imageMatrixVector)); numberOfChannels = numel(channels2use); timePoints = []; %run analysis for each channel for i = 1:numberOfChannels index = channels2use(i); imageMatrixName = imageMatrixVector{index}; imageMatrix = evalin('base',imageMatrixName); timePoints = size(imageMatrix); timePoints = timePoints(4); finalTracks = dotQuant( imageMatrix, maskXY, maskZ, maxLinkingDistance, maxGap, minimumTrackLength, pixelSize, stepSize, maxNoOfParticles, threshold ); trackName = ['finalTracks_' imageMatrixName]; assignin('base', trackName, finalTracks); %save final tracks globally %set tracks to table data to allow user to show or hide tracks dims = ndims(finalTracks); tableName = ['tracksTable' num2str(i)]; tableHandle = findobj('tag', tableName); if dims == 2 set (tableHandle, 'data', {1 true}); else numberTracks = size(finalTracks); iVector = 1:numberTracks(3); iVector = iVector'; trueVector = true(numberTracks(3),1); data = [num2cell(iVector) num2cell(trueVector)]; set (tableHandle, 'data', data); end set (tableHandle, 'Visible', 'on'); titleName = ['showTrack' num2str(i) 'Title']; tableTitleHandle = findobj('tag', titleName); title = ['Show all ' imageMatrixName ' tracks']; set(tableTitleHandle, 'String', title); set(tableTitleHandle, 'Visible', 'on'); checkboxName = ['showAllTracks' num2str(i)]; checkboxHandle = findobj('tag', checkboxName); set(checkboxHandle, 'Visible', 'on'); end %allow slider maneuvering (slider has to stay inactive untill there's %something to present) sliderHandle = findobj('tag', 'timePointSlider'); set(sliderHandle, 'max', timePoints); set(sliderHandle, 'SliderStep',... [1/timePoints , 10/timePoints ]); set(sliderHandle, 'Enable', 'on'); timePointHandle = findobj('tag', 'timePoint'); set(timePointHandle, 'string', ['Time Point: ' '1' ' / ' num2str(timePoints)]); figHandle = findobj('tag', 'figure'); set(figHandle, 'Visible', 'on'); analysisFigHandle = findobj('tag', 'statisticalAnalysisFigure'); set(analysisFigHandle, 'Visible', 'on'); alignTracksHandle = findobj('tag', 'alignTracks'); set(alignTracksHandle, 'Enable', 'on'); close(waitBar); %profile viewer end end function [] = analyze(calling_button, eventData) %runs the data analysis box = msgbox('Analyzing data and preparing files. Go treat yourself to something nice. You deserve it after all this hard work.','Program is running'); %check which analyses protocol to perform sumPixelsHandle = findobj('tag','chooseSumPixels'); sumPixels = get(sumPixelsHandle, 'value'); %check for sum of neighboring pixels selectCubeHandle = findobj('tag','selectCube'); selectCube = get(selectCubeHandle, 'value'); %check for selection cube fitGaussianHandle = findobj('tag','chooseFitGaussian'); fitGaussian = get(fitGaussianHandle, 'value'); %check for gaussian fit individualHandle = findobj('tag','individualAnalysis'); individualAnalysis = get(individualHandle, 'value'); alignedHandle = findobj('tag','alignedAnalysis'); alignedAnalysis = get(alignedHandle, 'value'); %check if user wishes to analyze aligned tracks or individual tracks %create saver matrix tracks = cell(3,3); if individualAnalysis == 1 %look up input image channles from user useChannel1Handle = findobj('tag','chooseChannel1'); useChannel1 = get(useChannel1Handle, 'value'); useChannel2Handle = findobj('tag','chooseChannel2'); useChannel2 = get(useChannel2Handle, 'value'); useChannel3Handle = findobj('tag','chooseChannel3'); useChannel3 = get(useChannel3Handle, 'value'); if useChannel1 == 1 channel1Handle = findobj('tag','Channel1'); dataName = get(channel1Handle,'string'); imageMatrix = evalin('base',dataName); tracks{1,1} = imageMatrix; %find intensities matrix finalTracks = evalin('base',['finalTracks_' dataName]); tracks{2,1} = finalTracks; tracks{3,1} = dataName; %find tracks end if useChannel2 == 1 channel2Handle = findobj('tag','Channel2'); dataName = get(channel2Handle,'string'); imageMatrix = evalin('base',dataName); tracks{1,2} = imageMatrix; %find intensities matrix finalTracks = evalin('base',['finalTracks_' dataName]); tracks{2,2} = finalTracks; tracks{3,2} = dataName; %find tracks end if useChannel3 == 1 channel3Handle = findobj('tag','Channel3'); dataName = get(channel3Handle,'string'); imageMatrix = evalin('base',dataName); tracks{1,3} = imageMatrix; %find intensities matrix finalTracks = evalin('base',['finalTracks_' dataName]); tracks{2,3} = finalTracks; tracks{3,3} = dataName; %find tracks end elseif alignedAnalysis == 1 alignedTracksNames = evalin('base','alignedTracksNames'); name1 = strrep(alignedTracksNames(1), 'finalTracks_', ''); tracks(3,1) = alignedTracksNames(1); image1 = evalin('base', name1{1}); tracks{1,1} = image1; name2 = strrep(alignedTracksNames(2), 'finalTracks_', ''); tracks(3,2) = alignedTracksNames(2); image2 = evalin('base', name2{1}); tracks{1,2} = image2; %save names of channels and the original images alignedTracks = evalin('base','finalAlignedTracks'); tracks{2,1} = alignedTracks(:,5:8,:); tracks{2,2} = alignedTracks(:,9:12,:); %save individual aligned tracks resultNames = cell(1,2); resultNames_sumPixels = resultNames; resultNames_sumBrightest = resultNames; resultNames_sumPixelsAboveMedian = resultNames; resultNames_sumPixelsCloseToMax = resultNames; resultNames_fitGaussian = resultNames; fitSigmoid = get(findobj('tag', 'autoFitSigmoid'), 'Value'); if fitSigmoid == 1 minWindow = get(findobj('tag', 'autoFitWindowMin'), 'value'); maxWindow = get(findobj('tag', 'autoFitWindowMax'), 'value'); minDeltaT = get(findobj('tag', 'autoFitDeltaMin'), 'value'); maxDeltaT = get(findobj('tag', 'autoFitDeltaMax'), 'value'); end end indices = find(~cellfun(@isempty,tracks(1,:))); numberOfTracks = numel(indices); for i = 1:numberOfTracks index = indices(i); imageMatrix = tracks{1,index}; finalTracks = tracks{2,index}; channelName = tracks{3,index}; %find tracks and channels %find which analysis protocol the user chose if sumPixels == 1 handleXY = findobj('tag','sumPixelsXY'); handleZ = findobj('tag','sumPixelsZ'); xyPixels = get(handleXY, 'value'); zPixels = get(handleZ, 'value'); %get user defined variables flag = 2; resultName_sumPixels = [channelName '_sumNeighbors']; sumTrack(resultName_sumPixels, imageMatrix, finalTracks, xyPixels, zPixels, flag) %perform data analysis if alignedAnalysis == 1 if i == 2 resultNames_sumPixels{2} = resultName_sumPixels; if fitSigmoid == 1 [greenFit, redFit] = autoYeastAnalyzer(resultNames_sumPixels, minWindow, maxWindow, minDeltaT, maxDeltaT); writeData(resultNames_sumPixels, greenFit, redFit); else writeData(resultNames_sumPixels); end else resultNames_sumPixels{1} = resultName_sumPixels; end else writeData(resultName_sumPixels); %save data to file end end if selectCube == 1 selectionPixelsXYHandle = findobj('tag', 'selectionPixelsXY'); maskXY = get(selectionPixelsXYHandle, 'value'); selectionPixelsZHandle = findobj('tag', 'selectionPixelsZ'); maskZ = get(selectionPixelsZHandle, 'value'); %find size of selection cube %what protocol did the user choose sumBrightestPixelsHandle = findobj('tag', 'sumBrightestPixels'); sumBrightest = get(sumBrightestPixelsHandle, 'value'); if sumBrightest == 1 numberOfBrightestPixelsHandle = findobj('tag', 'numberOfBrightestPixels'); pixels = get(numberOfBrightestPixelsHandle, 'value'); flag = 3; resultName_sumBrightest = [channelName '_brightestNeighbors']; sumTrack(resultName_sumBrightest, imageMatrix, finalTracks, maskXY, maskZ, flag, pixels) if alignedAnalysis == 1 if i == 2 resultNames_sumBrightest{2} = resultName_sumBrightest; if fitSigmoid == 1 [greenFit, redFit] = autoYeastAnalyzer(resultNames_sumBrightest, minWindow, maxWindow, minDeltaT, maxDeltaT); writeData(resultNames_sumBrightest, greenFit, redFit); else writeData(resultNames_sumBrightest); end else resultNames_sumBrightest{1} = resultName_sumBrightest; end else writeData(resultName_sumBrightest); %save data to file end end sumPixelsAboveMedianHandle = findobj('tag', 'sumPixelsAboveMedian'); sumPixelsAboveMedian = get(sumPixelsAboveMedianHandle, 'value'); if sumPixelsAboveMedian == 1 percentAboveMedianHandle = findobj('tag', 'percentAboveMedian'); percentAboveMedian = get(percentAboveMedianHandle, 'value'); flag = 4; resultName_sumPixelsAboveMedian = [channelName '_aboveMedian']; sumTrack(resultName_sumPixelsAboveMedian, imageMatrix, finalTracks, maskXY, maskZ, flag, percentAboveMedian) if alignedAnalysis == 1 if i == 2 resultNames_sumPixelsAboveMedian{2} = resultName_sumPixelsAboveMedian; if fitSigmoid == 1 [greenFit, redFit] = autoYeastAnalyzer(resultNames_sumPixelsAboveMedian, minWindow, maxWindow, minDeltaT, maxDeltaT); writeData(resultNames_sumPixelsAboveMedian, greenFit, redFit); else writeData(resultNames_sumPixelsAboveMedian); end else resultNames_sumPixelsAboveMedian{1} = resultName_sumPixelsAboveMedian; end else writeData(resultName_sumPixelsAboveMedian); %save data to file end end sumPixelsCloseToMaxHandle = findobj('tag', 'sumPixelsCloseToMax'); sumPixelsCloseToMax = get(sumPixelsCloseToMaxHandle, 'value'); if sumPixelsCloseToMax == 1 percentOfMaxHandle = findobj('tag', 'percentOfMax'); percentOfMax = get(percentOfMaxHandle, 'value'); flag = 5; resultName_sumPixelsCloseToMax = [channelName '_closeToMax']; sumTrack(resultName_sumPixelsCloseToMax, imageMatrix, finalTracks, maskXY, maskZ, flag, percentOfMax) if alignedAnalysis == 1 if i == 2 resultNames_sumPixelsCloseToMax{2} = resultName_sumPixelsCloseToMax; if fitSigmoid == 1 [greenFit, redFit] = autoYeastAnalyzer(resultNames_sumPixelsCloseToMax, minWindow, maxWindow, minDeltaT, maxDeltaT); writeData(resultNames_sumPixelsCloseToMax, greenFit, redFit); else writeData(resultNames_sumPixelsCloseToMax); end else resultNames_sumPixelsCloseToMax{1} = resultName_sumPixelsCloseToMax; end else writeData(resultName_sumPixelsCloseToMax); %save data to file end end end if fitGaussian == 1 handleXY = findobj('tag','gaussianFitXY'); handleZ = findobj('tag','gaussianFitZ'); xyRange = get(handleXY, 'value'); zRange = get(handleZ, 'value'); pixelSizeHandle = findobj('tag','pixelSize'); pixelSize = get(pixelSizeHandle, 'value'); %look up user input for pixel size stepSizeHandle = findobj('tag','stepSize'); stepSize = get(stepSizeHandle, 'value'); %look up user input for step size %get user defined variables resultName_fitGaussian = [channelName '_gaussian']; sumTrack(resultName_fitGaussian, imageMatrix, finalTracks, xyRange, zRange, flag, pixelSize, stepSize) if alignedAnalysis == 1 if i == 2 resultNames_fitGaussian{2} = resultName_fitGaussian; if fitSigmoid == 1 [greenFit, redFit] = autoYeastAnalyzer(resultNames_fitGaussian, minWindow, maxWindow, minDeltaT, maxDeltaT); writeData(resultNames_fitGaussian, greenFit, redFit); else writeData(resultNames_fitGaussian); end else resultNames_fitGaussian{1} = resultName_fitGaussian; end else writeData(resultName_fitGaussian); %save data to file end end end close(box); %find text files in current folder currentFolder = pwd; title = 'Choose folder to save analysis files'; if ismac h = helpdlg(title, 'File saver'); end targetFolder = uigetdir(currentFolder, title); if ismac close(h); end files = [currentFolder '/' '*.xlsx']; folderInfo = dir(files); fileNames = {folderInfo(:).name}; numberFiles = numel(fileNames); for i = 1:numberFiles file = [currentFolder '/' fileNames{i}]; copyfile(file,targetFolder) end delete(files); set(findobj('tag', 'plotAnalysisResults'), 'enable', 'on'); end function [] = closepushbutton(calling_button, eventData, FigHandle) %Closes the main figure (quit button) close all; end %-------------------------------------------------------------------------% %-------------------------------- graphics -------------------------------% %-------------------------------------------------------------------------% function [] = showImage(imageMatrixVector, time, colorVector, axesHandle) %creates a gray scale maximum projection for a single time point %from a 3D time lapse. Does this to all data sets and shows them %in axes dataSetsIndices = find(~cellfun('isempty',colorVector)); dataSets = numel(dataSetsIndices); [y,x,~,~,~] = size(imageMatrixVector{dataSetsIndices(1)}); %find image dimensions grayMaxImage = zeros(y,x); %create saver matrix for maximum projection red = grayMaxImage; green = grayMaxImage; blue = grayMaxImage; gray = ones(y,x); transparencyMatrix = grayMaxImage; for i = 1:dataSets index = dataSetsIndices(i); image = imageMatrixVector{index}; maximumProjection = max(image(:,:,:,time),[],3); grayScaled = mat2gray(maximumProjection); %create a gray scale maximum projection grayMaxImage(:,:) = grayScaled; color = colorVector{index}; if strcmp(color, 'r') == 1 red = grayMaxImage; if get(findobj('Tag', 'enhanceContrastChannel3'), 'Value') == 1 red = adapthisteq(red); end elseif strcmp(color, 'g') == 1 green = grayMaxImage; if get(findobj('Tag', 'enhanceContrastChannel2'), 'Value') == 1 green = adapthisteq(green); end elseif strcmp(color, 'b') == 1 blue = grayMaxImage; if get(findobj('Tag', 'enhanceContrastChannel1'), 'Value') == 1 blue = adapthisteq(blue); end elseif strcmp(color, 'w') == 1 gray = grayMaxImage; if get(findobj('Tag', 'enhanceContrastChannel4'), 'Value') == 1 gray = adapthisteq(gray); end end end rgbImage = cat(3, red, green, blue); imshow(rgbImage, 'Parent', axesHandle); hold on; dic = imshow(gray, 'Parent', axesHandle); set(dic, 'AlphaData', (1-gray)); if get(findobj('Tag', 'subtractBackground'), 'Value') == 1 hold on; left = get(findobj('Tag', 'subtractBackgroundXstart'), 'Value'); if left < 1 set(findobj('Tag', 'subtractBackgroundXstart'), 'Value', 1, 'String', '1'); left = 1; end bottom = get(findobj('Tag', 'subtractBackgroundYstart'), 'Value'); if bottom < 1 set(findobj('Tag', 'subtractBackgroundYstart'), 'Value', 1, 'String', '1'); bottom = 1; end width = get(findobj('Tag', 'subtractBackgroundXend'), 'Value') - left; xMax = strsplit(get(findobj('Tag', 'subtractBackgroundXMax'), 'String'),' '); xMax = str2double(xMax{2}); if left+width >= xMax set(findobj('Tag', 'subtractBackgroundXend'), 'Value', (xMax-1), 'String', num2str(xMax-1)); width = xMax - (left+1); end height = get(findobj('Tag', 'subtractBackgroundYend'), 'Value') - bottom; yMax = strsplit(get(findobj('Tag', 'subtractBackgroundYMax'), 'String'),' '); yMax = str2double(yMax{2}); if bottom+height >= yMax set(findobj('Tag', 'subtractBackgroundYend'), 'Value', (yMax-1), 'String', num2str(yMax-1)); height = yMax - (bottom+1); end rectangle('Position', [left bottom width height], 'EdgeColor', 'w'); end end function [] = plotTracks(tracks, timePoint, axesHandle, show, color) %plots tracks over image %find all channels that require track plotting indicesTracks = find(~cellfun(@isempty,tracks(1,:))); indicesShow = find(~cellfun(@isempty,show)); indices = ismember(indicesTracks, indicesShow); indices = indicesTracks(indices); tracks2plot = numel(indices); for i = 1:tracks2plot index = indices(1,i); channelTracks = tracks{1,index}; tracksInTime = channelTracks(1,4,:)<=timePoint; %find if there are tracks that have current time point channelName = show{index}; if strcmp(channelName, 'Aligned_tracks') == 1 tag = 'tracksTable4'; else tableTitleName = ['Show all ' channelName ' tracks']; titleHandle = findobj('String', tableTitleName); tag = get(titleHandle, 'Tag'); tag = strrep(tag, 'Title', ''); tag = strrep(tag, 'showTrack', 'tracksTable'); end tableHandle = findobj('tag', tag); tableData = get(tableHandle, 'Data'); tableData = logical(~cellfun(@isempty,(cellfun(@find,tableData(:,2),'UniformOutput', 0)))); %find if there are tracks that the user wishes to show for x = 1:numel(tableData) tracksInTime(1,1,x) = tracksInTime(1,1,x)*tableData(x); end %if there are any tracks in the current time point that the user wishes to show %plot them up to that time point if isempty(tracksInTime) == 0 && isempty(find(tracksInTime,3)) == 0 tracksIndices = find(tracksInTime == 1); %which tracks are in current time point numberOfTracks = numel(tracksIndices); %how many tracks in total are in current time point sizeTracks = size(channelTracks); if numel(sizeTracks)<3 colorVector = hsv(1); else colorVector = hsv(sizeTracks(3)); end for track = 1:numberOfTracks %for each track trackColor = colorVector(track,:); %choose color for tracks currentTrack = tracksIndices(track); endRow = find(channelTracks(:,4,currentTrack) == timePoint); if strcmp(channelName, 'Aligned_tracks') == 1 iterations = 2; column = [5,6;9,10]; else iterations = 1; column = [1,2]; end for iteration = 1:iterations hold(axesHandle,'on') scatter(axesHandle, channelTracks(endRow,column(iteration,2),currentTrack), channelTracks(endRow,column(iteration,1), currentTrack),... 50,... 'LineWidth',2,... 'MarkerEdgeColor',color); %where to plot, x(2nd column), y(first column), style end s2 = num2str(currentTrack); %track number if strcmp(channelName, 'Aligned_tracks') == 1 s3 = strcat('Aligned\_track','\_'); else s3 = strcat(channelName,'\_'); end trackText = strcat(s3,s2); %create string for track number text( channelTracks(endRow,2,currentTrack), channelTracks(endRow,1,currentTrack),... trackText,... 'FontSize', 12,... 'HorizontalAlignment', 'left',... 'VerticalAlignment', 'bottom',... 'parent', axesHandle,... 'Color', 'c') %add track number reference if timePoint > 1 x = channelTracks(1:endRow,2,currentTrack); y = channelTracks(1:endRow,1,currentTrack); plot( axesHandle, x, y, ':', 'Color', trackColor, 'LineWidth',2) %connect the dots to form a track end end end end end %-------------------------------------------------------------------------% %-------------------------- statistical analysis -------------------------% %-------------------------------------------------------------------------% function [] = sumTrack(matrixName, image, tracks, xyPixels, zPixels, flag, threshold, pixelSize, stepSize) %sums the intensity of each time point for each track %flag = 2 : sum all neighboring pixels within range %flag = 3 : sum #n brightest neighboring pixels %flag = 4 : sum neighbors above median %flag = 5 : sum neighbors close to max value inputs = nargin; imageDimensions = size(image); dimensions = size(tracks); if numel(dimensions) == 2 numberOfTracks = 1; else numberOfTracks = dimensions(3); %find number of tracks end tracksSum = cell(numberOfTracks,1); for track = 1:numberOfTracks %analyze track by track timePoints = max(find(tracks(:,4,track) ~=0)); %find last non zero element intensities = zeros(timePoints,2); %create array the size of the number of actual coordinates %one column for intensity the other for time point: [intensity time] for time = 1:timePoints %calculate intensity for each time point x = tracks(time,2,track); y = tracks(time,1,track); z = tracks(time,3,track); t = tracks(time,4,track); indCoordinate = sub2ind(imageDimensions, y, x, z, t); %turn subscripted coordinates to indexed coordinates to use in %compareSubMatrix if inputs == 6 sumIntensity = compareSubMatrix( image, xyPixels, zPixels, indCoordinate, flag); elseif inputs == 7 sumIntensity = compareSubMatrix( image, xyPixels, zPixels, indCoordinate, flag, threshold); end intensities(time,1) = sumIntensity; intensities(time,2) = tracks(time,4,track); end %copy to outside saver matrix tracksSum{track} = intensities; end assignin('base', matrixName, tracksSum); %assign as a global variable end %-------------------------------------------------------------------------% %------------------------------ data export ------------------------------% %-------------------------------------------------------------------------% function [] = writeData(resultName, greenFit, redFit) %write results to file %different files for individual tracks. same files for aligned tracks pause('on'); dimensions = size(resultName,2); %if results has 2 entries then it's aligned tracks if dimensions == 2 data1 = evalin('base',resultName{1}); data2 = evalin('base',resultName{2}); %copy results data tracks = numel(data1); %find number of tracks analysisType = (strsplit(resultName{1},'_')); analysisType = analysisType {1,size(analysisType, 2)}; fileName = ['Aligned_tracks' '_' analysisType '.xlsx']; %create excel file name columnHeaders = {'Timepoint' 'Intensity' 'y' 'x' 'z'}; %create column headers: timepoint, intensity and coordinates for i = 1:tracks sheet = ['Track_' num2str(i)]; %open new sheet for each track coordinatesData = evalin('base','finalAlignedTracks'); trackData1 = data1{i}; coordinatesData1 = coordinatesData(1:size(trackData1, 1),5:7,i); trackData2 = data2{i}; coordinatesData2 = coordinatesData(1:size(trackData2, 1),9:11,i); tracksData1 = [trackData1(:,2) trackData1(:,1)]; tracksData2 = [trackData2(:,2) trackData2(:,1)]; rows = size(tracksData1,1); dataToExport = cell(rows+3,25); dataToExport(1,1) = {strjoin([resultName(1), 'aligned with', resultName(2)])}; dataToExport(2,1) = resultName(1); dataToExport(2,6) = resultName(2); dataToExport(3,1:10) = [columnHeaders columnHeaders]; dataToExport(4:end,1:10) = num2cell([tracksData1 coordinatesData1 tracksData2 coordinatesData2]); if nargin == 3 %if auto fit was applied fitHeader1 = strsplit(resultName{1},'_'); fitHeader2 = strsplit(resultName{2},'_'); fitColumnHeaders = {[fitHeader1{2} '_norm'] [fitHeader1{2} '_sigmoid'] [fitHeader2{2} '_norm'] [fitHeader2{2} '_sigmoid']}; dataToExport(3,11:14) = fitColumnHeaders; dataToExport(4:end,11:14) = num2cell([greenFit{i,1} greenFit{i,2} redFit{i,1} redFit{i,2}]); dataToExport(3:4,16) = [fitHeader1(2);fitHeader2(2)]; dataToExport(2,16:25) = {'Sigmoidal Fit:' 'Window Start' 'Window End' 'Minimum' 'Height' 'Slope' 'Midpoint' 'Score' '' 'delta T'}; dataToExport(3:4,17:23) = num2cell([greenFit{i,3};redFit{i,3}]); dataToExport(3,25) = num2cell(redFit{i,3}(6) - greenFit{i,3}(6)); end writecell(dataToExport,fileName,'Sheet',sheet,'Range','A1'); end else data = evalin('base',resultName); tracks = numel(data); fileName = [resultName '.xlsx']; columnHeaders = {'timePoint' 'Intensity' 'y' 'x' 'z'}; channel = (strsplit(resultName,'_')); channel = channel{1}; coordinatesData = evalin('base', ['finalTracks_' channel]); for i = 1:tracks sheet = ['Track_' num2str(i)]; %open new sheet for each track trackData = data{i}; tracksData = [trackData(:,2) trackData(:,1)]; rows = size(tracksData,1); coordinates = coordinatesData(1:rows,1:3,i); dataToExport = cell(rows+2,5); dataToExport(1,1) = {resultName}; dataToExport(2,1:5) = columnHeaders; dataToExport(3:end,1:5) = num2cell([tracksData coordinates]); writecell(dataToExport,fileName,'Sheet',sheet,'Range','A1'); end end end %-------------------------------------------------------------------------% %------------------------------ separate GUIs ----------------------------% %-------------------------------------------------------------------------% function [ ] = showSeparateFun(calling_button, eventData, tag ) %call back function %shows an image in seperate axes clicked = get(calling_button, 'Value'); imageNameHandle = findobj('tag', tag); imageName = get(imageNameHandle, 'String'); exists = any(strcmp(evalin('base','who'),imageName)); if clicked == 1 && exists == 1 separateWindow = figure('Position', [200, 200, 960, 720],... 'tag','sperateFigure','color', 'w', 'MenuBar','none',... 'name','','numbertitle','off', 'Visible', 'on'); separateAxes = subplot('position', [0.025 0.15 0.85 0.825], 'color', 'k',... 'parent', separateWindow, 'tag', 'mainAxes'); %[left,bottom,width,height] set(separateAxes,'XColor','w', 'xtick',[]); set(separateAxes,'YColor','w', 'ytick',[]); uicontrol('style' ,'slider',.... 'parent', separateWindow,... 'unit', 'norm',... 'position',[0.1 0.05 0.75 0.025],... %[left,bottom,width,height] 'Enable', 'on',... 'tag' ,'separateSlider',... 'max' ,100,... %change values to fit number of time points 'min' ,1,... 'sliderstep',[0.01 0.1],... %change to 1 time point per minor step 'value' ,1,... 'callback', {@changeSeparate, separateAxes, tag}); % Adds timepoint over slider uicontrol('Style','text',... 'parent', separateWindow,... 'String','Time point',... 'fontsize', 12,... 'HorizontalAlignment', 'left',... 'backgroundColor','w',... 'foregroundColor','b',... 'unit', 'norm',... 'Position',[0.125 0.1 0.2 0.025],... %[left,bottom,width,height] 'tag','separateTimePoint'); uicontrol('style' ,'pushbutton',... 'parent', separateWindow,... 'string', 'Close',... 'fontsize', 12,... 'unit', 'norm',... 'position',[0.9, 0.05 0.075 0.03],... %[left,bottom,width,height] 'tag','close',... 'callback', {@closeFig, separateWindow, 'showSeparate'}); uicontrol('Style','checkbox',... 'parent', separateWindow,... 'backgroundColor','w',... 'Value', 0,... 'foregroundColor','k',... 'fontsize', 12,... 'string', 'Zoom in',... 'unit', 'norm',... 'Position',[0.9 0.2 0.15 0.03],... %[left,bottom,width,height] 'tag','separateZoomIn',... 'callback', {@Zoom, 'separateZoomIn', separateWindow, 'on'}); uicontrol('style' ,'pushbutton',... 'parent', separateWindow,... 'String','Reset view' ,... 'Enable', 'on',... 'unit', 'norm',... 'fontsize', 12,... 'position',[0.9 0.15 0.075 0.03],... %[left,bottom,width,height] 'tag','separateResetView',... 'callback', {@Zoom, 'separateZoomIn', separateWindow, 'out'}); set(separateWindow, 'name', imageName); set(findobj('tag', 'separateSlider'), 'Max', get(findobj('tag', 'timePointSlider'), 'Max')); set(findobj('tag', 'separateSlider'), 'value', get(findobj('tag', 'timePointSlider'), 'value')); changeSeparate(calling_button, eventData, separateAxes, tag) else if ishandle(findobj('tag', 'sperateFigure')) == 1 close(findobj('tag', 'sperateFigure')); end end end function [] = changeSeparate(calling_button, eventData, axes, tag) %changes image in response to slider value = get(findobj('tag', 'separateSlider'), 'value'); imageNameHandle = findobj('tag', tag); imageName = get(imageNameHandle, 'String'); imageMatrix = evalin('base',imageName); imageMatrixVector = cell(1); imageMatrixVector{1} = imageMatrix; colorVector = cell(1); colorVector{1} = 'w'; showImage(imageMatrixVector, round(value), colorVector, axes); %change text to show current time point separateTimePointHandle = findobj('tag', 'separateTimePoint'); sliderMax = get(findobj('tag', 'separateSlider'), 'max'); set(separateTimePointHandle, 'string', ['Time Point: ' num2str(round(value)) ' / ' num2str(sliderMax)]); end function [] = closeFig(calling_button, eventData, FigHandle, checkbox) %Closes the window with handle FigHandle set(findobj('tag', checkbox), 'value', 0); close (FigHandle); end function [] = Zoom (calling_button, eventData, checkbox, fig, status) %allows the user to zoom in on axes if get(findobj('tag', checkbox), 'value') == 1 zoom(fig, status); else zoom(fig, 'out'); zoom(fig, 'off'); end end