Vasco summer start

.gitignore

@@ -21,3 +21,4 @@ variables.mat
 
 # System files on Mac.
 *.DS_Store
+BF_Functions/2022-05-16-IBK-Gal8/matlab.mat

Ai9DetermineCutoff.m

@@ -0,0 +1,16 @@
+Area=squeeze(Data(:,:,1,:));
+Tomato=squeeze(Data(:,:,2,:));
+TooLow=~(Tomato>0.1);
+Area2=Area;
+Tomato2=Tomato;
+Area2(TooLow) =[NaN];
+Tomato2(TooLow)=[NaN];
+% 
+TotArea=sum(Area2,'omitnan');
+AvTomato=(Tomato2);
+figure, plot3(1:384,Area2,Tomato2,'o')
+grid on
+% % Area=sum(squeeze(Data(:,:,1,:)),'omitnan');
+% % AvTomato=mean(squeeze(Data(:,:,2,:)),'omitnan');
+% figure, plot3(1:384,Area,AvTomato,'o')
+% grid on

Analysis/CellAnalysis/Plot_Fluorescence.m

@@ -66,6 +66,8 @@ function Plot_Fluorescence(aCells, aAxes, aChannel, varargin)
             fluor = c.regionProps.(['FluorMax' aChannel]);
         case 'avg'
             fluor = c.regionProps.(['FluorAvg' aChannel]);
+        case 'test'
+            fluor = c.regionProps.(['FluorAvg' aChannel]);    
         case 'tot'
             fluor = c.regionProps.(['FluorTot' aChannel]);
             if strcmpi(aYUnit, 'microns')

Analysis/CellAnalysis/Plot_Fluorescence3D.m

@@ -0,0 +1,155 @@
+function Plot_Fluorescence(aCells, aAxes, aChannel,aChannel2,Color, varargin)
+% Plots the fluorescence intensity of cells over time.
+%
+% The function can be used to plot the maximum intensity, the average
+% intensity or the integrated intensity. The function only works for cells
+% that come from the same image sequence. The function can only be used on
+% tracking results where there is a fluorescent channel. The function is
+% meant to be called by CellAnalysisPlayer. The function will only show up
+% in the CellAnalysisPlayer GUI if the dataset has one or more
+% fluorescence channels. The function PrintStyle is called to make the
+% plotting style consistent with other plots.
+%
+% Inputs:
+% aCells - Cells for which the fluorescence will be plotted.
+% aAxes - Axes object to plot the data in.
+% aChannel - The name of the fluorescence channel to be plotted.
+%
+% Property/Value inputs:
+% XUnit - The time unit used on the x-axis. The options are 'frames' and
+%         'hours', and the default is 'hours'.
+% YUnit - The length unit used to compute the integrated intensity. The
+%         options are 'pixels' and 'microns'. For 2D datasets, the
+%         resulting units on the y-axis are intensity * pixels and
+%         intensity * square microns respectively. For 3D datasets, the
+%         units are intensity * voxels or intensity * cubic microns. The
+%         default is 'microns'. Note that this input has an effect only if
+%         Metric is 'tot'.
+% Metric - What parameter of the fluorescence to plot. The options are
+%          'max', 'avg', and 'tot', and they correspond to the maximum,
+%          average, and the integrated fluorescence over the cell area. The
+%          default is 'max'.
+%
+% See also:
+% CellAnalysisPlayer, Plot_AxisRatio, Plot_CellSize, Plot_LinageTree,
+% Plot_TotalDistance, PrintStyle
+
+% Get property/value inputs.
+[aXUnit, aYUnit, aMetric1] = GetArgs(...
+    {'XUnit', 'YUnit', 'Metric'},...
+    {'hours', 'microns', 'max'},...
+    true, varargin);
+
+% Clear the previous plot.
+% cla(aAxes)
+% hold(aAxes, 'off')
+
+if isempty(aCells)
+    return
+end
+imData = aCells(1).imageData;
+%     BronkBox=cell(length(cells2),max([cells2.stopT]));
+for i = 1:length(aCells)
+    c = aCells(i);
+    % Time (x-coordinates of plot).
+%     switch aXUnit
+%         case 'hours'
+%             t = imData.FrameToT(c.firstFrame : c.lastFrame);
+%         case 'frames'
+%             t = c.firstFrame : c.lastFrame;
+%     end
+    t=1;
+    % Fluorescence (y-coordinates of plot).
+    aMetric1= 'avg';
+    switch lower(aMetric1)
+        case 'max'
+            fluor = c.regionProps.(['FluorMax' aChannel]);
+        case 'avg'
+            fluor = c.regionProps.(['FluorAvg' aChannel]);
+        case 'test'
+            fluor = c.regionProps.(['FluorAvg' aChannel]);    
+        case 'tot'
+            fluor = c.regionProps.(['FluorTot' aChannel]);
+            if strcmpi(aYUnit, 'microns')
+                if imData.GetDim() == 2
+                    fluor = imData.Pixel2ToMicroM2(fluor);
+                else
+                    fluor = imData.VoxelToMicroM3(fluor);
+                end
+            end
+    end
+    aMetric2= 'tot';
+    % Fluorescence (z-coordinates of plot).
+    switch lower(aMetric2)
+        case 'max'
+            fluor2 = c.regionProps.(['FluorMax' aChannel2]);
+        case 'avg'
+            fluor2 = c.regionProps.(['FluorAvg' aChannel2]);
+        case 'test'
+            fluor2 = c.regionProps.(['FluorAvg' aChannel2]);    
+        case 'tot'
+            fluor2 = c.regionProps.(['FluorTot' aChannel2]);
+            if strcmpi(aYUnit, 'microns')
+                if imData.GetDim() == 2
+                    fluor2 = imData.Pixel2ToMicroM2(fluor2);
+                else
+                    fluor2 = imData.VoxelToMicroM3(fluor2);
+                end
+            end
+    end
+    % Plot the fluorescence over time for one cell.
+    Color=Color;
+    Color2=Color+0.4*((i-1)/length(aCells));
+    Color2(Color2>1)=1;
+    Color2(Color2<0)=1;
+    PlotWithNan3D(aAxes, t, fluor,fluor2,'color',Color2,...
+        'LineWidth', 2);
+%     alpha(.5);
+    hold(aAxes, 'on')
+%     testing=Color;
+end
+
+% Set the limits of the plot.
+SetYLimits(aAxes)
+xlim(aAxes, imData.GetTLim(aXUnit, 'Margins', [0.01 0.01]))
+
+% x-label.
+switch lower(aXUnit)
+    case 'frames'
+        xlabel(aAxes, 'Time (frames)')
+    case 'hours'
+        xlabel(aAxes, 'Time (hours)')
+end
+
+% y-label and title.
+switch lower(aMetric1)
+    case 'max'
+        title(aAxes, sprintf('Maximum fluorescence (%s)',...
+            SpecChar(imData.GetSeqDir(), 'matlab')))
+        ylabel(aAxes, 'Fluorescence (relative to max)')
+    case 'avg'
+        title(aAxes, sprintf('Average fluorescence (%s)',...
+            SpecChar(imData.GetSeqDir(), 'matlab')))
+        ylabel(aAxes, 'Fluorescence (relative to max)')
+    case 'tot'
+        title(aAxes, sprintf('Integrated fluorescence (%s)',...
+            SpecChar(imData.GetSeqDir(), 'matlab')))
+        if imData.GetDim() == 2
+            switch aYUnit
+                case 'pixels'
+                    ylabel(aAxes, 'Fluorescence (relative to max) * Area in pixels')
+                case 'microns'
+                    ylabel(aAxes, 'Fluorescence (relative to max) * Area in \mum^2')
+            end
+        else
+            switch aYUnit
+                case 'pixels'
+                    ylabel(aAxes, 'Fluorescence (relative to max) * Volume in voxels')
+                case 'microns'
+                    ylabel(aAxes, 'Fluorescence (relative to max) * Volume in \mum^3')
+            end
+        end
+end
+
+PrintStyle(aAxes)
+end

Analysis/CellAnalysis/Plot_Fluorescence3D_2.m

@@ -0,0 +1,157 @@
+function Plot_Fluorescence3D_2(aCells, aAxes, aChannel,aChannel2,Color,x_in, varargin)
+% Plots the fluorescence intensity of cells over time.
+%
+% The function can be used to plot the maximum intensity, the average
+% intensity or the integrated intensity. The function only works for cells
+% that come from the same image sequence. The function can only be used on
+% tracking results where there is a fluorescent channel. The function is
+% meant to be called by CellAnalysisPlayer. The function will only show up
+% in the CellAnalysisPlayer GUI if the dataset has one or more
+% fluorescence channels. The function PrintStyle is called to make the
+% plotting style consistent with other plots.
+%
+% Inputs:
+% aCells - Cells for which the fluorescence will be plotted.
+% aAxes - Axes object to plot the data in.
+% aChannel - The name of the fluorescence channel to be plotted.
+%
+% Property/Value inputs:
+% XUnit - The time unit used on the x-axis. The options are 'frames' and
+%         'hours', and the default is 'hours'.
+% YUnit - The length unit used to compute the integrated intensity. The
+%         options are 'pixels' and 'microns'. For 2D datasets, the
+%         resulting units on the y-axis are intensity * pixels and
+%         intensity * square microns respectively. For 3D datasets, the
+%         units are intensity * voxels or intensity * cubic microns. The
+%         default is 'microns'. Note that this input has an effect only if
+%         Metric is 'tot'.
+% Metric - What parameter of the fluorescence to plot. The options are
+%          'max', 'avg', and 'tot', and they correspond to the maximum,
+%          average, and the integrated fluorescence over the cell area. The
+%          default is 'max'.
+%
+% See also:
+% CellAnalysisPlayer, Plot_AxisRatio, Plot_CellSize, Plot_LinageTree,
+% Plot_TotalDistance, PrintStyle
+
+% Get property/value inputs.
+[aXUnit, aYUnit, aMetric] = GetArgs(...
+    {'XUnit', 'YUnit', 'Metric'},...
+    {'hours', 'microns', 'max'},...
+    true, varargin);
+
+% Clear the previous plot.
+% cla(aAxes)
+% hold(aAxes, 'off')
+
+if isempty(aCells)
+    return
+end
+imData = aCells(1).imageData;
+%     BronkBox=cell(length(cells2),max([cells2.stopT]));
+for i = 1:length(aCells)
+    c = aCells(i);
+    % Time (x-coordinates of plot).
+    switch aXUnit
+        case 'hours'
+            t = imData.FrameToT(c.firstFrame : c.lastFrame);
+        case 'frames'
+            t = c.firstFrame : c.lastFrame;
+    end
+    t=x_in;
+    % Fluorescence (y-coordinates of plot).
+    aMetric= 'avg';
+    switch lower(aMetric)
+        case 'max'
+            fluor = c.regionProps.(['FluorMax' aChannel]);
+        case 'avg'
+            fluor = c.regionProps.(['FluorAvg' aChannel]);
+        case 'test'
+            fluor = c.regionProps.(['FluorAvg' aChannel]);    
+        case 'tot'
+            fluor = c.regionProps.(['FluorTot' aChannel]);
+            if strcmpi(aYUnit, 'microns')
+                if imData.GetDim() == 2
+                    fluor = imData.Pixel2ToMicroM2(fluor);
+                else
+                    fluor = imData.VoxelToMicroM3(fluor);
+                end
+            end
+    end
+    aMetric2= 'tot';
+    % Fluorescence (z-coordinates of plot).
+    switch lower(aMetric2)
+        case 'max'
+            fluor2 = c.regionProps.(['FluorMax' aChannel2]);
+        case 'avg'
+            fluor2 = c.regionProps.(['FluorAvg' aChannel2]);
+        case 'test'
+            fluor2 = c.regionProps.(['FluorAvg' aChannel2]);    
+        case 'tot'
+            fluor2 = c.regionProps.(['FluorTot' aChannel2]);
+            if strcmpi(aYUnit, 'microns')
+                if imData.GetDim() == 2
+                    fluor2 = imData.Pixel2ToMicroM2(fluor2);
+                else
+                    fluor2 = imData.VoxelToMicroM3(fluor2);
+                end
+            end
+    end
+    % Plot the fluorescence over time for one cell.
+    Color=Color;
+    Color2=Color+0.4*((i-1)/length(aCells));
+    Color2(Color2>1)=1;
+    Color2(Color2<0)=1;
+%     PlotWithNan3D(aAxes, t, fluor,fluor2,'color',Color2,...
+%         'LineWidth', 2);
+    PlotWithNan3D(aAxes, t, fluor,fluor2,'color',Color2,...
+        'LineWidth', 2);
+%     alpha(.5);
+%     hold(aAxes, 'on')
+%     testing=Color;
+end
+
+% % Set the limits of the plot.
+% % SetYLimits(aAxes)
+% xlim(aAxes, imData.GetTLim(aXUnit, 'Margins', [0.01 0.01]))
+% 
+% % x-label.
+% switch lower(aXUnit)
+%     case 'frames'
+%         xlabel(aAxes, 'Time (frames)')
+%     case 'hours'
+%         xlabel(aAxes, 'Time (hours)')
+% end
+% 
+% % y-label and title.
+% switch lower(aMetric1)
+%     case 'max'
+%         title(aAxes, sprintf('Maximum fluorescence (%s)',...
+%             SpecChar(imData.GetSeqDir(), 'matlab')))
+%         ylabel(aAxes, 'Fluorescence (relative to max)')
+%     case 'avg'
+%         title(aAxes, sprintf('Average fluorescence (%s)',...
+%             SpecChar(imData.GetSeqDir(), 'matlab')))
+%         ylabel(aAxes, 'Fluorescence (relative to max)')
+%     case 'tot'
+%         title(aAxes, sprintf('Integrated fluorescence (%s)',...
+%             SpecChar(imData.GetSeqDir(), 'matlab')))
+%         if imData.GetDim() == 2
+%             switch aYUnit
+%                 case 'pixels'
+%                     ylabel(aAxes, 'Fluorescence (relative to max) * Area in pixels')
+%                 case 'microns'
+%                     ylabel(aAxes, 'Fluorescence (relative to max) * Area in \mum^2')
+%             end
+%         else
+%             switch aYUnit
+%                 case 'pixels'
+%                     ylabel(aAxes, 'Fluorescence (relative to max) * Volume in voxels')
+%                 case 'microns'
+%                     ylabel(aAxes, 'Fluorescence (relative to max) * Volume in \mum^3')
+%             end
+%         end
+% end
+
+% PrintStyle(aAxes)
+end