diff --git a/Ai9DetermineCutoff.m b/Ai9DetermineCutoff.m
new file mode 100644
index 0000000..10cb092
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/Analysis/CellAnalysis/Plot_Fluorescence.m b/Analysis/CellAnalysis/Plot_Fluorescence.m
index 52cdc70..5e4a1c0 100644
--- a/Analysis/CellAnalysis/Plot_Fluorescence.m
+++ b/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')
diff --git a/Analysis/CellAnalysis/Plot_Fluorescence3D.m b/Analysis/CellAnalysis/Plot_Fluorescence3D.m
new file mode 100644
index 0000000..fa960fd
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/Analysis/CellAnalysis/Plot_Fluorescence3D_2.m b/Analysis/CellAnalysis/Plot_Fluorescence3D_2.m
new file mode 100644
index 0000000..255d8a8
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/Analysis/Plotting/PlotWithNan3D.m b/Analysis/Plotting/PlotWithNan3D.m
new file mode 100644
index 0000000..f85b494
--- /dev/null
+++ b/Analysis/Plotting/PlotWithNan3D.m
@@ -0,0 +1,58 @@
+function PlotWithNan3D(aAxes,aX, aY,aZ, varargin)
+% Plots a curve and fills in gaps of NaNs with dotted lines.
+%
+% The built in plot function in MATLAB will create gaps in the lines in
+% places where there are NaN-values. This function will instead connect the
+% end-points around the gaps with dotted lines. NaNs in the beginning and
+% at the end of an array are not plotted.
+%
+% Inputs:
+% aAxes - Axes object to plot in.
+% aX - Array of x-values.
+% aY - Array of y-values, that may contain NaN-values.
+% varargin - Extra input arguments passed to the built in function plot.
+
+% Make the function work for both row- and column vectors.
+aX = aX(:);
+aY = aY(:);
+aZ = aZ(:);
+if isempty(aX)
+    return
+end
+
+% Get the original hold-setting.
+% hSet = ishold(aAxes);
+
+% Find breakpoints between NaN-values and other values. There will be 1s at
+% each start of a new interval and at the first and the last element.
+bp = [1; find(abs(diff(isnan(aY))))+1; length(aY)+1];
+
+for i = 1:length(bp) - 1
+    if isnan(aY(bp(i)))
+        if i ~= 1 && i ~= length(bp) - 1
+            % Plot a dotted line over a NaN-gap.
+            start = bp(i)-1;
+            stop = bp(i + 1);
+            plot3([aX(start);  aX(stop)],...
+                [aY(start);  aY(stop)],...
+                [aZ(start);  aZ(stop)],...
+                varargin{:},...
+                'LineStyle', ':')
+            alpha(.1);
+            hold(aAxes, 'on')
+        end
+    else
+        % Plot a normal line.
+        start = bp(i);
+        stop = bp(i + 1) - 1;
+        plot3(aX(start : stop), aY(start : stop),aZ(start : stop),'o',varargin{:})
+        alpha(.1);
+        grid on
+%         hold(aAxes, 'on')
+    end
+end
+
+% Restore the original hold-setting.
+% if ~hSet
+%     hold(aAxes, 'off')
+end
diff --git a/Analysis/PopulationAnalysis/OverTime3D.m b/Analysis/PopulationAnalysis/OverTime3D.m
new file mode 100644
index 0000000..0e27a27
--- /dev/null
+++ b/Analysis/PopulationAnalysis/OverTime3D.m
@@ -0,0 +1,136 @@
+function OverTime(aAxes, aCellVec, aLabels, aProperty, aTitle, aPropertyLabel, ~, ~)
+% Plots time averaged cell properties against appearance times of cells.
+%
+% The appearance times are binned into intervals of 1 hour, and average
+% parameter values for the bins are computed and plotted against time. When
+% there are no cells in a bin, the value of that bin is interpolated from
+% surrounding values using linear interpolation. Lines that end in
+% interpolated points are plotted using a dashed line style.
+%
+% Inputs:
+% aAxes - Axes object to plot in.
+% aCellVec - Cell array where each cell contains a group of Cell objects
+%            that will be plotted in a separate color.
+% aLabels - Labels associated with the different cell groups. The groups
+%           are usually experimental conditions.
+% aProperty - The name of the cell property to be plotted. The property
+%             must be a property of the Cell class.
+% aTitle - Title describing the plotted property. The title will be placed
+%          at the top of the plot.
+% aPropertyLabel - The axis label associated with the plotted property.
+%
+% The function also takes two dummy inputs which make it possible to call
+% the function from PlotConditionProperty with the same input arguments as
+% Scatter.
+%
+% See also:
+% PlotConditionProperty
+
+% Colors used for plotting the different groups of cells. If there are more
+% groups than colors, the colors are recycled.
+colors = {'b', 'r', 'c', 'm', 'k', 'y', 'g'};
+
+% Get the maximum property value.
+cells = [aCellVec{:}];
+props = ExtractProperty(cells, aProperty);
+if all(isnan(props))
+    return
+end
+maxVal = max(props(~isnan(props)));
+
+numFrames = TimeSpan(cells);
+df = 3600/cells(1).dT;  % Number of frames in each bin.
+% Time points corresponding to the bins.
+t = cells(1).imageData.FrameToT(1:df:numFrames);
+
+propHist = cell(size(aCellVec));
+counts = cell(size(aCellVec));
+
+% Put the cells and their properties into the bins.
+for i = 1:length(aCellVec)
+    propHist{i} = zeros(ceil(numFrames / df), 1);
+    counts{i} = zeros(ceil(numFrames / df), 1);
+    for cIndex = 1:length(aCellVec{i})
+        c = aCellVec{i}(cIndex);
+        if ~isnan(ExtractProperty(c, aProperty))
+            % Bin that the cell belongs to.
+            bin = floor(c.firstFrame / df) + 1;
+            if strcmpi(aProperty, 'deltaT')
+                % For the property deltaT, each sister cell pair has a
+                % positive and a negative value (or two zeros). To deal
+                % with this, we take the absolute value of the property.
+                propHist{i}(bin) = propHist{i}(bin) +...
+                    abs(ExtractProperty(c, aProperty));
+            else
+                propHist{i}(bin) = propHist{i}(bin) +...
+                    ExtractProperty(c, aProperty);
+            end
+            counts{i}(bin) = counts{i}(bin) + 1;
+        end
+    end
+end
+
+% Compute the average property value in each bin, by dividing the summed
+% property values by the number of cells.
+propHistNorm = cell(size(propHist));
+for i = 1:length(aCellVec)
+    propHistNorm{i} = propHist{i} ./ counts{i};
+end
+
+% Create label strings, and make fake lines at the origin with the
+% corresponding line styles, so that the correct lines are drawn in the
+% legend.
+labelStrings = {};
+for i = 1:length(aCellVec)
+    if all(isnan(propHistNorm{i}))
+        continue
+    end
+    
+    colorIndex = mod(i-1,length(colors)) + 1;
+    
+    % Solid line.
+    plot(aAxes, 0, 0, 'LineWidth', 4, 'Color', colors{colorIndex})
+    hold(aAxes, 'on')
+    labelStrings = [labelStrings {num2str(aLabels{i})}]; %#ok<AGROW>
+    
+    % Dashed line.
+    if any(isnan(propHistNorm{i}))
+        plot(aAxes, 0, 0,...
+            'LineWidth', 4,...
+            'Color', colors{colorIndex},...
+            'LineStyle', '--')
+        labelStrings = [labelStrings...
+            {[num2str(aLabels{i}) ' (interpolated)']}]; %#ok<AGROW>
+    end
+end
+
+% Plot observed values with solid lines and interpolated values with dotted
+% lines. The bins that need to be interpolated have NaN-values.
+for i = 1:length(aCellVec)
+    colorIndex = mod(i-1,length(colors)) + 1;
+    bronkx=t'
+    bronky=propHistNorm{i}'
+    PlotWithNan(aAxes, t', propHistNorm{i}',...
+        'LineWidth', 4,...
+        'Color', colors{colorIndex})
+end
+
+% Set axis limits for the time axes.
+if length(t) == 1
+    % Avoids a crash when the plot is empty.
+    xlim(aAxes, [t t+1])
+else
+    xlim(aAxes, [t(1) t(end)])
+end
+
+% Set y-axis limits so that there is a 10 % Margin at the top.
+if maxVal > 0
+    set(aAxes, 'ylim', [0, maxVal*1.1])
+end
+
+grid(aAxes, 'on')
+xlabel(aAxes, 'Time (hours)')
+ylabel(aAxes, aPropertyLabel)
+legend(aAxes, labelStrings, 'Location', 'Best')
+title(aAxes, aTitle)
+end
\ No newline at end of file
diff --git a/BF_Functions/BronkOpeningWindow.mlapp b/BF_Functions/BronkOpeningWindow.mlapp
new file mode 100644
index 0000000..910f5e6
Binary files /dev/null and b/BF_Functions/BronkOpeningWindow.mlapp differ
diff --git a/BF_Functions/CytDrug.m b/BF_Functions/CytDrug.m
new file mode 100644
index 0000000..e97bc53
--- /dev/null
+++ b/BF_Functions/CytDrug.m
@@ -0,0 +1,25 @@
+  %%Drugmine Code 
+  
+function [DrugBright,areaDrug, Drugsum, DrugAvgInCell, DrugAvgOutCell,Drug_eq,DrugMask] = Drug(Img, Drug_threshold, cyt_bw4)
+
+    Drug_eq =imadjust(Img,[0 0.4],[]);
+       
+    Drug_threshold = Drug_threshold *intmax(class(drug));
+    
+    Drugweiner=wiener2(Img);
+    RhodMask=Drugweiner>Drug_threshold;
+    areaDrug = sum(RhodMask,'all');
+    if 
+    Drug_in_cell = drug(cyt_bw4);
+    Drug_out_cell = drug(cyt_bw4 == 0);
+    
+    cell_area = sum(sum(cyt_bw4));
+    not_cell_area = size(cyt_bw4,1) * size(cyt_bw4, 2) - cell_area;
+    
+    Rhodsum = sum(rhod_eq(RhodMask));
+    RhodBright=drug;
+    RhodBright(~RhodMask)=0;
+    DrugvgInCell = sum(Drug_in_cell) / cell_area;
+    DrugvgOutCell = sum(Drug_out_cell) / not_cell_area;
+    
+  
\ No newline at end of file
diff --git a/BF_Functions/CytNucWaterShed.m b/BF_Functions/CytNucWaterShed.m
new file mode 100644
index 0000000..ff0c048
--- /dev/null
+++ b/BF_Functions/CytNucWaterShed.m
@@ -0,0 +1,21 @@
+function [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4)
+%UNTITLED4 Summary of this function goes here
+%   Detailed explanation goes here
+cytsize=size(cyt);
+	border = ones(cytsize);
+    border(2:end-1,2:end-1) = 0;
+    n_maxs=imerode(Nuc_bw4,strel('disk',1));
+    n_maxs=bwareaopen(n_maxs,100);
+    h=imhmin(CytTopHat,1);
+    h_c=imcomplement(h);
+    h_c_min=imimposemin(h_c, n_maxs);
+    L_n = watershed(h_c_min);
+    L_n(~cyt_bw4) = 0;
+    borderInverse=~border;
+    L_n(~borderInverse) = 0;
+    howdy=L_n;
+    Cyt_WS=imfill((howdy),4,'holes');
+    Cyt_WS_perim = imdilate(bwperim(Cyt_WS),strel('disk',1));
+    
+end
+
diff --git a/BF_Functions/Cytosol.m b/BF_Functions/Cytosol.m
new file mode 100644
index 0000000..4fe5036
--- /dev/null
+++ b/BF_Functions/Cytosol.m
@@ -0,0 +1,27 @@
+function [CytBright,CytArea,CytCytOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+ CytTopHat=imtophat(cyt,CytTophatDisk); % Clean image with tophat filter for thresholding 
+    CytOpen=imerode(CytTopHat,CytOpenDisk);
+     CytOpen=imreconstruct(CytOpen,CytTopHat);
+    cyt_eq =imadjust(CytTopHat,[0 0.25],[]);   %Make it easy to see
+    
+    CytMaxValue= CytMax*intmax(class(cyt));
+    CytOverbright=CytOpen>CytMaxValue;
+    CytBright=CytOpen;
+    CytBright(CytOverbright)=0;
+        CytMT1=multithresh(CytBright,20); %Calculate 20 brightness thresholds for image 
+        CytQuant1=imquantize(CytBright,CytMT1); %Divide Image into the 20 brightness baskets
+        CytBrightEnough=CytQuant1>CytLow;
+        
+        CytPos=CytBright;
+        CytPos(~CytBrightEnough)=0;
+          cyt_bw2=imerode(CytPos,CytErodeDisk);
+          cyt_bw3 = bwareaopen(cyt_bw2, 2000); %%Be sure to check this threshold
+          cyt_bw4 = imclose(cyt_bw3, CytCloseDisk);
+          CytPos(~cyt_bw4)=0;
+        cyt_bw4_perim = imdilate(bwperim(cyt_bw4),strel('disk',2));
+       CytArea = imoverlay(cyt_eq, cyt_bw4_perim, [.3 1 .3]);
+        CytCytOverlay = imoverlay(cyt_eq, cyt_bw4_perim, [.3 1 .3]);
+end
+
diff --git a/BF_Functions/Drug.m b/BF_Functions/Drug.m
new file mode 100644
index 0000000..ff3cf5d
--- /dev/null
+++ b/BF_Functions/Drug.m
@@ -0,0 +1,12 @@
+  %%BasicThresh Code 
+  
+function [DrugBright,areaDrug, Drugsum, DrugMask] = Drug(Img, Drug_threshold)
+
+    Drug_threshold = Drug_threshold *intmax(class(drug));
+    DrugMask=Img>Drug_threshold;
+    areaDrug = sum(DrugMask,'all');
+    Drugsum = sum(Img(DrugMask));
+    DrugBright(~DrugMask)=0;
+   
+    
+  
\ No newline at end of file
diff --git a/BF_Functions/Gal8.m b/BF_Functions/Gal8.m
new file mode 100644
index 0000000..3584c1d
--- /dev/null
+++ b/BF_Functions/Gal8.m
@@ -0,0 +1,31 @@
+function [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+
+Gal8=wiener2(Img);
+Gal8TH=imtophat(Gal8,Gal8TophatDisk);
+Gal8Open=imopen(Gal8TH,Gal8OpenDisk);
+
+Gal8MinValue= Gal8MinThreshold*intmax(class(Img));
+Gal8Quant2=Gal8Open-Gal8MinValue;
+Gal8Quant2(Gal8Quant2<=0)=0;
+Gal8Quant3=bwareaopen(Gal8Quant2,4);
+% Gal8Quant3(~Cyt_WS)=0;
+Gal8Quant3(~CytPos)=0;
+Gal8Quant3=imdilate(Gal8Quant3,Gal8DilateDisk);
+Gal8Quant4=imdilate(Gal8Quant3,Gal8OutlineDisk);
+Gal8Quant5=imbinarize(Gal8Quant4-Gal8Quant3);
+GalPals=Img;
+GalPals(~Gal8Quant3)=0;
+
+Puncta=regionprops(Gal8Quant3,Img,'Area','Centroid','MeanIntensity');
+Ring=regionprops(Gal8Quant5,Img,'Area','Centroid','MeanIntensity'); %need to figure out way to subtract out surrounding brightness for each individual Point
+RingMeanInt=2; %need to figure out way to subtract out surrounding brightness for each individual Point
+Gal8Signal=sum((vertcat(Puncta.MeanIntensity).*vertcat(Puncta.Area)));
+% Gal8Signal=Gal8Signal';
+end
+
diff --git a/BF_Functions/NuclearStain.m b/BF_Functions/NuclearStain.m
new file mode 100644
index 0000000..ae8496c
--- /dev/null
+++ b/BF_Functions/NuclearStain.m
@@ -0,0 +1,34 @@
+function [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+    NucWeiner=wiener2(Nuc);
+    NucTopHat=imtophat(NucWeiner,NucTophatDisk); % Clean image with tophat filter for thresholding 
+%     NucOpen=imerode(NucTopHat,NucOpenDisk);
+%      NucOpen=imreconstruct(NucOpen,NucTopHat);
+    Nuc_eq =imadjust(NucTopHat);   %Make it easy to see
+    NucOpen=imopen(NucTopHat,NucOpenDisk);
+    NucMaxValue= NucMax*intmax(class(Nuc));
+    NucOverbright=NucTopHat>NucMaxValue;
+    
+    NucOpen(NucOverbright)=0;
+%         NucMT1=multithresh(NucOpen,20); %Calculate 20 brightness thresholds for image 
+%         NucQuant1=imquantize(NucOpen,NucMT1); %Divide Image into the 20 brightness baskets
+        NucMT1=1;
+        NucQuant1=1;
+%         NucBrightEnough=NucQuant1>NucLow;
+        NucBrightEnough=NucOpen>NucLow;
+        NucPos=NucOpen;
+        NucPos(~NucBrightEnough)=0;
+%         NucPos=imadjust(NucPos);
+          Nuc_bw2=imerode(NucPos,NucErodeDisk);
+          Nuc_bw3 = bwareaopen(Nuc_bw2, 250); %%Be sure to check this threshold
+          Nuc_bw4 = imclose(Nuc_bw3, NucCloseDisk);
+          Nuc_bw4 = imfill(Nuc_bw4,'holes');
+        Nuc_bw4_perim = imdilate(bwperim(Nuc_bw4),strel('disk',3));
+       
+       NucConn=bwconncomp(Nuc_bw4);
+       NucLabel = labelmatrix(NucConn);
+       NucArea = imoverlay(Nuc_eq, Nuc_bw4_perim, [.3 1 .3]);
+       
+end
+
diff --git a/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-07.m b/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-07.m
new file mode 100644
index 0000000..086eada
--- /dev/null
+++ b/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-07.m	
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-10.m b/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-10.m
new file mode 100644
index 0000000..086eada
--- /dev/null
+++ b/BF_Functions/Old Files/RunLogbackup_2022-02-09-02-21-10.m	
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_2021_12_30.m b/BF_Functions/Old Files/m_2021_12_30.m
new file mode 100644
index 0000000..211e2ba
--- /dev/null
+++ b/BF_Functions/Old Files/m_2021_12_30.m	
@@ -0,0 +1,257 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\20211002BigProteinScreen001.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2022-01-04_Demo';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    InputPlanes={'Nuc','cyt','drug'};
+    
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.08;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.4; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=1:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+            for n=              
+                ImagePlane(n)= bitConvert*bfGetPlane(reader,iplane+n);
+            end
+            
+    
+                %% Analyze Images
+            %%Nuclear Stain Code    
+            [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+            %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+
+            %%Cytosol Code
+            [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+
+            %WaterShed Segmentation of Individual Cells
+            [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+            %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+            %Gal8 Puncta Segmentation
+            [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+            %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+
+            %Rhodamine Code
+            [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+            rhodPerim=bwperim(RhodMask);
+
+                %All Data Images
+                RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+                WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+                ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+                    ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+                    ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+                areacell=bwarea(Nuc_bw4(:));
+                CellSum=sum(Nuc(Nuc_bw4));
+                areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    %% Write Images to File
+     %overlaid Image
+    BaxterName=strcat('w',Well,'t',Timepoint)
+     
+     exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+    
+    
+    fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+    imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    ImageName=fullfile(BaxWellFolder,BaxterName);    
+    imwrite(Nuc, strcat(ImageName,'c01','.tif'),'tif');
+    imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+    imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+    imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+    imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+     
+    
+    SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+    imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+    
+    
+    SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+    imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+    
+    
+    end   
+end
+%% Write Analysis Data to File
+ 
+D=[Categories;C];
+WritingHere=strcat(exportdir,'\','Gal8','_',run);
+ writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_Bronk_2022_01_05.m b/BF_Functions/Old Files/m_Bronk_2022_01_05.m
new file mode 100644
index 0000000..c0fa4f0
--- /dev/null
+++ b/BF_Functions/Old Files/m_Bronk_2022_01_05.m	
@@ -0,0 +1,255 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-11-BigProteinFollowUp\Ai9Lipo48hrs002.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-11-BigProteinFollowUp\Analysis';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=1.36;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=1000;%
+     %Cytosol    
+        CytMax= 1.1; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=1;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 1; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=0:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+
+            Nuc = bitConvert*bfGetPlane(reader,iplane+2);
+
+            cyt = bitConvert*bfGetPlane(reader,iplane+2);
+
+            drug = bitConvert*bfGetPlane(reader,iplane+1);
+    
+                %% Analyze Images
+            %%Nuclear Stain Code    
+            [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+            %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+
+            %%Cytosol Code
+            [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+
+            %WaterShed Segmentation of Individual Cells
+            [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+            %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+            %Gal8 Puncta Segmentation
+            [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+            %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+
+            %Rhodamine Code
+            [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+            rhodPerim=bwperim(RhodMask);
+
+                %All Data Images
+                RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+                WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+                ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+                    ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+                    ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+                areacell=bwarea(Nuc_bw4(:));
+                CellSum=sum(Nuc(Nuc_bw4));
+                areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    %% Write Images to File
+     %overlaid Image
+    BaxterName=strcat('w',Well,'t',Timepoint)
+     
+     exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+    
+    
+    fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+    imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    ImageName=fullfile(BaxWellFolder,BaxterName);    
+    imwrite(Nuc, strcat(ImageName,'c01','.tif'),'tif');
+    imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+    imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+    imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+    imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+     
+    
+    SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+    imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+    
+    
+    SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+    imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+    
+    
+    end   
+end
+%% Write Analysis Data to File
+ 
+D=[Categories;C];
+WritingHere=strcat(exportdir,'\','Gal8','_',run);
+ writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_Bronk_2022_01_05_bigChanges.m b/BF_Functions/Old Files/m_Bronk_2022_01_05_bigChanges.m
new file mode 100644
index 0000000..8484300
--- /dev/null
+++ b/BF_Functions/Old Files/m_Bronk_2022_01_05_bigChanges.m	
@@ -0,0 +1,273 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\20211002BigProteinScreen001.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2022-01-04_Demo';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    ImagePlanes=[1,2,3];
+    ImageAnalyses={{'nuc'},{'cyt' 'gal'},{'drug'}};
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.08;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.4; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=1:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+            Img=[];
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+                n
+                if contains(CurrPlane,'nuc')
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                x='hell0'
+                end
+                if contains(CurrPlane,'cyt')
+                [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end
+                 if contains(CurrPlane,'gal')
+                [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(Img,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);  
+                end
+                 if contains(CurrPlane,'drug')
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                   end  
+                   
+                
+                   
+%                 %% Analyze Images
+%             %%Nuclear Stain Code    
+%             [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+%             %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+            end
+%             %%Cytosol Code
+%             
+% 
+%             %WaterShed Segmentation of Individual Cells
+%             [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+%             %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+%             %Gal8 Puncta Segmentation
+%             [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+%             %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+% 
+%             %Rhodamine Code
+%             [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+%             rhodPerim=bwperim(RhodMask);
+% 
+%                 %All Data Images
+%                 RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+%                 WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+%                 ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+%             %         figure; imshow(ExportImage);
+%             %
+% 
+%                 %% Measure Image Data
+% 
+%                 % measurement
+%                 areacell=bwarea(Nuc_bw4(:));
+%                 CellSum=sum(Nuc(Nuc_bw4));
+%                 areaGal8=sum((vertcat(Puncta.Area)));
+%             %    
+%             % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+%     %% Write Images to File
+%      %overlaid Image
+%     BaxterName=strcat('w',Well,'t',Timepoint)
+%      
+%      exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+%     
+%     
+%     fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+%     imwrite(ExportImage, fulldestination);  %save the file there directory
+%     
+%     %BaxterImages    
+%     ImageName=fullfile(BaxWellFolder,BaxterName);    
+%     imwrite(Nuc, strcat(ImageName,'c01','.tif'),'tif');
+%     imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+%     imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+%     imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+%     imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+%      
+%     
+%     SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+%     imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+%     
+%     
+%     SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+%     imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+%     
+    
+    end   
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_Bronk_2022_01_06_for11_15_assay.m b/BF_Functions/Old Files/m_Bronk_2022_01_06_for11_15_assay.m
new file mode 100644
index 0000000..f2c7b99
--- /dev/null
+++ b/BF_Functions/Old Files/m_Bronk_2022_01_06_for11_15_assay.m	
@@ -0,0 +1,278 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+%hello world
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-11-15-Ai9CMAX PRotein Screen\ProteinScreen.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-11-15-Ai9CMAX PRotein Screen\Analysis';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    ImagePlanes=[1,2];
+    ImageAnalyses={{'Bax'},{'Bax'}};
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.08;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.4; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries-1% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=1:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()));
+            Img=[];
+            %overlaid Image
+                        BaxterName=strcat('w',Well,'t',Timepoint) ;
+                         exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+                        fulldestination = strcat(exportbase,'.png');
+                        ImageName=fullfile(BaxWellFolder,BaxterName);
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+                 
+                
+                if contains(CurrPlane,'Bax')
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                end
+                if contains(CurrPlane,'nuc')
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                x='hell0'
+                end
+                if contains(CurrPlane,'cyt')
+                [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end
+                 if contains(CurrPlane,'gal')
+                [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(Img,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);  
+                end
+                 if contains(CurrPlane,'drug')
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                   end  
+                   
+            end    
+                 %% Test  
+%                 %% Analyze Images
+%             %%Nuclear Stain Code    
+%             [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+%             %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+                
+%             %%Cytosol Code
+%             
+% 
+%             %WaterShed Segmentation of Individual Cells
+%             [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+%             %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+%             %Gal8 Puncta Segmentation
+%             [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+%             %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+% 
+%             %Rhodamine Code
+%             [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+%             rhodPerim=bwperim(RhodMask);
+% 
+%                 %All Data Images
+%                 RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+%                 WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+%                 ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+%             %         figure; imshow(ExportImage);
+%             %
+% 
+%                 %% Measure Image Data
+% 
+%                 % measurement
+%                 areacell=bwarea(Nuc_bw4(:));
+%                 CellSum=sum(Nuc(Nuc_bw4));
+%                 areaGal8=sum((vertcat(Puncta.Area)));
+%             %    
+%             % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    %% Write Images to File
+       %name file relative to that directory
+%     imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    
+    
+%     imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+%     imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+%     imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+%      
+%     
+%     SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+%     imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+%     
+%     
+%     SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+%     imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+%     
+    
+    end   
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_Bronk_2022_02_04_for2021_06_29_assay.m b/BF_Functions/Old Files/m_Bronk_2022_02_04_for2021_06_29_assay.m
new file mode 100644
index 0000000..2dc0757
--- /dev/null
+++ b/BF_Functions/Old Files/m_Bronk_2022_02_04_for2021_06_29_assay.m	
@@ -0,0 +1,325 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+%hello world
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear all, close all
+string()
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze #Integrate with 
+    ImageAnalyses={{'Bax'},{},{'Bax'}}; %Which Image analysis/functions to call. NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=1;%Logical Yes or no to make overlay image
+    % Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % Add selection for data of interest from each analysis
+    %
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+%j=0:NumSeries-1%
+
+for j=0:NumSeries-1% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value
+
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()));
+            Img=[];
+            %overlaid Image
+                        BaxterName=strcat('w',Well,'t',Timepoint) ;
+                         exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+                        fulldestination = strcat(exportbase,'.png');
+                        ImageName=fullfile(BaxWellFolder,BaxterName);
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(Img,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,CytPos,Gal8OutlineDisk);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end   
+                 
+                 if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+% UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH COLOR            
+% RGBExportImage=imoverlay(RGBExportImage,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');    
+%             
+%             
+            imshow(RGBExportImage)
+            end
+                 %% Test  
+                
+                %All Data Images
+                
+%                 WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+%                 ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+%                 areacell=bwarea(Nuc_bw4(:));
+%                 CellSum=sum(Nuc(Nuc_bw4));
+%                 areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    % Write Images to File
+%        name file relative to that directory
+%     imwrite(ExportImage, fulldestination);  %save the file there directory
+%     
+%     BaxterImages    
+    
+    
+   
+%     imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+%     imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+%      
+%     
+%     SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+%     imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+%     
+%     
+%     SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+%     imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+% %     
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/Old Files/m_Bronk_2022_02_07_for2021_06_29_assay.m b/BF_Functions/Old Files/m_Bronk_2022_02_07_for2021_06_29_assay.m
new file mode 100644
index 0000000..bf025f0
--- /dev/null
+++ b/BF_Functions/Old Files/m_Bronk_2022_02_07_for2021_06_29_assay.m	
@@ -0,0 +1,309 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+%hello world
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('/Users/sarahreilly/Desktop/PolyScreen004.nd2');
+exportdir='/Users/sarahreilly/Desktop/TestExport';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    ImagePlanes=[1,3];
+    ImageAnalyses={{'Bax'},{},{'Bax'}};
+    MakeOverlayImage=1;
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+%j=0:NumSeries-1%
+for j=0:NumSeries - 1% Number of images in ND2 File  
+    place='series for loop'
+    
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=0:T_Value
+        place = 'inside time for loop'
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()));
+            Img=[];
+            %overlaid Image
+                        BaxterName=strcat('w',Well,'t',Timepoint) ;
+                         exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+                        fulldestination = strcat(exportbase,'.png');
+                        ImageName=fullfile(BaxWellFolder,BaxterName);
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                    test='Hello'
+                    
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end
+                
+                if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(Img,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,CytPos,Gal8OutlineDisk);  
+                        
+                end
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+                 
+                 if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+%               RGBExportImage=imoverlay(RGBExportImage,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');    
+%             
+%             
+            imshow(RGBExportImage)
+            end
+                 %% Test  
+                
+                %All Data Images
+                
+%                 WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+%                 ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+%                     ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+%                     ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+%                 areacell=bwarea(Nuc_bw4(:));
+%                 CellSum=sum(Nuc(Nuc_bw4));
+%                 areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    % Write Images to File
+%        name file relative to that directory
+%     imwrite(ExportImage, fulldestination);  %save the file there directory
+%     
+%     BaxterImages    
+    
+    
+   
+%     imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+%     imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+%      
+%     
+%     SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+%     imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+%     
+%     
+%     SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+%     imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+% %     
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/BF_Functions/Rhoda.m b/BF_Functions/Rhoda.m
new file mode 100644
index 0000000..fde251b
--- /dev/null
+++ b/BF_Functions/Rhoda.m
@@ -0,0 +1,25 @@
+  %%Rhodamine Code 
+  
+function [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4)
+
+    rhod_eq =imadjust(drug,[0 0.4],[]);
+       
+    Rhoda_threshold = Rhoda_threshold *intmax(class(drug));
+    
+    rhodaweiner=wiener2(drug);
+    RhodMask=rhodaweiner>Rhoda_threshold;
+    areaRhod = sum(RhodMask,'all');
+    
+    rhoda_in_cell = drug(cyt_bw4);
+    rhoda_out_cell = drug(cyt_bw4 == 0);
+    
+    cell_area = sum(sum(cyt_bw4));
+    not_cell_area = size(cyt_bw4,1) * size(cyt_bw4, 2) - cell_area;
+    
+    Rhodsum = sum(rhod_eq(RhodMask));
+    RhodBright=drug;
+    RhodBright(~RhodMask)=0;
+    RhodAvgInCell = sum(rhoda_in_cell) / cell_area;
+    RhodAvgOutCell = sum(rhoda_out_cell) / not_cell_area;
+    
+  
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-23-12.m b/BF_Functions/RunLog/backup_2022-02-09-02-23-12.m
new file mode 100644
index 0000000..61fb464
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-23-12.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-23-14.m b/BF_Functions/RunLog/backup_2022-02-09-02-23-14.m
new file mode 100644
index 0000000..61fb464
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-23-14.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-23-19.m b/BF_Functions/RunLog/backup_2022-02-09-02-23-19.m
new file mode 100644
index 0000000..61fb464
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-23-19.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-25-04.m b/BF_Functions/RunLog/backup_2022-02-09-02-25-04.m
new file mode 100644
index 0000000..52e549a
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-25-04.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')]
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-25-31.m b/BF_Functions/RunLog/backup_2022-02-09-02-25-31.m
new file mode 100644
index 0000000..52e549a
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-25-31.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')]
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-26-32.m b/BF_Functions/RunLog/backup_2022-02-09-02-26-32.m
new file mode 100644
index 0000000..52e549a
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-26-32.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')]
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-26-43.m b/BF_Functions/RunLog/backup_2022-02-09-02-26-43.m
new file mode 100644
index 0000000..52e549a
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-26-43.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')]
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_2022-02-09-02-27-51.m b/BF_Functions/RunLog/backup_2022-02-09-02-27-51.m
new file mode 100644
index 0000000..52e549a
--- /dev/null
+++ b/BF_Functions/RunLog/backup_2022-02-09-02-27-51.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')]
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/backup_LiveEditorEvaluationHelperESectionEval2ef0f50d.m2022-02-09-02-24-29backup_ b/BF_Functions/RunLog/backup_LiveEditorEvaluationHelperESectionEval2ef0f50d.m2022-02-09-02-24-29backup_
new file mode 100644
index 0000000..93dc60f
--- /dev/null
+++ b/BF_Functions/RunLog/backup_LiveEditorEvaluationHelperESectionEval2ef0f50d.m2022-02-09-02-24-29backup_
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,mfilename,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m b/BF_Functions/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m
new file mode 100644
index 0000000..045a8c9
--- /dev/null
+++ b/BF_Functions/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m
@@ -0,0 +1,281 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+RunLog=fullfile(pwd,'RunLog');
+mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,RunLog);
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah.m b/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah.m
new file mode 100644
index 0000000..b574c8a
--- /dev/null
+++ b/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah.m
@@ -0,0 +1,283 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+Gitdir=fullfile(pwd,'RunLog\');
+GitLog=sprintf('%sbackup_%s.m',Gitdir,Version);
+% GitLog=sprintf('%sbackup_%s.m',LogFolder,Version);
+% mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,GitLog)
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+% sr1=strel('square',1);
+% se1=strel('disk',1);
+% sr2=strel('square',2);
+% se2=strel('disk',2);
+% se3=strel('disk',3);
+% sr3=strel('square',3);
+% se4=strel('disk',4);
+% se5=strel('disk',5);
+% se6=strel('disk',6);
+% se7=strel('disk',7);
+% se8=strel('disk',8);
+% se9=strel('disk',9);
+% se10=strel('disk',10);
+% se12=strel('disk',12);
+% se20=strel('disk',20);
+% se25=strel('disk',25);
+% se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Drugamine
+        Drug_threshold = 0.01; %Number 0-1, removes Drugmine signal dimmer than threshold
+%         Drug_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaDrug'},{'Drugsum'},{'DrugAvgInCell'},{'DrugAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [DrugBright,areaDrug, Drugsum, DrugAvgInCell, DrugAvgOutCell,Drug_eq,DrugMask] = Drug(Img, Drug_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m b/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m
new file mode 100644
index 0000000..ea10e3a
--- /dev/null
+++ b/BF_Functions/m_2022_02_08_Commented_byBF_forMichaelSarah/RunLog/m_2022_02_08_Commented_byBF_forMichaelSarah.m
@@ -0,0 +1,281 @@
+%% Gal8 Recruitment MATLAB Program
+%% Image Folder Location
+clc, clear all, close all
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\PolyScreen004.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-06-29-PolymerScreen\2022_02_04_SarahHelp';
+
+%% Directory Code
+
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+          
+readeromeMeta=reader.getMetadataStore();
+RunDirectory= fullfile(exportdir,run);
+mkdir(RunDirectory); 
+
+destdirectory1 = fullfile(RunDirectory,'Overlaid');
+mkdir(destdirectory1); 
+
+BaxtDirectory = fullfile(RunDirectory,'Baxter');
+mkdir(BaxtDirectory);
+
+LogDirectory = fullfile(RunDirectory,'Log');
+mkdir(LogDirectory);
+
+SegDirectory = fullfile(RunDirectory,'Segmentation');
+mkdir(SegDirectory);
+
+exportbaseBAXTSegNuc=fullfile(SegDirectory,'Segmentation_Nuc');
+mkdir(exportbaseBAXTSegNuc);
+
+exportbaseBAXTSegCell=fullfile(SegDirectory,'Segmentation_Cell');
+mkdir(exportbaseBAXTSegCell);
+            %##Need to universalize the Segmentation stuff for whatever the
+            %GUI needs, so that it can be arbitrarily named and assigned.
+            %Might be a good idea to write this all into a function
+
+%%Log Data
+Version=run;
+LogFile=strcat(LogDirectory,'\');
+FileNameAndLocation=[mfilename('fullpath')];
+newbackup=sprintf('%sbackup_%s.m',LogFile,Version);
+RunLog=fullfile(FileNameAndLocation,'RunLog');
+mkdir(RunLog);
+currentfile=strcat(FileNameAndLocation, '.m');
+copyfile(currentfile,newbackup);
+copyfile(currentfile,RunLog);
+% A = exist(newbackup,'file');
+% if (A~=0)
+% warning('Backup already exists for the current version')
+% end
+%##This may not be the best way to be logging the data and directory, since
+%it's in a new folder every time, but we can figure htis otu later. Also
+%might be possible to write this all into a function
+
+
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+%## Can probably delete this section after checking on all of the functions
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+            
+            %##Probabloy possible and better to integrate all of this into
+            %a single function for the "round" section and then have ll of
+            %the indivual disks just created in each function based on the
+            %relative pixel size with a cell size correction
+%% Analysis Functions
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    bitConvert=(2^16/2^bitdepthin); %This assures that whatever the bit depth of the input image, the analyzed images are all 16 bit.
+%Input Planes
+    ImagePlanes=[1,2,3]; %Which image Planes to analyze ##Integrate with GUI 
+    ImageAnalyses={{'cytgal'},{},{}}; %Which Image analysis/functions to call. ##NEed to solve problem of secondary analyses like watershed of Nuc and Cytosol or gal8 and cytosol
+    MakeOverlayImage=0;%Logical Yes or no to make overlay image #Integrate with GUI
+    % ##Add selection for what to overlay on the overlay image, for example,
+    % showing the cytosol perimeter analysis or Not
+
+    % ##Add selection for data of interest from each analysis, i.e. what to
+    % export from each function
+    %
+    
+%% Image Thresholding EDIT HERE BASIC 
+    %##Need to make these into GUI, and make universal so that as we call
+    %each function we can set the function parameters in the GUI. I believe
+    %Baxter has a very good solution for doing this
+    %Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=0; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.2;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.01; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}]; 
+%##Categories are manually typed out here, but it should integrate so that
+%these are auto-populated or selectable within the GUI, might have to get
+%clever for this to work
+
+NumSeries=reader.getSeriesCount(); %The number of different wells you imaged
+NumColors=reader.getEffectiveSizeC(); %The number of colors of each well you imaged
+NumTimepoint=(reader.getImageCount())/NumColors; %The number of timepoints you imaged
+NumImg=NumSeries*NumTimepoint*NumColors; %The total number of images, combining everything
+
+C = cell(NumImg,length(Categories)); 
+%##C is something that will probably have be edited to allow data output
+%from this scale of the analysis. Don't even know if it's correct right now
+%or even neccessary at all
+%% Analysis Program 
+for j=0:NumSeries-1% Number of wells in ND2 File  
+    % Set Current Well and other important values
+    %##Would be very useful to figure out how to make this work as a parfor
+    %loop, but might be quite difficult
+    CurrSeries=j; %The current well that we're looking at
+    reader.setSeries(CurrSeries); %##uses BioFormats function, can be swapped with something else (i forget what) if it's buggy with the GUI
+    fname = reader.getSeries; %gets the name of the series using BioFormats
+    Well=num2str(fname,'%05.f'); %Formats the well name for up to 5 decimal places of different wells, could increase but 5 already feels like overkill 
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value(); %May be useful someday, but not needed here
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value(); %May be useful someday, but not needed yet. Get's the position of the actual image. Useful for checking stuff
+    T_Value = reader.getSizeT()-1; %Very important, the timepoints of the images. Returns the total number of timepoints, the -1 is important.
+    
+    %CreateFolders for Baxter to read data
+        %##Important work: generalize this folder creation and put into GUI, so
+        %that whatever segmentations the user creates can be saved for baxter
+        %analysis. The "BaxSegFolderCell" is probably the most important and
+        %default, but this should be customizable
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well); %Creates a filename that's compatible with both PC and Mac (##Check and see if any of the strcat functions need to be replaced with fullfile functions) 
+    mkdir(BaxWellFolder); %makes a new folder on your hard drive for the baxter stuff   
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderNuc); %makes a new folder on your hard drive for the nuclear segmentaiton for Baxter
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well); %Creates a filename that's compatible with both PC and Mac
+    mkdir(BaxSegFolderCell);
+
+    for i=0:T_Value %For all of the time points in the series, should start at zero if T_Value has -1 built in, which it should
+            %Set up the particular timepoint image
+        Timepoint = num2str(i,'%03.f'); %Creates a string so taht the BioFormats can read it
+       iplane=reader.getIndex(0,0,i); %Gets the particular timepoint image, so now we're in a particular well at a particular timepoint
+       WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value())); %The time that the well image was taken. Very useful for sanity checks
+       Img=[];%Creates an empty array for the image ##Check and see if this is necessary or if there's a more efficient way of doing this.
+                         
+                        BaxterName=strcat('w',Well,'t',Timepoint) ; %Very important, creates a name in the format that Baxter Algorithms prefers
+                        
+                        ImageName=fullfile(BaxWellFolder,BaxterName); %Creates a name for each particular image
+                        
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                CurrPlane=ImageAnalyses{n};
+              
+             %Primary Analyses   
+                if any(contains(CurrPlane,'Bax'))
+                    my_field = strcat('c',num2str(n,'%02.f'));
+                    imwrite(Img, strcat(ImageName,my_field,'.tif'),'tif');
+                 
+                end
+                if any(contains(CurrPlane,'nuc'))
+                [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+                
+                end
+                                          
+                if any(contains(CurrPlane,'cyt'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                end           
+                
+                 if any(contains(CurrPlane,'drug'))
+                [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(Img, Rhoda_threshold, cyt_bw4);
+                 end
+
+                 %Secondary Analyses
+                     if any(contains(CurrPlane,'cytgal'))
+                    [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);    
+                    [GalPals,Gal8Signal,Gal8Quant5] = Gal8(Img,Gal8MinThreshold,CytPos,MiPerPix);  
+                     end
+
+                     if any(contains(CurrPlane,'nucWS'))
+                      [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk); 
+                     end
+                    if any(contains(CurrPlane,'cytWS'))
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                    end
+                    
+            %Make RGB Image
+                    
+                    if any(contains(CurrPlane,'blue'))
+                 blue=imadjust(Img);
+%                  else
+%                      blue=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'green'))
+                 green=imadjust(Img);
+%                  else
+%                      green=zeros(size(Img),'like',Img);
+                 end  
+                 if any(contains(CurrPlane,'red'))
+                 red=imadjust(Img);
+%                   else
+%                      red=zeros(size(Img),'like',Img);
+                 end  
+                 
+            end
+            
+        %Make Overlay Image
+            %#UNIVERSALIZE THIS CODE AND MAKE IT SO THAT WE FROM THE GUI 
+            %CALL WHICH PERIMETER OF WHICH MASK WE WANT TO OVERLAY IN WHICH
+            %COLOR
+            
+            if logical(MakeOverlayImage)
+            if ~exist('blue','var')
+                blue=zeros(size(Img),'like',Img);
+            end
+            if ~exist('green','var')
+                green=zeros(size(Img),'like',Img);
+            end
+            if ~exist('red','var')
+                red=zeros(size(Img),'like',Img);
+            end
+            RGBExportImage=cat(3,red,green,blue);
+             if exist('cyt_bw4_perim','var')
+               RGBExportImage=imoverlay(RGBExportImage,cyt_bw4_perim,[0.8500 0.3250 0.0980]);
+             end
+             imshow(RGBExportImage)
+            end
+                %% Measure Image Data
+            %##Write Code here that uses parameters set in the GUI to take
+            %all of the data we'd be interested in analyzing. Will probably
+            %need to get clever with the analysis function output names in
+            %order to make it all work with an arbitrary number of analyses
+            %and image planes
+    
+    end   
+    
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
+% 
+%% add code that writes the text of this code with the timestamp to a record every time it is run
\ No newline at end of file
diff --git a/BF_Gal8_Settings.csv b/BF_Gal8_Settings.csv
new file mode 100644
index 0000000..c20bdcc
--- /dev/null
+++ b/BF_Gal8_Settings.csv
@@ -0,0 +1,84 @@
+setting,A20,F08
+numZ,1,1
+bits,16,16
+minWellR,NaN,NaN
+maxWellR,NaN,NaN
+channelNames,Dapi:Gal8:RNA:TD,Dapi:Gal8:RNA
+channelTags,c1:c2:c3:c4,c1:c2:c3
+channelColors,0  0  1:0  1  0:1         0.5           0:1  1  1,0  0  1:0  1  0:1         0.5           0:1  1  1
+channelMin,0:0:0:0,0:0:0:0
+channelMax,0.32022:0.58192:0.69413:1,0.32022:0.58192:0.69413:1
+use,1,1
+sequenceLength,,
+SegOldVersion,none,none
+SegSave,1,1
+SegAlgorithm,Segment_bandpass,Segment_bandpass
+SegChannel,Gal8,Gal8
+SegLightCorrect,none,none
+SegBgSubAlgorithm,none,none
+SegTopHatRadius,Inf,Inf
+SegFillHoles,1,1
+SegMinHoleArea,Inf,Inf
+SegMinArea,1000,1000
+SegMaxArea,Inf,Inf
+SegMinSumIntensity,0,0
+SegClipping,1,1
+SegClippingBelow,0,0
+SegSmooth,2,2
+SegMedFilt,1,1
+SegWatershed,intermediate,intermediate
+SegWSmooth,5,5
+SegWHMax,6,6
+SegWThresh,-Inf,-Inf
+SegWatershed2,darkness,darkness
+SegWLocMaxCentroids,0,0
+SegCellMorphOp,none,none
+BPSegHighStd,5,5
+BPSegLowStd,2,2
+BPSegBgFactor,1,1
+BPSegThreshold,1e-06,1e-06
+BPSegDarkOrBright,bright,bright
+TrackXSpeedStd,12,12
+countClassifier,none,none
+splitClassifier,none,none
+deathClassifier,none,none
+migClassifier,none,none
+pCnt0,0.2,0.2
+pCnt1,0.7,0.7
+pCnt2,0.1,0.1
+pCntExtrap,0.25,0.25
+pSplit,0.01,0.01
+pDeath,0.01,0.01
+TrackPAppear,0,0
+TrackPDisappear,0,0
+TrackMotionModel,none,none
+TrackMigLogLikeList,MigLogLikeList_uniformClutter,MigLogLikeList_uniformClutter
+TrackDeathShift,2e-05,2e-05
+TrackMaxDeathProb,1,1
+TrackMaxMigScore,0,0
+TrackMigInOut,1,1
+TrackNumNeighbours,3,3
+TrackSingleIdleState,0,0
+TrackBipartiteMatch,1,1
+TrackFalsePos,1,1
+TrackSaveFPAsCells,0,0
+TrackCentroidOffset,0,0
+TrackMergeWatersheds,1,1
+TrackMergeOverlapMaxIter,0,0
+TrackMergeBrokenMaxArea,0,0
+TrackMergeBrokenRatio,0.75,0.75
+foiErosion,0,0
+TrackSaveIterations,0,0
+TrackSavePTC,0,0
+TrackSaveCTC,0,0
+TrackEvaluateCTC,0,0
+TrackSelectFromGT,0,0
+condition,Unspecified,Unspecified
+pixelSize,1,1
+magnification,1,1
+dT,1,1
+startT,0,0
+authorStr,,
+SegWSmooth2,7,7
+SegWHMax2,0.1,0.1
+SegWThresh2,-Inf,-Inf
diff --git a/Copy_of_BF_Functions/CytNucWaterShed.m b/Copy_of_BF_Functions/CytNucWaterShed.m
new file mode 100644
index 0000000..ff0c048
--- /dev/null
+++ b/Copy_of_BF_Functions/CytNucWaterShed.m
@@ -0,0 +1,21 @@
+function [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4)
+%UNTITLED4 Summary of this function goes here
+%   Detailed explanation goes here
+cytsize=size(cyt);
+	border = ones(cytsize);
+    border(2:end-1,2:end-1) = 0;
+    n_maxs=imerode(Nuc_bw4,strel('disk',1));
+    n_maxs=bwareaopen(n_maxs,100);
+    h=imhmin(CytTopHat,1);
+    h_c=imcomplement(h);
+    h_c_min=imimposemin(h_c, n_maxs);
+    L_n = watershed(h_c_min);
+    L_n(~cyt_bw4) = 0;
+    borderInverse=~border;
+    L_n(~borderInverse) = 0;
+    howdy=L_n;
+    Cyt_WS=imfill((howdy),4,'holes');
+    Cyt_WS_perim = imdilate(bwperim(Cyt_WS),strel('disk',1));
+    
+end
+
diff --git a/Copy_of_BF_Functions/Cytosol.m b/Copy_of_BF_Functions/Cytosol.m
new file mode 100644
index 0000000..029f0ea
--- /dev/null
+++ b/Copy_of_BF_Functions/Cytosol.m
@@ -0,0 +1,27 @@
+function [CytBright,CytArea,CytCytOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+ CytTopHat=imtophat(cyt,CytTophatDisk); % Clean image with tophat filter for thresholding 
+    CytOpen=imerode(CytTopHat,CytOpenDisk);
+     CytOpen=imreconstruct(CytOpen,CytTopHat);
+    cyt_eq =imadjust(CytTopHat,[0 0.25],[]);   %Make it easy to see
+    
+    CytMaxValue= CytMax*intmax(class(cyt));
+    CytOverbright=CytOpen>CytMaxValue;
+    CytBright=CytOpen;
+    CytBright(CytOverbright)=0;
+        CytMT1=multithresh(CytBright,20); %Calculate 20 brightness thresholds for image 
+        CytQuant1=imquantize(CytBright,CytMT1); %Divide Image into the 20 brightness baskets
+        CytBrightEnough=CytQuant1>CytLow;
+        
+        CytPos=CytBright;
+        CytPos(~CytBrightEnough)=0;
+          cyt_bw2=imerode(CytPos,CytErodeDisk);
+          cyt_bw3 = bwareaopen(cyt_bw2, 2000); %%Be sure to check this threshold
+          cyt_bw4 = imclose(cyt_bw3, CytCloseDisk);
+          CytPos(~cyt_bw4)=0;
+        cyt_bw4_perim = imdilate(bwperim(cyt_bw4),strel('disk',3));
+       CytArea = imoverlay(cyt_eq, cyt_bw4_perim, [.3 1 .3]);
+        CytCytOverlay = imoverlay(cyt_eq, cyt_bw4_perim, [.3 1 .3]);
+end
+
diff --git a/Copy_of_BF_Functions/Gal8.m b/Copy_of_BF_Functions/Gal8.m
new file mode 100644
index 0000000..7a57b30
--- /dev/null
+++ b/Copy_of_BF_Functions/Gal8.m
@@ -0,0 +1,25 @@
+function [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,CytPos,Gal8OutlineDisk)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+Gal8=wiener2(cyt);
+Gal8TH=imtophat(Gal8,Gal8TophatDisk);
+Gal8Open=imopen(Gal8TH,Gal8OpenDisk);
+
+Gal8MinValue= Gal8MinThreshold*intmax(class(cyt));
+Gal8Quant2=Gal8Open-Gal8MinValue;
+Gal8Quant2(Gal8Quant2<=0)=0;
+Gal8Quant3=bwareaopen(Gal8Quant2,4);
+Gal8Quant3(~CytPos)=0;
+Gal8Quant3=imdilate(Gal8Quant3,Gal8DilateDisk);
+Gal8Quant4=imdilate(Gal8Quant3,Gal8OutlineDisk);
+Gal8Quant5=imbinarize(Gal8Quant4-Gal8Quant3);
+GalPals=cyt;
+GalPals(~Gal8Quant3)=0;
+
+Puncta=regionprops(Gal8Quant3,cyt,'Area','Centroid','MeanIntensity');
+Ring=regionprops(Gal8Quant5,cyt,'Area','Centroid','MeanIntensity'); %need to figure out way to subtract out surrounding brightness for each individual Point
+RingMeanInt=2; %need to figure out way to subtract out surrounding brightness for each individual Point
+Gal8Signal=sum((vertcat(Puncta.MeanIntensity).*vertcat(Puncta.Area)));
+% Gal8Signal=Gal8Signal';
+end
+
diff --git a/Copy_of_BF_Functions/NuclearStain.m b/Copy_of_BF_Functions/NuclearStain.m
new file mode 100644
index 0000000..ae8496c
--- /dev/null
+++ b/Copy_of_BF_Functions/NuclearStain.m
@@ -0,0 +1,34 @@
+function [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk)
+%UNTITLED2 Summary of this function goes here
+%   Detailed explanation goes here
+    NucWeiner=wiener2(Nuc);
+    NucTopHat=imtophat(NucWeiner,NucTophatDisk); % Clean image with tophat filter for thresholding 
+%     NucOpen=imerode(NucTopHat,NucOpenDisk);
+%      NucOpen=imreconstruct(NucOpen,NucTopHat);
+    Nuc_eq =imadjust(NucTopHat);   %Make it easy to see
+    NucOpen=imopen(NucTopHat,NucOpenDisk);
+    NucMaxValue= NucMax*intmax(class(Nuc));
+    NucOverbright=NucTopHat>NucMaxValue;
+    
+    NucOpen(NucOverbright)=0;
+%         NucMT1=multithresh(NucOpen,20); %Calculate 20 brightness thresholds for image 
+%         NucQuant1=imquantize(NucOpen,NucMT1); %Divide Image into the 20 brightness baskets
+        NucMT1=1;
+        NucQuant1=1;
+%         NucBrightEnough=NucQuant1>NucLow;
+        NucBrightEnough=NucOpen>NucLow;
+        NucPos=NucOpen;
+        NucPos(~NucBrightEnough)=0;
+%         NucPos=imadjust(NucPos);
+          Nuc_bw2=imerode(NucPos,NucErodeDisk);
+          Nuc_bw3 = bwareaopen(Nuc_bw2, 250); %%Be sure to check this threshold
+          Nuc_bw4 = imclose(Nuc_bw3, NucCloseDisk);
+          Nuc_bw4 = imfill(Nuc_bw4,'holes');
+        Nuc_bw4_perim = imdilate(bwperim(Nuc_bw4),strel('disk',3));
+       
+       NucConn=bwconncomp(Nuc_bw4);
+       NucLabel = labelmatrix(NucConn);
+       NucArea = imoverlay(Nuc_eq, Nuc_bw4_perim, [.3 1 .3]);
+       
+end
+
diff --git a/Copy_of_BF_Functions/Rhoda.m b/Copy_of_BF_Functions/Rhoda.m
new file mode 100644
index 0000000..606771e
--- /dev/null
+++ b/Copy_of_BF_Functions/Rhoda.m
@@ -0,0 +1,14 @@
+  %%Rhodamine Code 
+  
+function [area,Thresh_eq,DrugMask,ThreshHigh] = ThreshSeg(Img, threshold)
+
+    Thresh_eq =imadjust(Img,[0 0.4],[]);
+       
+    threshold = threshold *intmax(class(Img));
+    
+    rhodaweiner=wiener2(Img);
+    DrugMask=rhodaweiner>threshold;
+    
+    area = sum(DrugMask,'all');
+    
+  
\ No newline at end of file
diff --git a/Copy_of_BF_Functions/ThreshSeg.m b/Copy_of_BF_Functions/ThreshSeg.m
new file mode 100644
index 0000000..d8aa2d6
--- /dev/null
+++ b/Copy_of_BF_Functions/ThreshSeg.m
@@ -0,0 +1,15 @@
+  %%Rhodamine Code 
+  
+function [area,Thresh_eq,DrugMask,ThreshHigh] = ThreshSeg(Img, threshold)
+
+    Thresh_eq =imadjust(Img,[0 0.4],[]);
+       
+    threshold = threshold *intmax(class(Img));
+    
+    rhodaweiner=wiener2(Img);
+    DrugMask=rhodaweiner>threshold;
+    ThreshHigh=Img;
+    ThreshHigh(~DrugMask)=0;
+    area = sum(DrugMask,'all');
+    
+  
\ No newline at end of file
diff --git a/Copy_of_BF_Functions/m_2021_12_30.m b/Copy_of_BF_Functions/m_2021_12_30.m
new file mode 100644
index 0000000..211e2ba
--- /dev/null
+++ b/Copy_of_BF_Functions/m_2021_12_30.m
@@ -0,0 +1,257 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\20211002BigProteinScreen001.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2022-01-04_Demo';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    InputPlanes={'Nuc','cyt','drug'};
+    
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.08;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 0.4; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=1:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+            for n=              
+                ImagePlane(n)= bitConvert*bfGetPlane(reader,iplane+n);
+            end
+            
+    
+                %% Analyze Images
+            %%Nuclear Stain Code    
+            [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+            %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+
+            %%Cytosol Code
+            [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+
+            %WaterShed Segmentation of Individual Cells
+            [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+            %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+            %Gal8 Puncta Segmentation
+            [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+            %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+
+            %Rhodamine Code
+            [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+            rhodPerim=bwperim(RhodMask);
+
+                %All Data Images
+                RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+                WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+                ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+                    ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+                    ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+                areacell=bwarea(Nuc_bw4(:));
+                CellSum=sum(Nuc(Nuc_bw4));
+                areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    %% Write Images to File
+     %overlaid Image
+    BaxterName=strcat('w',Well,'t',Timepoint)
+     
+     exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+    
+    
+    fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+    imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    ImageName=fullfile(BaxWellFolder,BaxterName);    
+    imwrite(Nuc, strcat(ImageName,'c01','.tif'),'tif');
+    imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+    imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+    imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+    imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+     
+    
+    SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+    imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+    
+    
+    SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+    imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+    
+    
+    end   
+end
+%% Write Analysis Data to File
+ 
+D=[Categories;C];
+WritingHere=strcat(exportdir,'\','Gal8','_',run);
+ writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/Copy_of_BF_Functions/m_Bronk_2022_01_05.m b/Copy_of_BF_Functions/m_Bronk_2022_01_05.m
new file mode 100644
index 0000000..c0fa4f0
--- /dev/null
+++ b/Copy_of_BF_Functions/m_Bronk_2022_01_05.m
@@ -0,0 +1,255 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-11-BigProteinFollowUp\Ai9Lipo48hrs002.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-11-BigProteinFollowUp\Analysis';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=1.36;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=1000;%
+     %Cytosol    
+        CytMax= 1.1; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=1;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        Rhoda_threshold = 1; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=0:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+
+            Nuc = bitConvert*bfGetPlane(reader,iplane+2);
+
+            cyt = bitConvert*bfGetPlane(reader,iplane+2);
+
+            drug = bitConvert*bfGetPlane(reader,iplane+1);
+    
+                %% Analyze Images
+            %%Nuclear Stain Code    
+            [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Nuc,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);   
+            %     NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+
+            %%Cytosol Code
+            [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(cyt,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+
+            %WaterShed Segmentation of Individual Cells
+            [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+            %   figure; imshow(imoverlay(cyt_eq,Cyt_WS, [.3 .3 1]));
+            %Gal8 Puncta Segmentation
+            [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(cyt,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,Cyt_WS,CytPos,Gal8OutlineDisk);    
+            %     figure; imshow(imoverlay(cyt_eq,Gal8Quant5, [.3 .3 1]));
+
+            %Rhodamine Code
+            [RhodBright,areaRhod, Rhodsum, RhodAvgInCell, RhodAvgOutCell,rhod_eq,RhodMask] = Rhoda(drug, Rhoda_threshold, cyt_bw4);
+            rhodPerim=bwperim(RhodMask);
+
+                %All Data Images
+                RGBExportImage=cat(3,rhod_eq,cyt_eq,Nuc_eq);
+                WSArea = imoverlay(RGBExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+                ExportImage=imoverlay(WSArea,Gal8Quant5,'m');
+                    ExportImage=imoverlay(ExportImage,Nuc_bw4_perim, [0.3010 0.7450 0.9330]);
+                    ExportImage=imoverlay(ExportImage,rhodPerim, 'y');
+            %         figure; imshow(ExportImage);
+            %
+
+                %% Measure Image Data
+
+                % measurement
+                areacell=bwarea(Nuc_bw4(:));
+                CellSum=sum(Nuc(Nuc_bw4));
+                areaGal8=sum((vertcat(Puncta.Area)));
+            %    
+            % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+    %% Write Images to File
+     %overlaid Image
+    BaxterName=strcat('w',Well,'t',Timepoint)
+     
+     exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+    
+    
+    fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+    imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    ImageName=fullfile(BaxWellFolder,BaxterName);    
+    imwrite(Nuc, strcat(ImageName,'c01','.tif'),'tif');
+    imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+    imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+    imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+    imwrite(RhodBright, strcat(ImageName,'c05','.tif'),'tif');
+     
+    
+    SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+    imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+    
+    
+    SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+    imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+    
+    
+    end   
+end
+%% Write Analysis Data to File
+ 
+D=[Categories;C];
+WritingHere=strcat(exportdir,'\','Gal8','_',run);
+ writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/Copy_of_BF_Functions/m_Bronk_2022_01_05_bigChanges.m b/Copy_of_BF_Functions/m_Bronk_2022_01_05_bigChanges.m
new file mode 100644
index 0000000..65aff67
--- /dev/null
+++ b/Copy_of_BF_Functions/m_Bronk_2022_01_05_bigChanges.m
@@ -0,0 +1,279 @@
+%% Gal8 Recruitment MATLAB Program
+
+% Written by Brock Fletcher in the Biomedical Engineering Department at
+% Vanderbilt University 2017 - 2022 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/). 
+%Adapted from work by Kameron V Kilchrist, 2015 - 2018 in the course of his PhD studies
+% advised by Craig Duvall (https://my.vanderbilt.edu/duvall/), published in
+% Kilchrist, Dimobi, ..., Duvall; "Gal8
+% Visualization of Endosome Disruption Predicts Carrier-mediated Biologic
+% Drug Intracellular Bioavailability".
+
+% University Email: brock.fletcher@vanderbilt.edu 
+% Permanent Email: brockfletch@gmail.com 
+
+% This code may be reused at will for non-commercial purposes. 
+% Licensed under a Creative Commons Attribution 4.0 International License.
+
+% Derivative code should be published at GitHub or FigShare. Derivative
+% scientific works should cite _______________
+%% Usage Guide (TL/DR):
+    %Steps
+        %Export your fluorescent microscopy as multipage TIFs
+        %Grab a few example TIFs to test your parameters and put them
+        %into a folder. (..\Test)
+        %Create a Second Folder to output to (..\TestExports)
+        
+        %Copy the file paths from file explorer and paste them into the
+        %"workingdir" and "exportdir"
+        
+        %Enter your "Calibration" value
+        %Enter what programs to run on each Channel ("C1=[]")
+        %Set your thresholds to a starting value
+        %Run Program
+        %Check output Images and Excel File
+        %Change Threshold Values and Re-Run until results are good enough
+            %If good analysis cannot be reached, edit advanced Values
+            %If still not good enough, edit actual bulk of code
+        %Once ready, change "workingdir" to a folder containing all images
+        %to be analyzed, and "exportdir" to a new, empty folder
+        
+        %Run Program and wait. If too hard on your CPU, change "parfor" to
+        %"for"
+        
+        %Review output images and analyze Data. 
+            %Reccomended Analysis Steps:
+                %Label Each row of Data using VLOOKUP in Excel.
+                %Explore Data using JMP's Graphbuilder.
+                %Graph Data in Prism.
+%% Image Folder Location
+clc, clear;
+reader = bfGetReader('D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\20211002BigProteinScreen001.nd2');
+exportdir='D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2022-01-04_Demo';
+% filetype='tif';
+% listing=dir(strcat(workingdir,'*.TIF'));
+% ds=imageDatastore(workingdir);
+%% Directory Code
+readeromeMeta=reader.getMetadataStore();
+destdirectory1 = fullfile(exportdir,'Overlaid');
+BaxtDirectory= fullfile(exportdir,'Baxter');
+exportbaseBAXTSegNuc=fullfile(BaxtDirectory,'Analysis','Segmentation_Nuc');
+exportbaseBAXTSegCell=fullfile(BaxtDirectory,'Analysis','Segmentation_Cell');
+mkdir(destdirectory1);   %create the directory
+mkdir(BaxtDirectory);
+mkdir(exportbaseBAXTSegNuc);
+mkdir(exportbaseBAXTSegCell);
+%% 
+% This will measure the total Gal8 recruited to puncta and count cell
+% nuclei or cytosol in each frame.
+
+% This code assumes you have exported images as multipage TIF files, with
+% any of the following stains in each channel:
+    % nuclear Stain
+    % Difuse Cytosolic Stain
+    % Punctate Cytosolic Stain
+    % Labeled Drug or other exogenous molecule (Cas9, siRNA)
+
+% Images were exported to 2 page TIF images using Nikon NIS Elements. If
+% you use alternate file formats or use separate export files for each
+% channel, please edit the code as appropriate.
+
+% You *must* edit the workingdir and exportdir variables for this code to
+% work. 
+%% Structuring Elements
+% For conveience, a number of sizes of disk shaped structural elements are
+% generated for data exploration.
+sr1=strel('square',1);
+se1=strel('disk',1);
+sr2=strel('square',2);
+se2=strel('disk',2);
+se3=strel('disk',3);
+sr3=strel('square',3);
+se4=strel('disk',4);
+se5=strel('disk',5);
+se6=strel('disk',6);
+se7=strel('disk',7);
+se8=strel('disk',8);
+se9=strel('disk',9);
+se10=strel('disk',10);
+se12=strel('disk',12);
+se20=strel('disk',20);
+se25=strel('disk',25);
+se100=strel('disk',100);
+%% Sizing/Resolution Parameters EDIT HERE ADVANCED
+
+        %NEED TO ADD microns per Pixel %NEED TO ADD Cell size (Small, Medium, Large)%Go through this and make all disks calculated on the microns per pixel and %the Cell Size
+
+MiPerPix=0.34;        
+CellSize=1; %Scale as needed for different Cells        
+            %Disks
+            NucTophatDisk=strel('disk',round(250*(0.34/MiPerPix)));
+            NucOpenDisk= strel('disk',round(5*(0.34/MiPerPix)));
+            NucErodeDisk=strel('disk',round(6*(0.34/MiPerPix)));
+            NucCloseDisk=strel('disk',round(4*(0.34/MiPerPix)));
+
+            CytTophatDisk=strel('disk',round(250*(0.34/MiPerPix))); % EditHere
+            CytOpenDisk =strel('disk',round(5*(0.34/MiPerPix)));
+            CytErodeDisk=strel('disk',round(5*(0.34/MiPerPix)));
+            CytCloseDisk=strel('disk',round(5*(0.34/MiPerPix)));
+
+            Gal8TophatDisk=strel('disk',round(6*(0.34/MiPerPix)));% EditHere
+            Gal8OpenDisk =strel('square',round(2*(0.34/MiPerPix)));
+            Gal8DilateDisk=strel('disk',round(1*(0.34/MiPerPix)));
+            Gal8OutlineDisk=strel('disk',round(2*(0.34/MiPerPix)));
+%% Image Thresholding EDIT HERE BASIC
+%Bit Depth    
+    bitdepthin= 12; %Bit depth of original image, usually 8, 12, or 16
+    
+%Input Planes
+    ImagePlanes=[1,2,3];
+    FirstAnalyses={{'nuc'},{'cyt'},{'thresh'}};
+    SecondAnalyses={{},{'SeededWS' 'gal' },{}};
+%Nuclear Stain
+        NucMax=0.8;%Number 0-1, removes Cell Debris brighter than this value in order to allow low end to remain visible. 0.2 is usually a good start 
+        NucLow=100;%
+     %Cytosol    
+        CytMax= 0.5; %Number 0-1, removes Cell Debris brighter than this value. 0.2 is usually a good start  
+        CytLow=1; %Choose number 0-20, start at 0. Higher numbers remove more dim cells and background.
+    %Gal8
+        Gal8MinThreshold=0.08;%Number 0-1, removes Puncta Dimmer than this value. 0.05 is usually a good start 
+    %Rhodamine
+        thresh = 0.4; %Number 0-1, removes rhodamine signal dimmer than threshold
+%         Rhoda_threshold_Big = 100;
+%% Analysis Variables
+bitConvert=(2^16/2^bitdepthin);
+run=char(datetime(clock),"yyyy-MM-dd-hh-mm-ss");    % The Run number is used to track multiple runs of the software, and is used in
+            % export file names and in the DataCells array. Note: it is a character
+            % array / string!
+Categories=[{'run'},{'well'},{'areacell'},{'CellSum'},{'areaGal8'},{'galsum'},{'areaRhod'},{'Rhodsum'},{'RhodAvgInCell'},{'RhodAvgOutCell'}];
+NumSeries=reader.getSeriesCount();
+NumColors=reader.getEffectiveSizeC();
+NumTimepoint=(reader.getImageCount())/NumColors;
+NumImg=NumSeries*NumTimepoint*NumColors;
+
+C = cell(NumImg,length(Categories));
+%% Analysis Program 
+for j=0:NumSeries% Number of images in ND2 File  
+    %% Import TIFs
+    % %The next few lines are specific to 2 page TIF images. Edit from here
+    % if you have alternate arrangements.
+%     currfile=strcat(workingdir,listing(j,1).name);
+    CurrSeries=j;
+    reader.setSeries(CurrSeries);
+    fname = reader.getSeries;
+    Well=num2str(fname,'%05.f');  
+    
+    BaxWellFolder=fullfile(BaxtDirectory,Well);
+    mkdir(BaxWellFolder);
+    PositionX = readeromeMeta.getPlanePositionX(CurrSeries,1).value();
+    PositionY = readeromeMeta.getPlanePositionY(CurrSeries,1).value();
+    T_Value = reader.getSizeT()-1;
+    
+    BaxSegFolderNuc=fullfile(exportbaseBAXTSegNuc,Well);
+    mkdir(BaxSegFolderNuc);
+    
+    BaxSegFolderCell=fullfile(exportbaseBAXTSegCell,Well);
+    mkdir(BaxSegFolderCell);
+    
+    for i=1:T_Value
+    
+%     T_Value = reader.getSizeT();
+            Timepoint = num2str(i,'%03.f');
+            iplane=reader.getIndex(0,0,i);
+            WellTime = round(str2double(readeromeMeta.getPlaneDeltaT(CurrSeries,iplane).value()))
+            Img=[];
+%             Red=zeros(imsize);
+%             Green=zeros(imsize);
+%             Blue=zeros(imsize);
+            for n=ImagePlanes             
+                Img= bitConvert*bfGetPlane(reader,iplane+n);
+                imsize=size(Img);    
+                CurrPlane=FirstAnalyses{n};
+                for c=1:length(CurrPlane)
+                    Analysis=CurrPlane{c}
+                     
+                     if contains(Analysis,'nuc')
+                        [NucLabel,Nuc_bw4,NucPos,NucBrightEnough,NucMT1,NucOpen,Nuc_eq,NucTopHat,Nuc_bw4_perim,NucOverbright,NucQuant1,NucWeiner,NucArea] = NuclearStain(Img,NucTophatDisk,NucMax,NucOpenDisk,NucErodeDisk,NucLow,NucCloseDisk);  
+        %                 x='hell0'
+                        nuc=Img;
+                        Blue=Nuc_eq;
+                        NucStats=regionprops(Nuc_bw4,'Centroid','Area');
+                        end
+                        if contains(Analysis,'cyt')
+                        [CytBright,CytArea,CytNucOverlay,cyt_bw4,CytPos,CytBrightEnough,CytMT1,CytOpen,cyt_eq,CytTopHat,cyt_bw4_perim] = Cytosol(Img,CytTophatDisk,CytMax,CytOpenDisk,CytErodeDisk,CytLow,CytCloseDisk);
+                        x='hell0';
+                        cyt=Img;
+                        Green=cyt_eq;
+                        end
+                         if contains(Analysis,'thresh')
+                            [areaThresh,Thresh_eq,ThreshMask,ThreshHigh] = ThreshSeg(Img, thresh);
+                            drug=Img;
+                            Red=Thresh_eq;
+                            ThreshPerim=bwperim(ThreshMask);
+                         end
+                       
+                end
+                 
+                    
+%                  ExportImage=cat(3,Red,Green,Blue);
+%                 ExportImage=imoverlay(ExportImage,ThreshPerim, 'y');
+                CurrPlane2=SecondAnalyses{n};
+                for d=1:length(CurrPlane2)
+                    Analysis2=CurrPlane2{d}
+                         if contains(Analysis2,'SeededWS')
+                           [Cyt_WS,Cyt_WS_perim,L_n] = CytNucWaterShed(cyt,Nuc_bw4,CytTopHat,cyt_bw4);
+                         
+                         end
+                         if contains(Analysis2,'gal')
+                          [GalPals,Gal8Signal,RingMeanInt,Gal8Quant5,Gal8Quant4,Gal8Quant3,Gal8Open,Gal8TH,Gal8Quant2,Puncta,Ring] = Gal8(Img,Gal8TophatDisk,Gal8OpenDisk,Gal8DilateDisk,Gal8MinThreshold,CytPos,Gal8OutlineDisk);  
+                         
+                         end
+                
+             
+                end
+            end
+                  ExportImage=cat(3,Red,Green,Blue);
+                  ExportImage = imoverlay(ExportImage, Cyt_WS_perim,[0.8500 0.3250 0.0980]);
+                  ExportImage=imoverlay(ExportImage,Gal8Quant5,'m');
+           %% Measure Image Data
+
+                % measurement
+%                 areacell=bwarea(Nuc_bw4(:));
+%                 CellSum=sum(Nuc(Nuc_bw4));
+%                 areaGal8=sum((vertcat(Puncta.Area)));
+% %             %    
+%             % C(j,:)=[{run},{WellTime},{areacell},{CellSum},{areaGal8},{Gal8Signal},{areaRhod},{Rhodsum},{RhodAvgInCell},{RhodAvgOutCell}];
+%     %% Write Images to File
+%      %overlaid Image
+    BaxterName=strcat('w',Well,'t',Timepoint);
+%      
+     exportbase=strcat(destdirectory1,'\',run,'_',BaxterName);
+%     
+%     
+    fulldestination = strcat(exportbase,'.png');  %name file relative to that directory
+    imwrite(ExportImage, fulldestination);  %save the file there directory
+    
+    %BaxterImages    
+    ImageName=fullfile(BaxWellFolder,BaxterName);    
+    imwrite(nuc, strcat(ImageName,'c01','.tif'),'tif');
+    imwrite(cyt, strcat(ImageName,'c02','.tif'),'tif');
+    imwrite(GalPals, strcat(ImageName,'c03','.tif'),'tif');
+    imwrite(drug, strcat(ImageName,'c04','.tif'),'tif');
+    imwrite(ThreshHigh, strcat(ImageName,'c05','.tif'),'tif');
+     
+    
+    SegNameNuc=fullfile(BaxSegFolderNuc,BaxterName);
+    imwrite(NucLabel, strcat(SegNameNuc,'c01','.tif'),'tif');
+    
+    
+    SegNameCell=fullfile(BaxSegFolderCell,BaxterName);
+    imwrite(Cyt_WS, strcat(SegNameCell,'c01','.tif'),'tif');
+%     
+    
+    end   
+end
+%% Write Analysis Data to File
+%  
+% D=[Categories;C];
+% WritingHere=strcat(exportdir,'\','Gal8','_',run);
+%  writecell(D,strcat(WritingHere,'.xlsx')); % Exports an XLSX sheet of your data
\ No newline at end of file
diff --git a/DataWriteTest.m b/DataWriteTest.m
new file mode 100644
index 0000000..382421c
--- /dev/null
+++ b/DataWriteTest.m
@@ -0,0 +1,17 @@
+for i=0:2
+    seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2021-12-31-TestMultiTimepoint\Baxter\';
+        Run=num2str(i)
+        seqPath=strcat(seqPath,'0000',num2str(i));
+        cells = LoadCells (seqPath , '_211231_152842','AreCells', true, 'Compact', true);
+%         cells2=AreCells(cells);
+properties=cells(1).regionProps.Area(2)
+% % [cellVec2, labels2] = PartitionCells(cells, 'firstFrame');
+% Test=a;
+fluorProps = {cells.regionProps};
+fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+fluorProps = unique(cat(1,fluorProps{:}))';
+% fluorProps = regexp(fluorProps, '^Fluor.*', 'match', 'once');
+% fluorProps(cellfun(@isempty, fluorProps)) = [];
+
+        Plot_Fluorescence3D(cells,ax1,'Drug','Gal',rand(1,3));
+end
diff --git a/DetermineCutoff.m b/DetermineCutoff.m
new file mode 100644
index 0000000..e69de29
diff --git a/Files/Settings/Brock/Settings.csv b/Files/Settings/Brock/Settings.csv
new file mode 100644
index 0000000..c20bdcc
--- /dev/null
+++ b/Files/Settings/Brock/Settings.csv
@@ -0,0 +1,84 @@
+setting,A20,F08
+numZ,1,1
+bits,16,16
+minWellR,NaN,NaN
+maxWellR,NaN,NaN
+channelNames,Dapi:Gal8:RNA:TD,Dapi:Gal8:RNA
+channelTags,c1:c2:c3:c4,c1:c2:c3
+channelColors,0  0  1:0  1  0:1         0.5           0:1  1  1,0  0  1:0  1  0:1         0.5           0:1  1  1
+channelMin,0:0:0:0,0:0:0:0
+channelMax,0.32022:0.58192:0.69413:1,0.32022:0.58192:0.69413:1
+use,1,1
+sequenceLength,,
+SegOldVersion,none,none
+SegSave,1,1
+SegAlgorithm,Segment_bandpass,Segment_bandpass
+SegChannel,Gal8,Gal8
+SegLightCorrect,none,none
+SegBgSubAlgorithm,none,none
+SegTopHatRadius,Inf,Inf
+SegFillHoles,1,1
+SegMinHoleArea,Inf,Inf
+SegMinArea,1000,1000
+SegMaxArea,Inf,Inf
+SegMinSumIntensity,0,0
+SegClipping,1,1
+SegClippingBelow,0,0
+SegSmooth,2,2
+SegMedFilt,1,1
+SegWatershed,intermediate,intermediate
+SegWSmooth,5,5
+SegWHMax,6,6
+SegWThresh,-Inf,-Inf
+SegWatershed2,darkness,darkness
+SegWLocMaxCentroids,0,0
+SegCellMorphOp,none,none
+BPSegHighStd,5,5
+BPSegLowStd,2,2
+BPSegBgFactor,1,1
+BPSegThreshold,1e-06,1e-06
+BPSegDarkOrBright,bright,bright
+TrackXSpeedStd,12,12
+countClassifier,none,none
+splitClassifier,none,none
+deathClassifier,none,none
+migClassifier,none,none
+pCnt0,0.2,0.2
+pCnt1,0.7,0.7
+pCnt2,0.1,0.1
+pCntExtrap,0.25,0.25
+pSplit,0.01,0.01
+pDeath,0.01,0.01
+TrackPAppear,0,0
+TrackPDisappear,0,0
+TrackMotionModel,none,none
+TrackMigLogLikeList,MigLogLikeList_uniformClutter,MigLogLikeList_uniformClutter
+TrackDeathShift,2e-05,2e-05
+TrackMaxDeathProb,1,1
+TrackMaxMigScore,0,0
+TrackMigInOut,1,1
+TrackNumNeighbours,3,3
+TrackSingleIdleState,0,0
+TrackBipartiteMatch,1,1
+TrackFalsePos,1,1
+TrackSaveFPAsCells,0,0
+TrackCentroidOffset,0,0
+TrackMergeWatersheds,1,1
+TrackMergeOverlapMaxIter,0,0
+TrackMergeBrokenMaxArea,0,0
+TrackMergeBrokenRatio,0.75,0.75
+foiErosion,0,0
+TrackSaveIterations,0,0
+TrackSavePTC,0,0
+TrackSaveCTC,0,0
+TrackEvaluateCTC,0,0
+TrackSelectFromGT,0,0
+condition,Unspecified,Unspecified
+pixelSize,1,1
+magnification,1,1
+dT,1,1
+startT,0,0
+authorStr,,
+SegWSmooth2,7,7
+SegWHMax2,0.1,0.1
+SegWThresh2,-Inf,-Inf
diff --git a/Make4DMatrix.m b/Make4DMatrix.m
new file mode 100644
index 0000000..520c4ff
--- /dev/null
+++ b/Make4DMatrix.m
@@ -0,0 +1,46 @@
+seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-11-15-Ai9CMAX PRotein Screen\Analysis\Baxter';
+TrackVersion='_220106_115446';
+FilePath=fullfile(seqPath,'Analysis',strcat('CellData',TrackVersion),'Compact');
+a=dir(fullfile(FilePath,'*.mat'));
+b={a.name};
+HasCells=[a.bytes];
+blank=~(HasCells>185);
+d=b;
+d(blank) =[];
+
+for m=1:length(b)
+    Run=b{1,m};
+    Run=Run(1:end-4)
+    if blank(m)
+        BronkBox{1,1,1,m}={};    
+    else
+    cellPath=strcat(seqPath,'\',Run);
+    cells = LoadCells(cellPath, TrackVersion, 'Compact', true);
+    fluorProps = {cells.regionProps};
+    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+    fluorProps = unique(cat(1,fluorProps{:}))';
+    BronkBox=cell(length(cells),max([cells.stopT]),length(fluorProps),NumWells);
+for k=1:length(fluorProps)
+    currProp=fluorProps{k};
+    Test='MinorAxisLength';
+for j=1:length(cells)
+    c = cells(j);
+    t = c.firstFrame : c.lastFrame;  
+    tp=1;
+    for i=t
+        BronkBox{j,i,k,m}=cells(1,j).regionProps.(currProp)(tp);
+        tp=tp+1;
+    end
+end
+end
+    end
+end
+empties=cellfun('isempty',BronkBox);
+BronkBox(empties) = {NaN};
+Data=cell2mat(BronkBox);
+means=mean(Data(:,:,:,:),'omitnan');
+medians=median(Data(:,:,:,:),'omitnan');
+stds=std(Data(:,:,:,:),'omitnan');
+vars=var(Data(:,:,:,:),'omitnan');
+sums=sum(Data(:,:,:,:),'omitnan');
+CVs=stds./means;
\ No newline at end of file
diff --git a/PlotTest.m b/PlotTest.m
new file mode 100644
index 0000000..d38bb81
--- /dev/null
+++ b/PlotTest.m
@@ -0,0 +1,13 @@
+figure, ax1 = axes('Position',[0.1 0.1 0.7 0.7]);
+for i=0:2
+    seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2021-12-31-TestMultiTimepoint\Baxter\';
+        Run=num2str(i)
+        seqPath=strcat(seqPath,'0000',num2str(i));
+        cells2 = LoadCells (seqPath , '_211231_152842','AreCells', true, 'Compact', true);
+%         cells2=AreCells(cells);
+        Plot_Fluorescence3D(cells2,ax1,'Drug','Gal',rand(1,3));
+end
+% for i = 1:length(cells2)
+%     c = cells2(i)
+%     
+% end    
\ No newline at end of file
diff --git a/TestApp.mlapp b/TestApp.mlapp
new file mode 100644
index 0000000..3c508ad
Binary files /dev/null and b/TestApp.mlapp differ
diff --git a/WriteTest.m b/WriteTest.m
new file mode 100644
index 0000000..a8fbbd0
--- /dev/null
+++ b/WriteTest.m
@@ -0,0 +1,53 @@
+seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2021-12-31-TestMultiTimepoint\Baxter\';
+TrackVersion='_211231_152842';
+FilePath=fullfile(seqPath,'Analysis',strcat('CellData',TrackVersion),'Compact');
+a=dir(fullfile(FilePath,'*.mat'));
+b={a.name};
+HasCells=[a.bytes];
+c=~(HasCells>185);
+d=b;
+d(c) =[];
+
+
+figure, ax2 = axes('Position',[0.1 0.1 0.7 0.7]);
+for m=1:length(d)
+        Run=d{1,m};
+        Run=Run(1:end-4)
+        cellPath=strcat(seqPath,Run);
+        cells = LoadCells(cellPath , TrackVersion,'AreCells', true, 'Compact', true);
+        fluorProps = {cells.regionProps};
+    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+    fluorProps = unique(cat(1,fluorProps{:}))';
+    
+    Plot_Fluorescence3D(cells,ax2,'Cyt','Debris',rand(1,3));
+%      BronkBox=cell(length(cells),max([cells.stopT]),length(fluorProps),NumWells);
+for k=1:length(fluorProps);
+    currProp=fluorProps{k};
+    Test='MinorAxisLength';
+for j=1:length(cells)
+    c = cells(j);
+    t = c.firstFrame : c.lastFrame;  
+    tp=1;
+    for i=t
+        BronkBox{j,i,k,m}=cells(1,j).regionProps.(currProp)(tp);
+        tp=tp+1;
+    end
+end
+end
+end
+empties=cellfun('isempty',BronkBox);
+BronkBox(empties) = {NaN};
+Data=cell2mat(BronkBox);
+means=mean(Data(:,:,:,:),'omitnan');
+medians=median(Data(:,:,:,:),'omitnan');
+stds=std(Data(:,:,:,:),'omitnan');
+vars=var(Data(:,:,:,:),'omitnan');
+sums=sum(Data(:,:,:,:),'omitnan');
+CVs=stds./means;
+figure, ax1 = axes('Position',[0.1 0.1 0.7 0.7]);
+% figure,
+for n=1:length(d)
+PlotWithNan3D(ax1,1:length(d),means(:,:,1,n),means(:,:,6,n));
+%   scatter(means(:,:,1,n),means(:,:,6,n));
+hold on
+end
\ No newline at end of file
diff --git a/WriteTest2.m b/WriteTest2.m
new file mode 100644
index 0000000..b8a1108
--- /dev/null
+++ b/WriteTest2.m
@@ -0,0 +1,34 @@
+Bigbox=cell(1,3);
+NumWells=3;
+for m=0:NumWells-1
+     seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Isa\2021-10-02-BigPRoteinScreen\2021-12-31-TestMultiTimepoint\Baxter\';
+        Run=num2str(m,'%05.f');
+        seqPath=strcat(seqPath,Run);
+        cells = LoadCells (seqPath , '_211231_152842','AreCells', true, 'Compact', true);
+        fluorProps = {cells.regionProps};
+    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+    fluorProps = unique(cat(1,fluorProps{:}))';
+    BronkBox=cell(length(cells),max([cells.stopT]));
+for k=1:length(fluorProps)
+%     k=1:length(fluorProps);
+    currProp=fluorProps{k};
+    Test='MinorAxisLength';
+for j=1:length(cells)
+    c = cells(j);
+    t = c.firstFrame : c.lastFrame;  
+    tp=1;
+    for i=t
+%         BronkBox{j,i}=cells(1,j).regionProps;
+        BronkBox{j,i}=cells(1,j).regionProps.(currProp)(tp);
+        tp=tp+1;
+        LilBox{k,1}=[BronkBox];
+        
+        Bigbox{1,m+1}=[LilBox];
+    end
+end
+end 
+LilStruct=cell2struct(LilBox,fluorProps,1);
+Bigbox{1,m+1}=[LilStruct];
+ Count{1,m+1}=char(Run);
+end
+% BigStruct=cell2struct(Bigbox,{'zero','One','Tree'},2);
\ No newline at end of file
diff --git a/WriteTest3.m b/WriteTest3.m
new file mode 100644
index 0000000..998642c
--- /dev/null
+++ b/WriteTest3.m
@@ -0,0 +1,75 @@
+% Update seqpath with image location
+% Leave trailing slash
+seqPath = 'C:\Users\Owner\Dropbox (VU Basic Sciences)\LabConfocalOld\Duvall Lab\Isa\2021-10-11-BigProteinFollowUp\Analysis\Baxter\'; 
+% Update track number here from BaxterAlgorithms.m GUI
+TrackVersion='_220105_121225'; 
+FilePath=fullfile(seqPath,'Analysis',strcat('CellData',TrackVersion),'Compact');
+a=dir(fullfile(FilePath,'*.mat'));
+b={a.name};
+% Rough way of gating / filtering cells by file size (bytes)
+HasCells=[a.bytes]; 
+c=~(HasCells>185);
+d=b;
+d(c) =[];
+
+
+figure, ax2 = axes('Position',[0.1 0.1 0.7 0.7]);
+for m=1:length(d)
+        Run=d{1,m};
+        Run=Run(1:end-4)
+        cellPath=strcat(seqPath,Run); % Appends Cell Path
+        cells = LoadCells (cellPath , TrackVersion,'AreCells', true, 'Compact', true);
+        fluorProps = {cells.regionProps};
+    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+    fluorProps = unique(cat(1,fluorProps{:}))';
+    
+     Plot_Fluorescence3D(cells,ax2,'Cyt','Debris',rand(1,3));
+   %   BronkBox=cell(length(cells),max([cells.stopT]),length(fluorProps),NumWells);
+for k=1:length(fluorProps);
+    currProp=fluorProps{k};
+    Test='MinorAxisLength';
+for j=1:length(cells)
+    c = cells(j);
+    t = c.firstFrame : c.lastFrame;  
+    tp=1;
+    for i=t
+        BronkBox{j,i,k,m}=cells(1,j).regionProps.(currProp)(tp);
+        tp=tp+1;
+    end
+end
+end
+end
+
+% Replaces all BronkBox 'empty' data with NaN
+empties=cellfun('isempty',BronkBox);
+BronkBox(empties) = {NaN};
+
+% Data holds BronkBox in a matrix
+% cell2mat converts cell array to one standard array
+Data=cell2mat(BronkBox); 
+
+means=mean(Data(:,:,:,:),'omitnan');
+medians=median(Data(:,:,:,:),'omitnan');
+stds=std(Data(:,:,:,:),'omitnan');
+vars=var(Data(:,:,:,:),'omitnan');
+sums=sum(Data(:,:,:,:),'omitnan');
+CVs=stds./means;
+
+figure, ax1 = axes('Position',[0.1 0.1 0.7 0.7]);
+xbar=categorical(d);
+ybar=[];
+for n=1:length(d)
+<<<<<<< HEAD
+% PlotWithNan3D(ax1,n*ones(size(Data(:,:,6,n))),Data(:,:,1,n),Data(:,:,6,n));
+swarmchart(n*ones(size(sums(:,:,6,n))),sums(:,:,1,n));
+ybar=cat(2,ybar,[sums(:,:,1,n)]);
+=======
+PlotWithNan3D(ax1,n*ones(size(Data(:,:,5,n))),Data(:,:,1,n),Data(:,:,5,n));
+% swarmchart(n*ones(size(sums(:,:,6,n))),sums(:,:,1,n));
+ % ybar=cat(2,ybar,[sums(:,:,1,n)]);
+%  Plot_Fluorescence3D(cells2,ax1,'Drug','Gal',rand(1,3));
+>>>>>>> c1e554047a8962cae6cafd1ca8a96a7c2015188b
+
+ % scatter(means(:,:,1,n),means(:,:,6,n));
+hold on
+end
\ No newline at end of file
diff --git a/WriteTest4.m b/WriteTest4.m
new file mode 100644
index 0000000..c5e3539
--- /dev/null
+++ b/WriteTest4.m
@@ -0,0 +1,64 @@
+seqPath = 'D:\Dropbox (VU Basic Sciences)\Duvall Confocal\Duvall Lab\Brock Fletcher\2021-11-15-Ai9CMAX PRotein Screen\Analysis\Baxter';
+TrackVersion='_220106_115446';
+FilePath=fullfile(seqPath,'Analysis',strcat('CellData',TrackVersion),'Compact');
+a=dir(fullfile(FilePath,'*.mat'));
+b={a.name};
+HasCells=[a.bytes];
+blank=~(HasCells>185);
+d=b;
+d(blank) =[];
+
+
+ax2 = axes;
+for m=1:length(b)
+    Run=b{1,m};
+    Run=Run(1:end-4)
+    if blank(m)
+        BronkBox{1,1,1,m}={};    
+    else
+    
+        cellPath=strcat(seqPath,'\',Run);
+        cells = LoadCells(cellPath, TrackVersion, 'Compact', true);
+        fluorProps = {cells.regionProps};
+    fluorProps = cellfun(@fieldnames, fluorProps,'UniformOutput', false);
+    fluorProps = unique(cat(1,fluorProps{:}))';
+        x_in=m;
+%      Plot_Fluorescence3D_2(cells,ax2,'c01','c01',rand(1,3),x_in);
+     hold on
+%      BronkBox=cell(length(cells),max([cells.stopT]),length(fluorProps),NumWells);
+for k=1:length(fluorProps)
+    currProp=fluorProps{k};
+    Test='MinorAxisLength';
+for j=1:length(cells)
+    c = cells(j);
+    t = c.firstFrame : c.lastFrame;  
+    tp=1;
+    for i=t
+        BronkBox{j,i,k,m}=cells(1,j).regionProps.(currProp)(tp);
+        tp=tp+1;
+    end
+end
+end
+    end
+end
+empties=cellfun('isempty',BronkBox);
+BronkBox(empties) = {NaN};
+Data=cell2mat(BronkBox);
+means=mean(Data(:,:,:,:),'omitnan');
+medians=median(Data(:,:,:,:),'omitnan');
+stds=std(Data(:,:,:,:),'omitnan');
+vars=var(Data(:,:,:,:),'omitnan');
+sums=sum(Data(:,:,:,:),'omitnan');
+CVs=stds./means;
+% figure, ax1 = axes('Position',[0.1 0.1 0.7 0.7]);
+% % figure,
+% xbar=categorical(d);
+% ybar=[];
+% for n=1:length(d)
+% % PlotWithNan3D(ax1,n*ones(size(Data(:,:,6,n))),Data(:,:,1,n),Data(:,:,6,n));
+% % swarmchart(n*ones(size(sums(:,:,6,n))),sums(:,:,1,n));
+% % ybar=cat(2,ybar,[sums(:,:,1,n)]);
+% 
+% %   scatter(means(:,:,1,n),means(:,:,6,n));
+% hold on
+% end
\ No newline at end of file