Regi_Nuance_HE_GUI.m

classdef Regi_Nuance_HE_GUI < matlab.apps.AppBase
    
    % Properties that correspond to app components
    properties (Access = public)
        figure1                     matlab.ui.Figure
        ImportPanel                 matlab.ui.container.Panel
        GridLayout3                 matlab.ui.container.GridLayout
        AADEditFieldLabel           matlab.ui.control.Label
        AADEditField                matlab.ui.control.EditField
        HEEditFieldLabel            matlab.ui.control.Label
        HEEditField                 matlab.ui.control.EditField
        LOADButton                  matlab.ui.control.Button
        TabGroup                    matlab.ui.container.TabGroup
        ManuallyTab                 matlab.ui.container.Tab
        loadtformButton             matlab.ui.control.Button
        savePanel                   matlab.ui.container.Panel
        save_pushbutton             matlab.ui.control.Button
        tformfileCheckBox           matlab.ui.control.CheckBox
        FeaturepointsCheckBox       matlab.ui.control.CheckBox
        cpselect_pushbutton         matlab.ui.control.Button
        AutoTab                     matlab.ui.container.Tab
        InitailregistrationButton   matlab.ui.control.Button
        precessingPanel             matlab.ui.container.Panel
        GridLayout                  matlab.ui.container.GridLayout
        Binarize7aadimagePanel      matlab.ui.container.Panel
        wiener2EditField_3          matlab.ui.control.NumericEditField
        bwareaopenEditField         matlab.ui.control.EditField
        bwareaopenEditFieldLabel    matlab.ui.control.Label
        wiener2EditField            matlab.ui.control.NumericEditField
        wiener2EditFieldLabel       matlab.ui.control.Label
        greythretholdSlider         matlab.ui.control.Slider
        greythretholdSliderLabel    matlab.ui.control.Label
        BinarizeheimagePanel_2      matlab.ui.container.Panel
        wiener2EditField_4          matlab.ui.control.NumericEditField
        greythretholdSlider_3       matlab.ui.control.Slider
        greythretholdSlider_3Label  matlab.ui.control.Label
        bwareaopenEditField_2       matlab.ui.control.NumericEditField
        bwareaopenEditField_2Label  matlab.ui.control.Label
        wiener2EditField_2          matlab.ui.control.NumericEditField
        wiener2EditField_2Label     matlab.ui.control.Label
        refreshButton               matlab.ui.control.Button
        saveButton                  matlab.ui.control.Button
        SlidiingwindowPanel         matlab.ui.container.Panel
        GridLayout2                 matlab.ui.container.GridLayout
        coreEditFieldLabel          matlab.ui.control.Label
        coreEditField               matlab.ui.control.NumericEditField
        topEditFieldLabel           matlab.ui.control.Label
        topEditField                matlab.ui.control.NumericEditField
        stepEditFieldLabel          matlab.ui.control.Label
        stepEditField               matlab.ui.control.NumericEditField
        RunButton                   matlab.ui.control.Button
        HECheckBox                  matlab.ui.control.CheckBox
        axes2                       matlab.ui.control.UIAxes
        axes1                       matlab.ui.control.UIAxes
    end
    
    % Callbacks that handle component events
    methods (Access = private)
        
        % Code that executes after component creation
        function main_gui_OpeningFcn(app, varargin)
            % Create GUIDE-style callback args - Added by Migration Tool
            [hObject, eventdata, handles] = convertToGUIDECallbackArguments(app); %#ok<ASGLU>
            
            % This function has no output args, see OutputFcn.
            % hObject    handle to figure
            % eventdata  reserved - to be defined in a future version of MATLAB
            % handles    structure with handles and user data (see GUIDATA)
            % varargin   command line arguments to main_gui (see VARARGIN)
            
            % Choose default command line output for main_gui
            handles.output = hObject;
            
            % Update handles structure
            guidata(hObject, handles);
        end
        
        % Button pushed function: LOADButton
        function LOAD_putshbutton_Callback(app, event)
            % Create GUIDE-style callback args - Added by Migration Tool
            [hObject, eventdata, handles] = convertToGUIDECallbackArguments(app, event); %#ok<ASGLU>
            
            % hObject    handle to LOAD_putshbutton (see GCBO)
            % eventdata  reserved - to be defined in a future version of MATLAB
            % handles    structure with handles and user data (see GUIDATA)
            global image
            [filename1, filepath]=uigetfile('*.*','please choose a Nuance image');%filename?????filepath?????
            image{1}=imread(strcat(filepath,filename1));
            str1=[filepath filename1];      %????????
            app.AADEditField.Value = str1;
            %             set( handles.edit1,'String',str1);   % ??????????????
            
            [filename2, filepath]=uigetfile('*.*','please choose a H&E image');%filename?????filepath?????
            image{2}=imread(strcat(filepath,filename2));
            str2=[filepath filename2];
            %             set( handles.edit2,'String',str2);
            app.HEEditField.Value = str2;
            
            axes(app.axes1);
            imshow(image{1});
            axes(app.axes2);
            imshow(image{2})
 
        end
        
        % Callback function
        function Savepoint_pushbutton_Callback(app, event)
            % Create GUIDE-style callback args - Added by Migration Tool
            [hObject, eventdata, handles] = convertToGUIDECallbackArguments(app, event); %#ok<ASGLU>
            
            % hObject    handle to Savepoint_pushbutton (see GCBO)
            % eventdata  reserved - to be defined in a future version of MATLAB
            % handles    structure with handles and user data (see GUIDATA)
            % [filename, foldername] = uiputfile('Where do you want the file saved?');
            % complete_name = fullfile(foldername, filename);
            global movingPoints fixedPoints
            % save(complete_name, movingPoints fixedPoints);
            [filename ,pathname]=uiputfile({'*.mat','MAT-files(*.mat)'},'Where do you want the file saved?');
            str=strcat(pathname,filename);
            save(char(str), 'movingPoints', 'fixedPoints');
        end
        
        % Button pushed function: cpselect_pushbutton
        function cpselect_pushbutton_Callback(app, event)
            % Create GUIDE-style callback args - Added by Migration Tool
            [hObject, eventdata, handles] = convertToGUIDECallbackArguments(app, event); %#ok<ASGLU>
            
            % hObject    handle to cpselect_pushbutton (see GCBO)
            % eventdata  reserved - to be defined in a future version of MATLAB
            % handles    structure with handles and user data (see GUIDATA)
            
            
            global image t_concord
            global movingPoints fixedPoints
            [movingPoints,fixedPoints] = cpselect(image{1},image{2},'Wait',true);
            fix = image{2};
            remove = image{1};
            % imshowpair(fix,remove,'blend');
            t_concord = fitgeotrans(fixedPoints,movingPoints,'similarity');
            remove_ref = imref2d(size(remove)); %relate intrinsic and world coordinates
            global aerial_registered
            aerial_registered = imwarp(fix,t_concord,'OutputView',remove_ref);
            axes(handles.axes1);
            imshow(aerial_registered);
            axes(handles.axes2);
            imshowpair(aerial_registered,remove,'blend')
            
            
        end
        
        % Button pushed function: loadtformButton
        function loadtformButtonPushed(app, event)
            
            global image t_concord aerial_registered
            
            [filename1, filepath]=uigetfile('*.*','please load tform data');%filename?????filepath?????
            load(strcat(filepath,filename1),'tform_nu2he');
            t_concord = invert(tform_nu2he);
            
            fix7aad = image{2};
            movehe = image{1};
            remove_ref = imref2d(size(movehe)); %relate intrinsic and world coordinates
            aerial_registered = imwarp(fix7aad,t_concord,'OutputView',remove_ref);
            
            axes(app.axes1);
            imshow(aerial_registered);
            axes(app.axes2);
            imshowpair(aerial_registered,movehe,'blend')
            
        end
        
        % Button pushed function: save_pushbutton
        function save_pushbutton_Callback(app, event)
            % Create GUIDE-style callback args - Added by Migration Tool
            [hObject, eventdata, handles] = convertToGUIDECallbackArguments(app, event); %#ok<ASGLU>
            
            % hObject    handle to save_pushbutton (see GCBO)
            % eventdata  reserved - to be defined in a future version of MATLAB
            % handles    structure with handles and user data (see GUIDATA)
            global savehe savepoint savetform aerial_registered movingPoints fixedPoints t_concord
            
            if savehe
                %global aerial_registered
                %combination and file name
                [filename, pathname]=uiputfile({'*.jpg';'*.bmp';'*.gif';'*.tif'},'Save H&E as');
                str = [pathname filename];
                if (filename~=0)
                    imwrite(aerial_registered,str);
                else
                    warndlg('You must input a file name!','Warning')
                end
            end
            
            if savepoint
                % save(complete_name, movingPoints fixedPoints);
                [filename ,pathname]=uiputfile({'*.mat','MAT-files(*.mat)'},'Save featurepoints as');
                str=strcat(pathname,filename);
                if (filename~=0)
                    save(char(str), 'movingPoints', 'fixedPoints');
                else
                    warndlg('You must input a file name!','Warning')
                end
                
            end
            
            if savetform
                [filename ,pathname]=uiputfile({'*.mat','MAT-files(*.mat)'},'Save tform as');
                str=strcat(pathname,filename);
                tform_nu2he = invert(t_concord);
                if (filename~=0)
                    save(char(str), 'tform_nu2he');
                else
                    warndlg('You must input a file name!','Warning')
                end
            end
            
        end
        
        
        % Button pushed function: save_pushbutton
        function SAVE_pushbutton_Callback(app, event)
            global tform_nu2he movingRegistered_he region
            [filename, pathname]=uiputfile({'*.jpg';'*.bmp';'*.gif';'*.tif'},'Save H&E as');
            str = [pathname filename];
            if (filename~=0)
                    imwrite(movingRegistered_he,str);
            else
                    warndlg('You must input a file name!','Warning')
            end
            
            [filename ,pathname]=uiputfile({'*.mat','MAT-files(*.mat)'},'Save tform as as');
                str=strcat(pathname,filename);
                if (filename~=0)
                    if exist('region','var')
                    save(char(str), 'tform_nu2he','region');
                    else
                        save(char(str), 'tform_nu2he');
                    end
                else
                    warndlg('You must input a file name!','Warning')
                end

            
        end
        
        % Value changed function: FeaturepointsCheckBox,
        % HECheckBox, tformfileCheckBox
        function CheckBoxValueChanged(app, event)
            
            global savehe savepoint savetform
            savehe =  app.HECheckBox.Value;
            savepoint =  app.FeaturepointsCheckBox.Value;
            savetform  =  app.tformfileCheckBox.Value;
            
        end
        
        % auto registration:
        % Button pushed function: refreshButton
        function refreshButtonPushed(app, event)
            global image bw4_7aad bw4_HE nu_he_img
            nucleus_img = image{1};
            movehe = image{2};
            
            %parameters of 7AAD
            gtaad = app.greythretholdSlider.Value;
            w2_1 = app.wiener2EditField.Value;
            w2_2 = app.wiener2EditField_3.Value;
            %             NHOOD = app.bwareaopenEditField.Value;
            NHOOD= regexp(app.bwareaopenEditField.Value,'\d*','Match');
            
            %parameters of H&E
            gtaadhe = app.greythretholdSlider_3.Value;
            w2he_1 = app.wiener2EditField_2.Value;
            w2he_2 = app.wiener2EditField_4.Value;
            NHOODhe = app.bwareaopenEditField_2.Value;
            
            %  Binarize 7AAD image
            nucleus_size=size(nucleus_img);
            if numel(nucleus_size)>2
                nucleus_img=rgb2gray(nucleus_img);
            end
            nucleus_img = imadjust(nucleus_img);
            nucleus_img = adapthisteq(nucleus_img);
            nucleus_img = imclearborder(nucleus_img);
            nucleus_img = wiener2(nucleus_img,[w2_1 w2_2]);
            bw = imbinarize(nucleus_img,'adaptive', 'Sensitivity', gtaad);
            bw2 = imfill(bw,'holes');
            bw3 = imclose(bw2,strel('disk', str2double(NHOOD{1})));
            bw4_7aad = imopen(bw3,strel('disk', str2double(NHOOD{2})));
            bw4_7aad=double(bw4_7aad);
            
            %  Binarize HE image
            % parameters
            pxsize=0.5476190448; % per pixel um % per pixel 0.5 um
            nu_px=0.5;
            nu_he_img=imresize(movehe,pxsize/nu_px);
            
            img_nuance=255-rgb2gray(nu_he_img);
            bw_img_nuance = adapthisteq(img_nuance);
            bw_img_nuance = imclearborder(bw_img_nuance);
            bw_img_nuance = wiener2(bw_img_nuance,[w2he_1 w2he_2]);
            bw_img_nuance = im2bw(bw_img_nuance, gtaadhe);
            bw2_img_nuance = imfill(bw_img_nuance,'holes');
            bw3_img_nuance = imopen(bw2_img_nuance,strel('disk',NHOODhe));
            bw4_img_nuance = bwareaopen(bw3_img_nuance,70);
            bw4_HE=double(bw4_img_nuance);
            
            axes(app.axes1);
            imshow(bw4_7aad);
            axes(app.axes2);
            imshow(bw4_HE)
            
        end
        
        
        % Button pushed function: InitailregistrationButton
        function InitailregistrationButtonPushed(app, event)
            global bw4_7aad bw4_HE movingRegistered_he tform_nu2he nu_he_img
%             img_he = image{2};
            
            [optimizer, metric] = imregconfig('multimodal');
            optimizer.InitialRadius = optimizer.InitialRadius/3.5;
            optimizer.MaximumIterations = 400;
            
            tform_nu2he = imregtform(bw4_7aad, bw4_HE, 'similarity', optimizer, metric);
            movingRegistered_7aad = imwarp(bw4_7aad,tform_nu2he,'OutputView',imref2d(size(bw4_HE)));
            
            invtform = invert(tform_nu2he);
            uialert(app.figure1,'Done!','Message','Icon','success');
            
            movingRegistered_he = imwarp(nu_he_img,invtform,'OutputView',imref2d(size(bw4_7aad)));
            axes(app.axes1);
            imshowpair(movingRegistered_7aad,nu_he_img);
            axes(app.axes2);
            imshow(movingRegistered_he);
            
        end
        
        % function: Sliding window
        function Slidewindow(app, event)
            global step top core
            step = app.stepEditField;
            top = app.topEditField.value;
            core = app.coreEditField.Value;
        end
        
        % Button pushed function: Sliding window
        function RunButtonPushed(app, event)
            global bw4_7aad bw4_HE tform_nu2he nu_he_img  movingRegistered_he image
             
            
            if ~exist('step','var')
            step = 20;
            end
            if ~exist('top','var')
            top = 10;
            end
            if ~exist('core','var')
            core = 4;  
            end
            
            global step top core 
%             img_he = image{2};
            nucleus_img= image{1};
            
            [nucleus_h,nucleus_w]=size(nucleus_img);
            windowsize=[nucleus_h nucleus_w];

            addpath(genpath('fun'));
            tic;
            region = SlideWindowDetector(bw4_HE ,bw4_7aad, windowsize, step, top,core);
            
            
            bw_he_img_jj= bw4_HE(region(3):region(4),region(1):region(2));
            
            [optimizer, metric] = imregconfig('multimodal');
            optimizer.InitialRadius = optimizer.InitialRadius/4;
            optimizer.MaximumIterations = 400;
            % movingRegistered = imregister(bw4, image, 'similarity', optimizer, metric);
            tform_nu2he = imregtform(bw4_7aad, bw_he_img_jj, 'similarity', optimizer, metric);
            
            toc;
            uialert(app.figure1,'Done!','Message','Icon','success');
            
            movingRegistered_7aad = imwarp(bw4_7aad,tform_nu2he,'OutputView',imref2d(size(bw_he_img_jj))); 
            img = nu_he_img(region(3):region(4),region(1):region(2),:);
            invtform = invert(tform_nu2he);
            movingRegistered_he = imwarp(img,invtform,'OutputView',imref2d(size(bw4_7aad)));
            axes(app.axes1);
            imshowpair(movingRegistered_7aad,img);
            axes(app.axes2);
            imshow(movingRegistered_he);            
        end
    end
    
    

% Component initialization
methods (Access = public)

    % Create UIFigure and components
    function createComponents(app)

    % Create figure1 and hide until all components are created
    app.figure1 = uifigure('Visible', 'off');
    app.figure1.CloseRequestFcn = createCallbackFcn(app, @InitailregistrationButtonPushed, true);
    app.figure1.Position = [500 100 942 797];
    app.figure1.Name = 'Registration';
    app.figure1.Resize = 'off';
    app.figure1.HandleVisibility = 'callback';
    app.figure1.Tag = 'Registration';

    % Create axes1
    app.axes1 = uiaxes(app.figure1);
    app.axes1.XTick = [];
    app.axes1.YTick = [];
    app.axes1.FontSize = 13.3333333333333;
    app.axes1.NextPlot = 'replace';
    app.axes1.Tag = 'axes1';
    app.axes1.Position = [460 404 461 345];

    % Create axes2
    app.axes2 = uiaxes(app.figure1);
    app.axes2.XTick = [];
    app.axes2.YTick = [];
    app.axes2.FontSize = 13.3333333333333;
    app.axes2.NextPlot = 'replace';
    app.axes2.Tag = 'axes2';
    app.axes2.Position = [463 35 458 345];

    % Create TabGroup
    app.TabGroup = uitabgroup(app.figure1);
    app.TabGroup.Position = [39 29 390 598];

    % Create ManuallyTab
    app.ManuallyTab = uitab(app.TabGroup);
    app.ManuallyTab.Title = 'Manually';

    % Create cpselect_pushbutton
    app.cpselect_pushbutton = uibutton(app.ManuallyTab, 'push');
    app.cpselect_pushbutton.ButtonPushedFcn = createCallbackFcn(app, @cpselect_pushbutton_Callback, true);
    app.cpselect_pushbutton.Tag = 'cpselect_pushbutton';
    app.cpselect_pushbutton.FontSize = 16;
    app.cpselect_pushbutton.FontWeight = 'bold';
    app.cpselect_pushbutton.Position = [44 491 88 37];
    app.cpselect_pushbutton.Text = 'cpselect';

    % Create savePanel
    app.savePanel = uipanel(app.ManuallyTab);
    app.savePanel.Title = 'save';
    app.savePanel.FontWeight = 'bold';
    app.savePanel.FontSize = 16;
    app.savePanel.Position = [26 325 341 118];

    % Create HECheckBox
    app.HECheckBox = uicheckbox(app.savePanel);
    app.HECheckBox.ValueChangedFcn = createCallbackFcn(app, @CheckBoxValueChanged, true);
    app.HECheckBox.Text = 'H&E';
    app.HECheckBox.Position = [8 62 47 22];

    % Create FeaturepointsCheckBox
    app.FeaturepointsCheckBox = uicheckbox(app.savePanel);
    app.FeaturepointsCheckBox.ValueChangedFcn = createCallbackFcn(app, @CheckBoxValueChanged, true);
    app.FeaturepointsCheckBox.Text = 'Feature points';
    app.FeaturepointsCheckBox.Position = [8 33 99 22];

    % Create tformfileCheckBox
    app.tformfileCheckBox = uicheckbox(app.savePanel);
    app.tformfileCheckBox.ValueChangedFcn = createCallbackFcn(app, @CheckBoxValueChanged, true);
    app.tformfileCheckBox.Text = 'tform file';
    app.tformfileCheckBox.Position = [8 4 68 22];

    % Create save_pushbutton
    app.save_pushbutton = uibutton(app.savePanel, 'push');
    app.save_pushbutton.ButtonPushedFcn = createCallbackFcn(app, @save_pushbutton_Callback, true);
    app.save_pushbutton.Tag = 'save_pushbutton';
    app.save_pushbutton.FontSize = 16;
    app.save_pushbutton.FontWeight = 'bold';
    app.save_pushbutton.Position = [189 39 88 36];
    app.save_pushbutton.Text = 'SAVE';

    % Create loadtformButton
    app.loadtformButton = uibutton(app.ManuallyTab, 'push');
    app.loadtformButton.ButtonPushedFcn = createCallbackFcn(app, @loadtformButtonPushed, true);
    app.loadtformButton.FontSize = 16;
    app.loadtformButton.FontWeight = 'bold';
    app.loadtformButton.Position = [197 491 100 35];
    app.loadtformButton.Text = 'load tform';

    % Create AutoTab
    app.AutoTab = uitab(app.TabGroup);
    app.AutoTab.Title = 'Auto';

    % Create precessingPanel
    app.precessingPanel = uipanel(app.AutoTab);
    app.precessingPanel.TitlePosition = 'centertop';
    app.precessingPanel.Title = 'precessing';
    app.precessingPanel.FontWeight = 'bold';
    app.precessingPanel.FontSize = 16;
    app.precessingPanel.Position = [20 210 353 348];

    % Create GridLayout
    app.GridLayout = uigridlayout(app.precessingPanel);
    app.GridLayout.ColumnWidth = {'1.33x', 100, '1x'};
    app.GridLayout.RowHeight = {125, 125, 26};
    app.GridLayout.ColumnSpacing = 5.75;
    app.GridLayout.RowSpacing = 11.75;
    app.GridLayout.Padding = [5.75 11.75 5.75 11.75];

    % Create SlidiingwindowPanel
    app.SlidiingwindowPanel = uipanel(app.AutoTab);
    app.SlidiingwindowPanel.Title = 'Slidiing window';
    app.SlidiingwindowPanel.FontWeight = 'bold';
    app.SlidiingwindowPanel.FontSize = 16;
    app.SlidiingwindowPanel.Position = [16 62 357 97];

    % Create GridLayout2
    app.GridLayout2 = uigridlayout(app.SlidiingwindowPanel);
    app.GridLayout2.ColumnWidth = {29, '1.33x', '1x', 25, 77};
    app.GridLayout2.RowHeight = {22, 26};
    app.GridLayout2.RowSpacing = 8;
    app.GridLayout2.Padding = [10 8 10 8];

    % Create RunButton
    app.RunButton = uibutton(app.GridLayout2, 'push');
    app.RunButton.ButtonPushedFcn = createCallbackFcn(app, @RunButtonPushed, true);
    app.RunButton.FontSize = 16;
    app.RunButton.Layout.Row = 2;
    app.RunButton.Layout.Column = [4 5];
    app.RunButton.Text = 'Run';

    % Create stepEditField
    app.stepEditField = uieditfield(app.GridLayout2, 'numeric');
    app.stepEditField.ValueChangedFcn = createCallbackFcn(app, @Slidewindow, true);
    app.stepEditField.Layout.Row = 1;
    app.stepEditField.Layout.Column = 2;
    app.stepEditField.Value = 20;

    % Create stepEditFieldLabel
    app.stepEditFieldLabel = uilabel(app.GridLayout2);
    app.stepEditFieldLabel.HorizontalAlignment = 'right';
    app.stepEditFieldLabel.Layout.Row = 1;
    app.stepEditFieldLabel.Layout.Column = 1;
    app.stepEditFieldLabel.Text = 'step';

    % Create topEditField
    app.topEditField = uieditfield(app.GridLayout2, 'numeric');
    app.topEditField.ValueChangedFcn = createCallbackFcn(app, @Slidewindow, true);
    app.topEditField.Layout.Row = 1;
    app.topEditField.Layout.Column = 5;
    app.topEditField.Value = 10;

    % Create topEditFieldLabel
    app.topEditFieldLabel = uilabel(app.GridLayout2);
    app.topEditFieldLabel.HorizontalAlignment = 'right';
    app.topEditFieldLabel.Layout.Row = 1;
    app.topEditFieldLabel.Layout.Column = 4;
    app.topEditFieldLabel.Text = 'top';

    % Create coreEditField
    app.coreEditField = uieditfield(app.GridLayout2, 'numeric');
    app.coreEditField.ValueChangedFcn = createCallbackFcn(app, @Slidewindow, true);
    app.coreEditField.Layout.Row = 2;
    app.coreEditField.Layout.Column = 2;
    app.coreEditField.Value = 4;

    % Create coreEditFieldLabel
    app.coreEditFieldLabel = uilabel(app.GridLayout2);
    app.coreEditFieldLabel.HorizontalAlignment = 'right';
    app.coreEditFieldLabel.Layout.Row = 2;
    app.coreEditFieldLabel.Layout.Column = 1;
    app.coreEditFieldLabel.Text = 'core';

    % Create saveButton
    app.saveButton = uibutton(app.AutoTab, 'push');
    app.saveButton.ButtonPushedFcn = createCallbackFcn(app, @SAVE_pushbutton_Callback, true);
    app.saveButton.FontSize = 16;
    app.saveButton.FontWeight = 'bold';
    app.saveButton.Position = [156 15 100 26];
    app.saveButton.Text = 'save';


    % Create BinarizeheimagePanel_2
    app.BinarizeheimagePanel_2 = uipanel(app.GridLayout);
    app.BinarizeheimagePanel_2.Title = ' Binarize H&E image';
    app.BinarizeheimagePanel_2.Layout.Row = 2;
    app.BinarizeheimagePanel_2.Layout.Column = [1 3];
    app.BinarizeheimagePanel_2.Position = [7 51 340 125];

    % Create wiener2EditField_2Label
    app.wiener2EditField_2Label = uilabel(app.BinarizeheimagePanel_2);
    app.wiener2EditField_2Label.HorizontalAlignment = 'right';
    app.wiener2EditField_2Label.Position = [14 17 48 22];
    app.wiener2EditField_2Label.Text = 'wiener2';

    % Create wiener2EditField_2
    app.wiener2EditField_2 = uieditfield(app.BinarizeheimagePanel_2, 'numeric');
    app.wiener2EditField_2.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.wiener2EditField_2.Position = [77 17 34 22];
    app.wiener2EditField_2.Value = 5;

    % Create wiener2EditField_4
    app.wiener2EditField_4 = uieditfield(app.BinarizeheimagePanel_2, 'numeric');
    app.wiener2EditField_4.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.wiener2EditField_4.Position = [122 17 33 22];
    app.wiener2EditField_4.Value = 5;

    % Create bwareaopenEditField_2Label
    app.bwareaopenEditField_2Label = uilabel(app.BinarizeheimagePanel_2);
    app.bwareaopenEditField_2Label.HorizontalAlignment = 'right';
    app.bwareaopenEditField_2Label.Position = [178 17 72 22];
    app.bwareaopenEditField_2Label.Text = 'Strel:Nhood';


    % Create bwareaopenEditField_2
    app.bwareaopenEditField_2 = uieditfield(app.BinarizeheimagePanel_2, 'numeric');
    app.bwareaopenEditField_2.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.bwareaopenEditField_2.Position = [265 17 45 22];
    app.bwareaopenEditField_2.Value = 3;

    % Create greythretholdSlider_3Label
    app.greythretholdSlider_3Label = uilabel(app.BinarizeheimagePanel_2);
    app.greythretholdSlider_3Label.HorizontalAlignment = 'right';
    app.greythretholdSlider_3Label.Position = [19 73 72 22];
    app.greythretholdSlider_3Label.Text = 'greythrethold';

    % Create greythretholdSlider_3
    app.greythretholdSlider_3 = uislider(app.BinarizeheimagePanel_2);
    app.greythretholdSlider_3.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.greythretholdSlider_3.Limits = [0 1];
    app.greythretholdSlider_3.MajorTicks = [0 0.2 0.4 0.6 0.8 1];
    app.greythretholdSlider_3.MajorTickLabels = {'0', '0.2', '0.4', '0.6', '0.8', '1'};
    app.greythretholdSlider_3.Position = [104 85 187 3];




    % Create Binarize7aadimagePanel
    app.Binarize7aadimagePanel = uipanel(app.GridLayout);
    app.Binarize7aadimagePanel.Title = ' Binarize 7AAD image';
    app.Binarize7aadimagePanel.Layout.Row = 1;
    app.Binarize7aadimagePanel.Layout.Column = [1 3];

    % Create greythretholdSliderLabel
    app.greythretholdSliderLabel = uilabel(app.Binarize7aadimagePanel);
    app.greythretholdSliderLabel.HorizontalAlignment = 'right';
    app.greythretholdSliderLabel.Position = [20 70 72 22];
    app.greythretholdSliderLabel.Text = 'Greythrethold';

    % Create greythretholdSlider
    app.greythretholdSlider = uislider(app.Binarize7aadimagePanel);
    app.greythretholdSlider.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.greythretholdSlider.Limits = [0 1];
    app.greythretholdSlider.MajorTicks = [0 0.2 0.4 0.6 0.8 1];
    app.greythretholdSlider.MajorTickLabels = {'0', '0.2', '0.4', '0.6', '0.8', '1'};
    app.greythretholdSlider.Position = [105 82 187 3];
    app.greythretholdSlider.Value = 0.2;

    % Create wiener2EditFieldLabel
    app.wiener2EditFieldLabel = uilabel(app.Binarize7aadimagePanel);
    app.wiener2EditFieldLabel.HorizontalAlignment = 'right';
    app.wiener2EditFieldLabel.Position = [16 13 48 22];
    app.wiener2EditFieldLabel.Text = 'wiener2';

    % Create wiener2EditField
    app.wiener2EditField = uieditfield(app.Binarize7aadimagePanel, 'numeric');
    app.wiener2EditField.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.wiener2EditField.Position = [79 13 37 22];
    app.wiener2EditField.Value = 5;

    % Create wiener2EditField_3
    app.wiener2EditField_3 = uieditfield(app.Binarize7aadimagePanel, 'numeric');
    app.wiener2EditField_3.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.wiener2EditField_3.Position = [124 13 33 22];
    app.wiener2EditField_3.Value = 5;

    % Create bwareaopenEditFieldLabel
    app.bwareaopenEditFieldLabel = uilabel(app.Binarize7aadimagePanel);
    app.bwareaopenEditFieldLabel.HorizontalAlignment = 'right';
    app.bwareaopenEditFieldLabel.Position = [178 7 72 40];
    app.bwareaopenEditFieldLabel.Text = sprintf('Nhood\n(close,open)');

    % Create bwareaopenEditField
    app.bwareaopenEditField = uieditfield(app.Binarize7aadimagePanel);
    app.bwareaopenEditField.ValueChangedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.bwareaopenEditField.Position = [265 11 45 22];
    app.bwareaopenEditField.Value = '3,4';


  

    % Create Initial Registration Button
    app.InitailregistrationButton = uibutton(app.AutoTab, 'push');
    app.InitailregistrationButton.ButtonPushedFcn = createCallbackFcn(app, @InitailregistrationButtonPushed, true);
    app.InitailregistrationButton.FontSize = 16;
    app.InitailregistrationButton.FontWeight = 'bold';
    app.InitailregistrationButton.Position = [136 173 150 26];
    app.InitailregistrationButton.Text = 'Quick Registration';

    % Create ImportPanel
    app.ImportPanel = uipanel(app.figure1);
    app.ImportPanel.Title = 'Import';
    app.ImportPanel.FontWeight = 'bold';
    app.ImportPanel.FontSize = 15;
    app.ImportPanel.Position = [39 642 389 107];

    % Create GridLayout3
    app.GridLayout3 = uigridlayout(app.ImportPanel);
    app.GridLayout3.ColumnWidth = {37, '1.58x', '1x', 65};
    app.GridLayout3.RowHeight = {26, 22};

    % Create refreshButton
    app.refreshButton = uibutton(app.GridLayout, 'push');
    app.refreshButton.ButtonPushedFcn = createCallbackFcn(app, @refreshButtonPushed, true);
    app.refreshButton.FontSize = 16;
    app.refreshButton.FontWeight = 'bold';
    app.refreshButton.Layout.Row = 3;
    app.refreshButton.Layout.Column = 2;
    app.refreshButton.Position = [143 13 100 26];
    app.refreshButton.Text = 'refresh';

    % Create LOADButton
    app.LOADButton = uibutton(app.GridLayout3, 'push');
    app.LOADButton.ButtonPushedFcn = createCallbackFcn(app, @LOAD_putshbutton_Callback, true);
    app.LOADButton.FontSize = 16;
    app.LOADButton.FontWeight = 'bold';
    app.LOADButton.Layout.Row = 1;
    app.LOADButton.Layout.Column = 4;
    app.LOADButton.Position = [313 48 65 26];
    app.LOADButton.Text = 'LOAD';

    % Create HEEditFieldLabel
    app.HEEditFieldLabel = uilabel(app.GridLayout3);
    app.HEEditFieldLabel.HorizontalAlignment = 'right';
    app.HEEditFieldLabel.Layout.Row = 1;
    app.HEEditFieldLabel.Layout.Column = 1;
    app.HEEditFieldLabel.Position = [11 48 37 26];
    app.HEEditFieldLabel.Text = 'H&E';

    % Create HEEditField
    app.HEEditField = uieditfield(app.GridLayout3, 'text');
    app.HEEditField.Layout.Row = 1;
    app.HEEditField.Layout.Column = 2;
    app.HEEditField.Position = [58 48 144 26];

    % Create AADEditFieldLabel
    app.AADEditFieldLabel = uilabel(app.GridLayout3);
    app.AADEditFieldLabel.HorizontalAlignment = 'right';
    app.AADEditFieldLabel.Layout.Row = 2;
    app.AADEditFieldLabel.Layout.Column = 1;
    app.AADEditFieldLabel.Position = [11 16 37 22];
    app.AADEditFieldLabel.Text = '7AAD';

    % Create AADEditField
    app.AADEditField = uieditfield(app.GridLayout3, 'text');
    app.AADEditField.Layout.Row = 2;
    app.AADEditField.Layout.Column = 2;
    app.AADEditField.Position = [58 16 144 22];


    % Create LOADButton
    app.LOADButton = uibutton(app.GridLayout3, 'push');
    app.LOADButton.ButtonPushedFcn = createCallbackFcn(app, @LOAD_putshbutton_Callback, true);
    app.LOADButton.FontSize = 16;
    app.LOADButton.FontWeight = 'bold';
    app.LOADButton.Layout.Row = 1;
    app.LOADButton.Layout.Column = 4;
    app.LOADButton.Text = 'LOAD';

    % Create HEEditField
    app.HEEditField = uieditfield(app.GridLayout3, 'text');
    app.HEEditField.Layout.Row = 1;
    app.HEEditField.Layout.Column = 2;

    % Create HEEditFieldLabel
    app.HEEditFieldLabel = uilabel(app.GridLayout3);
    app.HEEditFieldLabel.HorizontalAlignment = 'right';
    app.HEEditFieldLabel.Layout.Row = 1;
    app.HEEditFieldLabel.Layout.Column = 1;
    app.HEEditFieldLabel.Text = 'H&E';

    % Create AADEditField
    app.AADEditField = uieditfield(app.GridLayout3, 'text');
    app.AADEditField.Layout.Row = 2;
    app.AADEditField.Layout.Column = 2;

    % Create AADEditFieldLabel
    app.AADEditFieldLabel = uilabel(app.GridLayout3);
    app.AADEditFieldLabel.HorizontalAlignment = 'right';
    app.AADEditFieldLabel.Layout.Row = 2;
    app.AADEditFieldLabel.Layout.Column = 1;
    app.AADEditFieldLabel.Text = '7AAD';

    % Show the figure after all components are created
    app.figure1.Visible = 'on';
    end
end

    % App creation and deletion
    methods (Access = public)

        % Construct app
        function app = Regi_Nuance_HE_GUI(varargin)

            runningApp = getRunningApp(app);

            % Check for running singleton app
            if isempty(runningApp)

                % Create UIFigure and components
                createComponents(app)

                % Register the app with App Designer
                registerApp(app, app.figure1)

                % Execute the startup function
                runStartupFcn(app, @(app)main_gui_OpeningFcn(app, varargin{:}))
            else

                % Focus the running singleton app
                figure(runningApp.figure1)

                app = runningApp;
            end

            if nargout == 0
                clear app
            end
        end

        % Code that executes before app deletion
        function delete(app)
        % Delete UIFigure when app is deleted
        delete(app.figure1)
        end
    end
end