diff --git a/urchin_compare/+Dev/VersionInfo.m b/urchin_compare/+Dev/VersionInfo.m
new file mode 100644
index 0000000000000000000000000000000000000000..2002fa5fbb50dbde8291e29c1913bdaa6285cbb8
--- /dev/null
+++ b/urchin_compare/+Dev/VersionInfo.m
@@ -0,0 +1,10 @@
+% versionInfo = VersionInfo()
+% Return the version info structure
+%
+% Note: This file is autogenerated by build script DO NOT MODIFY!!
+
+function versionInfo = VersionInfo()
+ jsonVer = '{"name":"urchin_compare","majorVersion":2,"minorVersion":0,"branchName":"master","buildNumber":"2020.12.07.07","buildMachine":"bioimage28","commitHash":[" : 15410c6b7251a6890057e04366431f0286b90d70"," : 07f725fe7b1c500a2743e016d119a7b0f059561e"]}';
+
+ versionInfo = Utils.ParseJSON(jsonVer);
+end
diff --git a/urchin_compare/.gitignore b/urchin_compare/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..4051d2a75c4484099154eca55f55295928e90b7c
--- /dev/null
+++ b/urchin_compare/.gitignore
@@ -0,0 +1,6 @@
+# Ignore matlab data files
+*.mat
+
+# Ignore some image formats
+*.jpg
+*.nd2
\ No newline at end of file
diff --git a/urchin_compare/compile_urchin.m b/urchin_compare/compile_urchin.m
new file mode 100644
index 0000000000000000000000000000000000000000..b1e40b68891aa442a13bc2b0bac0d7ff35cdb062
--- /dev/null
+++ b/urchin_compare/compile_urchin.m
@@ -0,0 +1,46 @@
+function compile_urchin()
+ %% General compiler setup: Deals with version updates and pulls external dependencies
+ initStruct = Dev.InitCompiler('urchin_compare','2.0');
+ if ( isempty(initStruct) )
+ % User exited the build due to error or uncommited dependencies.
+ return;
+ end
+
+ compileMATLAB('urchin_compare','urchin_compare','', initStruct.javaList, initStruct.toolboxList);
+end
+
+function outputFile = compileMATLAB(projectName, mainscript, outputdir, extrasList, toolboxList)
+ compileTime = tic();
+
+ outputFile = [projectName '.exe'];
+
+ if ( ~exist('extrasList','var') )
+ extrasList = {};
+ end
+
+ extraCommand = '';
+ if ( ~isempty(extrasList) )
+ extraElems = cellfun(@(x)([' -a ' x]),extrasList, 'UniformOutput',0);
+ extraCommand = [extraElems{:}];
+ end
+
+ if ( ~exist('toolboxList','var') )
+ toolboxList = {};
+ end
+
+ toolboxAddCommand = '';
+ if ( ~isempty(toolboxList) )
+ toolboxElems = cellfun(@(x)([' -p "' x '"']), toolboxList, 'UniformOutput',0);
+ toolboxAddCommand = ['-N' toolboxElems{:}];
+ end
+
+ fprintf('\nMATLAB Compiling: %s...\n', outputFile);
+ result = system(['mcc -v -R -startmsg -m ' mainscript '.m -o ' projectName ' ' toolboxAddCommand extraCommand]);
+ if ( result ~= 0 )
+ error([projectName ': MATLAB compile failed.']);
+ end
+
+ system(['copy ' projectName '.exe ' fullfile(outputdir,'.')]);
+
+ fprintf('Done (%f sec)\n', toc(compileTime));
+end
diff --git a/urchin_compare/helpdlg.fig b/urchin_compare/helpdlg.fig
new file mode 100644
index 0000000000000000000000000000000000000000..e48d4f55d39dda373ec42b2bf8b1e20511c2e014
Binary files /dev/null and b/urchin_compare/helpdlg.fig differ
diff --git a/urchin_compare/helpdlg.m b/urchin_compare/helpdlg.m
new file mode 100644
index 0000000000000000000000000000000000000000..c58ee283ab96fea102b203b2f4ab03ec27159adc
--- /dev/null
+++ b/urchin_compare/helpdlg.m
@@ -0,0 +1,86 @@
+function varargout = helpdlg(varargin)
+% HELPDLG MATLAB code for helpdlg.fig
+% HELPDLG, by itself, creates a new HELPDLG or raises the existing
+% singleton*.
+%
+% H = HELPDLG returns the handle to a new HELPDLG or the handle to
+% the existing singleton*.
+%
+% HELPDLG('CALLBACK',hObject,eventData,handles,...) calls the local
+% function named CALLBACK in HELPDLG.M with the given input arguments.
+%
+% HELPDLG('Property','Value',...) creates a new HELPDLG or raises the
+% existing singleton*. Starting from the left, property value pairs are
+% applied to the GUI before helpdlg_OpeningFcn gets called. An
+% unrecognized property name or invalid value makes property application
+% stop. All inputs are passed to helpdlg_OpeningFcn via varargin.
+%
+% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
+% instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help helpdlg
+
+% Last Modified by GUIDE v2.5 18-Jun-2019 03:23:18
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name', mfilename, ...
+ 'gui_Singleton', gui_Singleton, ...
+ 'gui_OpeningFcn', @helpdlg_OpeningFcn, ...
+ 'gui_OutputFcn', @helpdlg_OutputFcn, ...
+ 'gui_LayoutFcn', [] , ...
+ 'gui_Callback', []);
+if nargin && ischar(varargin{1})
+ gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+ [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+ gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before helpdlg is made visible.
+function helpdlg_OpeningFcn(hObject, eventdata, handles, varargin)
+% 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 helpdlg (see VARARGIN)
+
+% Choose default command line output for helpdlg
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+
+% UIWAIT makes helpdlg wait for user response (see UIRESUME)
+% uiwait(handles.help_fig);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = helpdlg_OutputFcn(hObject, eventdata, handles)
+% varargout cell array for returning output args (see VARARGOUT);
+% hObject handle to figure
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+
+% --- Executes on key press with focus on help_fig and none of its controls.
+function help_fig_KeyPressFcn(hObject, eventdata, handles)
+% hObject handle to help_fig (see GCBO)
+% eventdata structure with the following fields (see MATLAB.UI.FIGURE)
+% Key: name of the key that was pressed, in lower case
+% Character: character interpretation of the key(s) that was pressed
+% Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
+% handles structure with handles and user data (see GUIDATA)
+if ( strcmpi(eventdata.Key,'escape') )
+ close(hObject);
+end
diff --git a/urchin_compare/settings.json b/urchin_compare/settings.json
new file mode 100644
index 0000000000000000000000000000000000000000..0a04ea2ea1046977c8663c03147abeecae8dbb84
--- /dev/null
+++ b/urchin_compare/settings.json
@@ -0,0 +1,8 @@
+{
+ "imagePath" : "H:\\Smadar\\2020-10-Phallodin_Myo",
+ "dataPath" : "H:\\Smadar\\2020-10-Phallodin_Myo",
+ "channelColors" : [
+ [0, 1, 0],
+ [1, 0, 0]
+ ]
+}
diff --git a/urchin_compare/toolsdlg.fig b/urchin_compare/toolsdlg.fig
new file mode 100644
index 0000000000000000000000000000000000000000..be3cc86a14f3b050d531c93ae21c3d150b0c3cd6
Binary files /dev/null and b/urchin_compare/toolsdlg.fig differ
diff --git a/urchin_compare/toolsdlg.m b/urchin_compare/toolsdlg.m
new file mode 100644
index 0000000000000000000000000000000000000000..4c2151738a95f23da57048d96dd62efdccade42c
--- /dev/null
+++ b/urchin_compare/toolsdlg.m
@@ -0,0 +1,537 @@
+function varargout = toolsdlg(varargin)
+% TOOLSDLG MATLAB code for tools.fig
+% TOOLSDLG, by itself, creates a new TOOLSDLG or raises the existing
+% singleton*.
+%
+% H = TOOLSDLG returns the handle to a new TOOLSDLG or the handle to
+% the existing singleton*.
+%
+% TOOLSDLG('CALLBACK',hObject,eventData,handles,...) calls the local
+% function named CALLBACK in TOOLSDLG.M with the given input arguments.
+%
+% TOOLSDLG('Property','Value',...) creates a new TOOLSDLG or raises the
+% existing singleton*. Starting from the left, property value pairs are
+% applied to the GUI before toolsdlg_OpeningFcn gets called. An
+% unrecognized property name or invalid value makes property application
+% stop. All inputs are passed to toolsdlg_OpeningFcn via varargin.
+%
+% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
+% instance to run (singleton)".
+%
+% See also: GUIDE, GUIDATA, GUIHANDLES
+
+% Edit the above text to modify the response to help toolsdlg
+
+% Last Modified by GUIDE v2.5 01-Dec-2020 18:35:44
+
+% Begin initialization code - DO NOT EDIT
+gui_Singleton = 1;
+gui_State = struct('gui_Name', mfilename, ...
+ 'gui_Singleton', gui_Singleton, ...
+ 'gui_OpeningFcn', @toolsdlg_OpeningFcn, ...
+ 'gui_OutputFcn', @toolsdlg_OutputFcn, ...
+ 'gui_LayoutFcn', [] , ...
+ 'gui_Callback', []);
+if nargin && ischar(varargin{1})
+ gui_State.gui_Callback = str2func(varargin{1});
+end
+
+if nargout
+ [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+else
+ gui_mainfcn(gui_State, varargin{:});
+end
+% End initialization code - DO NOT EDIT
+
+
+% --- Executes just before toolsdlg is made visible.
+function toolsdlg_OpeningFcn(hObject, eventdata, handles, varargin)
+% 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 toolsdlg (see VARARGIN)
+
+% Choose default command line output for toolsdlg
+handles.output = hObject;
+
+% Update handles structure
+guidata(hObject, handles);
+
+% UIWAIT makes toolsdlg wait for user response (see UIRESUME)
+% uiwait(handles.tools_fig);
+
+
+% --- Outputs from this function are returned to the command line.
+function varargout = toolsdlg_OutputFcn(hObject, eventdata, handles)
+% varargout cell array for returning output args (see VARARGOUT);
+% hObject handle to figure
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Get default command line output from handles structure
+varargout{1} = handles.output;
+
+% Helpers for updating editbox/sliders
+function v = clamp(v, minv,maxv)
+ v = max(minv, min(v, maxv));
+
+% --- Executes on slider movement.
+function update_editbox(hTxt,hSlider)
+ val = get(hSlider, 'Value');
+ if ( ~isempty(hTxt) )
+ set(hTxt, 'String',num2str(val));
+ end
+
+% --- Executes on slider movement.
+function update_slider(hTxt,hSlider)
+ strval = get(hTxt, 'String');
+ val = str2double(strval);
+ if ( ~isempty(hSlider) )
+ val = clamp(val, get(hSlider,'Min'),get(hSlider,'Max'));
+ set(hSlider, 'Value',val);
+ end
+
+% --- Executes on slider movement.
+function contrast_ch2_Callback(hObject, eventdata, handles)
+% hObject handle to contrast_ch2 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','contrast_ch2_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function contrast_ch2_CreateFcn(hObject, eventdata, handles)
+% hObject handle to contrast_ch2 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes on slider movement.
+function bright_ch2_Callback(hObject, eventdata, handles)
+% hObject handle to bright_ch2 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','bright_ch2_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function bright_ch2_CreateFcn(hObject, eventdata, handles)
+% hObject handle to bright_ch2 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes on button press in color_ch2.
+function color_ch2_Callback(hObject, eventdata, handles)
+% hObject handle to color_ch2 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+global UIInfo
+newC = uisetcolor(get(hObject, 'BackgroundColor'));
+set(hObject, 'BackgroundColor', newC);
+UIInfo.updateFcn();
+
+
+% --- Executes on button press in color_ch1.
+function color_ch1_Callback(hObject, eventdata, handles)
+% hObject handle to color_ch1 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+global UIInfo
+newC = uisetcolor(get(hObject, 'BackgroundColor'));
+set(hObject, 'BackgroundColor', newC);
+UIInfo.updateFcn();
+
+
+% --- Executes on slider movement.
+function bright_ch1_Callback(hObject, eventdata, handles)
+% hObject handle to bright_ch1 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','bright_ch1_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function bright_ch1_CreateFcn(hObject, eventdata, handles)
+% hObject handle to bright_ch1 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes on slider movement.
+function contrast_ch1_Callback(hObject, eventdata, handles)
+% hObject handle to contrast_ch1 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','contrast_ch1_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function contrast_ch1_CreateFcn(hObject, eventdata, handles)
+% hObject handle to contrast_ch1 (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes on button press in show_regions.
+function show_regions_Callback(hObject, eventdata, handles)
+% hObject handle to show_regions (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of show_regions
+global UIInfo
+UIInfo.updateFcn();
+
+
+% --- Executes on button press in show_ch1px.
+function show_ch1px_Callback(hObject, eventdata, handles)
+% hObject handle to show_ch1px (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of show_ch1px
+global UIInfo
+UIInfo.updateFcn();
+
+
+% --- Executes on button press in show_ch2px.
+function show_ch2px_Callback(hObject, eventdata, handles)
+% hObject handle to show_ch2px (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hint: get(hObject,'Value') returns toggle state of show_ch2px
+global UIInfo
+UIInfo.updateFcn();
+
+
+% --- Executes on slider movement.
+function ch1_thresh_Callback(hObject, eventdata, handles)
+% hObject handle to ch1_thresh (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','ch1_thresh_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateThresh();
+
+
+% --- Executes during object creation, after setting all properties.
+function ch1_thresh_CreateFcn(hObject, eventdata, handles)
+% hObject handle to ch1_thresh (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes on slider movement.
+function ch2_thresh_Callback(hObject, eventdata, handles)
+% hObject handle to ch2_thresh (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'Value') returns position of slider
+% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
+global UIInfo
+hTxt = findobj('Tag','ch2_thresh_edit');
+update_editbox(hTxt,hObject);
+UIInfo.updateThresh();
+
+
+% --- Executes during object creation, after setting all properties.
+function ch2_thresh_CreateFcn(hObject, eventdata, handles)
+% hObject handle to ch2_thresh (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: slider controls usually have a light gray background.
+if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor',[.9 .9 .9]);
+end
+
+
+% --- Executes when selected cell(s) is changed in cells_table.
+function cells_table_CellSelectionCallback(hObject, eventdata, handles)
+% hObject handle to cells_table (see GCBO)
+% eventdata structure with the following fields (see MATLAB.UI.CONTROL.TABLE)
+% Indices: row and column indices of the cell(s) currently selecteds
+% handles structure with handles and user data (see GUIDATA)
+global UIInfo
+
+regionID = -1;
+if ( ~isempty(eventdata.Indices) )
+ Data = get(hObject, 'Data');
+ regionID = Data{eventdata.Indices(1),1};
+end
+
+UIInfo.updateRegionSelect(regionID);
+
+
+% --- Executes when entered data in editable cell(s) in cells_table.
+function cells_table_CellEditCallback(hObject, eventdata, handles)
+% hObject handle to cells_table (see GCBO)
+% eventdata structure with the following fields (see MATLAB.UI.CONTROL.TABLE)
+% Indices: row and column indices of the cell(s) edited
+% PreviousData: previous data for the cell(s) edited
+% EditData: string(s) entered by the user
+% NewData: EditData or its converted form set on the Data property. Empty if Data was not changed
+% Error: error string when failed to convert EditData to appropriate value for Data
+% handles structure with handles and user data (see GUIDATA)
+global UIInfo
+
+Data = get(hObject, 'Data');
+
+editData = eventdata.EditData;
+if ( ischar(editData) )
+ %% Support empty if space-bar is used
+ editData = strtrim(editData);
+end
+
+if ( isempty(editData) )
+ %% Allow user to set empty data
+ Data{eventdata.Indices(1),eventdata.Indices(2)} = [];
+ set(hObject, 'Data',Data);
+end
+% % User modifiable count variable
+% cellID = Data{eventdata.Indices(1),1};
+% newCount = Data{eventdata.Indices(1),eventdata.Indices(2)};
+
+% UIInfo.updateCellCount(cellID,newCount);
+
+
+% --- Executes when user attempts to close tools_fig.
+function tools_fig_CloseRequestFcn(hObject, eventdata, handles)
+% hObject handle to tools_fig (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hint: delete(hObject) closes the figure
+global UIInfo
+set(hObject, 'Visible','off');
+UIInfo.updateMenu();
+
+
+
+function ch1_thresh_edit_Callback(hObject, eventdata, handles)
+% hObject handle to ch1_thresh_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ch1_thresh_edit as text
+% str2double(get(hObject,'String')) returns contents of ch1_thresh_edit as a double
+global UIInfo
+hSlider = findobj('Tag','ch1_thresh');
+update_slider(hObject,hSlider);
+UIInfo.updateThresh();
+
+
+% --- Executes during object creation, after setting all properties.
+function ch1_thresh_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to ch1_thresh_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','ch1_thresh');
+update_editbox(hObject,hSlider);
+
+
+
+function ch2_thresh_edit_Callback(hObject, eventdata, handles)
+% hObject handle to ch2_thresh_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of ch2_thresh_edit as text
+% str2double(get(hObject,'String')) returns contents of ch2_thresh_edit as a double
+global UIInfo
+hSlider = findobj('Tag','ch2_thresh');
+update_slider(hObject,hSlider);
+UIInfo.updateThresh();
+
+
+% --- Executes during object creation, after setting all properties.
+function ch2_thresh_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to ch2_thresh_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','ch2_thresh');
+update_editbox(hObject,hSlider);
+
+
+
+function bright_ch2_edit_Callback(hObject, eventdata, handles)
+% hObject handle to bright_ch2_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of bright_ch2_edit as text
+% str2double(get(hObject,'String')) returns contents of bright_ch2_edit as a double
+global UIInfo
+hSlider = findobj('Tag','bright_ch2');
+update_slider(hObject,hSlider);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function bright_ch2_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to bright_ch2_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','bright_ch2');
+update_editbox(hObject,hSlider);
+
+
+
+function contrast_ch2_edit_Callback(hObject, eventdata, handles)
+% hObject handle to contrast_ch2_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of contrast_ch2_edit as text
+% str2double(get(hObject,'String')) returns contents of contrast_ch2_edit as a double
+global UIInfo
+hSlider = findobj('Tag','contrast_ch2');
+update_slider(hObject,hSlider);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function contrast_ch2_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to contrast_ch2_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','contrast_ch2');
+update_editbox(hObject,hSlider);
+
+
+function bright_ch1_edit_Callback(hObject, eventdata, handles)
+% hObject handle to bright_ch1_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of bright_ch1_edit as text
+% str2double(get(hObject,'String')) returns contents of bright_ch1_edit as a double
+global UIInfo
+hSlider = findobj('Tag','bright_ch1');
+update_slider(hObject,hSlider);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function bright_ch1_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to bright_ch1_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','bright_ch1');
+update_editbox(hObject,hSlider);
+
+
+
+function contrast_ch1_edit_Callback(hObject, eventdata, handles)
+% hObject handle to contrast_ch1_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of contrast_ch1_edit as text
+% str2double(get(hObject,'String')) returns contents of contrast_ch1_edit as a double
+global UIInfo
+hSlider = findobj('Tag','contrast_ch1');
+update_slider(hObject,hSlider);
+UIInfo.updateFcn();
+
+
+% --- Executes during object creation, after setting all properties.
+function contrast_ch1_edit_CreateFcn(hObject, eventdata, handles)
+% hObject handle to contrast_ch1_edit (see GCBO)
+% eventdata reserved - to be defined in a future version of MATLAB
+% handles empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+% See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+ set(hObject,'BackgroundColor','white');
+end
+hSlider = findobj('Tag','contrast_ch1');
+update_editbox(hObject,hSlider);
diff --git a/urchin_compare/urchin_compare.m b/urchin_compare/urchin_compare.m
new file mode 100644
index 0000000000000000000000000000000000000000..d38f4ab2c931b789f9c9feb6f29194fe9949141f
--- /dev/null
+++ b/urchin_compare/urchin_compare.m
@@ -0,0 +1,1232 @@
+function urchin_compare()
+ init_globals();
+ load_config();
+
+ ui_initialize_main();
+end
+
+function init_globals()
+ global CONSTANTS UIInfo RegionInfo imC bwCh
+
+ imC = [];
+ bwCh = [];
+
+ RegionInfo = [];
+ CONSTANTS = [];
+
+ UIInfo.mainFig = figure();
+ UIInfo.toolFig = [];
+
+ reset_ui_fields();
+end
+
+function reset_ui_fields()
+ global UIInfo
+
+ UIInfo.pad = zeros(1,2);
+ UIInfo.padDelta = zeros(1,2);
+
+ UIInfo.mousePt = zeros(1,2);
+ UIInfo.zoom = 0;
+ UIInfo.selectedRegion = -1;
+
+ UIInfo.edited = false;
+ UIInfo.panning = false;
+
+ clf(UIInfo.mainFig);
+end
+
+function imPath = get_image_path(rootDir)
+ imPath = '';
+
+ [filename,pathname] = uigetfile(fullfile(rootDir, '*.*'), 'Open image file');
+ if ( filename == 0 )
+ return;
+ end
+
+ imPath = fullfile(pathname,filename);
+end
+
+function [im,imD] = fixup_im_channels(im,imD)
+ chNames = {};
+ if ( isfield(imD,'ChannelNames') )
+ chNames = imD.ChannelNames;
+ end
+
+ if ( ~isempty(chNames) )
+ keepNames = {'Alexa 488'; 'Cy3.5'};
+ sidx = zeros(length(chNames),1);
+ for i=1:length(keepNames)
+ bkn = startsWith(chNames, keepNames{i});
+ sidx(bkn) = i;
+ end
+
+ srtCh = zeros(length(keepNames),1);
+ for i=1:length(keepNames)
+ srtCh(i) = find(sidx==i,1,'first');
+ end
+
+ imD.ChannelNames = chNames(srtCh);
+ else
+ srtCh = [1;2];
+ end
+
+ imD.NumberOfChannels = 2;
+ im = im(:,:,:,srtCh,:);
+end
+
+function [im,imD,imPath] = load_image(imPath)
+ im = [];
+
+ [pathname,filename,fext] = fileparts(imPath);
+ imD = MicroscopeData.Original.ReadMetadata(pathname,[filename fext]);
+ if ( isempty(imD) )
+ return;
+ end
+
+ im = MicroscopeData.Original.ReadImages(pathname,[filename fext], [], 'zList',[1]);
+ if ( isempty(im) )
+ return;
+ end
+
+ [im,imD] = fixup_im_channels(im,imD);
+end
+
+%% ---- Size compat-helper
+function sz_dims = size_dims(A, dims)
+ sz_dims = arrayfun(@(x)(size(A,x)), dims);
+end
+
+%% ---- Config handling ----
+function load_config()
+ global Config
+
+ Config = struct('imagePath',{''},...
+ 'dataPath',{''},...
+ 'channelColors',{[0,1,0; 1,0,0]});
+
+ % Check for a valid settings file
+ if ( ~exist('settings.json','file') )
+ return;
+ end
+
+ jsonData = fileread('settings.json');
+ settings = jsondecode(jsonData);
+
+ if ( isempty(settings) )
+ return;
+ end
+
+ fields = fieldnames(settings);
+ for i=1:length(fields)
+ Config.(fields{i}) = settings.(fields{i});
+ end
+end
+
+function save_config()
+ global Config
+
+ jsonData = Utils.CreateJSON(Config);
+ fid = fopen('settings.json','wt');
+ if ( fid >= 0 )
+ fprintf(fid, '%s\n', jsonData);
+ fclose(fid);
+ end
+end
+
+function set_datapath(datapath)
+ global Config
+
+ pathname = fileparts(datapath);
+ Config.dataPath = pathname;
+end
+
+function set_imagepath(imagepath)
+ global Config
+
+ pathname = fileparts(imagepath);
+ Config.imagePath = pathname;
+end
+
+
+%% ---- Draw Functions ----
+function draw_image()
+ global imC UIInfo
+
+ if ( isempty(imC) )
+ return;
+ end
+
+ imR = im_composite_channels(imC, UIInfo.Cmap,UIInfo.Tfn);
+
+ render_image(UIInfo.mainFig, imR);
+ draw_regions();
+end
+
+function xor_cmap = color_xor(cmap)
+ xor_cmap = sum(cmap,1);
+ while ( any(xor_cmap > 1.0) )
+ bgo = (xor_cmap > 1.0);
+ xor_cmap(bgo) = xor_cmap(bgo) - 1.0;
+ end
+end
+
+function draw_regions()
+ global UIInfo RegionInfo
+
+ curAx = get(UIInfo.mainFig, 'CurrentAxes');
+
+ if ( UIInfo.bShowRegions )
+ for i=1:length(RegionInfo)
+ if ( isempty(RegionInfo(i).id) )
+ continue;
+ end
+
+ [~,uridx] = sortrows(RegionInfo(i).pts);
+
+ drawStyle = '-';
+ if ( UIInfo.selectedRegion == i )
+ drawStyle = ':';
+ end
+ plot(RegionInfo(i).pts(:,1),RegionInfo(i).pts(:,2), 'w',...
+ 'LineWidth',2,...
+ 'LineStyle',drawStyle,...
+ 'Parent',curAx,...
+ 'ButtonDownFcn',@(src,evt)(set_region_select(i)));
+
+ text(curAx,...
+ RegionInfo(i).pts(uridx(end),1)+1,...
+ RegionInfo(i).pts(uridx(end),2)+1,...
+ num2str(RegionInfo(i).id),...
+ 'Color','w',...
+ 'VerticalAlignment','top');
+ end
+ end
+
+ % Figure out a distinctive overlap color (if all channels on)
+ bShowCh = [UIInfo.bShowChPx, any(UIInfo.bShowChPx)];
+ % NOTE/HACK: color_xor runs across all channels passed in so it's important to start with [0,0,0] for overlap
+ pxCmap = [UIInfo.Cmap; 0 0 0];
+ pxCmap(3,:) = color_xor(pxCmap(bShowCh,:));
+ for c=1:3
+ if ( ~bShowCh(c) )
+ continue;
+ end
+
+ for i=1:length(RegionInfo)
+ if ( isempty(RegionInfo(i).id) )
+ continue;
+ end
+
+ if ( isempty(RegionInfo(i).chPts{c}) )
+ continue;
+ end
+
+ plot(RegionInfo(i).chPts{c}(:,1),RegionInfo(i).chPts{c}(:,2), '.',...
+ 'Color',pxCmap(c,:),...
+ 'Parent',curAx,...
+ 'ButtonDownFcn',@(src,evt)(set_region_select(i)));
+ end
+ end
+
+ drawnow();
+end
+
+function render_image(hFig, imRender)
+ global UIInfo
+
+ %% Compute padding info
+ imSize = size(imRender);
+ imPad = pad_image(imRender, UIInfo.pad);
+
+ imLims = [1-UIInfo.pad(2) imSize(2)+UIInfo.pad(2);
+ 1-UIInfo.pad(1) imSize(1)+UIInfo.pad(1)];
+
+ %% Setup current image axis and get limits
+ xl = [];
+ yl = [];
+
+ curAx = get(hFig, 'CurrentAxes');
+ if ( isempty(curAx) )
+ curAx = axes('Parent', hFig);
+ set(hFig, 'CurrentAxes',curAx);
+ else
+ %% Get current axis limit sets
+ xl = xlim(curAx);
+ yl = ylim(curAx);
+
+ im_xy = (imLims(:,2)-imLims(:,1));
+ prevIm_xy = im_xy - 2*[UIInfo.padDelta(2);UIInfo.padDelta(1)];
+
+ view_xy = [xl(2)-xl(1); yl(2)-yl(1)];
+
+ ssrd_xy = 0.5 * view_xy .* (im_xy - prevIm_xy) ./ prevIm_xy;
+
+ xl = xl + [-ssrd_xy(1), ssrd_xy(1)];
+ yl = yl + [-ssrd_xy(2), ssrd_xy(2)];
+ end
+
+ % Reset pad delta
+ UIInfo.padDelta = zeros(1,2);
+
+ %% render image
+ hold(curAx, 'off');
+ hIm = imagesc(imLims(1,:),imLims(2,:),imPad, 'Parent',curAx, [0 1]);
+ set(hIm, 'ButtonDownFcn', @click_down_event);
+
+ %% Axis positions
+ set(curAx, 'Position',[0 0 1 1]);
+
+ %% Setup axis defaults
+ axis(curAx, 'off');
+ axis(curAx, 'fill');
+ axis(curAx, 'ij');
+ zoom(hFig, 'reset');
+
+ %% Reset limits
+ if ( ~isempty(xl) )
+ xlim(curAx, xl);
+ ylim(curAx, yl);
+ end
+
+ %% Hold for further drawing
+ hold(curAx, 'all');
+end
+
+
+%% ---- Handle aspect-ratio padding
+function imPad = pad_image(im, pad)
+ imSize = size(im);
+ imPad = zeros(imSize + 2*[pad, 0]);
+
+ imX = pad(2) + (1:imSize(2));
+ imY = pad(1) + (1:imSize(1));
+
+ imPad(imY,imX,:) = im;
+end
+
+function [pad,finalAR] = compute_pad(hFig, im)
+ imSize = size(im);
+ pos = get(hFig, 'Position');
+
+ fAR = pos(3) / pos(4);
+ imAR = imSize(2) / imSize(1);
+
+ pad = zeros(1,2);
+ if ( imAR <= fAR )
+ pad(2) = ceil((fAR * imSize(1) - imSize(2)) / 2);
+ else
+ pad(1) = ceil((imSize(2) / fAR - imSize(1)) / 2);
+ end
+
+ finalAR = (imSize(2) + 2*pad(2)) / (imSize(1) + 2*pad(1));
+end
+
+%% ---- Image rendering functions
+function imRender = im_composite_channels(imC, cmap,tfn)
+ imSize = size_dims(imC, 1:4);
+
+ %% Create normalized images
+ imNrm = zeros([imSize(1:2), imSize(4)]);
+ for c=1:imSize(4)
+ imNrm(:,:,c) = mat2gray(imC(:,:,1,c));
+ end
+
+ %% Transform channels
+ imT = im_apply_tfn(imNrm, tfn);
+
+ % Use a default alpha and normalize at the end
+ % NOTE: Alpha = 0.1 makes all channels pretty transparent
+ alpha = 0.1;
+ %% Composite colors
+ imRender = zeros([imSize(1:2), 3]);
+ imTrn = ones([imSize(1:2), 1]);
+ for c=imSize(4):-1:1
+ oppacity = alpha * imT(:,:,c);
+
+ imPremul = oppacity .* repmat(reshape(cmap(c,:),[1,1,3]), [imSize(1:2), 1]);
+ imRender = (1-oppacity).*imRender + imPremul;
+ imTrn = imTrn .* (1-oppacity);
+ end
+
+ imRender = clamp(imRender ./ alpha, 0.0,1.0);
+end
+
+function imT = im_apply_tfn(im,tfn)
+ alpha = tfn(:,1).';
+ beta = tfn(:,2).';
+ % gamma = tfn(:,3).';
+
+ imR = reshape(im, [size(im,1)*size(im,2), size(im,3)]);
+ imTl = clamp(alpha .* (clamp(imR + beta,0.0,1.0) - 0.5) + 0.5, 0.0, 1.0);
+% imTl = clamp(clamp(alpha .* ((imR.^gamma) - 0.5),-0.5,0.5) + 0.5 + beta, 0.0, 1.0);
+
+ imT = reshape(imTl, size(im));
+end
+
+function outV = clamp(inV, minV, maxV)
+ outV = min(max(inV, minV), maxV);
+end
+
+
+%% ---- UI Init Functions ----
+function ui_initialize_main()
+ global UIInfo
+
+ set(UIInfo.mainFig,...
+ 'SizeChangedFcn', @resize_event,...
+ 'WindowScrollWheelFcn', @scroll_event,...
+ 'WindowButtonMotionFcn',@move_event,...
+ 'KeyPressFcn', @key_event,...
+ 'CloseRequestFcn', @close_event,...
+ 'Menu', 'none',...
+ 'ToolBar', 'none',...
+ 'BusyAction', 'cancel',...
+ 'Interruptible', 'off',...
+ 'NumberTitle', 'off',...
+ 'Name', 'Sea Urchin Calcein Counter');
+
+ ui_create_menubar(UIInfo.mainFig);
+end
+
+function ui_create_menubar(hFig)
+ global UIInfo
+
+ fileMenu = uimenu(...
+ 'Parent', hFig,...
+ 'Label', 'File',...
+ 'HandleVisibility', 'callback');
+
+ toolsMenu = uimenu(...
+ 'Parent', hFig,...
+ 'Label', 'Tools',...
+ 'HandleVisibility', 'callback');
+
+ helpMenu = uimenu(...
+ 'Parent', hFig,...
+ 'Label', 'Help',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @(src,evt)(helpdlg()));
+
+ uimenu(...
+ 'Parent', fileMenu,...
+ 'Label', 'Open Image',...
+ 'HandleVisibility', 'callback', ...
+ 'Callback', @open_image_event,...
+ 'Accelerator', 'o');
+
+ uimenu(...
+ 'Parent', fileMenu,...
+ 'Label', 'Save Data',...
+ 'HandleVisibility', 'callback', ...
+ 'Callback', @save_data_event,...
+ 'Accelerator', 's',...
+ 'Separator', 'on');
+
+ uimenu(...
+ 'Parent', fileMenu,...
+ 'Label', 'Load Data',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @open_data_event,...
+ 'Accelerator', 'l');
+
+ showTools = uimenu(...
+ 'Parent', toolsMenu,...
+ 'Label', 'Show Tools',...
+ 'HandleVisibility', 'callback',...
+ 'Callback', @(src,evt)(ui_toggle_tools()),...
+ 'Accelerator', 't',...
+ 'Enable', 'off',...
+ 'Checked', 'off');
+
+ UIInfo.handles.showTools = showTools;
+end
+
+function ui_update_title()
+ global CONSTANTS UIInfo
+
+ datasetName = CONSTANTS.imageData.DatasetName;
+
+ title = datasetName;
+ if ( is_edited() )
+ title = [title ' *'];
+ end
+
+ set(UIInfo.mainFig, 'NumberTitle','off');
+ set(UIInfo.mainFig, 'Name',title);
+end
+
+function ui_create_tooldlg()
+ global UIInfo
+
+ if ( ~check_valid_handle(UIInfo.toolFig) )
+ UIInfo.toolFig = toolsdlg();
+ UIInfo.updateMenu = @ui_update_toolsmenu;
+ UIInfo.updateFcn = @ui_update_fcn;
+ UIInfo.updateThresh = @ui_update_thresh_fcn;
+ UIInfo.updateRegionSelect = @set_region_select;
+ % UIInfo.updateCellCount = @ui_update_cellcount;
+ end
+
+ ui_setup_toolhandles();
+ ui_set_channel_names();
+
+ ui_update_region_table();
+ ui_init_chthresh();
+
+ ui_update_from_info();
+ ui_update_toolsmenu();
+end
+
+function ui_toggle_tools()
+ global UIInfo
+
+ if ( check_valid_handle(UIInfo.toolFig) )
+ visible = get(UIInfo.toolFig, 'Visible');
+ if ( strcmpi(visible,'on') )
+ set(UIInfo.toolFig, 'Visible','off');
+ else
+ set(UIInfo.toolFig, 'Visible','on');
+ end
+ else
+ ui_create_tooldlg();
+ end
+
+ ui_update_toolsmenu();
+end
+
+function ui_update_toolsmenu()
+ global UIInfo CONSTANTS
+
+ strEn = 'off';
+ if ( ~isempty(CONSTANTS) )
+ strEn = 'on';
+ end
+
+ if ( check_valid_handle(UIInfo.toolFig) )
+ strCh = get(UIInfo.toolFig, 'Visible');
+ end
+
+ set(UIInfo.handles.showTools, 'Checked',strCh);
+ set(UIInfo.handles.showTools, 'Enable',strEn);
+end
+
+function bValid = check_valid_handle(chkHandle)
+ bValid = false;
+ if ( isempty(chkHandle) )
+ return;
+ end
+
+ if ( ~isvalid(chkHandle) )
+ return;
+ end
+
+ bValid = true;
+end
+
+
+%% ---- Tools UI Helpers ----
+function ui_update_fcn()
+ ui_update_tool_values();
+ draw_image();
+end
+
+function ui_update_tool_values()
+ ui_load_colors();
+ ui_load_display_settings();
+ ui_compute_transferfcn();
+end
+
+function ui_update_thresh_fcn()
+ ui_update_chthresh();
+
+ edit_op(@update_region_chbw);
+ ui_update_region_table();
+ draw_image();
+end
+
+function ui_setup_toolhandles()
+ global CONSTANTS UIInfo
+
+ UIInfo.tools = [];
+ UIInfo.tools.hShowCh = findobj(UIInfo.toolFig, 'Tag','show_regions');
+
+ minChan = min(2,CONSTANTS.imageData.NumberOfChannels);
+
+ UIInfo.tools.hChColor = zeros(1,minChan);
+ UIInfo.tools.hChBright = zeros(1,minChan);
+ UIInfo.tools.hChContrast = zeros(1,minChan);
+
+ for c=1:minChan
+ UIInfo.tools.hChColor(c) = findobj(UIInfo.toolFig, 'Tag',['color_ch' num2str(c)]);
+ UIInfo.tools.hChBright(c) = findobj(UIInfo.toolFig, 'Tag',['bright_ch' num2str(c)]);
+ UIInfo.tools.hChContrast(c) = findobj(UIInfo.toolFig, 'Tag',['contrast_ch' num2str(c)]);
+
+ UIInfo.tools.hShowChPx(c) = findobj(UIInfo.toolFig, 'Tag',['show_ch' num2str(c) 'px']);
+ UIInfo.tools.hChThresh(c) = findobj(UIInfo.toolFig, 'Tag', ['ch' num2str(c) '_thresh']);
+ end
+
+ UIInfo.tools.hRegionTable = findobj(UIInfo.toolFig, 'Tag','cells_table');
+end
+
+function ui_set_channel_names()
+ global CONSTANTS UIInfo
+
+ for c=1:2
+ hChPanel = findobj(UIInfo.toolFig, 'Tag',['uipanel_ch' num2str(c)]);
+ if ( ~isempty(hChPanel) && ~isempty(CONSTANTS.imageData.ChannelNames{c}) )
+ set(hChPanel, 'Title',CONSTANTS.imageData.ChannelNames{c});
+ end
+ end
+end
+
+function ui_init_chthresh()
+ ui_update_chthresh();
+ update_bw_ch();
+end
+
+function ui_set_channel_colors()
+ global UIInfo Config CONSTANTS
+
+ if ( isfield(CONSTANTS.imageData,'ChannelColors') && ~isempty(CONSTANTS.imageData.ChannelColors) )
+ UIInfo.Cmap = CONSTANTS.imageData.ChannelColors;
+ else
+ UIInfo.Cmap = Config.channelColors;
+ end
+end
+
+function ui_reset_display_settings()
+ global UIInfo
+
+ UIInfo.bShowRegions = true;
+ UIInfo.bShowChPx = [true, true];
+
+ UIInfo.ThrScale = [1.0, 1.0];
+
+ UIInfo.Tfn(1,:) = [1,0,1];
+ UIInfo.Tfn(2,:) = [1,0,1];
+
+ ui_set_channel_colors();
+end
+
+function ui_update_from_info()
+ global UIInfo
+
+ %% Setup display settings
+ set(UIInfo.tools.hShowCh, 'Value',UIInfo.bShowRegions);
+ for c=1:length(UIInfo.tools.hShowChPx)
+ set(UIInfo.tools.hShowChPx(c), 'Value',UIInfo.bShowChPx(c));
+ end
+
+ %% Setup colors
+ for c=1:size(UIInfo.Cmap,1)
+ set(UIInfo.tools.hChColor(c), 'BackgroundColor',UIInfo.Cmap(c,:));
+ end
+
+ %% Setup transfer functions
+ for c=1:size(UIInfo.Tfn,1)
+ alpha = UIInfo.Tfn(c,1);
+ beta = UIInfo.Tfn(c,2);
+
+ vBr = beta;
+ vCon = 1-2.^(-alpha);
+
+ set(UIInfo.tools.hChBright(c), 'Value',vBr);
+ set(UIInfo.tools.hChContrast(c), 'Value',vCon);
+ end
+
+ %% Setup threshold
+ for c=1:length(UIInfo.tools.hChThresh)
+ tSc = UIInfo.ThrScale(c);
+ vCt = 1-2.^(-tSc);
+ set(UIInfo.tools.hChThresh(c), 'Value',vCt);
+ end
+end
+
+function ui_load_display_settings()
+ global UIInfo
+
+ UIInfo.bShowRegions = (get(UIInfo.tools.hShowCh, 'Value') > 0.0);
+ for c=1:length(UIInfo.tools.hShowChPx)
+ UIInfo.bShowChPx(c) = (get(UIInfo.tools.hShowChPx(c), 'Value') > 0.0);
+ end
+end
+
+function ui_load_colors()
+ global UIInfo Config
+ cmap = [1,0,0; 0,1,0];
+
+ for c=1:length(UIInfo.tools.hChColor)
+ cmap(c,:) = get(UIInfo.tools.hChColor(c), 'BackgroundColor');
+ end
+
+ UIInfo.Cmap = cmap;
+ Config.channelColors = cmap;
+end
+
+function ui_compute_transferfcn()
+ global UIInfo
+ gamma = 1.2;
+ tfn = [1,0,gamma;1,0,gamma];
+
+ for c=1:length(UIInfo.tools.hChBright)
+ vBr = get(UIInfo.tools.hChBright(c), 'Value');
+ vCon = get(UIInfo.tools.hChContrast(c), 'Value');
+
+ alpha = -log2(1-vCon);
+ beta = vBr;
+
+ tfn(c,:) = [alpha,beta,1];
+ end
+
+ UIInfo.Tfn = tfn;
+end
+
+function ui_update_chthresh()
+ global UIInfo
+
+ thrScale = zeros(1,2);
+ for c=1:length(UIInfo.tools.hChThresh)
+ tVal = get(UIInfo.tools.hChThresh(c), 'Value');
+ thrScale(c) = -log2(1-tVal);
+ end
+
+ UIInfo.ThrScale = thrScale;
+end
+
+
+%% ---- Partial region (drawing) handling ----
+function update_cell_edge(point_xy)
+ global PartialCell
+
+ updateLine = PartialCell.lines(end);
+ set(updateLine, 'XData', [PartialCell.pts(end,1) point_xy(1)]);
+ set(updateLine, 'YData', [PartialCell.pts(end,2) point_xy(2)]);
+end
+
+function start_cell(curAx, point_xy)
+ global PartialCell
+
+ PartialCell = [];
+ PartialCell.pts = point_xy;
+
+ newLine = line([PartialCell.pts(end,1) point_xy(1)], [PartialCell.pts(end,2) point_xy(2)], 'Parent',curAx, 'color','w');
+ PartialCell.lines = newLine;
+end
+
+function chk_next_edge(curAx, point_xy)
+ global PartialCell
+
+ if ( isempty(PartialCell) )
+ return;
+ end
+
+ if ( sum((PartialCell.pts(end,:) - point_xy).^2,1) < 0.6 )
+ return;
+ end
+
+ next_cell_edge(curAx, point_xy);
+end
+
+function next_cell_edge(curAx, point_xy)
+ global PartialCell
+
+ if ( isempty(PartialCell) )
+ return;
+ end
+
+ PartialCell.pts = [PartialCell.pts; point_xy];
+
+ newLine = line([PartialCell.pts(end,1) point_xy(1)], [PartialCell.pts(end,2) point_xy(2)], 'Parent',curAx, 'color','w');
+ PartialCell.lines = [PartialCell.lines; newLine];
+end
+
+function delete_partial_cell()
+ global PartialCell
+
+ if ( ~isempty(PartialCell) )
+ for i=1:length(PartialCell.lines)
+ delete(PartialCell.lines(i));
+ end
+ end
+
+ PartialCell = [];
+end
+
+
+%% ---- Region handling ----
+function ui_update_region_table()
+ global RegionInfo UIInfo
+
+ data = {};
+ if ( isempty(RegionInfo) )
+ set(UIInfo.tools.hRegionTable, 'Data',data);
+ else
+ bValidRegions = arrayfun(@(x)(~isempty(x.id)), RegionInfo);
+ validRegions = RegionInfo(bValidRegions);
+
+ % Channel counts 1x3 array: [ch1Count,ch2Count,overlapCount]
+ % NOTE: The channel 1/2 counts are only the disjoint non-overlapping pixels so we add 3 to both
+ chCounts = arrayfun(@(x)([x.chCount(1) x.chCount(2) 0] + x.chCount(3)), validRegions, 'UniformOutput',false);
+ chCounts = vertcat(chCounts{:});
+
+ data = cell(length(validRegions),5);
+ [data{:,1}] = deal(validRegions.id);
+ [data{:,2}] = deal(validRegions.area);
+ data(:,3) = num2cell(chCounts(:,1));
+ data(:,4) = num2cell(chCounts(:,2));
+ data(:,5) = num2cell(chCounts(:,3));
+
+ set(UIInfo.tools.hRegionTable, 'Data',data);
+ end
+end
+
+function update_region_chpoints(regionIDs)
+ global RegionInfo bwCh
+
+ %% Get above-threshold points for each region (handle overlap as well)
+ pts = [];
+ chansz = zeros(1,3);
+ bOverlap = all(bwCh,3);
+ % These are disjoint (non-overlapping points)
+ for ch=1:size(bwCh,3)
+ [r,c] = find(bwCh(:,:,ch) & ~bOverlap);
+
+ pts = [pts; c,r];
+ chansz(ch) = size(r,1);
+ end
+ % Handle overlap points
+ [ro,co] = find(bOverlap);
+ pts = [pts; co,ro];
+ chansz(3) = size(ro,1);
+ % Starts for channel/overlap points
+ startidx = [0,cumsum(chansz)];
+ % Make a bool map for point sets
+ bChPx = false(sum(chansz),3);
+ for i=1:3
+ bChPx(startidx(i)+(1:chansz(i)),i) = true;
+ end
+
+ %% Compute counts and channel points for all valid regions in region list
+ for i=1:length(regionIDs)
+ idx = regionIDs(i);
+ if ( isempty(RegionInfo(idx).id) )
+ continue;
+ end
+
+ bInR = inpolygon(pts(:,1),pts(:,2), RegionInfo(idx).pts(:,1),RegionInfo(idx).pts(:,2));
+ RegionInfo(idx).chCount = zeros(1,3);
+ for ch=1:3
+ bch = bInR & bChPx(:,ch);
+ chPts = pts(bch,:);
+
+ RegionInfo(idx).chPts{ch} = chPts;
+ RegionInfo(idx).chCount(ch) = size(chPts,1);
+ end
+ end
+end
+
+function update_region_chbw()
+ global RegionInfo
+
+ update_bw_ch();
+ update_region_chpoints(1:length(RegionInfo));
+end
+
+function update_bw_ch()
+ global UIInfo imC bwCh
+
+ bwCh = false(size_dims(imC,[1,2,4]));
+ for c=1:size(imC,4)
+ imN = mat2gray(imC(:,:,1,c));
+ mt = multithresh(imN(:),2);
+ thresh = UIInfo.ThrScale(c) * mt(2);
+
+ bwCh(:,:,c) = (imN >= thresh);
+ end
+end
+
+function create_region(partialRegion)
+ global RegionInfo
+
+ if ( isempty(partialRegion) )
+ return;
+ end
+
+ newID = 1;
+ if ( ~isempty(RegionInfo) )
+ newID = size(RegionInfo,1) + 1;
+ end
+
+ newRegion = make_empty_cell();
+ newRegion.id = newID;
+ newRegion.pts = [partialRegion.pts; partialRegion.pts(1,:)];
+ newRegion.area = polyarea(newRegion.pts(:,1),newRegion.pts(:,2));
+
+ RegionInfo = [RegionInfo; newRegion];
+ update_region_chpoints(newID);
+
+ ui_update_region_table();
+end
+
+function delete_region(cellID)
+ global RegionInfo
+
+ RegionInfo(cellID) = make_empty_cell();
+end
+
+function cellStruct = make_empty_cell()
+ cellStruct = struct('id',{[]}, 'pts',{[]}, 'area',{[]}, 'chPts',{[]},'chCount',{[]}, 'count',{[]});
+end
+
+function regionID = check_region_select(point_xy)
+ global RegionInfo
+
+ bValidRegions = arrayfun(@(x)(~isempty(x.id)), RegionInfo);
+ validRegions = RegionInfo(bValidRegions);
+
+ regionID = -1;
+ for i=1:length(validRegions)
+ [bIn,bOn] = inpolygon(point_xy(1),point_xy(2), validRegions(i).pts(:,1),validRegions(i).pts(:,2));
+ if ( any(bIn | bOn) )
+ regionID = validRegions(i).id;
+ return
+ end
+ end
+end
+
+%% ---- Editor support ----
+function edit_op(editfcn, varargin)
+ editfcn(varargin{:});
+ set_edited(true);
+end
+
+function bEdited = is_edited()
+ global UIInfo
+ bEdited = UIInfo.edited;
+end
+
+function set_edited(bEdited)
+ global UIInfo
+
+ UIInfo.edited = bEdited;
+ ui_update_title();
+end
+
+
+%% ---- Menu Events ----
+function open_image_event(hSrc,evt)
+ global CONSTANTS Config imC
+
+ chk_const = [];
+ if ( ~check_continue_unsaved() )
+ return;
+ end
+
+ imPath = get_image_path(Config.imagePath);
+ if ( isempty(imPath) )
+ return;
+ end
+
+ [imC,chk_const.imageData] = load_image(imPath);
+ if ( isempty(imC) )
+ msgbox('Unable to read image data from file', 'Error reading image', 'warn');
+ return;
+ end
+
+ chk_const.imagePath = imPath;
+ chk_const.dataPath = '';
+
+ CONSTANTS = chk_const;
+
+ set_imagepath(imPath);
+ set_datapath(imPath);
+
+ clear_data();
+ reset_ui_fields();
+
+ ui_update_title();
+ ui_reset_display_settings();
+ ui_create_tooldlg();
+
+ resize_padding();
+ draw_image();
+end
+
+function open_data_event(hSrc,evt)
+ global CONSTANTS Config
+
+ if ( ~check_continue_unsaved() )
+ return;
+ end
+
+ [filename,pathname] = uigetfile(fullfile(Config.dataPath,'*.mat'));
+ if ( filename == 0 )
+ return;
+ end
+
+ datapath = fullfile(pathname,filename);
+
+ open_data(datapath)
+ CONSTANTS.dataPath = datapath;
+
+ ui_create_tooldlg();
+ draw_image();
+end
+
+function save_data_event(hSrc,evt)
+ global CONSTANTS Config
+
+ if ( isempty(CONSTANTS) )
+ return;
+ end
+
+ if ( isempty(CONSTANTS.dataPath) )
+ [filename,pathname] = uiputfile(fullfile(Config.dataPath,'*.mat'));
+ if ( filename == 0 )
+ return;
+ end
+
+ CONSTANTS.dataPath = fullfile(pathname,filename);
+ end
+
+ save_data(CONSTANTS.dataPath);
+end
+
+
+function bContinue = check_continue_unsaved()
+ bContinue = true;
+ if ( is_edited() )
+ bContinue = unsaved_verify();
+ end
+end
+
+function bContinue = unsaved_verify()
+ userSel = questdlg('You have unsaved data, are you sure you wish to continue without saving?','Unsaved Data','Continue','Cancel','Cancel');
+ bContinue = ~strcmpi(userSel,'Cancel');
+end
+
+%% ---- Data handling ----
+function clear_data()
+ global RegionInfo
+
+ RegionInfo = [];
+end
+
+function open_data(datapath)
+ global CONSTANTS RegionInfo UIInfo imC
+
+ s = load(datapath);
+ CONSTANTS = s.CONSTANTS;
+ RegionInfo = s.RegionInfo;
+
+ imC = s.CONSTANTS.im;
+
+ %% Update from ui after load
+ fields = fieldnames(s.displayInfo);
+ for i=1:length(fields)
+ UIInfo.(fields{i}) = s.displayInfo.(fields{i});
+ end
+
+ set_edited(false);
+ set_datapath(datapath);
+end
+
+function save_data(datapath)
+ global CONSTANTS RegionInfo UIInfo imC
+
+ CONSTANTS.im = imC;
+ displayInfo = struct('Tfn',{UIInfo.Tfn}, 'Cmap',{UIInfo.Cmap},...
+ 'ThrScale',{UIInfo.ThrScale},...
+ 'bShowRegions',{UIInfo.bShowRegions},...
+ 'bShowChPx',{UIInfo.bShowChPx});
+
+ save(datapath, 'CONSTANTS','RegionInfo','displayInfo');
+
+ set_edited(false);
+ set_datapath(datapath);
+end
+
+
+%% ---- UI Events ----
+function click_down_event(hSrc,evt)
+ global UIInfo PartialCell
+ curAx = get(UIInfo.mainFig, 'CurrentAxes');
+ currentPoint = get(curAx, 'CurrentPoint');
+ point_xy = currentPoint(1,1:2);
+
+ selectType = get(UIInfo.mainFig, 'SelectionType');
+ cellID = check_region_select(point_xy);
+
+ set_region_select(cellID);
+
+ if ( isempty(PartialCell) && strcmpi(selectType,'normal') && (cellID < 0) )
+ start_cell(curAx, point_xy);
+ set(UIInfo.mainFig, 'WindowButtonUpFcn',@click_up_event);
+ elseif ( strcmpi(selectType,'alt') )
+ UIInfo.panning = true;
+ set(UIInfo.mainFig, 'WindowButtonUpFcn',@click_up_event);
+ end
+end
+
+function click_up_event(hSrc,evt)
+ global UIInfo PartialCell
+
+ UIInfo.panning = false;
+ set(UIInfo.mainFig, 'WindowButtonUpFcn','');
+
+ if ( ~isempty(PartialCell) )
+ %% Don't create a cell if it's only a local click
+ if ( size(PartialCell.pts,1) > 2 )
+ edit_op(@create_region, PartialCell);
+ end
+
+ delete_partial_cell();
+ draw_image();
+ end
+end
+
+function set_region_select(regionID)
+ global UIInfo
+
+ if ( UIInfo.selectedRegion ~= regionID )
+ UIInfo.selectedRegion = regionID;
+ draw_image();
+ end
+end
+
+function move_event(hSrc,evt)
+ global UIInfo PartialCell
+
+ curAx = get(hSrc, 'CurrentAxes');
+ if ( UIInfo.panning )
+ stable_mouse_xlat(curAx);
+ end
+
+ if ( ~isempty(curAx) )
+ curPt = get(curAx, 'CurrentPoint');
+ UIInfo.mousePt = curPt(1,1:2);
+ end
+
+ if ( ~isempty(PartialCell) )
+ update_cell_edge(UIInfo.mousePt);
+ chk_next_edge(curAx,UIInfo.mousePt);
+ end
+end
+
+function key_event(hSrc,evt)
+ global UIInfo
+
+ if ( strcmpi(evt.Key,'escape') )
+ delete_partial_cell();
+ set(UIInfo.mainFig, 'WindowButtonUpFcn','');
+ elseif ( strcmpi(evt.Key,'backspace') || strcmpi(evt.Key,'delete') )
+ if ( UIInfo.selectedRegion > 0 )
+ edit_op(@delete_region, UIInfo.selectedRegion)
+
+ UIInfo.selectedRegion = -1;
+ ui_update_region_table();
+ draw_image();
+ end
+ end
+end
+
+function scroll_event(hSrc,evt)
+ global UIInfo
+
+ zBase = 1.4;
+
+ curAx = get(UIInfo.mainFig, 'CurrentAxes');
+ if ( isempty(curAx) )
+ return;
+ end
+
+ currentPoint = get(curAx, 'CurrentPoint');
+ point_xy = currentPoint(1,1:2);
+
+ wheelDelta = -evt.VerticalScrollCount;
+ newZoom = clamp(wheelDelta + UIInfo.zoom, 0, 10);
+ zoomDelta = newZoom - UIInfo.zoom;
+
+ if ( abs(zoomDelta) > 0 )
+ xl = xlim(curAx);
+ yl = ylim(curAx);
+
+ UIInfo.zoom = UIInfo.zoom + zoomDelta;
+ zoomFactor = zBase ^ zoomDelta;
+
+ lims_xy = [xl.', yl.'];
+ zoomlims_xy = compute_smooth_zoom(zoomFactor, lims_xy, point_xy);
+
+ xlim(curAx, zoomlims_xy(:,1));
+ ylim(curAx, zoomlims_xy(:,2));
+ elseif ( wheelDelta < 0 )
+ UIInfo.zoom = 0;
+ zoom(curAx, 'out')
+ end
+end
+
+function zm_lims_xy = compute_smooth_zoom(zoomFactor, lims_xy, point_xy)
+ %% Compute zoomed xy-limits such that point_xy is fixed (doesn't move)
+ % NOTE: lims_xy = [xmin ymin
+ % xmax ymax]
+
+ loc_xy = point_xy - lims_xy(1,:);
+ vsz_xy = lims_xy(2,:) - lims_xy(1,:);
+
+ delta_xy = loc_xy - (loc_xy / zoomFactor);
+ zoomsz_xy = vsz_xy / zoomFactor;
+
+ zm_lims_xy = [lims_xy(1,:); lims_xy(1,:) + zoomsz_xy] + delta_xy;
+end
+
+function stable_mouse_xlat(curAx)
+ global UIInfo
+
+ xl = xlim(curAx);
+ yl = ylim(curAx);
+
+ currentPoint = get(curAx, 'CurrentPoint');
+ point_xy = currentPoint(1,1:2);
+
+ delta_xy = UIInfo.mousePt - point_xy;
+ xl = xl + delta_xy(1);
+ yl = yl + delta_xy(2);
+
+ xlim(curAx, xl);
+ ylim(curAx, yl);
+end
+
+function resize_padding()
+ global UIInfo imC
+
+ if ( isempty(imC) )
+ return;
+ end
+
+ padding = compute_pad(UIInfo.mainFig, imC);
+
+ UIInfo.padDelta = padding - UIInfo.pad;
+ UIInfo.pad = padding;
+end
+
+function resize_event(hFig,evt)
+ resize_padding();
+ draw_image();
+end
+
+function close_event(hFig,evt)
+ global UIInfo
+
+ if ( ~check_continue_unsaved() )
+ return;
+ end
+
+ save_config();
+
+ if ( check_valid_handle(UIInfo.toolFig) )
+ delete(UIInfo.toolFig);
+ end
+
+ delete(hFig);
+end
diff --git a/urchin_compare/version.json b/urchin_compare/version.json
new file mode 100644
index 0000000000000000000000000000000000000000..ff8f7bf05c33c2d12446661bd1f05a5f61149bd4
--- /dev/null
+++ b/urchin_compare/version.json
@@ -0,0 +1,12 @@
+{
+ "name" : "urchin_compare",
+ "majorVersion" : 2,
+ "minorVersion" : 0,
+ "branchName" : "master",
+ "buildNumber" : "2020.12.07.07",
+ "buildMachine" : "bioimage28",
+ "commitHash" : [
+ " : 15410c6b7251a6890057e04366431f0286b90d70",
+ " : 07f725fe7b1c500a2743e016d119a7b0f059561e"
+ ]
+}