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im_browser.m
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function varargout = im_browser(varargin)
% @mainpage Microscopy Image Browser
% @section intro Introduction
% @b Microscopy @b Image @b Browser is is a high-performance software package for advanced image processing, segmentation and visualization of multidimentional (2D-4D) datasets.
% Microscopy Image Browser is written in Matlab, but has a user friendly graphical interface that does not requre knowledge of Matlab and can be used by anybody.
% @section features Key Features
% - Works as a Matlab program under Windows/Linux/MacOS Matlab, or as a standalone application (Windows 64bit);
% - Open source, no license/fee required;
% - Extendable with custom plugins;
% - Generation of multidimentional image stacks;
% - Alignment of 3D stacks and images within these stacks;
% - Brightness, contrast, gamma, image mode adjustments, resize, crop functions;
% - Automatic/manual image segmentation with help of filters and interpolation in XY, XZ, or YZ planes;
% - Quantification and statistics for 2D/3D objects;
% - Export of images or models to Matlab, Amira, IMOD, TIF, NRRD formats;
% - Direct 3D visualization using Matlab isosurfaces or Fiji 3D viewer;
% - Log of performed actions;
% - Customizable Undo option
% - Colorblind friendly default color modeling scheme
% @section description Description
% Recent years witnessed a rapid development of 3D electron microscopy
% imaging techniques applied for the life science research. In addition to electron tomography
% (ET) that is effective on a subcellular level, several other alternative methods that extend the
% imaging up to the tissue level have been developed. Among these are new scanning electron microscopy (SEM)
% techniques that allow automated sequential imaging of a freshly cut block face of resin-embedded specimens
% using a back scatter detector. A fresh block face is created by an ultramicrotome inserted in the imaging
% chamber (Serial-Block Face SEM) or by focused ion beam (FIB-SEM). As a result, the amount and volumes of
% 3D datasets increases extensively raising a question of effective image processing and modeling.
% With development of Microscopy Image Browser (MIB) we address this problem and present a free,
% open-source software package, which can be used for image processing, analysis, segmentation and
% visualization of multidimensional datasets.
%
% @page install Download and installbination
% Please follow instructions on Microscopy Image Browser web page:
% http://mib.helsinki.fi
% Copyright (C) 2010-2015 Ilya Belevich, University of Helsinki (ilya.belevich @ helsinki.fi)
% part of Microscopy Image Browser, http:\\mib.helsinki.fi
% This program is free software; you can redistribute it and/or
% modify it under the terms of the GNU General Public License
% as published by the Free Software Foundation; either version 2
% of the License, or (at your option) any later version.
% Begin initialization code - DO NOT EDIT
gui_Singleton = 0;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @im_browser_OpeningFcn, ...
'gui_OutputFcn', @im_browser_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
end
function im_browser_OpeningFcn(hObject, eventdata, handles, varargin)
% function im_browser_OpeningFcn(hObject, eventdata, handles, varargin)
% Opening function of im_browser
%
% Parameters:
% 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 im_browser (see VARARGIN)
%
% Return values:
% add path to other directories
if ~isdeployed
func_name='im_browser.m';
func_dir=which(func_name);
func_dir=fileparts(func_dir);
addpath(func_dir);
addpath(fullfile(func_dir, 'Classes'));
addpath(fullfile(func_dir, 'GuiTools'));
addpath(fullfile(func_dir, 'GuiTools', 'volren'));
addpath(fullfile(func_dir, 'ImageFilters'));
addpath(fullfile(func_dir, 'ImageFilters', 'Coherence_filter'));
addpath(fullfile(func_dir, 'ImageFilters', 'Coherence_filter','functions'));
addpath(fullfile(func_dir, 'ImageFilters', 'Coherence_filter','functions2D'));
addpath(fullfile(func_dir, 'ImageFilters', 'Coherence_filter','functions3D'));
addpath(fullfile(func_dir, 'ImageFilters', 'FastMarching'));
addpath(fullfile(func_dir, 'ImageFilters', 'FastMarching','functions'));
addpath(fullfile(func_dir, 'ImageFilters', 'FastMarching','shortestpath'));
addpath(fullfile(func_dir, 'ImageFilters', 'Frangi'));
addpath(fullfile(func_dir, 'ImageFilters', 'RandomForest'));
addpath(fullfile(func_dir, 'ImageFilters', 'RandomForest','RF_Class_C'));
addpath(fullfile(func_dir, 'ImageFilters', 'RandomForest','RF_Reg_C'));
addpath(fullfile(func_dir, 'ImageFilters', 'RandomForest','MembraneDetection'));
addpath(fullfile(func_dir, 'ImageFilters', 'Supervoxels'));
addpath(fullfile(func_dir, 'ImportExportTools'));
addpath(fullfile(func_dir, 'ImportExportTools', 'BioFormats'));
addpath(fullfile(func_dir, 'ImportExportTools', 'export_fig'));
addpath(fullfile(func_dir, 'ImportExportTools', 'Fiji'));
addpath(fullfile(func_dir, 'ImportExportTools', 'HDF5'));
addpath(fullfile(func_dir, 'ImportExportTools', 'Imaris'));
addpath(fullfile(func_dir, 'ImportExportTools', 'MatTomo'));
addpath(fullfile(func_dir, 'ImportExportTools', 'MatTomo', 'Utils'));
addpath(fullfile(func_dir, 'ImportExportTools', 'nrrd'));
addpath(fullfile(func_dir, 'ImportExportTools', 'Omero'));
addpath(fullfile(func_dir, 'Misc_func'));
addpath(fullfile(func_dir, 'Misc_func', 'imclipboard'));
addpath(fullfile(func_dir, 'techdoc'));
addpath(fullfile(func_dir, 'Tools'));
addpath(fullfile(func_dir, 'Tools', 'Align'));
addpath(fullfile(func_dir, 'Tools', 'AreaAnalysis'));
addpath(fullfile(func_dir, 'Tools', 'RegionGrowing'));
end
% get the current version of matlab; keep this variable to be faster and
% not call ver function
v = ver('matlab');
handles.matlabVersion = str2double(v(1).Version);
if handles.matlabVersion >= 8.4 % R2014b
set(handles.im_browser,'GraphicsSmoothing','off'); % turn off smoothing and turn opengl renderer
set(handles.im_browser, 'Renderer','opengl');
set(handles.imageAxes,'FontSmoothing','off');
else
%set(handles.im_browser,'Renderer','painters');
set(handles.im_browser,'Renderer','opengl');
end
dateTag = 'ver. 1.305 / 23.12.2016'; % ATTENTION! it is important to have the version number between "ver." and "/"
%dateTag = ''; % it is important to have the version number between "ver." and "/"
title = ['Microscopy Image Browser ' dateTag];
if isdeployed; title = [title ' deployed version']; end;
set(handles.im_browser,'Name',title);
% show splash screen
try
if isdeployed
if isunix()
%[~, user_name] = system('whoami');
%pathName = fullfile('./Users', user_name(1:end-1), 'Documents/MIB');
[status, result] = system('path');
pathName = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
% the code above does not work on Mac OS X Yosemite and R2016a
% so fix MIB location
if isempty(pathName)
pathName = '/Applications/MIB/application/';
end
else
%pathName = pwd;
% USERPROFILE_PATH = getenv('USERPROFILE');
% mibDataPath = fullfile(USERPROFILE_PATH, 'AppData', 'Local', 'Microscopy Image Browser');
% if isdir(mibDataPath) == 0
% mkdir(mibDataPath);
% end
[status, result] = system('path');
pathName = char(regexpi(result, 'Path=(.*?);', 'tokens', 'once'));
end
handles.pathMIB = pathName;
img = imread(fullfile(handles.pathMIB, 'Resources', 'splash')); % load splash screen
% get numbers for the brush size change
handles.brushSizeNumbers = 1 - imread(fullfile(handles.pathMIB, 'Resources', 'numbers.png')); % height=16, letter size = 8, +1 pixel border
handles.dejavufont = 1 - imread(fullfile(handles.pathMIB, 'Resources', 'DejaVuSansMono.png')); % table with DejaVu font, Pt = 8, 10, 12, 14, 16, 18, 20
else
handles.pathMIB = fileparts(which('im_browser'));
img = imread(fullfile(handles.pathMIB, 'Resources', 'splash')); % load splash screen
% get numbers for the brush size change
handles.brushSizeNumbers = 1-imread(fullfile(handles.pathMIB, 'Resources', 'numbers.png')); % height=16, letter size = 8, +1 pixel border
handles.dejavufont = 1-imread(fullfile(handles.pathMIB, 'Resources', 'DejaVuSansMono.png')); % table with DejaVu font, Pt = 8, 10, 12, 14, 16, 18, 20
end
%dateTagCrop = dateTag(strfind(dateTag, 'ver.')+5:end);
%img = rendertext(img, dateTagCrop,[255 255 255], [30, 392],'bnd','right');
addTextOptions.color = [1 1 0];
addTextOptions.fontSize = 2;
addTextOptions.markerText = 'text';
img = ib_addText2Img(img, dateTag, [1,425], handles.dejavufont, addTextOptions);
% if handles.matlabVersion >= 8.4 && isdeployed && ~ismac() % R2014b
% % do not show the splash screen
% else
jimg = im2java(img);
frame = javax.swing.JFrame;
frame.setUndecorated(true);
icon = javax.swing.ImageIcon(jimg);
label = javax.swing.JLabel(icon);
frame.getContentPane.add(label);
frame.pack;
imgSize = size(img);
frame.setSize(imgSize(2),imgSize(1));
screenSize = get(0,'ScreenSize');
frame.setLocation((screenSize(3)-imgSize(2))/2,...
(screenSize(4)-imgSize(1))/2);
frame.show;
% end
catch err
sprintf('%s', err.identifier);
disp(err);
end
%% Adding listeners, using Yair Altman, suggestion:
% http://undocumentedmatlab.com/blog/continuous-slider-callback/#Event_Listener
% to change layer slider
% % keep the code under im_browser
if handles.matlabVersion < 8.4 % R2014a or earlier
% for z-slider
handles.changelayerSliderListener = handle.listener(handles.changelayerSlider,'ActionEvent',@changelayerSlider_Callback);
handles.changelayerSliderListener.Enabled = 'off'; % disactivate the listener for Z=1;
% for t-slider
handles.changeTimeSliderListener = handle.listener(handles.changeTimeSlider,'ActionEvent',@changeTimeSlider_Callback);
handles.changeTimeSliderListener.Enabled = 'off'; % disactivate the listener for Z=1;
% to transparency sliders
handles.modelTransSliderListener = handle.listener(handles.modelTransSlider,'ActionEvent',@imageRedraw);
handles.modelmaskTransSliderListener = handle.listener(handles.maskTransSlider,'ActionEvent',@imageRedraw);
handles.selectionTransparencySliderListener = handle.listener(handles.selectionTransparencySlider,'ActionEvent',@imageRedraw);
% to the LowLim and HighLim sliders of the BW thresholding
handles.segmLowSliderListener = handle.listener(handles.segmLowSlider,'ActionEvent',@segmBW_Update);
handles.segmHighSliderListener = handle.listener(handles.segmHighSlider,'ActionEvent',@segmBW_Update);
else
% for z-slider
handles.changelayerSliderListener = addlistener(handles.changelayerSlider,'ContinuousValueChange',@changelayerSlider_Callback);
handles.changelayerSliderListener.Enabled = 0; % disactivate the listener for Z=1;
% for t-slider
handles.changeTimeSliderListener = addlistener(handles.changeTimeSlider,'ContinuousValueChange',@changeTimeSlider_Callback);
handles.changeTimeSliderListener.Enabled = 0; % disactivate the listener for Z=1;
% to transparency sliders
handles.modelTransSliderListener = addlistener(handles.modelTransSlider,'ContinuousValueChange',@imageRedraw);
handles.modelmaskTransSliderListener = addlistener(handles.maskTransSlider,'ContinuousValueChange',@imageRedraw);
handles.selectionTransparencySliderListener = addlistener(handles.selectionTransparencySlider,'ContinuousValueChange',@imageRedraw);
% to the LowLim and HighLim sliders of the BW thresholding
handles.segmLowSliderListener = addlistener(handles.segmLowSlider,'ContinuousValueChange',@segmBW_Update);
handles.segmHighSliderListener = addlistener(handles.segmHighSlider,'ContinuousValueChange',@segmBW_Update);
end
% Choose default command line output for im_browser
handles.output = hObject;
% get default or load last session parameters
[handles, start_path] = im_browser_getDefaultParameters(handles);
handles.U = imageUndo(handles.preferences.maxUndoHistory, handles.preferences.max3dUndoHistory); % create instanse for keeping undo information
% resize all elements x1.25 times for macOS
mib_rescaleWidgets(handles.im_browser);
% initializa image buffer with dummy images
handles.Id = 1; % number of the selected buffer
for i=1:8
if handles.preferences.uint8
handles.Img{i}.I = imageData(handles, 'uint8'); % create instanse for keeping images;
else
handles.Img{i}.I = imageData(handles, 'uint6'); % create instanse for keeping images;
end
handles = handles.Img{i}.I.updateAxesLimits(handles, 'resize');
end;
if strcmp(handles.preferences.undo, 'no')
handles.U.enableSwitch = 0;
else
handles.U.enableSwitch = 1;
end
% % adding menus to some widgets
% adding context menu for filesListbox
handles.filesListbox_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.filesListbox_cm, 'Label', 'Combine selected datasets...', 'Callback', {@filesListboxContext_cb, 'load'});
uimenu(handles.filesListbox_cm, 'Label', 'Load part of the dataset (*.am only)...', 'Callback', {@filesListboxContext_cb, 'loadPart'});
uimenu(handles.filesListbox_cm, 'Label', 'Load each N-th dataset...', 'Callback', {@filesListboxContext_cb, 'nth'});
uimenu(handles.filesListbox_cm, 'Label', 'Insert into the open dataset...', 'Callback', {@filesListboxContext_cb, 'insertData'});
uimenu(handles.filesListbox_cm, 'Label', 'Combine files as color channels...', 'Separator', 'on', 'Callback', {@filesListboxContext_cb, 'combinecolors'});
uimenu(handles.filesListbox_cm, 'Label', 'Add as a new color channel...', 'Callback', {@filesListboxContext_cb, 'addchannel'});
uimenu(handles.filesListbox_cm, 'Label', 'Add each N-th dataset as a new color channel...', 'Callback', {@filesListboxContext_cb, 'addchannel_nth'});
uimenu(handles.filesListbox_cm, 'Label', 'Rename selected file...', 'Separator', 'on', 'Callback', {@filesListboxContext_cb, 'rename'});
uimenu(handles.filesListbox_cm, 'Label', 'Delete selected files...', 'Callback', {@filesListboxContext_cb, 'delete'});
uimenu(handles.filesListbox_cm, 'Label', 'File properties', 'Separator', 'on', 'Callback', {@filesListboxContext_cb, 'file_properties'});
set(handles.filesListbox,'uicontextmenu',handles.filesListbox_cm);
% adding context menu for buffer toggles
for i=1:8
eval(sprintf('handles.bufferToggle%d_cm = uicontextmenu(''Parent'', handles.im_browser);', i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Duplicate dataset'', ''Callback'', {@bufferToggles_cb, ''duplicate'',%d});', i, i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Sync view (x,y) with...'', ''Separator'',''on'',''Callback'', {@bufferToggles_cb, ''sync_xy'',%d});', i, i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Sync view (x,y,z) with...'', ''Callback'', {@bufferToggles_cb, ''sync_xyz'',%d});', i, i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Sync view (x,y,z,t) with...'', ''Callback'', {@bufferToggles_cb, ''sync_xyzt'',%d});', i, i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Clear dataset'', ''Separator'',''on'',''Callback'', {@bufferToggles_cb, ''clear'',%d});', i, i));
eval(sprintf('uimenu(handles.bufferToggle%d_cm, ''Label'', ''Clear all stored datasets'', ''Callback'', {@bufferToggles_cb, ''clearAll'',%d});', i, i));
eval(sprintf('set(handles.bufferToggle%d,''uicontextmenu'',handles.bufferToggle%d_cm);', i, i));
end
% adding context menu to ROI List
handles.roiList_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.roiList_cm, 'Label', 'Rename', 'Callback', {@roiList_cm_Callback, 'rename'});
uimenu(handles.roiList_cm, 'Label', 'Edit', 'Callback', {@roiList_cm_Callback, 'edit'});
uimenu(handles.roiList_cm, 'Label', 'Remove', 'Callback', {@roiList_cm_Callback, 'remove'}, 'Separator','on');
set(handles.roiList,'uicontextmenu',handles.roiList_cm);
% adding context menu to pixel information
handles.pixInfo_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.pixInfo_cm, 'Label', 'Jump to...', 'Callback', {@pixInfo_cb, 'jump'});
set(handles.pixelinfoTxt2,'uicontextmenu',handles.pixInfo_cm);
set(handles.pixelinfoTxt,'uicontextmenu',handles.pixInfo_cm);
% adding context menus for Change layer slider
handles.changelayer_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.changelayer_cm, 'Label', 'Default', 'Callback', {@changelayerSliderContext_cb, 'def'});
uimenu(handles.changelayer_cm, 'Label', 'Set step...', 'Callback', {@changelayerSliderContext_cb, 'set'});
set(handles.changelayerSlider,'uicontextmenu',handles.changelayer_cm);
% adding context menus for Min and Max threshold sliders
handles.threshold_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.threshold_cm, 'Label', 'Default', 'Callback', {@changeThresholdValueContext_cb, 'def'});
uimenu(handles.threshold_cm, 'Label', 'Set step...', 'Callback', {@changeThresholdValueContext_cb, 'set'});
set(handles.segmLowSlider,'uicontextmenu',handles.threshold_cm);
set(handles.segmHighSlider,'uicontextmenu',handles.threshold_cm);
% adding context menus for Contrast adjustment
handles.contrast_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.contrast_cm, 'Label', 'Show histogram', 'Callback', {@mib_contrastContext_cb, 'showhist'});
uimenu(handles.contrast_cm, 'Label', 'Contrast-limited adaptive histogram equalization for shown slice', 'Callback', {@mib_contrastContext_cb, 'CLAHE_2D'});
uimenu(handles.contrast_cm, 'Label', 'Contrast-limited adaptive histogram equalization for current stack', 'Callback', {@mib_contrastContext_cb, 'CLAHE_3D'});
uimenu(handles.contrast_cm, 'Label', 'Contrast-limited adaptive histogram equalization for complete volume', 'Callback', {@mib_contrastContext_cb, 'CLAHE_4D'});
set(handles.contrastBtn,'uicontextmenu',handles.contrast_cm);
% adding context menus for Mask Do it button
handles.mask_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.mask_cm, 'Label', 'Do new mask', 'Callback', {@maskGenBtn_Callback, NaN, 'new'});
uimenu(handles.mask_cm, 'Label', 'Generate new mask and add it to the existing mask', 'Callback', {@maskGenBtn_Callback, NaN, 'add'});
set(handles.maskGenBtn,'uicontextmenu',handles.mask_cm);
% adding context menus for Materials table
handles.segmTable_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.segmTable_cm, 'Label', 'Show selected material only', 'Callback', {@model_cm_Callback, 'showselected'});
uimenu(handles.segmTable_cm, 'Label', 'Rename...', 'Separator', 'on', 'Callback', {@model_cm_Callback, 'rename'});
uimenu(handles.segmTable_cm, 'Label', 'Set color...', 'Callback', {@model_cm_Callback, 'set color'});
uimenu(handles.segmTable_cm, 'Label', 'Get statistics...', 'Callback', {@model_cm_Callback, 'statistics'});
h1=uimenu(handles.segmTable_cm,'label','Material to Selection...','Separator','on');
uimenu(h1,'label','NEW (CURRENT)','callback', {@ib_moveLayers, NaN,'model','selection','2D','replace'});
uimenu(h1,'label','ADD (CURRENT)','callback', {@ib_moveLayers, NaN, 'model','selection','2D','add'});
uimenu(h1,'label','REMOVE (CURRENT)','callback', {@ib_moveLayers, NaN,'model','selection','2D','remove'});
uimenu(h1,'label','NEW (ALL SLICES)','Separator','on','callback', {@ib_moveLayers, NaN,'model','selection','3D','replace'});
uimenu(h1,'label','ADD (ALL SLICES)','callback', {@ib_moveLayers, NaN, 'model','selection','3D','add'});
uimenu(h1,'label','REMOVE (ALL SLICES)','callback', {@ib_moveLayers, NaN,'model','selection','3D','remove'});
h2=uimenu(handles.segmTable_cm,'label','Material to Mask...');
uimenu(h2,'label','NEW (CURRENT)','callback', {@ib_moveLayers, NaN,'model','mask','2D','replace'});
uimenu(h2,'label','ADD (CURRENT)','callback', {@ib_moveLayers, NaN, 'model','mask','2D','add'});
uimenu(h2,'label','REMOVE (CURRENT)','callback', {@ib_moveLayers, NaN,'model','mask','2D','remove'});
uimenu(h2,'label','NEW (ALL SLICES)','Separator','on','callback', {@ib_moveLayers, NaN,'model','mask','3D','replace'});
uimenu(h2,'label','ADD (ALL SLICES)','callback', {@ib_moveLayers, NaN, 'model','mask','3D','add'});
uimenu(h2,'label','REMOVE (ALL SLICES)','callback', {@ib_moveLayers, NaN,'model','mask','3D','remove'});
uimenu(handles.segmTable_cm, 'Label', 'Show isosurface (Matlab)...', 'Separator', 'on', 'Callback', {@model_cm_Callback, 'isosurface'});
uimenu(handles.segmTable_cm, 'Label', 'Show as volume (Fiji)...', 'Callback', {@model_cm_Callback, 'volumeFiji'});
uimenu(handles.segmTable_cm, 'Label', 'Unlink material from Add to', 'Separator', 'on', 'Callback', {@model_cm_Callback, 'unlinkaddto'});
set(handles.segmTable, 'uicontextmenu', handles.segmTable_cm);
% adding context menu for Color channels table
handles.channelMixerTable_cm = uicontextmenu('Parent',handles.im_browser);
uimenu(handles.channelMixerTable_cm, 'Label', 'Insert empty channel', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'insert'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Copy channel', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'copy'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Invert channel', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'invert'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Rotate channel', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'rotate'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Swap channels', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'swap'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Delete channel', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'delete'});
uimenu(handles.channelMixerTable_cm, 'Label', 'Set LUT color', 'Callback', {@ib_channelMixerTable_Callback, NaN, 'set color'}, 'Separator','on');
set(handles.channelMixerTable,'uicontextmenu',handles.channelMixerTable_cm);
% set callback for the mode selection in the Mask Generator panel
set(handles.maskGenPanelModeRadioPanel,'SelectionChangeFcn',@maskGenPanelModeRadioPanel_Callback);
set(0,'CurrentFigure',handles.im_browser);
update_drives(handles,start_path,1); % get available disk drives
update_filelist(handles);
%handles = handles.Img{handles.Id}.I.updateAxesLimits(handles, 'resize');
handles = updateGuiWidgets(handles);
handles = handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 1);
%handles.changelayerSliderListener = addlistener(handles.changelayerSlider,'Value','PostSet', @(s,e) changelayerSlider_Callback(handles.changelayerSlider, [], handles));
set(handles.im_browser,'Visible','on');
% remove focus from the menu
uicontrol(handles.updatefilelistBtn);
drawnow;
if exist('frame','var') % put again to the top
frame.show;
frame.toFront();
end
uiwait(handles.im_browser, 1);
% find java object for the segmentation table
userData = get(handles.segmTable,'userData');
userData.jScroll = findjobj(handles.segmTable);
try
userData.jTable = userData.jScroll.getViewport.getComponent(0);
catch err
warndlg('Please wait for MIB to load completely before interacting with the main window!');
sprintf('%s', err.identifier);
sprintf('%s', err.message);
disp(err);
disp('Trying again...')
userData.jScroll = findjobj(handles.segmTable);
userData.jTable = userData.jScroll.getViewport.getComponent(0);
end
userData.jScroll.setVerticalScrollBarPolicy(javax.swing.ScrollPaneConstants.VERTICAL_SCROLLBAR_ALWAYS); % add vertical scroll bar
userData.jTable.setAutoResizeMode(userData.jTable.AUTO_RESIZE_SUBSEQUENT_COLUMNS);
set(handles.segmTable, 'UserData', userData);
% resize the column width
set(handles.segmTable, 'Units', 'Pixels');
tablePosition = get(handles.segmTable, 'position');
currentColWidth = {25, 'auto', 50};
currentColWidth{2} = tablePosition(3)-currentColWidth{1}-currentColWidth{3}-6;
set(handles.segmTable, 'ColumnWidth', currentColWidth);
set(handles.segmTable, 'Units', 'Points');
% add right mouse click callbacks for the sliders of the widgets,
% see more http://undocumentedmatlab.com/blog/setting-listbox-mouse-actions
try
jFilesListbox = findjobj(handles.filesListbox); % jScrollPane
jFilesListbox = jFilesListbox.getVerticalScrollBar;
jFilesListbox = handle(jFilesListbox, 'CallbackProperties');
set(jFilesListbox, 'MousePressedCallback',{@scrollbarClick_Callback, handles.filesListbox, 1});
catch err
sprintf('%s', err.identifier);
disp(err);
end
if exist('frame','var') % close splash window
frame.hide;
clear frame;
end
% UIWAIT makes im_browser wait for user response (see UIRESUME)
%uiwait(handles.im_browser);
end
% --- Outputs from this function are returned to the command line.
function varargout = im_browser_OutputFcn(~, ~, handles)
% Get default command line output from handles structure
varargout{1} = handles.output;
end
function drivePopup_Callback(hObject, eventdata, handles)
% change the logical drive
drives = get(handles.drivePopup,'String');
if ischar(class(drives(1))); drives = cellstr(drives); end;
value = get(handles.drivePopup,'Value');
handles.mypath = cell2mat(drives(value));
set(handles.pathEdit,'String',drives(value));
update_filelist(handles);
end
function folderselectBtn_Callback(~, ~, handles)
% directory selection via GUI tool
dirname = uigetdir(get(handles.pathEdit, 'String'),'Choose Directory');
if ischar(dirname)
handles.mypath = dirname;
set(handles.pathEdit,'String',dirname);
update_filelist(handles);
drives = get(handles.drivePopup,'String');
if ischar(class(drives(1))); drives = cellstr(drives); end;
if ispc()
for i = 1:numel(drives)
if strcmpi(cell2mat(drives(i)),dirname(1:2))
set(handles.drivePopup,'Value',i);
return;
end
end
end
end
guidata(handles.im_browser, handles);
end
function updatefilelistBtn_Callback(~, ~, handles)
% manually update the list of file in the current directory
update_filelist(handles);
guidata(handles.im_browser, handles);
end
function im_filterPopup_Callback(~, ~, handles)
% Filter the files with a new selected extension
update_filelist(handles);
end
function segmShowTypePopup_Callback(~, ~, handles)
% Toggle model shape: filled/countour
if strcmp(handles.Img{handles.Id}.I.model_type,'uint8') || strcmp(handles.Img{handles.Id}.I.model_type,'uint6')
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
end
% can't take to a separate file due to imageRedraw function
function addMaterialBtn_Callback(hObject, eventdata, handles)
% Add a new object to a model
unFocus(hObject); % remove focus from hObject
% do nothing is selection is disabled
if strcmp(handles.preferences.disableSelection, 'yes')
warndlg(sprintf('The models are switched off!\n\nPlease make sure that the "Disable selection" option in the Preferences dialog (Menu->File->Preferences) is set to "no" and try again...'),'The models are disabled');
return;
end;
list = handles.Img{handles.Id}.I.modelMaterialNames;
if isempty(list); list = cell(0); end; % remove empty entry from the list
number = numel(list);
answer = mib_inputdlg(handles, sprintf('Please add a new name for this material:'),'Rename material', num2str(number+1));
if ~isempty(answer)
list(end+1,1) = cellstr(answer(1));
else
return;
end
if ~handles.Img{handles.Id}.I.modelExist
createModelBtn_Callback(handles.createModelBtn,eventdata, handles); % make an empty model
end
handles.Img{handles.Id}.I.modelMaterialNames = list;
handles.Img{handles.Id}.I.generateModelColors();
userData = get(handles.segmTable, 'UserData');
userData.prevAddTo = numel(list)+2;
userData.prevMaterial = numel(list)+2;
set(handles.segmTable, 'UserData',userData);
updateSegmentationTable(handles);
imageRedraw(hObject, NaN, handles);
guidata(handles.im_browser, handles);
end
function magicwandConnectCheck_Callback(~, ~, handles)
% --- Executes on button press in magicwandConnectCheck.
set(handles.magicwandConnectCheck4,'Value',0);
end
% --- Executes on selection change in filterTypePopup.
function filterTypePopup_Callback(~, ~, handles)
pos = get(handles.filterTypePopup,'Value');
fulllist = get(handles.filterTypePopup,'String');
text_str = fulllist{pos};
set(handles.maskGeneratorsPanel,'Visible','off');
set(handles.corrPanel,'Visible','off');
set(handles.fijiPanel,'Visible','off');
set(handles.backgroundPanel,'Visible','off');
set(handles.imageFiltersPanel,'Visible','off');
switch text_str
case 'Image Filters'
set(handles.imageFiltersPanel,'Visible','on');
case 'Mask generators'
set(handles.maskGeneratorsPanel,'Visible','on');
case 'Correlation analysis'
set(handles.corrPanel,'Visible','on');
case 'Fiji connect' % connect to Fiji
set(handles.fijiPanel,'Visible','on');
case 'Background removal' % background removal
set(handles.backgroundPanel,'Visible','on');
end
end
function mainPanPopup_Callback(~, ~, handles)
% update panels after mainPanPopup change
pos = get(handles.mainPanPopup,'Value');
switch pos
case 1 % Segmentation
set(handles.segmentationPanel,'Visible','on');
set(handles.roiPanel,'Visible','off');
case 2 % ROI
set(handles.segmentationPanel,'Visible','off');
set(handles.roiPanel,'Visible','on');
end
end
function brightnessBtn_Callback(~, ~, handles)
% Auto brightness Rment
handles = ib_autoBrightness(handles);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function roiList_Callback(~, eventdata, handles)
% show selected ROI
set(handles.roiShowCheck,'Value',1);
roiShowCheck_Callback(handles.roiShowCheck, eventdata, handles);
end
function bioformatsCheck_Callback(~, ~, handles)
% Bioformats that can be read with loci toolbox
val = get(handles.bioformatsCheck,'Value');
position = handles.im_filterLast;
handles.im_filterLast = get(handles.im_filterPopup,'Value');
if val == 1 % use bioformats reader
extentions = {'mov','pic','ics','ids','lei','stk','nd','nd2','sld','pict'...
,'lsm','mdb','psd','img','hdr','svs','dv','r3d','dcm','dicom','fits','liff'...
,'jp2','lif','l2d','mnc','mrc','oib','oif','pgm','zvi','gel','ims','dm3','naf'...
,'seq','xdce','ipl','mrw','mng','nrrd','ome','amiramesh','labels','fli'...
,'arf','al3d','sdt','czi','c01','flex','ipw','raw','ipm','xv','lim','nef','apl','mtb'...
,'tnb','obsep','cxd','vws','xys','xml','dm4'};
extentions = ['all known',sort(extentions)];
set(handles.im_filterPopup,'String',extentions);
set(handles.im_filterPopup,'Value',position);
else
image_formats = imformats; % get readable image formats
if handles.matlabVersion < 8.0
video_formats = mmreader.getFileFormats(); %#ok<DMMR> % get readable image formats
else
video_formats = VideoReader.getFileFormats(); % get readable image formats
end
extentions = ['all known' sort([image_formats.ext 'mrc' 'rec' 'am' 'nrrd' 'h5' 'xml' 'st' 'preali' {video_formats.Extension}])];
set(handles.im_filterPopup,'String',extentions);
set(handles.im_filterPopup,'Value',position);
end
update_filelist(handles);
guidata(handles.im_browser, handles);
end
function AdaptiveDilateCheck_Callback(~, ~, handles)
% Enable/disable adaptive coefficient edit box
if get(handles.AdaptiveDilateCheck,'Value') == 1
set(handles.dilateAdaptCoefEdit,'Enable','on');
set(handles.adaptiveSmoothCheck,'Enable','on');
else
set(handles.dilateAdaptCoefEdit,'Enable','off');
set(handles.adaptiveSmoothCheck,'Enable','off');
end
end
function changelayerSliderContext_cb(hObject, ~, parameter)
handles = guidata(hObject);
switch parameter
case 'def' % set brightness on the screen to be the same as in the image
handles.sliderStep = 1; % parameters for slider movement
handles.sliderShiftStep = 10;
case 'set'
prompt = {'Enter step for use with arrows or Q/W buttons:','Enter step for use with Shift+arrows or Shift+Q/W buttons:'};
def = {num2str(handles.sliderStep),num2str(handles.sliderShiftStep)};
answer = inputdlg(prompt,'Set step...',1,def);
if isempty(answer); return; end;
handles.sliderStep = round(str2double(cell2mat(answer(1)))); % parameters for slider movement
handles.sliderShiftStep = round(str2double(cell2mat(answer(2))));
end
guidata(handles.im_browser, handles);
end
function changeThresholdValueContext_cb(hObject, ~, parameter)
handles = guidata(hObject);
switch parameter
case 'def' % set brightness on the screen to be the same as in the image
set(handles.segmLowSlider, 'SliderStep', [0.01 0.1]);
set(handles.segmHighSlider, 'SliderStep', [0.01 0.1]);
case 'set'
sliderStep = get(handles.segmLowSlider, 'SliderStep');
prompt = {'Enter step the step for the slider:'};
maxVal = double(intmax(class(handles.Img{handles.Id}.I.img)));
defaultAnswer = {num2str(round(sliderStep(1)*maxVal))};
%answer = inputdlg(prompt,'Set step...',1,defaultAnswer);
answer = mib_inputdlg(handles, prompt, 'Set step...', defaultAnswer);
if isempty(answer); return; end;
if str2double(answer{1})/maxVal > 1 || str2double(answer{1}) <= 0
errordlg(sprintf('The step should be between 1 and %d!', maxVal),'Wrong step!');
return;
end
set(handles.segmLowSlider, 'SliderStep', [str2double(answer{1})/maxVal str2double(answer{1})/maxVal*10]);
set(handles.segmHighSlider, 'SliderStep', [str2double(answer{1})/maxVal str2double(answer{1})/maxVal*10]);
end
end
function magicwandConnectCheck4_Callback(~, ~, handles)
% --- Executes on button press in magicwandConnectCheck4.
set(handles.magicwandConnectCheck,'Value',0);
end
function contrastBtn_Callback(~, ~, handles)
% Contrast button callback
handles = ib_linearContrast(handles);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function backgroundProfileChk_Callback(~, ~, handles)
% defines whether to show a profile after background removal for a certatin row
if get(handles.backgroundProfileChk,'Value')
set(handles.backgroundProfileLineEdit,'Enable','on');
val = str2double(get(handles.backgroundProfileLineEdit,'String'));
if val > size(handles.Img{handles.Id}.I.img,1)
val = size(handles.Img{handles.Id}.I.img,1)/2;
set(handles.backgroundProfileLineEdit,'String',num2str(val));
end;
else
set(handles.backgroundProfileLineEdit,'Enable','off');
end
end
% --- Executes on button press in backgroundRemoveBtn.
function backgroundRemoveBtn_Callback(~, ~, handles)
if handles.Img{handles.Id}.I.orientation ~= 4;
msgbox('Please rotate the dataset to the XY orientation!','Error!','error','modal');
return;
end
handles = ib_removeBackground(handles);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function bwFilterGridCheck_Callback(hObject, ~, handles)
% black and white filter grid check callback
val = get(hObject, 'value');
set(handles.bwConversionCoefTxt,'Visible','off');
set(handles.bwConversionCoefEdit,'Visible','off');
if strcmp(get(hObject,'tag'),'bwFilterGridCheck') && val == 1
set(handles.bwConversionCoefTxt,'Visible','on');
set(handles.bwConversionCoefEdit,'Visible','on');
set(handles.bwFilterThrasMinEdit,'String', '0');
set(handles.bwFilterThrasMaxEdit,'String', '0');
set(handles.bwFilterManGridCheck,'Value',0);
elseif strcmp(get(hObject,'tag'),'bwFilterManGridCheck') && val == 1
set(handles.bwFilterGridCheck,'Value',0);
end
if val == 1
%answer = inputdlg('Input square grid size, px','Grid settings',1,cellstr(num2str(handles.corrGridrunSize)));
answer = mib_inputdlg(handles, 'Input square grid size, px', 'Grid settings', num2str(handles.corrGridrunSize));
if isempty(answer)
set(handles.corrGridrunCheck,'Value',0);
return;
end
handles.corrGridrunSize = str2double(cell2mat(answer));
end
guidata(handles.im_browser, handles);
end
function menuSelectionSizeFilter(~, ~, handles, type)
% - Run size exclusion filter -
% do nothing is selection is disabled
if strcmp(handles.preferences.disableSelection, 'yes');
warndlg(sprintf('The selection layer is switched off!\n\nPlease make sure that the "Disable selection" option in the Preferences dialog (Menu->File->Preferences) is set to "no" and try again...'),'The selection layer is disabled','modal');
return;
end;
handles = ib_sizeExclusionFilter(handles, type);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function imAdjustBtn_Callback(~, ~, handles)
% Open image adjustments dialog
if strcmp(handles.Img{handles.Id}.I.img_info('ColorType'),'indexed')
msgbox(sprintf('Please convert to grayscale or truecolor data format first!\nMenu->Image->Mode->'),'Change format!','error','modal');
return;
end
imAdjustments(handles);
guidata(handles.im_browser, handles);
end
% --- Executes on button press in backgroundLocNormSw.
function backgroundLocNormSw_Callback(hObject, eventdata, handles)
if get(handles.backgroundLocNormSw,'Value')
else
set(handles.backgroundStrelSmoothingChk,'Value',1);
backgroundStrelSmoothingChk_Callback(handles.backgroundStrelSmoothingChk, NaN, handles);
end
end
function anDiffDoBtn_Callback(~, ~, handles)
% Filter image with coherence filter, anisotropic diffusion
handles = ib_anisotropicDiffusion(handles, 'coherence_filter');
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function handles = anDiffOptionsBtn_Callback(~, ~, handles)
% Update Paramters for Coherence filter, anisotropic diffusion
anDiffOptionsDlg('options', NaN);
end
function anDiffTestrunBtn_Callback(~, ~, handles)
% Do a test run of image filtering with coherence filter, anisotropic diffusion
handles = ib_anisotropicDiffusion(handles, 'coherence_filter_test');
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
function corrModeCombo_Callback(~, ~, handles)
% --- Executes on selection change in corrModeCombo.
contents = cellstr(get(handles.corrModeCombo,'String'));
selmode = contents{get(handles.corrModeCombo,'Value')};
if strcmp(selmode,'Absolute')
set(handles.corrAbsvsEdit,'Enable','on');
set(handles.vsText,'Enable','on');
else
set(handles.corrAbsvsEdit,'Enable','off');
set(handles.vsText,'Enable','off');
end;
end
function corrManualRadio_Callback(hObject, ~, handles)
% --- Executes on button press in corrManualRadio.
val = get(handles.corrManualRadio,'Value');
if val == 1
set(handles.corrManualThresEdit,'Enable','on');
else
set(handles.corrManualThresEdit,'Enable','off');
end
if get(hObject,'Value') == 0
set(hObject,'Value',1);
end
end
function corrCalculateButton_Callback(~, ~, handles)
% Calculate correlation coefficients between
handles = ib_calcCorrelation(handles);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
% --- Executes on button press in corrGridCheck.
function corrGridCheck_Callback(~, ~, handles)
val = get(handles.corrGridCheck,'Value');
if val == 1
%answer = inputdlg('Input square grid size, px','Grid settings',1,cellstr(num2str(handles.corrGridrunSize)));
answer = mib_inputdlg(handles, 'Input square grid size, px', 'Grid settings', num2str(handles.corrGridrunSize));
if isempty(answer)
set(handles.corrGridrunCheck,'Value',0);
return;
end
handles.corrGridrunSize = str2double(cell2mat(answer));
end
guidata(handles.im_browser, handles);
end
function corrTypeCombo_Callback(~, ~, handles)
% --- Executes on selection change in corrTypeCombo.
selected = get(handles.corrTypeCombo,'Value');
list_of_options = get(handles.corrTypeCombo,'String');
if strcmp(list_of_options{selected}, 'Image Displacement')
set(handles.corrMaskRadio,'Enable','off');
set(handles.corrAutoRadio,'Enable','off');
set(handles.corrManualRadio,'Value',1);
set(handles.corrManualThresEdit,'Enable','on');
else
set(handles.corrMaskRadio,'Enable','on');
set(handles.corrAutoRadio,'Enable','on');
end
end
function corrAbsvsEdit_Callback(~, eventdata, handles)
% --- Executes on selection change in corrAbsvsEdit_Callback.
status = editbox_Callback(handles.corrAbsvsEdit,eventdata,handles,'pint','1',[1 handles.Img{handles.Id}.I.no_stacks]);
if status == 0
return;
end;
end
function handles = getMaskStats(handles)
% calculate statistics of objects in the Mask/Model layers
wb = waitbar(0, 'Calculating statistics, please wait...','WindowStyle','modal');
getDataOptions.blockModeSwitch = 0;
if get(handles.segmMaskClickModelCheck, 'value')
type = 'model';
userData = get(handles.segmTable,'UserData');
colchannel = userData.prevMaterial - 2;
if colchannel < 0; % do not continue when All is selected
msgbox(sprintf('Please select Material in the ''Select from list'' and press the ''Recalc.'' button in the Segmentation panel, Object Picker tool again!'),'Warning!','warn');
delete(wb);
return;
end
else
type = 'mask';
colchannel = 0;
end
if get(handles.magicwandConnectCheck4,'Value')
connectionType = 6; % 6-neighbour points
else
connectionType = 26; % 26-neighbour points
end
handles.Img{handles.Id}.I.maskStat = bwconncomp(handles.Img{handles.Id}.I.getData3D(type, NaN, 4, colchannel, getDataOptions), connectionType);
handles.Img{handles.Id}.I.maskStat.L = labelmatrix(handles.Img{handles.Id}.I.maskStat); % create a label matrix for fast search of the indices
handles.Img{handles.Id}.I.maskStat.bb = regionprops(handles.Img{handles.Id}.I.maskStat, 'BoundingBox'); % create a label matrix for fast search of the indices
handles.Img{handles.Id}.I.maskStat = rmfield(handles.Img{handles.Id}.I.maskStat, 'PixelIdxList'); % remove PixelIdxList it is not needed anymore
guidata(handles.im_browser, handles);
delete(wb);
end
function maskRecalcStatsBtn_Callback(~, ~, handles)
% recalculate Mask statistics for right mouse selection
tic
getMaskStats(handles);
toc
end
function maskGenTypePopup_Callback(~, ~, handles)
% --- Executes on selection change in maskGenTypePopup.
pos = get(handles.maskGenTypePopup,'Value');
fulllist = get(handles.maskGenTypePopup,'String');
text_str = fulllist{pos};
set(handles.frangiPanel,'Visible','off');
set(handles.strelPanel,'Visible','off');
set(handles.bwFilterPanel,'Visible','off');
set(handles.morphPanel,'Visible','off');
set(handles.maskGenPanel3DAllRadio, 'enable', 'on');
switch text_str
case 'Frangi filter'
set(handles.maskGeneratorsPanel,'Title','Mask generators (Frangi filter)');
set(handles.frangiPanel,'Visible','on');
case 'Strel filter'
set(handles.maskGeneratorsPanel,'Title','Mask generators (Strel filter)');
set(handles.strelPanel,'Visible','on');
case 'BW thresholding'
set(handles.maskGeneratorsPanel,'Title','Mask generators (BW threshold filter)');
set(handles.bwFilterPanel,'Visible','on');
set(handles.maskGenPanel3DAllRadio, 'enable', 'off');
set(handles.maskGenPanel2DCurrentRadio, 'value', 1);
case 'Morphological filters'
set(handles.maskGeneratorsPanel,'Title','Mask generators (Morphological filters)');
set(handles.morphPanel,'Visible','on');
end
end
function maskGenBtn_Callback(hObject, ~, ~, type)
% Automatic generation of the Mask layer
handles = guidata(hObject);
handles = ib_maskGenerator(handles, type);
handles.Img{handles.Id}.I.maskExist = 1;
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
listing = get(handles.seltypePopup,'String');
if strcmp(listing(get(handles.seltypePopup,'Value')),'Mask');
getMaskStats(handles); % get shapes statistics
end;
end
function logBtn_Callback(~, ~, handles)
% Show Log list window
logList(handles);
guidata(handles.im_browser, handles);
end
% --- Executes on button press in adaptiveSmoothCheck.
function adaptiveSmoothCheck_Callback(hObject, eventdata, handles)
if get(handles.adaptiveSmoothCheck, 'Value')
%answer = inputdlg('Enter the smoothing factor value, (>2)','Smoothing factor',1,{num2str(handles.adaptiveSmoothingFactor)});
answer = mib_inputdlg(handles, 'Enter the smoothing factor value, (>2)', 'Smoothing factor', num2str(handles.adaptiveSmoothingFactor));
if isempty(answer); return; end;
handles.adaptiveSmoothingFactor = str2double(answer{1});
guidata(handles.im_browser, handles);
end
end
% --- Executes when entered data in editable cell(s) in channelMixerTable.
function channelMixerTable_CellEditCallback(hObject, eventdata, handles)
% hObject handle to channelMixerTable (see GCBO)
% eventdata structure with the following fields (see UITABLE)
% 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)
data = get(handles.channelMixerTable,'Data');
selected = find(cell2mat(data(:,2))==1)';
if isempty(selected);
data{eventdata.Indices(1), 2} = eventdata.PreviousData;
set(handles.channelMixerTable,'Data', data);
return;
end;
if strcmp(get(handles.im_browser,'currentModifier'), 'control') % toggle between two color channels using the Ctrl modifier
for i=1:size(data,1); data{i,2} = 0; end; % clear selected channels
data{eventdata.Indices(1,1),2} = 1;
set(handles.channelMixerTable,'data', data);
end
handles.Img{handles.Id}.I.slices{3} = find(cell2mat(data(:,2))==1)';
if numel(handles.Img{handles.Id}.I.slices{3}) == 1
set(handles.ColChannelCombo, 'value', handles.Img{handles.Id}.I.slices{3}+1); % update color channel combo box in the Selection panel
end
redrawChannelMixerTable(handles);
handles.Img{handles.Id}.I.plotImage(handles.imageAxes, handles, 0);
end
% --- Executes on button press in segmTrackStraightChk.
function segmTrackStraightChk_Callback(hObject, eventdata, handles)
val = get(handles.segmTrackStraightChk, 'Value');
if val == 1
set(handles.segmTracScaleEdit, 'Enable', 'off');
set(handles.segmTrackBlackChk, 'Enable', 'off');
else
set(handles.segmTracScaleEdit, 'Enable', 'on');
set(handles.segmTrackBlackChk, 'Enable', 'on');
end
end
% --- Executes during object deletion, before destroying properties.
function im_browser_DeleteFcn(hObject, eventdata, handles)
global running;
running = 0;