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AxonSeg.m
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AxonSeg.m
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function varargout = AxonSeg(varargin)
% AxonSeg: Axon Segmentation Toolbox
% AxonSeg() starts the Graphical User Interface (GUI)
%
% AxonSeg( fname ) starts the GUI and load image fname (e.g. image.tif)
% AxonSeg( fname, SegParameters ) load the parameters from SegParameters
% file (e.g. SegParameters.mat)
% AxonSeg( fname, SegParameters, '-nogui' ) starts the segmentation
% of the myelin (nogui)
% AxonSeg( fname, SegParameters, '-nogui', '-skipmyelin' ) starts the segmentation
% of the axons only (nogui)
% AxonSeg( {fname, axon_mask_fname}, SegParameters, '-nogui' ) starts the
% myelin segmentation
% ----------------------------------------------------------------------------------------------------
% Example:
% Segment and generate a SegParameters.mat file:
% AxonSeg test_image_OM_2.tif
%
% Segment a new image using the same SegParameters:
% AxonSeg test_image_OM_2.tif SegParameters.mat -nogui
%
% Segment myelin using a corrected axon mask:
% AxonSeg({'RawImage.tif','Seg_mask_axon_corr.tif'}, 'SegParameters.mat', '-nogui')
% ----------------------------------------------------------------------------------------------------
%
% Reference: Zaimi A, Duval T, Gasecka A, Cote D, Stikov N and Cohen-Adad J (2016). AxonSeg: open source software for axon and myelin segmentation and morphometric analysis. Front. Neuroinform. 10:37. doi: 10.3389/fninf.2016.00037
% Copyright (c) 2016 NeuroPoly (Polytechnique Montreal) and DCClab (Universite Laval)
%
% See Also : as_Segmentation_full_image, myelinInitialSegmention
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @AxonSeg_OpeningFcn, ...
'gui_OutputFcn', @AxonSeg_OutputFcn, ...
'gui_LayoutFcn', [], ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if ~nargin
FileName= uigetimagefile_v2;
if isempty(FileName), return; end
varargin{1}=FileName;
end
nogui = strcmp(varargin,'-nogui');
if nargin>2 && max(nogui)
varargin(nogui) = [];
skipmyelin = strcmp(varargin,'-skipmyelin');
if max(skipmyelin)
varargin(skipmyelin) = [];
as_Segmentation_full_image(varargin{1},varargin{2},[],[],[],true)
else
as_Segmentation_full_image(varargin{:})
end
return;
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 AxonSeg is made visible.
function AxonSeg_OpeningFcn(hObject, eventdata, handles, varargin)
% read input
handles.varargin=varargin{1};
set(handles.go_full_image,'String', '<html>Segment full image <br>(uncropped)</html>');
[handles.outputdir,handles.fname]=fileparts(handles.varargin); if isempty(handles.outputdir), handles.outputdir=[pwd filesep]; else handles.outputdir = [handles.outputdir, filesep]; end
handles.fname = matlab.lang.makeValidName(handles.fname);
if length(varargin)>1, LoadSegParam_Callback(hObject, eventdata, handles, varargin{2}); end
% read image
if ~isfield(handles,'data') || ~isfield(handles.data,'raw')
handles.data.raw=imresize(imread(handles.varargin),2);
end
handles.data.img=handles.data.raw;
if length(size(handles.data.img))==3
handles.data.img=rgb2gray(handles.data.img(:,:,1:3));
end
axes(handles.plotseg);
handles.reducefactor=max(1,floor(size(handles.data.img,1)/1000));
imshow(handles.data.img(1:handles.reducefactor:end,1:handles.reducefactor:end));
% undock figure
set(gcf,'windowstyle','modal');
set(gcf,'windowstyle','normal');
% Update handles structure
set(gcf,'windowStyle','normal');
movegui(gcf,'center')
guidata(hObject, handles);
% --- Outputs from this function are returned to the command line.
function AxonSeg_OutputFcn(hObject, eventdata, handles)
% --- Executes on slider movement.
function Transparency_Callback(hObject, eventdata, handles)
if handles.display.type==2
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
else
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
end
guidata(hObject, handles);
function PixelSize_Callback(hObject, eventdata, handles)
px_tmp=str2num(get(hObject,'String'));
if max(isempty(px_tmp)) || (length(px_tmp(:))>1) %if text --> put default value
set(hObject,'String',num2str(get(hObject,'Value')));
else
set(hObject,'Value',px_tmp);
end
handles.segParam.PixelSize=str2num(get(handles.PixelSize,'String'));
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function PixelSize_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in PixelSize_button.
function PixelSize_button_Callback(hObject, eventdata, handles)
% hObject handle to PixelSize_button (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
PixelSize=as_improc_pixelsize/handles.reducefactor;
PixelSize = PixelSize*2; % Image is oversampled by 2 in AxonSeg.
if PixelSize
set(handles.PixelSize,'String',PixelSize);
set(handles.PixelSize,'Value',PixelSize);
end
handles.segParam.PixelSize=str2num(get(handles.PixelSize,'String'));
guidata(hObject, handles);
% --- Executes on button press in cropImage.
function cropImage_Callback(hObject, eventdata, handles)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.histEq, handles.invertColor, handles.Smoothing, handles.Go_0_to_1, handles.resetStep0, handles.Deconv];
set(handleArray,'Enable','off');
drawnow;
handles.data.img=as_improc_cutFromRect(handles.data.img, handles.reducefactor);
axes(handles.plotseg);
handles.reducefactor=max(1,floor(size(handles.data.img,1)/1000)); % Max 1000 pixels size set for imshow
imshow(handles.data.img(1:handles.reducefactor:end,1:handles.reducefactor:end));
set(handleArray,'Enable','on');
guidata(hObject, handles);
function show_pre_process(handles)
% function that controls the pre-processing options of the GUI and updates
% the displays
im_pre=handles.data.img;
if get(handles.invertColor,'Value')==1
im_pre=imcomplement(handles.data.img);
end
if get(handles.histEq,'Value')==1
im_pre=histeq(im_pre,1);
end
if get(handles.Smoothing,'Value')==1
im_pre=as_gaussian_smoothing(im_pre);
end
axes(handles.plotseg);
imshow(im_pre(1:handles.reducefactor:end,1:handles.reducefactor:end));
% --- Executes on button press in invertColor.
function handles=invertColor_Callback(hObject, eventdata, handles)
show_pre_process(handles);
guidata(hObject, handles);
% --- Executes on button press in histEq.
function handles=histEq_Callback(hObject, eventdata, handles)
show_pre_process(handles);
guidata(hObject, handles);
% --- Executes on button press in Smoothing.
function Smoothing_Callback(hObject, eventdata, handles)
show_pre_process(handles);
guidata(hObject,handles);
% --- Executes on slider movement.
function Deconv_Callback(hObject, eventdata, handles)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.histEq, handles.invertColor, handles.Smoothing, handles.Go_0_to_1, handles.resetStep0, handles.cropImage];
set(handleArray,'Enable','off');
drawnow;
fprintf('*** Warning *** : Computing deconvolution. This may take time. Please wait. \n');
tic;
set(handles.Deconv,'Value',round(get(handles.Deconv,'Value'))); % ensure int
tmp=handles.data.img;
if get(handles.invertColor,'Value'), tmp=imcomplement(tmp); end
if get(handles.Smoothing,'Value'), tmp=as_gaussian_smoothing(tmp); end
if get(handles.histEq,'Value'), tmp=histeq(tmp,get(handles.histEq,'Value')); end
% if get(handles.histEq,'Value'), tmp=histeq(handles.data.img,1); else tmp=handles.data.img; end
tmp=Deconv(tmp,get(handles.Deconv,'Value'));
axes(handles.plotseg);
imshow(tmp(1:handles.reducefactor:end,1:handles.reducefactor:end));
toc;
set(handleArray,'Enable','on');
guidata(hObject, handles);
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% --- Executes during object creation, after setting all properties.
function Deconv_CreateFcn(hObject, eventdata, handles)
% hObject handle to Deconv (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 roi_add.
function roi_add_Callback(hObject, eventdata, handles)
% hObject handle to roi_add (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[~, roi]=as_tools_getroi(handles.data.img);
handles.data.img(~roi)=0;
axes(handles.plotseg)
imshow(handles.data.img(1:handles.reducefactor:end,1:handles.reducefactor:end));
guidata(hObject, handles);
% --- Executes on button press in cut_greymatter.
function roi_substract_Callback(hObject, eventdata, handles)
% hObject handle to cut_greymatter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[~, roi]=as_tools_getroi(handles.data.img);
handles.data.img(roi)=0;
axes(handles.plotseg)
imshow(handles.data.img(1:handles.reducefactor:end,1:handles.reducefactor:end));
guidata(hObject, handles);
% --- Executes on button press in Go_0_to_1.
function Go_0_to_1_Callback(hObject, eventdata, handles)
handles.data.Step1=handles.data.img;
if get(handles.invertColor,'Value'), handles.data.Step1=imcomplement(handles.data.Step1); end
if get(handles.Smoothing,'Value'), handles.data.Step1=as_gaussian_smoothing(handles.data.Step1); end
if get(handles.histEq,'Value'), handles.data.Step1=histeq(handles.data.Step1,get(handles.histEq,'Value')); end
handles.data.Step1=Deconv(handles.data.Step1,get(handles.Deconv,'Value'));
imshow(handles.data.Step1(1:handles.reducefactor:end,1:handles.reducefactor:end));
% set(handles.panel_LS, 'Visible', 'on');
set(handles.uipanel1, 'Visible', 'on');
set(handles.uipanel0, 'Visible', 'off');
guidata(hObject, handles);
% --- Executes on button press in resetStep0.
function resetStep0_Callback(hObject, eventdata, handles)
AxonSeg_OpeningFcn(hObject, eventdata, handles, handles.varargin)
function LoadSegParam_Callback(hObject, eventdata, handles, Param_fname)
% Select segmentation parameters file to load
if ~exist('Param_fname','var') || ~exist(Param_fname,'file')
[FileName,PathName] = uigetfile('*.mat*','Select the segmentation parameters you want to use');
else
[PathName,FileName] = fileparts(Param_fname);
end
segparam_filepath = [PathName FileName];
load(segparam_filepath);
% Get parameters from a SegParameters file
set(handles.PixelSize,'String',SegParameters.PixelSize)
set(handles.invertColor,'Value',SegParameters.invertColor);
set(handles.histEq,'Value',SegParameters.histEq);
set(handles.Deconv,'Value',SegParameters.Deconv);
set(handles.Smoothing,'Value',SegParameters.Smoothing);
set(handles.initSeg,'Value',SegParameters.initSeg);
set(handles.diffMaxMin,'Value',SegParameters.diffMaxMin);
set(handles.threshold,'Value',SegParameters.threshold);
set(handles.minSize,'Value',SegParameters.minSize);
set(handles.Solidity,'Value',SegParameters.Solidity);
set(handles.Ellipticity,'Value',SegParameters.Ellipticity);
if isfield(SegParameters,'parameters')
handles.parameters=SegParameters.parameters;
if isfield(SegParameters,'DA_classifier')
handles.classifier_final=SegParameters.DA_classifier;
end
end
% Update handles
guidata(hObject,handles);
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
%%%------------------- STEP 1 ------------------------------------------%%%
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% --- Executes on slider movement.
function initSeg_Callback(hObject, eventdata, handles)
% hObject handle to initSeg (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.diffMaxMin, handles.Go_1_to_2, handles.resetStep1];
set(handleArray,'Enable','off');
drawnow;
%--------------------------------------------------------------------------
tmp=initseg(handles.data.Step1, get(handles.initSeg,'Value'));
tmp=imfill(tmp,'holes'); %imshow(initialBW)
%--------------------------------------------------------------------------
axes(handles.plotseg)
% -1-
handles.display.opt1=[1 1 0];
handles.display.seg1=tmp;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% example inputs: transparency=get(handles.Transparency,'Value'), img=handles.data.img,
% seg1=handles.display.seg1, opt1=handles.display.opt1, ...
% sc(get(handles.Transparency,'Value')*sc(tmp,'y',tmp)+sc(handles.data.Step1));
% imshow(imfuse(handles.data.Step1,tmp))
set(handleArray,'Enable','on');
guidata(hObject, handles);
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
% Function initseg
function im_out=initseg(im_in,heigthThresh)
% Performs initial segmentation of axons & outputs the resulting image
% (binary image with axon separation vs background)
[im_out, handles.data.initialRejectBW] = axonInitialSegmentation(im_in, heigthThresh);
% --- Executes when user moves the diffmaxMin slider
function diffMaxMin_Callback(hObject, eventdata, handles)
% hObject handle to diffMaxMin (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.initSeg, handles.Go_1_to_2, handles.resetStep1];
set(handleArray,'Enable','off');
drawnow;
% Perform initial segmentation of the axons based on diffMaxMin value
tmp=initseg(handles.data.Step1, get(handles.diffMaxMin,'Value'));
% Show updated axon segmentation on screen
axes(handles.plotseg);
handles.display.opt1=[1 1 0];
handles.display.seg1=tmp;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% -1-
% sc(get(handles.Transparency,'Value')*sc(tmp,'y',tmp)+sc(handles.data.Step1));
% imshow(imfuse(handles.data.Step1,tmp));
set(handleArray,'Enable','on');
% Update handles
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function diffMaxMin_CreateFcn(hObject, eventdata, handles)
% hObject handle to diffMaxMin (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 threshold_Callback(hObject, eventdata, handles)
% hObject handle to threshold (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
tmp=handles.data.Step1<prctile(handles.data.Step1(:),100*get(handles.threshold,'Value'));
tmp=bwmorph(tmp,'fill'); tmp=bwmorph(tmp,'close'); tmp=bwmorph(tmp,'hbreak'); tmp = bwareaopen(tmp,5); %imshow(tmp)
% -4-
handles.display.opt1=[1 1 0];
handles.display.seg1=tmp;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% --- Executes on button press in Go_1_to_2.
function Go_1_to_2_Callback(hObject, eventdata, handles)
handles.data.Step2_seg=step1(handles);
[handles.stats_step2, handles.stats_cc]=axon_stats_step2(handles.data.Step2_seg);
%--------------------------------------------------------------------------
axes(handles.plotseg);
handles.display.opt1=[1 1 0];
handles.display.seg1=handles.data.Step2_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
guidata(hObject, handles);
fprintf('Step 1 Done \n');
% set(handles.panel_LS, 'Visible', 'off');
set(handles.uipanel2, 'Visible', 'on');
set(handles.uipanel1, 'Visible', 'off');
set(handles.text_legend, 'Visible','on');
guidata(hObject, handles);
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in resetStep1.
function resetStep1_Callback(hObject, eventdata, handles)
axes(handles.plotseg);
imshow(handles.data.img(1:handles.reducefactor:end,1:handles.reducefactor:end));
set(handles.uipanel0, 'Visible', 'on')
set(handles.uipanel1, 'Visible', 'off')
guidata(hObject, handles);
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
%%%------------------- STEP 2 ------------------------------------------%%%
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% --- Executes on button press in Go_2_to_3.
function Go_2_to_3_Callback(hObject, eventdata, handles)
% DO SAVE HERE FOR INITIAL SEG IMAGE---------------------------------------
handles.data.Step3_seg=step2(handles);
% DO SAVE HERE FOR INITIAL SEG IMAGE---------------------------------------
axes(handles.plotseg);
handles.display.opt1=[0 0.75 0];
handles.display.seg1=handles.data.Step3_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% Segmentation parameters to save for future use (full image seg.)---------
handles.segParam.invertColor=get(handles.invertColor,'Value');
handles.segParam.histEq=get(handles.histEq,'Value');
handles.segParam.Deconv=get(handles.Deconv,'Value');
handles.segParam.Smoothing=get(handles.Smoothing,'Value');
handles.segParam.initSeg=get(handles.initSeg,'Value');
handles.segParam.diffMaxMin=get(handles.diffMaxMin,'Value');
handles.segParam.threshold=get(handles.threshold,'Value');
handles.segParam.minSize=get(handles.minSize,'Value');
handles.segParam.Solidity=get(handles.Solidity,'Value');
% handles.segParam.AreaRatio=get(handles.AreaRatio,'Value');
handles.segParam.Ellipticity=get(handles.Ellipticity,'Value');
handles.segParam.Regularize=get(handles.Regularize,'Value');
% handles.segParam.parameters=get(handles.parameters,'Value');
% handles.segParam.DA_classifier=get(handles.DA_classifier,'Value');
fprintf('Step 2 Done \n');
set(handles.uipanel3, 'Visible', 'on');
set(handles.uipanel2, 'Visible', 'off');
set(handles.text_legend, 'Visible','on');
guidata(hObject, handles);
% --- Executes on button press in resetStep2.
function resetStep2_Callback(hObject, eventdata, handles)
% hObject handle to resetStep2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
axes(handles.plotseg);
handles.display.opt1=[1 1 0];
handles.display.seg1=handles.data.Step2_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
set(handles.uipanel1, 'Visible', 'on');
set(handles.uipanel2, 'Visible', 'off');
set(handles.text_legend, 'Visible','off');
guidata(hObject, handles);
% --- Executes on slider movement.
function maxSize_Callback(hObject, eventdata, handles)
% hObject handle to maxSize (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handle.data.proc=maxSize(handles.data.Step2_seg,get(handles.maxSize,'Value'));
axes(handles.plotseg)
%-1-
imshowpair(sc(get(handles.Transparency,'Value')*sc(handles.data.Step2_seg,'y',handles.data.Step2_seg)+sc(handles.data.Step1)),sc(get(handles.Transparency,'Value')*sc(tmp,'y',tmp)+sc(handles.data.Step1)),'montage');
guidata(hObject, handles);
function im_out=maxSize(im_in,sizeMax)
eqDiam=regionprops(im_in,'EquivDiameter');
rm=find([eqDiam.EquivDiameter]<sizeMax);
[axonLabel, numAxon] = bwlabel(im_in);
im_out(ismember(axonLabel,rm))=false;
function maxSize_CreateFcn(hObject, eventdata, handles)
% hObject handle to maxSize (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
function im_out=circTest(im_in,Circ)
im_out = axonValidateCircularity(im_in, Circ);
% --- Executes on slider movement.
function Solidity_Callback(hObject, eventdata, handles)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.minSize, handles.Ellipticity, handles.Go_2_to_3, handles.resetStep2];
set(handleArray,'Enable','off');
drawnow;
tmp=handles.data.Step2_seg;
metric=handles.stats_step2.Solidity;
p=find(metric<get(handles.Solidity,'Value'));
tmp(ismember(handles.stats_cc,p)==1)=0;
axes(handles.plotseg);
handles.display.opt1=[1 0.5 0];
handles.display.seg1=im2bw(handles.data.Step2_seg-tmp);
handles.display.opt2=[0 0.75 0];
handles.display.seg2=tmp;
handles.display.type=2;
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
set(handleArray,'Enable','on');
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function Solidity_CreateFcn(hObject, eventdata, handles)
% hObject handle to Solidity (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 minSize_Callback(hObject, eventdata, handles)
% hObject handle to minSize (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.Ellipticity, handles.Solidity, handles.Go_2_to_3, handles.resetStep2];
set(handleArray,'Enable','off');
drawnow;
% tmp ---> the axons accepted
% handles.data.step2_seg ---> all axons
tmp=handles.data.Step2_seg;
metric=handles.stats_step2.EquivDiameter;
p=find(metric<get(handles.minSize,'Value'));
tmp(ismember(handles.stats_cc,p)==1)=0;
% tmp=sizeTest(handles.data.Step2_seg,get(handles.minSize,'Value'));
% handles.state.minSize = get(handles.minSize,'Value'); % ajoutee
axes(handles.plotseg);
handles.display.opt1=[1 0.5 0];
handles.display.seg1=im2bw(handles.data.Step2_seg-tmp);
handles.display.opt2=[0 0.75 0];
handles.display.seg2=tmp;
handles.display.type=2;
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
set(handleArray,'Enable','on');
guidata(hObject, handles);
% --- Executes on slider movement.
function Ellipticity_Callback(hObject, eventdata, handles)
% hObject handle to Ellipticity (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handleArray = [handles.LoadSegParam, handles.PixelSize_button, handles.Transparency,...
handles.minSize, handles.Solidity, handles.Go_2_to_3, handles.resetStep2];
set(handleArray,'Enable','off');
drawnow;
tmp=handles.data.Step2_seg;
metric=handles.stats_step2.MinorMajorRatio;
p=find(metric<get(handles.Ellipticity,'Value'));
tmp(ismember(handles.stats_cc,p)==1)=0;
% Only select axons that validate the circularity criterion defined by user
% tmp = axonValidateMinorAxis(handles.data.Step2_seg, get(handles.Ellipticity,'Value'));
% Show side-by-side segmentation obtained after step 2 VS segmentation
% corrected by the circularity criterion
axes(handles.plotseg);
handles.display.opt1=[1 0.5 0];
handles.display.seg1=im2bw(handles.data.Step2_seg-tmp);
handles.display.opt2=[0 0.75 0];
handles.display.seg2=tmp;
handles.display.type=2;
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
set(handleArray,'Enable','on');
guidata(hObject,handles);
% --- Executes during object creation, after setting all properties.
function Ellipticity_CreateFcn(hObject, eventdata, handles)
% hObject handle to Ellipticity (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 MajorAxis_Callback(hObject, eventdata, handles)
% hObject handle to MajorAxis (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
% Only select axons that validate the circularity criterion defined by user
tmp = axonValidateMajorAxis(handles.data.Step2_seg, get(handles.MajorAxis,'Value'));
% Show side-by-side segmentation obtained after step 2 VS segmentation
% corrected by the circularity criterion
axes(handles.plotseg)
imshowpair(sc(get(handles.Transparency,'Value')*sc(handles.data.Step2_seg,'y',handles.data.Step2_seg)+sc(handles.data.Step1)),sc(get(handles.Transparency,'Value')*sc(tmp,'y',tmp)+sc(handles.data.Step1)),'montage');
guidata(hObject,handles);
% --- Executes during object creation, after setting all properties.
function MajorAxis_CreateFcn(hObject, eventdata, handles)
% hObject handle to MajorAxis (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
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
%%%----------------- STEP 3 --------------------------------------------%%%
%%% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
% --- Executes on button press in Add.
function Add_Callback(hObject, eventdata, handles)
% hObject handle to Add (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
axes(handles.plotseg);
set(findall(handles.uipanel3, '-property', 'enable'), 'enable', 'off')
handles.display.opt1=[0 0.75 0];
handles.display.seg1=handles.data.Step3_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
manualBW=as_axonSeg_manual;
handles.data.Step3_seg = imresize(manualBW,size(handles.data.Step3_seg)) | handles.data.Step3_seg;
%--------------------------------------------------------------------------
axes(handles.plotseg);
handles.display.opt1=[0 0.75 0];
handles.display.seg1=handles.data.Step3_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
set(findall(handles.uipanel3, '-property', 'enable'), 'enable', 'on')
guidata(hObject, handles);
% --- Executes on button press in remove.
function remove_Callback(hObject, eventdata, handles)
% hObject handle to remove (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
axes(handles.plotseg);
handles.display.opt1=[0 0.75 0];
handles.display.seg1=handles.data.Step3_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% -1-
% imshow(sc(get(handles.Transparency,'Value')*sc(handles.data.Step3_seg,[0 0.75 0],handles.data.Step3_seg)...
% +sc(handles.data.Step1)));
[Label, ~] = bwlabel(handles.data.Step3_seg);
set(findall(handles.uipanel3, '-property', 'enable'), 'enable', 'off')
[c,r,err] = impixel; err = max(isnan(err),[],2);
c = c(~err); r=r(~err);
rm=diag(Label(r*handles.reducefactor,c*handles.reducefactor));
rejected=im2bw(handles.data.Step3_seg-(~ismember(Label,[0;rm])));
handles.data.Step3_seg=~ismember(Label,[0;rm]);
%--------------------------------------------------------------------------
guidata(hObject, handles);
% axes(handles.plotseg);
% imshow(sc(get(handles.Transparency,'Value')*sc(handles.data.Step3_seg,[0 0.75 0],handles.data.Step3_seg)...
% +sc(handles.data.Step1)));
axes(handles.plotseg);
handles.display.opt1=[1 0.5 0];
handles.display.seg1=rejected;
handles.display.opt2=[0 0.75 0];
handles.display.seg2=handles.data.Step3_seg;
handles.display.type=2;
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
% -1-
% imshow(sc(get(handles.Transparency,'Value')*sc(rejected,[1 0.5 0],rejected)...
% +get(handles.Transparency,'Value')*sc(handles.data.Step3_seg,[0 0.75 0],handles.data.Step3_seg)+sc(handles.data.Step1)));
set(findall(handles.uipanel3, '-property', 'enable'), 'enable', 'on')
guidata(hObject, handles);
% --- Executes on button press in resetStep3.
function resetStep3_Callback(hObject, eventdata, handles)
% hObject handle to resetStep3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isfield(handles.segParam,'DA_classifier')
handles.segParam=rmfield(handles.segParam,{'parameters', 'DA_classifier'});
set(handles.DiscriminantAnalysis,'Value',0)
end
set(handles.slider_ROC_plot, 'Visible','off');
set(handles.text_slider_ROC_plot, 'Visible','off');
set(handles.Panel_manual_modifs, 'Visible','on');
set(handles.text_legend, 'Visible','on');
set(handles.ROC_Panel, 'Visible','off');
legend(handles.ROC_curve, 'hide');
cla(handles.ROC_curve);
set(handles.uipanel2, 'Visible', 'on')
set(handles.uipanel3, 'Visible', 'off')
axes(handles.plotseg)
handles.display.opt1=[1 1 0];
handles.display.seg1=handles.data.Step2_seg;
handles.display.type=1;
GUI_display(1,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1);
% imshow(sc(get(handles.Transparency,'Value')*sc(handles.data.Step2_seg,'y',handles.data.Step2_seg)+sc(handles.data.Step1)));
% imshow(imfuse(handles.data.Step1,handles.data.Step2_seg));
% --- Executes on button press in MyelinSeg.
function MyelinSeg_Callback(hObject, eventdata, handles)
% hObject handle to MyelinSeg (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%% Launch Seg
set(findobj('Name','AxonSeg'),'pointer', 'watch');
drawnow;
%---
if get(handles.DiscriminantAnalysis,'value')
AxSeg = handles.data.DA_accepted;
else
AxSeg = handles.data.Step3_seg;
end
AxSeg = imresize(AxSeg,0.5); % return to original size.
[AxSeg_noborder,border_removed_mask]=RemoveBorder(AxSeg,str2num(get(handles.PixelSize,'String')));
backBW=AxSeg & ~AxSeg_noborder;
img = imresize(handles.data.Step1,0.5); % return to original size.
[axonlist,handles.data.seg,Step3_seg] = myelinInitialSegmention(img, AxSeg_noborder, backBW,0,get(handles.Regularize,'Value'),2/3,0,str2num(get(handles.PixelSize,'String')));
axes(handles.plotseg);
handles.display.seg1 = imresize(handles.data.seg,2,'nearest');
handles.display.opt1 = cat(1,[0 0 0],jet(255));
handles.display.seg2 = imresize(border_removed_mask,2);
handles.display.opt2 = [0.5 0.4 0.4];
handles.display.type = 2;
GUI_display(2,handles.reducefactor,get(handles.Transparency,'Value'), handles.data.Step1, handles.display.seg1, handles.display.opt1, handles.display.seg2, handles.display.opt2);
%% SAVE
% save SegParam
odir = uigetdir(handles.outputdir,'Save Results in this directory');
if odir
handles.outputdir = odir;
handles.outputdir = [handles.outputdir filesep];
savedir=[handles.outputdir handles.fname '_AxonSeg_cropped' filesep];
mkdir(savedir);
currentdir=pwd;
cd(savedir);
% save SegParameters
PixelSize=str2num(get(handles.PixelSize,'String'));
handles.segParam.PixelSize=PixelSize;
SegParameters=handles.segParam;
save([pwd filesep 'SegParameters.mat'], 'SegParameters');
% axonlist structure
% clean axonlist (if 0 gRatio & 0 axon diameter)
axonlist=axonlist([axonlist.gRatio]~=0);
axonlist=axonlist([axonlist.axonEquivDiameter]~=0);
PixelSize = str2num(get(handles.PixelSize,'String'));
save('axonlist.mat', 'axonlist', 'img', 'PixelSize','-v7.3');
% excel
handles.stats = as_stats(handles.data.seg,str2num(get(handles.PixelSize,'String')));
handles.stats = struct2table(handles.stats);
writetable(handles.stats,'Stats.csv')
% AxonDiameter Labelled
img = imresize(handles.data.img,.5);
bw_axonseg_myelin=as_display_label(axonlist,size(img),'axonEquivDiameter','myelin',img);
imwrite(im2bw(bw_axonseg_myelin,0),'Seg_mask_myelin.tif');
bw_axonseg_axon=as_display_label(axonlist,size(img),'axonEquivDiameter','axon');
imwrite(im2bw(bw_axonseg_axon,0),'Seg_mask_axon.tif');