function varargout = cellcountGUI2(varargin)
% Programmed by Tian Zhou from Thayer School of Engineering
% this is a course project for digital image processing by Prof. Alex Hartov
% the overlay coding was borrowed from Steve
% http://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/
% CELLCOUNTGUI2 M-file for cellcountGUI2.fig
% CELLCOUNTGUI2, by itself, creates a new CELLCOUNTGUI2 or raises the existing
% singleton*.
%
% H = CELLCOUNTGUI2 returns the handle to a new CELLCOUNTGUI2 or the handle to
% the existing singleton*.
%
% CELLCOUNTGUI2('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in CELLCOUNTGUI2.M with the given input arguments.
%
% CELLCOUNTGUI2('Property','Value',...) creates a new CELLCOUNTGUI2 or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before cellcountGUI2_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to cellcountGUI2_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 cellcountGUI2
% Last Modified by GUIDE v2.5 05-Mar-2010 11:12:13
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @cellcountGUI2_OpeningFcn, ...
'gui_OutputFcn', @cellcountGUI2_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 cellcountGUI2 is made visible.
function cellcountGUI2_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 cellcountGUI2 (see VARARGIN)
% Choose default command line output for cellcountGUI2
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes cellcountGUI2 wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = cellcountGUI2_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 button press in browse.
function browse_Callback(hObject, eventdata, handles)
global im;
global imOld;
global map;
% hObject handle to browse (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
clc
[filename,pathname]=uigetfile({'*.tif';'*.png';'*.tiff';'*.jpg';'*.bmp';'*.gif'},'Open File');
[im,map]=imread(filename);
imOld=im;
axes(handles.axes1);
imshow(im,map);
axis off
title(filename,'fontsize',16)
set(handles.edit1,'string','');
% --- Executes on button press in count.
function count_Callback(hObject, eventdata, handles)
% hObject handle to count (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global im;
global imOld;
global imOut;
global level;
global overlay1;
% hObject handle to filter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[a b c]=size(im);
if(c>1) % color image
switch get(handles.popupmenu1,'Value')
case 2 % Red
im1=im(:,:,1);
case 3 % Green
im1=im(:,:,2);
case 4 % Blue
im1=im(:,:,3);
otherwise
im1=im(:,:,2);
end
else % grayscale image
im1=im;
end
% frequency filtering (band pass)
[row column]=size(im1);
imFFT=fft2(im1,row,column); % Fourier transformed image, same size as original image
imFFT=fftshift(imFFT); % Fourier transformed image centered
temp=min(row,column);
temp1=max(row,column);
% Build a bandpass filter. Everything within the pass band is one,
% everything outside is 0.0.
ri=repmat([1:temp]',1,temp); % the size of the original image is 1200X1600
ci=repmat([1:temp],temp,1);
ri=ri-temp/2.0;
ci=ci-temp/2.0;
r(1:temp,(temp1-temp)/2+1:(temp1+temp)/2)=sqrt(ri.*ri+ci.*ci);
r(1:temp,1:(temp1-temp)/2)=max(r(:)).*ones(temp,(temp1-temp)/2); % pad the margin
r(1:temp,(temp1+temp)/2+1:temp1)=r(1:temp,1:(temp1-temp)/2);
radius1=6;
radius2=30;
index=find(r<radius2 & r>radius1);
filt=zeros(row,column); % everything outside the pass band is 0
filt(index)=1.0;
% Apply the filter
imFFT2=imFFT.*filt; % Masked centered fft of image with bandpass filter
imOut=ifft2(fftshift(imFFT2));
imOut=real(imOut);
axes(handles.axes2);
if(min(imOut(:))<0) % make all values positive
imOut=imOut+abs(min(imOut(:)));
end
imOut=imOut./max(imOut(:));
level=graythresh(imOut);
BW=im2bw(imOut,level);
bw2 = imfill(BW,'holes');
bw3 = imopen(bw2, ones(5,5));
bw4 = bwareaopen(bw3, 40);
bw4_perim = bwperim(bw4,8);
SE=[0 1 0
1 1 1
0 1 0];
bw4_perim=imdilate(bw4_perim,SE);
colorV=get(handles.popupmenu1,'Value');
if(colorV==2)
rgbV=[0.3 1 0.3];
else
rgbV=[1 0.3 0.3];
end
overlay1=imoverlay(imOld,bw4_perim,rgbV);
axes(handles.axes2)
imshow(overlay1)
[L1,n1]=bwlabel(BW);
title(['N=',num2str(n1)],'color','red','fontsize',16)
% --- Executes on slider movement.
function slider1_Callback(hObject, eventdata, handles)
global imOld;
global imOut;
global level;
global overlay1;
global BW;
% hObject handle to slider1 (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
threshold=get(handles.slider1,'value');
set(handles.edit1,'string',num2str(threshold));
BW=im2bw(imOut,level+threshold);
bw2 = imfill(BW,'holes');
bw3 = imopen(bw2, ones(5,5));
bw4 = bwareaopen(bw3, 40);
bw4_perim = bwperim(bw4,8);
SE=[0 1 0
1 1 1
0 1 0];
bw4_perim=imdilate(bw4_perim,SE);
colorV=get(handles.popupmenu1,'Value');
if(colorV==2)
rgbV=[0.3 1 0.3];
else
rgbV=[1 0.3 0.3];
end
overlay1=imoverlay(imOld,bw4_perim,rgbV);
axes(handles.axes2)
imshow(overlay1)
[L1,n1]=bwlabel(BW);
title(['N=',num2str(n1)],'color','red','fontsize',16)
drawnow
% --- Executes during object creation, after setting all properties.
function slider1_CreateFcn(hObject, eventdata, handles)
% hObject handle to slider1 (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 edit1_Callback(hObject, eventdata, handles)
% hObject handle to edit1 (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 edit1 as text
% str2double(get(hObject,'String')) returns contents of edit1 as a double
% --- Executes during object creation, after setting all properties.
function edit1_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit1 (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
% --- Executes on button press in output.
function output_Callback(hObject, eventdata, handles)
global overlay1;
global map;
global BW;
% hObject handle to output (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
figure
imshow(overlay1,map)
[L1,n1]=bwlabel(BW);
title(['N=',num2str(n1)],'color','red','fontsize',16)
% --- Executes on selection change in popupmenu1.
function popupmenu1_Callback(hObject, eventdata, handles)
global im;
% hObject handle to popupmenu1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
se=strel('disk',20);
im=imtophat(im,se);
% Hints: contents = get(hObject,'String') returns popupmenu1 contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupmenu1
% --- Executes during object creation, after setting all properties.
function popupmenu1_CreateFcn(hObject, eventdata, handles)
% hObject handle to popupmenu1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu 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
