Demo1.m

%% Segmentation of a cell

% Display image
I = imread('AT3_1m4_10_small.tif');
imshow(I)

%% Interactive visualization
imtool(I)

%% Edge detection
BW = edge(I,'sobel');
imshow(BW);

%% Dilation
se = strel('square',5);
BWdil = imdilate(BW,se);
imshow(BWdil)

%% Fill in holes
BWfil = imfill(BWdil,'holes');
imshow(BWfil)



%% Visual inspection
imtool(BWfil)

%% Remove small objects
BWopen = bwareaopen(BWfil,140);
imshow(BWopen)



%% Region properties
% Label blobs
cc = bwconncomp(BWfil);
L = labelmatrix(cc);
imshow( ind2rgb(L, jet(47)) )

%% Calculate statistics
stats = regionprops(L,'Area');
idx = find([stats.Area] > 130);

% Filter out by area
BWopen = ismember(L, idx);
imshow(BWopen)



%% Erode edges
BWfinal = imerode(BWopen,se);
imshow(BWfinal)

%% Calculate perimeter
BWoutline = bwperim(BWfinal);
imshow(BWoutline)

%% Overlay on original
y = I;
y(BWoutline) = 255;
imshow(y)

% Copyright 2005-2009 The MathWorks, Inc.