watershed algorithm in matlab

Question

anyone knows how to write a function in matlab to segment the cells and compute the average cell area using the watershed algorithm? any help would be much appreciated. Than

Answer 1

See watershed in the Image Processing toolbox and this post on cell segmentation on the 'Steve on Image Processing' blog.

Answer 2

Here's one way to segment the image using watershed. There's plenty more you could do (e.g. fuse cells with two nuclei if they haven't completed cytokinesis yet), but the steps below should give you a first idea.

(1) Determine cell-background threshold, cell-nucleus threshold

%# read image
img = imread('http://i.stack.imgur.com/nFDkX.png');
%# normalize to 0...1
imgN = double(img-min(img(:)))/(max(img(:)-min(img(:))));
th1=graythresh(imgN);
th2 = graythresh(imgN(imgN>th1));

cellMsk = imgN>th1;
nucMsk = imgN>th2;

figure,imshow(cellMsk+nucMsk,[])

(2) Smooth the raw image (to avoid oversegmentation) and impose nuclei as minima

[xx,yy]=ndgrid(-5:5,-5:5);
gf = exp((-xx.^2-yy.^2)/20);
filtImg = conv2(imgN,gf,'same');

figure,imshow(filtImg,[])

filtImgM = imimposemin(-filtImg,nucMsk);

(3) Watershed, mask cells, and display

ws = watershed(filtImgM);
ws(~cellMsk) = 0;

lblImg = bwlabel(ws);

figure,imshow(label2rgb(lblImg,'jet','k','shuffle'));

(4) Now you can use REGIONPROPS on the labeled image to extract the statistics you want.