Try this:
binaryImage = grayImage > 128;
[labeledImage, numSpots] = bwlabel(binaryImage);
props = regionrops(labeledImage, 'Centroid');
props is a structure array where Centroid is a field of the structure. You can get a table variable out instead of a structure array if you want.
See my File Exchange for the Image Segmentation Tutorial: http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862&sort=downloads_desc
