If you have your 2xN dot matrix dots which presumably contain the x (row 1) and y (row 2) coordinates, then N is the number of dots in the whole image and
ni = nnz(dots(1,:)>=xi & dots(1,:)<xi+wi) & dots(2,:)>=yi & dots(1,:)<yi+hi));
Gives you the number of dots in image patch i, which has its lower left corner at (xi,yi) and has a width x size of wi x hi.