Please expand on your question.
Are you trying to find out how many of the points fall in to each square of a grid? If so, then you can use accumarray for that:
xgrid = 1 + floor(Nx * (x - min(x)) ./ (max(x) - min(x)));
ygrid = 1 + floor(Ny * (y - min(y)) ./ (max(y) - min(y)));
weights = accumarray([xgrid(:), ygrid(:)], 1);
This will produce an Nx by Ny grid of counts.