"The x = ... and y = ... is clearly wrong as it makes a seperate figure with lines and the lines are not on the picture. "
You need to specify the axis in your call to plot(). After calling imagesc() get the handle to you axis using gca()
h = gca;
hold(h, 'on')
plot(h, x', y')
If you want to draw a square, you'll need to add the first coordinate on to the end of each x and y vector to complete the square.
plot(h, [x;x(1)]', [y;y(1)]')
