In this work, we present a method providing real-time, low cost, three-dimensional imaging in a three-dimensional optical micromanipulation system. The three-dimensional imaging system is based on a small form factor LED based projector. The projector is used to dynamically shape the rear illumination light in a counter-propagating beam-trapping setup. This allows us to produce stereoscopic images, from which the human brain can construct a three-dimensional image, or alternatively image analysis can be applied by a computer, thereby obtaining true three-dimensional coordinates in real-time for the trapped objects.