1. A method for calibrating a three-dimensional imaging system having an optical apparatus for capturing an optical image of an object from at least a first position and a second position, comprising the steps of: projecting a virtual calibration pattern in the field of view of the object in relation to the optical apparatus in the first position and in the second position; capturing an optical image of the object together with an optical image of the virtual calibration pattern from the first position and from the second position; choosing one of the first position and the second position of the optical apparatus as a reference position; assigning coordinates of a coordinate system relative to either the virtual calibration pattern or the reference position; measuring differences in the virtual calibration pattern in the coordinate system from the first position to the second position of the optical apparatus; calculating calibration corrections relative to the reference position based on spatial locations and orientations of voxels in the reference position in relation to the optical image of the virtual calibration pattern; and adjusting images from the optical apparatus based on the calibration corrections.