The present invention provides a method and system for determining the position of the image of a target object or the position of the x-ray source in digital tomosynthesis, as the x-ray source is moved relative to the object so as to obtain multiple two-dimensional images of the object from multiple angles. At least one marker, characterized by a simple and known image pattern, is disposed between an x-ray source and a detector system. The shift in the image of the object, resulting from the movement of the x-ray source during tomosynthesis, is calculated to a desired resolution using the readily observable shift in the image of the marker. The x-ray source may be translated along a plane parallel to the plane of the detector system, or may be rotated about a fixed center.