In one aspect, in general, a measurement system includes a projector for illuminating a pattern on a surface of the object, at least two imaging devices for obtaining images of a portion of an object, wherein at least some of the images include representations of one or more illuminated reference markers, an instrument for identifying a predetermined feature of the object, and a computing device for determining first position information associated with the illuminated reference markers represented in the images, determining second position information associated with the instrument, and based on the first position information and the second position information, assigning a predetermined coordinate system of the object to the object.