1. A method for refining calibration of an imaging system comprising: acquiring image data with the imaging system from a measurement volume that includes a three-dimensional object having one or more known parameters; identifying a first projection contour of the three-dimensional object in the image data; analytically determining a second projection contour of the three-dimensional object using the one or more known parameters and a model of the imaging system; refining a calibration of the imaging system by minimizing a deviation between the first projection contour and the second projection contour; and storing the calibration in the imaging system for use in recovering calibrated coordinates during a three-dimensional scan.