A method of generating alignment data for a printhead. The method includes the steps of: printing a calibration pattern using the printhead, the calibration pattern including rows of spaced apart fiducials, each fiducial having a plurality of concentric shapes representing a code sequence; imaging the fiducials at a first resolution to generate imaged fiducials; cross-correlating a template fiducial with the imaged fiducials at a plurality of different displacement s relative to each imaged fiducial, the template fiducial having a configuration matching the imaged fiducials; determining a two-dimensional set of cross-correlation values for each imaged fiducial, each set of cross-correlation values indicating a center of a respective fiducial; and generating alignment data for the printhead using the sets of cross-correlation values.