A method for aligning multi-channel digital image data for a digital printer having a plurality at least one printhead is described. One or more spatial adjustment parameters are determined for each of the printheads. The spatial adjustment parameters can be determined by comparing locations of test pattern indicia in a printed test pattern to predefined reference indicia locations. Digital image data for the non-reference printheads is modified by designating an input pixel neighborhood within which an image pixel should be inserted or deleted, comparing the image pixels in the input pixel neighborhood to a plurality of predefined pixel patterns to identify a matching pixel pattern; and determining a modified pixel neighborhood responsive to the matching pixel pattern.