1. A method for aligning multi-channel digital image data for a digital printer having an array of printheads for each of a plurality of channels, the printheads for a particular channel being positioned across a width dimension of the digital printer, comprising: receiving one or more scanned test patterns formed by using an imaging device to capture an image of a test pattern printed using the digital printer, the test pattern including test pattern indicia printed using individual printheads; analyzing the scanned test patterns to detect locations of the printed test pattern indicia; for each of a plurality of array positions: determining reference test pattern indicia locations; designating at least one of the printheads at the array position to be non-reference printheads; and determining one or more spatial adjustment parameters for each of the non-reference printheads responsive to the detected locations of the printed test pattern indicia printed by the non-reference printhead and the reference test pattern indicia locations; receiving multi-channel digital image data for a multi-channel digital image; modifying the digital image data to be printed with the non-reference printheads in accordance with the determined spatial adjustment parameters; and printing the modified digital image data; wherein the modification of the digital image data provides improved alignment between image content printed with the different printheads.