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; applying spatial modifications to 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 spatial adjustment parameters are determined separately for each of the array positions, and wherein the spatial modification of the digital image data provides improved alignment between image content printed with the different printheads.