1. A method of aligning a plurality of lens stack arrays with a corresponding plurality of sensors, wherein each of the plurality of sensors includes a plurality of focal planes, where each of the plurality of focal planes comprises a plurality of rows of pixels that also form a plurality of columns of pixels and is contained within a region of the imager array that does not contain pixels from another focal plane, and wherein each particular one of the plurality of lens stack arrays comprises a plurality of lens stacks and each of plurality of lens stacks forms a separate optical channel for each focal plane in the one of the plurality of corresponding sensors that corresponds to the particular one of the plurality of lens stack arrays, the method comprising: aligning a first one of the plurality of lens stack arrays relative to a first one of the corresponding plurality of sensors that corresponds to the first one of the plurality of lens stack arrays in an initial position; varying the spatial relationship between the first lens stack array and the first sensor; capturing a plurality of images of a known target using a set of one or more active focal planes in the plurality of focal planes within the first one of the corresponding plurality of sensors wherein each of the plurality of images is captured having a different spatial relationship between the first one of the plurality of lens stack arrays and the first one of the corresponding plurality of sensors, and wherein the known target including at least one region of interest; scoring the plurality of images captured by the plurality of active focal planes, where the resulting scores provide a direct comparison of the extent to which at least one region of interest is focused in the plurality of images; and aligning at least a second one of the plurality of lens stack arrays relative to at least a second one of the plurality of corresponding sensors that corresponds to the second one of the plurality of lens stack arrays, based on the scores of the plurality of images captured by the set of active focal planes of the first one of the plurality of corresponding images and the corresponding spatial relationships by which the respective scored plurality of images were obtained.