1. A hyperspectral imaging system comprising: a plurality of illumination sources in fixed positions to output light toward a target scene; an imaging sensor array including an array of pixels configured for outputting electrical signals in response to receiving light reflected from, transmitted through, or scattered by the target scene; an array of light filters over the imaging sensor array, the array of light filters configured to filter light before reaching the pixels of the imaging sensor array; and a controller coupled to the imaging sensor array, the controller having a memory; wherein the controller is adapted to: acquire into the memory from the imaging sensor array a plurality of images of the target scene during movement or dithering of the combination of the imaging sensor array and the array of light filters, wherein said plurality of images as acquired are spatially shifted with respect to each other, and wherein at least one single image of the plurality of images includes hyperspectral information; and process the plurality of acquired images in the memory of the controller to spatially align said plurality of images based on at least one common image feature in said plurality of images.