1. A hyperspectral imaging system comprising: 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 a target scene; an array of light filters configured for filtering the light reaching the pixels of the imaging sensor; and a controller adapted to: acquire into a memory of the controller 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 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.