1. A method for resolving features on a probe array, comprising: acquiring a set of micro-shifted images of a region of a probe array comprising features, wherein the images are acquired using an image acquisition device comprising an objective lens and a sensing element having pixels, and wherein each image in the set is shifted from other images in the set by less than one half a size of a pixel of the sensing element; reconstructing an image of the probe array using the set of micro-shifted images, wherein reconstructing the image comprises: creating a single image from the set of micro-shifted images by taking a pixel from a common location within each of the micro-shifted images and tiling the pixels in the single image according to the spatial orientation corresponding to the shift direction and magnitude used during image acquisition, and repeating for each pixel associated with the set of micro-shifted images; and creating an unboxed image from the single image, wherein the unboxed image is made up of subpixels defined by the shifts used to produce the micro-shifted images, and wherein creating the unboxed image comprises solving a system of linear algebraic equations to determine the value of each subpixel from the values of the pixels in the single image; and deriving intensity values for one or more probe features on the region of the probe array from a reconstructed image, wherein the reconstructed image is created from at least one of the unboxed image or a deconvolved image.