1. A method for registering a visual image and a spectral image of a biological sample, comprising: receiving a first set of coordinates of a plurality of reference marks on a slide or a slide holder with the biological sample and a visual image of the biological sample, wherein the first set of coordinates are independent from features within the visual image; associating the first set of coordinates with the visual image; receiving a second set of coordinates of the plurality of reference marks on the slide or the slide holder with the biological sample and a spectral image of the biological sample, wherein the second set of coordinates are independent from features within the spectral image; associating the second set of coordinates with the spectral image; creating a common coordinate system by associating the first set of coordinates and the second set of coordinates; generating a registered image with the spectral image and the visual image based upon the common coordinate system; and refining the registered image by applying one or more optimizations to the registered image.