Method and systems for removing any inherent autofluorescence associated with a biological material, comprising: acquiring a first reference image of the biological material; acquiring a first set of one or more images of the biological material using one or more filters corresponding to one or more information dyes; applying the one or more additional dyes to the biological material and then acquiring a second set of one or more images comprising a separate image of the biological material with each of the filters corresponding to the information dyes and a second reference image of the biological material; coregistering the first and second reference images; and then removing any inherent autofluorescence exhibited in the informational images acquired.