1. A method for registering images of a biological material, comprising the steps of; applying one or more molecular probes, adapted to provide fluorescent molecular markers, to said biological material; obtaining a digital image of said biological material and the fluorescent molecular markers; applying a morphological stain to said biological material; obtaining a digital image of said biological material; and aligning and combining digital images, one of which is a moving image and one of which is a fixed image, into a single digital image, that comprises the fluorescent markers and the morphological stain, whereby aligning the digital images comprises identifying a plurality of feature points of the biological material in the moving image and the fixed image, and aligning one or more pixels in the moving and fixed images that correspond to the identified feature points, wherein the feature points comprise a cellular structure, a subcellular structure, or proteins, or combinations thereof.