1. A method for registering multi-channel images of a tissue micro array, comprising the steps of, providing a biological material on a substrate; applying one or more molecular probes, adapted to provide fluorescent molecular markers, to said biological material; obtaining a first digital image of said biological material and the fluorescent molecular markers; applying a morphological stain to said biological material; obtaining a second digital image of said biological material, and co-registering said second image with said first image based on one or more registration metrics.