1. An automated method for indexing a plurality of anatomical structures of interest in a plurality of digital images, comprising: determining organ level details of a plurality of anatomical structures of interest in a plurality of digital images of one or more biological tissue samples to which a chemical compound has been applied; determining cell level details of the plurality of anatomical structures of interest in the plurality of digital images; determining foreign material level details of the plurality of anatomical structures of interest in the plurality of digital images; and indexing the plurality of digital images using the plurality of determined details with a predetermined indexing scheme, thereby allowing a medical conclusion to be determined from the indexed plurality of digital images.