1. An automated system for identifying one or more stained targets in a biological sample comprising a slide scanner, and a view screen, and further, comprising, in combination: a database capable of including a plurality of digital representations of a plurality of biological samples, wherein said samples have been stained with a stain so as to define a stained target; and a software module for analyzing a plurality of pixels from at least one of said digital representations of said biological samples, and carrying out the following method for identifying one or more stained targets in said samples, said method comprising: a) providing at least one digital representation of the sample wherein the sample has been stained with a stain so as to define said stained target, and b) filtering the digital representation with at least three filters, each of said filters comprising filter constant(s), applying said filter constant(s) to each pixels in at least a subset of the digital representation and determining an eigensolution based on the filter output for each pixel in the subset, wherein said filters are capable of enhancing the stained targets obtaining a filtered representation, c) segmenting the digital representation based on information from the filtered representation into stained cell targets and background, thereby obtaining a segmented representation, wherein said segmented representation discriminates between stained targets and other structures in the digital representation, and; d) from said segmented representation, identifying the stained targets in the sample.