1. Specimen analysis apparatus comprising a machine readable storage medium containing a set of instructions for execution by a processing unit, the processing unit having access to a set of M images of a specimen stained with one or more quantum dots and imaged with a camera arranged as an array of pixels, the set of M images comprising an image of the specimen at M different wavelengths, where M is an integer greater than 2, wherein the instructions comprise a set of instructions for: (a) determining from the set of M images coefficients C 1. .. C N for each pixel, wherein the coefficients C 1. .. C N are related to the concentrations of the one or more quantum dots present in the specimen imaged by each pixel; (b) morphologically processing an image of the specimen to identify cells or cellular components in the specimen, (c) conducting a quantitative analysis of the specimen including calculating quantum dot concentrations for the cells or cellular components identified in step (b) from the coefficients C 1. .. C N ; and (d) generating data for display of the results of the quantitative analysis process (c) on a display associated with the processing unit.