1. A system for analysis of a biological specimen having between 1 and N different fluorophore(s) applied to the specimen, the fluorophores including at least one quantum dot, comprising, in combination: a microscope, spectral filters and an associated camera for imaging the specimen at a plurality (M) of discrete wavelengths and responsively generating a plurality of images, each of which is composed of a plurality of pixels, the M wavelengths including a plurality of discrete wavelengths at which the 1. .. N fluorophores produce a luminescent response to incident light; and a workstation including a processing unit for performing processing steps, comprising: a) interpolating fluorescence reference spectra for the 1. .. N fluorophores to the M wavelengths to generate a matrix (I) of illumination intensity at each wavelength for each fluorophore and an unmixing process processing the plurality of images and matrix I and responsively determining coefficients C 1. .. C N at each pixel location, wherein the coefficients C 1. .. C N are related to the concentrations of the 1. .. N fluorophores present in the sample at each pixel location; b) at least one morphological processing process identifying at least one biological structure in the specimen; c) a quantitative analysis process calculating fluorophore concentrations for the biological structures identified in step b) from the coefficients C 1. .. C N ; and d) a display process for displaying the results of the quantitative analysis process c) on a display associated with the workstation.