A biological sample such as a tissue section is stained with one or more quantum dots and possibly other fluorophores (total number of fluorophores N). A camera coupled to a microscope generates an image of the specimen at a plurality of different wavelengths within the emission spectral band of the N fluorophores. An analysis module calculates coefficients C1 . . . CN at each pixel which are related to the concentration of each of the individual fluorophores. Morphological processing instructions find biological structures. A display module displays quantitative analysis results to the user. The quantitative analysis display includes histograms of the biological structures, scatter plots of fluorophore concentrations, statistical data, spectral data, image data and still others.