Spectroscopy
Not only can we measure light amount, we can measure the color characteristics of the specimen. Micro-spectroscopy systems are available to determine the chemical characteristics of the specimen. These are just like the spectrometers in your lab, they are just connected to a microscope.
A micro-spectrophotometer is attached to the documentation port on a microscope. It consists of a grating monochrometer that breaks the light down into its wave length parts and a PMT or detector array that changes the light into voltage. This is read and controlled by a computer. The computer knows what the wave length of the light is that is being read and know the amount.
The computer then shows you the amount and the wavelength. This curve tell us a lot about the specimens make up. While this sounds relatively easy it isn't. There are a lot of practical considerations in using a micro-spectophotometer including specimen preparation and standardization.
Typically micro-spectophotometers are used by forensic labs to determine the characteristics of fibers found at crime scenes. This has proved over the years to be a fruitful use of the microscope. Another use has been in analyzing naturally occurring fluorochromes. These systems are capable of fluorescent analysis.
A really neat application of this technology is the FT-IR spectrographic microscopes used in industry, primarily textiles. This microscope uses infrared light to measure the transmission of particles. The analysis method uses Fourier transform math to provide quick and accurate results. With this type of microscope you can quickly tell what sort of particle contamination you have. These are very valuable and quite easy to use microscopes.
If this area interests you then read Inouye's book and find a local guru. This is not easy, simple stuff but there seems to me to be a area were a lot of good work can be done. Bring money too, these systems are not cheap or simple.
What this means to you
You can analyze the color content of a specimen but it is difficult.