Fluorescence is used to observe the distribution of specific molecules. Molecules that do not auto fluoresce are marked with fluorescing molecules called fluorochromes. Fluorochromes emit light when they are exited with light of a certain wavelength.

Fluorescene microscopes can be either upright or inverted but unline a typical brightfield microscope the illumination is provided by a mercury-vapor lamp, or a modern LED fluoresce light source.A fluorescence microscope will contain three filters, a excitation filter, a dichroic filter, and emission filter. These three filters are all contained into one fluorescence filter cub. An excitation filter transmits light that excites the specimen with its particular dye. Light emitted by the specimen passes through the emission filter before reaching the detector. The emission filter only allows light with a distinct wavelength, such as the light emitted by the specimen. The dichroic mirror allows light of a certain wavelength to pass though. Light of other wavelengths is reflected and will not pass.First light passes through the excitation filter, it is then passed to the dichroic mirror reflecting the light through the objective at the specimen. Fluorochromes in the specimen are then excited and emit photons. Then the emission light is passed through the objective and back to the dichroic mirror. The emitted liht with the appropriate wavelength is able to pass.

There are different types of fluorescence filters - short pass, band pass, and long pass. Short pass filters transmit short wavelengths while blocking long ones. Band pass filters transmit a band of wavelengths, blocking light that is outside this window. Long pass