Before we get into how a confocal microscope works, it is better to refresh you with the terms used in fluorescent microscopy for better understanding and the mechanics by which images are formed in fluorescent microscope. What is then fluorescence? If you shine light on some molecules, you may see light of a different color emitted from those molecules. This is known as fluorescence or luminescence. Those molecules absorb high energy light (blue, for example as reported). This increases the energy of the molecules, and they are called excited molecules. Some of the energy from the blue photon is lost internally. The molecules then emit a photon with less energy, green in this example. Fluorescence is a common dye that acts in exactly this way, emitting green light when hit with blue excitation light. The color of light emitted is material dependent, and likewise the excitation light wavelength depends on the material. There are other forms of inelastic scattering; fluorescence is particularly strong. (more…)