Fluorescence is a member of the ubiquitous luminescence family of processes in which susceptible molecules emit light from electronically excited states created by either a physical (for example, absorption of light), mechanical (friction), or chemical mechanism. Generation of luminescence through excitation of a molecule by ultraviolet or visible light photons is a phenomenon termed photoluminescence, which is formally divided into two categories, fluorescence and phosphorescence, depending upon the electronic configuration of the excited state and the emission pathway. Fluorescence is the property of some atoms and molecules to absorb light at a particular wavelength and to subsequently emit light of longer wavelength after a brief interval, termed the fluorescence lifetime. The process of phosphorescence occurs in a manner similar to fluorescence, but with a much longer excited state lifetime.

The fluorescence process is governed by three important events, all of which occur on timescales that are separated by several orders of magnitude (see Figure 1(a)). Excitation of a susceptible molecule by an incoming photon happens in femtoseconds (1015 seconds), while vibrational relaxation of excited state electrons to the lowest energy level is much slower and can be measured in picoseconds (1012 seconds). The final process, emission of a longer wavelength photon and return of the molecule to the ground state, occurs in the relatively long time period of nanoseconds (109 seconds). Although the entire molecular fluorescence lifetime, from excitation to emission, is measured in only billionths of a second, the phenomenon is a stunning manifestation of the interaction between light and matter that forms the basis for the expansive fields of steady state and time-resolved fluorescence spectroscopy and microscopy. Because of the tremendously sensitive emission profiles, spatial resolution, and high specificity of fluorescence investigations, the technique has become an important tool (cartoon in Figure 1(b)) in genetics and cell biology.
Several investigators reported luminescence phenomena during the seventeenth and eighteenth centuries, but it was British scientist Sir George G. Stokes who first described fluorescence in 1852 and was responsible for coining the term in honor of the blue-white fluorescent mineral fluorite (fluorspar). Stokes also discovered the wavelength shift to longer values in emission spectra that bears his name (known as the Stokes Shift; Figure 1(c) and Figure 2). Fluorescence was first encountered in optical microscopy during the early part of the twentieth century by several notable scientists, including August Köhler and Carl Reichert, who initially reported that fluorescence was a nuisance in ultraviolet microscopy. The first fluorescence microscopes were developed between 1911 and 1913 by German physicists Otto Heimstaedt and Heinrich Lehmann as a spin-off from the ultraviolet instrument. These microscopes were employed to observe autofluorescence in bacteria, animal, and plant tissues. Shortly thereafter, Stanislav Von Provazek launched a new era when he used fluorescence microscopy to study dye binding in fixed tissues and living cells. However, it wasn't until the early 1940s that Albert Coons developed a technique for labeling antibodies with fluorescent dyes, thus giving birth to the field of immunofluorescence. By the turn of the twenty-first century, the field of fluorescence microscopy was responsible for a revolution in cell biology, coupling the power of live cell imaging to highly specific multiple labeling of individual organelles and macromolecular complexes with synthetic and genetically encoded fluorescent probes.

In contrast to other modes of optical microscopy that are based on macroscopic specimen features, such as phase gradients, light absorption, and birefringence, fluorescence microscopy is capable of imaging the distribution of a single molecular species based solely on the properties of fluorescence emission. Thus, using fluorescence microscopy, the precise location of intracellular components labeled with specific fluorophores can be monitored, as well as their associated diffusion coefficients, transport characteristics, and interactions with other biomolecules. In addition, the dramatic response in fluorescence to localized environmental variables enables the investigation of pH, viscosity, refractive index, ionic concentrations, membrane potential, and solvent polarity in living cells and tissues.