Studying the dynamics in the cell is essential for understanding cell function. Fluorescence microscopy is one of the most used approaches in studying the location and movement of molecules and subcellular components in the cell using a fluorescence microscope. Usually, cellular components do not fluoresce themselves. Fluorescent markers are therefore introduced in the specimen to be viewed under a fluorescence microscope. Fluorescent dyes are directly taken up by the cells. They are incorporated and concentrated in specific subcellular compartments. The living cells are then mounted on a microscope slide and examined in a fluorescence microscope.

Immunofluorescence is another common fluorescence microscope technique. It involves the use of antibodies to which a fluorescent marker has been attached. Antibodies are molecules that recognize and bind selectively to specific target molecules in the cell being viewed under a fluorescence microscope. The fluorescent signal in the fluorescence microscope can be amplified by using an unlabelled primary antibody and detecting it with labeled secondary antibodies. It is possible to modify cells under fluorescence microscope so that they create their own fluorescing molecules. These protein molecules are tagged with a fluorescing marker. When a specific protein is modified in this way, the location of that protein can be studied under a fluorescence microscope. It is also possible to watch the movements of the proteins and its interactions with other cellular components inside under a fluorescence microscope.

The most economical and easy-to-use device available is Epi-Fluorescence. This fluorescence microscope technique offers a fast, sensitive and specific method for antibody identification. It works well for the diagnosis of smears and biopsies and can be used in bacteriological, immunological and viral studies in conjunction with a fluorescence microscope. This fluorescence microscope attachment is a favorite choice for budget-conscious laboratories, public health organizations, veterinary clinics, etc.

The fluorescence microscope performs especially well for Acridine Orange fluorescence and is very effective if combined with transmitted Phase Contrast observation. The bright 9V/70W halogen lamp provides uniform illumination adequate for fluorescence. Practically service-free when compared to more expensive high-pressure mercury systems, the fluorescence microscope attachment features a centerable lamp holder, a movable collector lens for focusing the filament, an field iris diaphragm, and filter slots to accommodate up to three excitation and heat-absorbing filters simultaneously. The fluorescence microscope is designed for observing and photographing specimens in visible fluorescence light in the green-blue violet part of the spectrum from above and in transmitted light using the phase contrast method or using mixed illumination. A total internal reflection fluorescence microscope is a type of microscope with which a thin region of a specimen, usually less than 200 nm, can be observed. In cell and molecular biology, a large number of molecular events in cellular surfaces such as cell adhesion, binding of cells by hormones, secretion of neurotransmitters, and membrane dynamics have been studied with conventional fluorescence microscopes. However, fluorophores that are bound to the specimen surface and those in the surrounding medium exist in an equilibrium state. When these molecules are excited and detected with a conventional fluorescence microscope, the resulting fluorescence from those fluorophores bound to the surface is often overwhelmed by the background fluorescence due to the much larger population of non-bound molecules.

To solve the problem, the TIRFM was developed by Daniel Axelrod at the University of Michigan, Ann Arbor in the early 1980s. A total internal reflection fluorescence microscope uses evanescent waves to selectively illuminate and excite fluorophores in a restricted region of the specimen immediately adjacent to the glass-water interface. Evanescent waves in the fluorescence microscopes are generated only when the incident light is totally reflected at the glass-water interface. The evanescent electromagnetic field decays exponentially from the interface, and thus propagates to a depth of only approximately 100 nm into the sample medium. Thus the total internal reflection fluorescence microscope enables a selective visualization of surface regions such as the basal plasma membrane which are about 7.5 nm thick of cells as shown in the figure above. The selective visualization of the plasma membrane renders the features and events on the plasma membrane in living cells with high axial resolution. The total internal reflection fluorescence microscope can also be used to observe the fluorescence of a single molecule, making it an important tool of biophysics and quantitative biology.