Fluorescence in the context of Optical sectioning

Ink is a gel, sol, or solution that contains at least one colorant, such as a dye or pigment, and is used to color a surface to produce an image, text, or design. Ink is used for drawing or writing with a pen, brush, reed pen, or quill. Thicker inks, in paste form, are used extensively in letterpress and lithographic printing.

Ink can be a complex medium, composed of solvents, pigments, dyes, resins, lubricants, solubilizers, surfactants, particulate matter, fluorescents, and other materials. The components of inks serve multiple purposes; the ink's carrier, colorants, and other additives affect the flow and thickness of the ink and its dry appearance.

A microscope (from Ancient Greek μικρός (mikrós) 'small' and σκοπέω (skopéō) 'to look (at); examine, inspect') is a laboratory instrument used to examine objects that are too small to be seen by the naked eye. Microscopy is the science of investigating small objects and structures using a microscope. Microscopic means being invisible to the eye unless aided by a microscope.

There are many types of microscopes, and they may be grouped in different ways. One way is to describe the method an instrument uses to interact with a sample and produce images, either by sending a beam of light or electrons through a sample in its optical path, by detecting photon emissions from a sample, or by scanning across and a short distance from the surface of a sample using a probe. The most common microscope (and the first to be invented) is the optical microscope, which uses lenses to refract visible light that passed through a thinly sectioned sample to produce an observable image. Other major types of microscopes are the fluorescence microscope, electron microscope (both the transmission electron microscope and the scanning electron microscope) and various types of scanning probe microscopes.

Selenium is a chemical element; it has symbol Se and atomic number 34. It has various physical appearances, including a brick-red powder, a vitreous black solid, and a grey metallic-looking form. It seldom occurs in this elemental state or as pure ore compounds in Earth's crust. Selenium (from σελήνη 'moon') was discovered in 1817 by Jöns Jacob Berzelius, who noted the similarity of the new element to the previously discovered tellurium (named for the Earth).

Selenium is found in metal sulfide ores, where it substitutes for sulfur. Commercially, selenium is produced as a byproduct in the refining of these ores. Minerals that are pure selenide or selenate compounds are rare. The chief commercial uses for selenium today are glassmaking and pigments. Selenium is a semiconductor and is used in photocells. Applications in electronics, once important, have been mostly replaced with silicon semiconductor devices. Selenium is still used in a few types of DC power surge protectors and one type of fluorescent quantum dot.

Mycobacterium tuberculosis (M. tb), also known as Koch's bacillus, is a species of pathogenic bacteria in the family Mycobacteriaceae and the causative agent of tuberculosis.

First discovered in 1882 by Robert Koch, M. tuberculosis has an unusual, waxy coating on its cell surface primarily due to the presence of mycolic acid. This coating makes the cells impervious to Gram staining, and as a result, M. tuberculosis can appear weakly Gram-positive. Acid-fast stains such as Ziehl–Neelsen, or fluorescent stains such as auramine are used instead to identify M. tuberculosis with a microscope. The physiology of M. tuberculosis is highly aerobic and requires high levels of oxygen. Primarily a pathogen of the mammalian respiratory system, it infects the lungs. The most frequently used diagnostic methods for tuberculosis are the tuberculin skin test, acid-fast stain, culture, and polymerase chain reaction.

A fluorescent lamp, or fluorescent tube, is a low-pressure mercury-vapor gas-discharge lamp that uses fluorescence to produce visible light. An electric current in the gas excites mercury vapor, to produce ultraviolet and make a phosphor coating in the lamp glow. Fluorescent lamps convert electrical energy into visible light much more efficiently than incandescent lamps, but are less efficient than most LED lamps. The typical luminous efficacy of fluorescent lamps is 50–100 lumens per watt, several times the efficacy of general lighting incandescent bulbs with comparable light output, which is on the close order of 16 lm/W.

Fluorescent lamp fixtures are more costly than incandescent lamps because, among other things, they require a ballast to regulate current through the lamp, but the initial cost is offset by a much lower running cost. Compact fluorescent lamps (CFL) made in the same sizes as incandescent lamp bulbs are used as an energy-saving alternative to incandescent lamps in homes.

A phosphor is a substance that exhibits the phenomenon of luminescence; it emits light when exposed to some type of radiant energy. The term is used both for fluorescent or phosphorescent substances which glow on exposure to ultraviolet or visible light, and cathodoluminescent substances which glow when struck by an electron beam (cathode rays) in a cathode-ray tube.

When a phosphor is exposed to radiation, the orbital electrons in its molecules are excited to a higher energy level; when they return to their former level they emit the energy as light of a certain color. Phosphors can be classified into two categories: fluorescent substances which emit the energy immediately and stop glowing when the exciting radiation is turned off, and phosphorescent substances which emit the energy after a delay, so they keep glowing after the radiation is turned off, decaying in brightness over a period of milliseconds to days.

Phosphorescence is a type of photoluminescence related to fluorescence. When exposed to light (radiation) of a shorter wavelength, a phosphorescent substance will glow, absorbing the light and reemitting it at a longer wavelength. Unlike fluorescence, a phosphorescent material does not immediately reemit the radiation it absorbs. Instead, a phosphorescent material absorbs some of the radiation energy and reemits it for a much longer time after the radiation source is removed.

In a general sense, there is no distinct boundary between the emission times of fluorescence and phosphorescence (i.e.: if a substance glows under a black light it is generally considered fluorescent, and if it glows in the dark it is often simply called phosphorescent). In a modern, scientific sense, the phenomena can usually be classified by the three different mechanisms that produce the light and the typical timescales at which they emit light: fluorescence, triplet phosphorescence, and persistent phosphorescence. Whereas fluorescent materials stop emitting light within nanoseconds (billionths of a second) after the excitation radiation is removed, phosphorescent materials may continue to emit an afterglow ranging from a few microseconds to many hours after the excitation is removed.

Photoluminescence (abbreviated as PL) is light emission from any form of matter after the absorption of photons (electromagnetic radiation). It is one of many forms of luminescence (light emission) and is initiated by photoexcitation (i.e. photons that excite electrons to a higher energy level in an atom), hence the prefix photo-. Following excitation, various relaxation processes typically occur in which other photons are re-radiated. Time periods between absorption and emission may vary: ranging from short femtosecond-regime for emission involving free-carrier plasma in inorganic semiconductors or metals up to milliseconds for phosphoresence processes in molecular systems; and under special circumstances delay of emission may even span to minutes or hours.

Observation of photoluminescence at a certain energy can be viewed as an indication that an electron transitioned between states separated by this transition energy. While this is generally true in atoms and similar systems, correlations and other more complex phenomena also act as sources for photoluminescence in many-body systems such as semiconductors or metals. A theoretical approach to handle this is given by the semiconductor luminescence equations.

The optical properties of a material define how it interacts with light. The optical properties of matter are studied in optical physics (a subfield of optics) and applied in materials science. The optical properties of matter include:

• Refractive index
• Dispersion
• Transmittance and Transmission coefficient
• Absorption
• Scattering
• Turbidity
• Reflectance and Reflectivity (reflection coefficient)
• Albedo
• Perceived color
• Fluorescence
• Phosphorescence
• Photoluminescence
• Optical bistability
• Dichroism
• Birefringence
• Optical activity
• Photosensitivity

A basic distinction is between isotropic materials, which exhibit the same properties regardless of the direction of the light, and anisotropic ones, which exhibit different properties when light passes through them in different directions.

Fluoroscopy (/flʊəˈrɒskəpi/), informally referred to as "fluoro", is an imaging technique that uses X-rays to obtain real-time moving images of the interior of an object. In its primary application of medical imaging, a fluoroscope (/ˈflʊərəˌskoʊp/) allows a surgeon to see the internal structure and function of a patient, so that the pumping action of the heart or the motion of swallowing, for example, can be watched. This is useful for both diagnosis and therapy and occurs in general radiology, interventional radiology, and image-guided surgery.

In its simplest form, a fluoroscope consists of an X-ray source and a fluorescent screen, between which a patient is placed. However, since the 1950s most fluoroscopes have included X-ray image intensifiers and cameras as well, to improve the image's visibility and make it available on a remote display screen. For many decades, fluoroscopy tended to produce live pictures that were not recorded, but since the 1960s, as technology improved, recording and playback became the norm.

An X-ray image intensifier (XRII) is an image intensifier that converts X-rays into visible light at higher intensity than the more traditional fluorescent screens can. Such intensifiers are used in X-ray imaging systems (such as fluoroscopes) to allow low-intensity X-rays to be converted to a conveniently bright visible light output. The device contains a low absorbency/scatter input window, typically aluminum, input fluorescent screen, photocathode, electron optics, output fluorescent screen and output window. These parts are all mounted in a high vacuum environment within glass or, more recently, metal/ceramic. By its intensifying effect, It allows the viewer to more easily see the structure of the object being imaged than fluorescent screens alone, whose images are dim. The XRII requires lower absorbed doses due to more efficient conversion of X-ray quanta to visible light. This device was originally introduced in 1948.

A scintillator (/ˈsɪntɪleɪtər/ SIN-til-ay-ter) is a material that exhibits scintillation, the property of luminescence, when excited by ionizing radiation. Luminescent materials, when struck by an incoming particle, absorb its energy and scintillate (i.e. re-emit the absorbed energy in the form of light). Sometimes, the excited state is metastable, so the relaxation back down from the excited state to lower states is delayed (necessitating anywhere from a few nanoseconds to hours depending on the material). The process then corresponds to one of two phenomena: delayed fluorescence or phosphorescence. The correspondence depends on the type of transition and hence the wavelength of the emitted optical photon.

A fluorescence microscope is an optical microscope that uses fluorescence instead of, or in addition to, scattering, reflection, and attenuation or absorption, to study the properties of organic or inorganic substances. A fluorescence microscope is any microscope that uses fluorescence to generate an image, whether it is a simple setup like an epifluorescence microscope or a more complicated design such as a confocal microscope, which uses optical sectioning to get better resolution of the fluorescence image.

Main article: Pyrimidine

A pyrimidine dimer is a type of molecular lesion that arises when adjacent thymine or cytosine bases are bonded together in an atypical way, often as a result of a photochemical reaction. Ultraviolet light (UV), particularly UVC, often causes this direct DNA damage, causing the formation of covalent bonds near the nucleotides' carbon–carbon double bonds. The resulting photo-coupled dimers are fluorescent, and are commonly classified as cyclobutane pyrimidine dimers (CPDs) and 6–4 photoproducts. These pre-mutagenic lesions modify the DNA helix structure by distorting it.

Polythiophenes (PTs) are polymerized thiophenes, a sulfur heterocycle. The parent PT is an insoluble colored solid with the formula (C₄H₂S)_n. The rings are linked through the 2- and 5-positions. Poly(alkylthiophene)s have alkyl substituents at the 3- or 4-position(s). They are also colored solids, but tend to be soluble in organic solvents.

PTs become conductive when oxidized. The electrical conductivity results from the delocalization of electrons along the polymer backbone. Conductivity however is not the only interesting property resulting from electron delocalization. The optical properties of these materials respond to environmental stimuli, with dramatic color shifts in response to changes in solvent, temperature, applied potential, and binding to other molecules. Changes in both color and conductivity are induced by the same mechanism, twisting of the polymer backbone and disrupting conjugation, making conjugated polymers attractive as sensors that can provide a range of optical and electronic responses.

Biofluorescence is fluorescence exhibited by a living organism: part of the organism absorbs light or other radiation at one wavelength and emits visible light at another, usually longer. The absorbed radiation is often blue or ultraviolet, while the light emitted is typically green, red, or anything in between. Biofluorescence requires an external light source and a fluorescent biomolecular substance, which is often one or more proteins, but can consist of other biomolecules.

A perceptible example of fluorescence occurs when the absorbed radiation is ultraviolet, thus invisible to the human eye, while the emitted light is in the visible spectrum; this gives the fluorescent substance a distinct color that can only be seen when it is exposed to UV light.