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Confocal Microscope
Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a spatial pinhole to block out-of-focus light in image formation. Capturing multiple two-dimensional images at different depths in a sample enables the reconstruction of three-dimensional structures (a process known as optical sectioning) within an object. This technique is used extensively in the scientific and industrial communities and typical applications are in life sciences, semiconductor inspection and materials science. Light travels through the sample under a conventional microscope as far into the specimen as it can penetrate, while a confocal microscope only focuses a smaller beam of light at one narrow depth level at a time. The CLSM achieves a controlled and highly limited depth of field. Basic concept The principle of co ...
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Fluorescent And Confocal Microscopes
Fluorescence is one of two kinds of photoluminescence, the emission of light by a substance that has absorbed light or other electromagnetic radiation. When exposed to ultraviolet radiation, many substances will glow (fluoresce) with colored visible light. The color of the light emitted depends on the chemical composition of the substance. Fluorescent materials generally cease to glow nearly immediately when the radiation source stops. This distinguishes them from the other type of light emission, phosphorescence. Phosphorescent materials continue to emit light for some time after the radiation stops. This difference in duration is a result of quantum spin effects. Fluorescence occurs when a photon from incoming radiation is absorbed by a molecule, exciting it to a higher energy level, followed by the emission of light as the molecule returns to a lower energy state. The emitted light may have a longer wavelength and, therefore, a lower photon energy than the absorbed radi ...
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Point Spread Function
The point spread function (PSF) describes the response of a focused optical imaging system to a point source or point object. A more general term for the PSF is the system's impulse response; the PSF is the impulse response or impulse response function (IRF) of a focused optical imaging system. The PSF in many contexts can be thought of as the shapeless blob in an image that should represent a single point object. We can consider this as a spatial impulse response function. In functional terms, it is the spatial domain version (i.e., the inverse Fourier transform) of the Optical transfer function, optical transfer function (OTF) of an imaging system. It is a useful concept in Fourier optics, astronomy, astronomical imaging, medical imaging, electron microscope, electron microscopy and other imaging techniques such as dimension, 3D microscopy (like in confocal laser scanning microscopy) and fluorescence microscopy. The degree of spreading (blurring) in the image of a point ob ...
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Green Fluorescent Protein
The green fluorescent protein (GFP) is a protein that exhibits green fluorescence when exposed to light in the blue to ultraviolet range. The label ''GFP'' traditionally refers to the protein first isolated from the jellyfish ''Aequorea victoria'' and is sometimes called ''avGFP''. However, GFPs have been found in other organisms including corals, sea anemones, zoanithids, copepods and lancelets. The GFP from ''A. victoria'' has a major excitation peak at a wavelength of 395 nm and a minor one at 475 nm. Its emission peak is at 509 nm, which is in the lower green portion of the visible spectrum. The fluorescence quantum yield (QY) of GFP is 0.79. The GFP from the sea pansy ('' Renilla reniformis'') has a single major excitation peak at 498 nm. GFP makes for an excellent tool in many forms of biology due to its ability to form an internal chromophore without requiring any accessory cofactors, gene products, or enzymes / substrates other than molecular ox ...
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Transgenic
A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change the phenotype of an organism. ''Transgene'' describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into a different organism. This non-native segment of DNA may either retain the ability to produce RNA or protein in the transgenic organism or alter the normal function of the transgenic organism's genetic code. In general, the DNA is incorporated into the organism's germ line. For example, in higher vertebrates this can be accomplished by injecting the foreign DNA into the nucleus of a fertilized ovum. This technique is routinely used to introduce human disease genes or other genes of interest into strains of laboratory mice to study the function or pathology involved with that part ...
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Fluorophore
A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds. Fluorophores are sometimes used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator (when its fluorescence is affected by environmental aspects such as polarity or ions). More generally they are covalently bonded to macromolecules, serving as a markers (or dyes, or tags, or reporters) for affine or bioactive reagents (antibodies, peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, such as fluorescent imaging and spectroscopy. Fluorescein, via its amine-reactive isothiocyanate derivative fluorescein isothiocyanate (FITC), has been one of the most popular fluorophores ...
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Objective Lens
In optical engineering, an objective is an optical element that gathers light from an object being observed and focuses the light rays from it to produce a real image of the object. Objectives can be a single lens or mirror, or combinations of several optical elements. They are used in microscopes, binoculars, telescopes, cameras, slide projectors, CD players and many other optical instruments. Objectives are also called object lenses, object glasses, or objective glasses. Microscope objectives The objective lens of a microscope is the one at the bottom near the sample. At its simplest, it is a very high-powered magnifying glass, with very short focal length. This is brought very close to the specimen being examined so that the light from the specimen comes to a focus inside the microscope tube. The objective itself is usually a cylinder containing one or more lenses that are typically made of glass; its function is to collect light from the sample. Magnification One of the ...
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Numerical Aperture
In optics, the numerical aperture (NA) of an optical system is a dimensionless number that characterizes the range of angles over which the system can accept or emit light. By incorporating index of refraction in its definition, has the property that it is constant for a beam as it goes from one material to another, provided there is no refractive power at the interface (e.g., a flat interface). The exact definition of the term varies slightly between different areas of optics. Numerical aperture is commonly used in microscopy to describe the acceptance cone of an Objective (optics), objective (and hence its light-gathering ability and Optical resolution, resolution), and in fiber optics, in which it describes the range of angles within which light that is incident on the fiber will be transmitted along it. General optics In most areas of optics, and especially in microscopy, the numerical aperture of an optical system such as an objective lens is defined by \mathrm = n \sin \t ...
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Contrast (vision)
Contrast is the difference in luminance or color that makes an object (or its representation in an image or display) visible against a background of different luminance or color. The human visual system is more sensitive to contrast than to absolute luminance; thus, we can perceive the world similarly despite significant changes in illumination throughout the day or across different locations. The maximum contrast of an image is termed the contrast ratio or dynamic range. In images where the contrast ratio approaches the maximum possible for the medium, there is a ''conservation of contrast''. In such cases, increasing contrast in certain parts of the image will necessarily result in a decrease in contrast elsewhere. Brightening an image increases contrast in darker areas but decreases it in brighter areas; conversely, darkening the image will have the opposite effect. Bleach bypass reduces contrast in the darkest and brightest parts of an image while enhancing luminance contr ...
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Signal-to-noise Ratio
Signal-to-noise ratio (SNR or S/N) is a measure used in science and engineering that compares the level of a desired signal to the level of background noise. SNR is defined as the ratio of signal power to noise power, often expressed in decibels. A ratio higher than 1:1 (greater than 0 dB) indicates more signal than noise. SNR is an important parameter that affects the performance and quality of systems that process or transmit signals, such as communication systems, audio systems, radar systems, imaging systems, and data acquisition systems. A high SNR means that the signal is clear and easy to detect or interpret, while a low SNR means that the signal is corrupted or obscured by noise and may be difficult to distinguish or recover. SNR can be improved by various methods, such as increasing the signal strength, reducing the noise level, filtering out unwanted noise, or using error correction techniques. SNR also determines the maximum possible amount of data that ...
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Latency (engineering)
Latency, from a general point of view, is a time delay between the Causality, cause and the effect of some physical change in the system being observed. Lag (video games), Lag, as it is known in Gaming culture, gaming circles, refers to the latency between the input to a simulation and the visual or auditory response, often occurring because of network delay in online games. The original meaning of “latency”, as used widely in psychology, medicine and most other disciplines, derives from “latent”, a word of Latin origin meaning “hidden”.  Its different and relatively recent meaning (this topic) of “lateness” or “delay” appears to derive from its superficial similarity to the word “late”, from the old English “laet”. Latency is physically a consequence of the limited velocity at which any Event (relativity), physical interaction can propagate. The magnitude of this velocity is always less than or equal to the speed of light. Therefore, every physical s ...
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Servomechanism
In mechanical and control engineering, a servomechanism (also called servo system, or simply servo) is a control system for the position and its time derivatives, such as velocity, of a mechanical system. It often includes a servomotor, and uses closed-loop control to reduce steady-state error and improve dynamic response. In closed-loop control, error-sensing negative feedback is used to correct the action of the mechanism. In displacement-controlled applications, it usually includes a built-in encoder or other position feedback mechanism to ensure the output is achieving the desired effect. Following a specified motion trajectory is called servoing, where "servo" is used as a verb. The ''servo'' prefix originates from the Latin word ''servus'' meaning slave. The term correctly applies only to systems where the feedback or error-correction signals help control mechanical position, speed, attitude or any other measurable variables. For example, an automotive power win ...
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Avalanche Photodiode
An avalanche photodiode (APD) is a highly sensitive type of photodiode, which in general are semiconductor diodes that convert light into electricity via the photovoltaic effect. APDs use materials and a structure optimised for operating with high reverse bias voltage, approaching the reverse breakdown voltage, such that charge carriers generated by the photovoltaic effect are multiplied by an avalanche breakdown; thus they can be used to detect relatively small amounts of light. From a functional standpoint, they can be regarded as the semiconductor analog of photomultiplier tubes; unlike solar cells, they are not optimised for ''generating'' electricity from light but rather for ''detection'' of incoming photons. Typical applications for APDs are laser rangefinders, long-range Optical fiber, fiber-optic telecommunication, positron emission tomography, and particle physics. History The avalanche photodiode was invented by Japanese engineer Jun-ichi Nishizawa in 1952. However, stu ...
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