Glossary
C
- camera
- A camera is a device used to capture an image. While cameras originally relied on the exposure of light-sensitive film to capture images, modern cameras are typically digital, featuring an area detector consisting of a large pixel array. Digital cameras typically feature either charge coupled device (CCD) or scientific complementary metal-oxide-semiconductor (sCMOS) detectors.
- See also: scientific complementary metal-oxide-semiconductor detector, charge coupled device, electron multiplying charge coupled device, area detector, detector, pixel, digital image
- cardinal points
- The focal points, principal points, and nodal points of a lens or lens system in geometric optics.
- See also: ray tracing, focal point, principal points, nodal points, geometric optics
- cardioid condenser
- A type of condenser for diascopic darkfield illumination that relies on internal mirrors to illuminate the object via reflection, minimizing optical aberrations.
- See also: darkfield, condenser, darkfield stop
- catadioptric
- An optical system utilizing both refraction (lenses) and reflection (mirrors).
- See also: optical train, catoptric
- catoptric
- An optical system utilizing only reflection from mirrors.
- See also: optical train, catadioptric
- cell culture
- see tissue culture
- cell painting
- A high content imaging based assay utilizing multiplex fluorescence detection of different cell components for automated morphological feature measurement and phenotyping.
- See also: high content imaging, phenotypic screening
- centering nosepiece
- A microscope objective lens nosepiece where each objective can be laterally translated for exact alignment with the optic axis.
- See also: nosepiece, body tube
- centering stage
- A type of rotating stage that can be adjusted such that the axis of rotation is aligned with the optical axis, especially important for polarized light observation.
- See also: stage, rotating stage
- centering telescope
- see phase telescope
- CF objective (CF)
- Nikon CF (chromatic aberration-free) objectives feature multilayer anti-reflection coatings and extra-low-dispersion glasses; designed for fixed tube length optical systems.
- See also: fixed tube length system, objective lens, optical coating, CFI60 objective
- CFI60 objective (CFI60)
- Nikon CFI60 (chromatic aberration-free infinity, 60mm parfocal distance) objectives features multilayer anti-reflection coatings and extra-low-dispersion glasses; designed for infinity optical systems with a tube length of 200 mm.
- See also: infinity optical system, infinity-corrected objective, objective lens, optical coating, CF objective
- CFI75 objective (CFI75)
- Nikon CFI75 (chromatic aberration-free infinity, 75mm parfocal distance) objectives features multilayer anti-reflection coatings and extra-low-dispersion glasses; designed for infinity optical systems with a tube length of 200 mm.
- See also: infinity optical system, infinity-corrected objective, objective lens, optical coating
- CFI90 objective (CFI90)
- Nikon CFI90 (chromatic aberration-free infinity, 90mm parfocal distance) objectives features multilayer anti-reflection coatings and extra-low-dispersion glasses; designed for infinity optical systems with a tube length of 200 mm.
- See also: infinity optical system, infinity-corrected objective, objective lens, optical coating
- channel
- In the context of microscopy, this usually refers to detection of a certain type of image information (e.g., brightfield, fluorescence in a defined waveband, etc.).
- characteristic rays
- A set of three rays typically used to define image formation in ray tracing: the principal ray (often referred to as the chief ray), the parallel ray, and the focal ray.
- See also: ray, ray tracing, principal ray, chief ray, parallel ray, focal ray, geometric optics
- charge coupled device (CCD)
- A class of area detector typified by the use of charge coupling to move photoelectrons generated at each pixel to a readout register for amplification and digitization.
- See also: area detector, electron multiplying charge coupled device, camera
- chief ray
- In ray tracing, a ray traveling from an off-axis point on the edge of the field of view and through the center of any aperture planes and entrance/exit pupils.
- See also: ray, ray tracing, characteristic rays, principal ray, geometric optics, marginal ray, microscope entrance pupil, microscope exit pupil
- chromatic aberration
- Aberrations arising from the wavelength dependence of refraction that result in different colors of light being focused to different points in the axial (Z) directions (all rays) and in the lateral (XY) directions (oblique rays).
- Synonyms: chromatic distortion, spherochromatism
- See also: lateral chromatic aberration, axial chromatic aberration, aberration
- chromatic distortion
- see axial chromatic aberration
- circle of confusion
- see circle of least confusion
- circle of indistinctness
- see circle of least confusion
- circle of least confusion
- The finest focal spot that can be created by an optical system given the presence of astigmatism and spherical aberration.
- Synonyms: circle of confusion, disk of confusion, circle of indistinctness, blur circle, blur spot
- See also: astigmatism, spherical aberration, aberration
- circularly polarized light
- see linearly-polarized light
- circularly-polarized light
- A specific type of elliptically polarized light where the X and Y components (eigenpolarizations) are of equal magnitude and out of phase by a quarter wavelength. It can be either left- or right-handed.
- See also: polarized light, elliptically-polarized light, quarter-wave plate
- coarse focus adjustment
- That part of microscope mechanical focusing mechanism that allows for large step sizes of the focus along the optic axis.
- Synonyms: coarse focusing
- See also: focus, fine focus adjustment
- coarse focusing
- see coarse focus adjustment
- coherence
- Coherence describes the ability of light waves to interfere. Interference is greatest when two or more waves have high monochromaticity (are a single color) and a constant phase relationship. Light can be coherent, incoherent, or partially coherent.
- See also: coherent imaging system, incoherent imaging system, spatially coherent illumination, temporally coherent illumination
- coherent
- see spatially coherent illumination
- coherent anti-stokes Raman scattering microscopy (CARS)
- A type of four-wave mixing where the combined action of a pump and Stokes beam results in occupation of a higher vibrational mode. Further mixing with the probe beam elevates the system to a second virtual state from which it can relax to the ground state, resulting in coherent emission at the anti-Stokes frequency.
- See also: Raman microscopy, Raman scattering, inelastic scattering, four-wave mixing
- coherent imaging system
- An imaging system where the illumination and detection light have a high degree of coherency, resulting in interference effects. The impulse response of such a system is the amplitude point-spread function, rather than the intensity point-spread function, as with incoherent imaging systems.
- See also: incoherent imaging system, spatially coherent illumination, temporally coherent illumination, interference, amplitude point-spread function
- coherent spread function
- see amplitude point-spread function
- coherent transfer function
- see amplitude transfer function
- collector
- see collector lens
- collector lens
- Lens in an optical system responsible for collecting light from the light source and imaging it onto the plane of the condenser aperture stop.
- Synonyms: collector
- See also: aperture stop, condenser, optical train
- collimation
- A beam of collimated light consists of parallel rays, minimizing the spread of the beam as it propagates. While no beam can ever be perfectly collimated, a laser beam are usually highly collimated.
- See also: laser, diffuser
- colocalization
- A family of image analysis techniques for assessing the pixel-wise co-occurrence of image features in different channels. Commonly applied metrics are the Pearson correlation coefficient and Mander's overlap coefficient.
- color balance filter
- see color conversion filter
- color contrast filter
- see color filter
- color conversion filter
- An optical filter used to adjust the color temperature of incident light from a broadband source, such as a halogen lamp.
- Synonyms: color balance filter
- See also: filter
- color filter
- An optical filter allowing the passage of a certain color or waveband of light.
- Synonyms: color contrast filter
- See also: filter
- coma
- A type of optical aberration arising from differences in magnification between light passing through different parts of a lens, causing the image of an off-axis point source to be shaped like a comet pointed away from the optic axis.
- Synonyms: comatic aberration
- See also: aberration
- comatic aberration
- see coma
- common main objective stereomicroscope (CMO)
- A stereomicroscope design using a single objective lens to image the object, with light in the back focal plane divided between two parallel optical paths leading to different eyepieces.
- See also: stereomicroscope, Greenough stereomicroscope
- comparison microscope
- A system where a pair of multiple microscopes are optically connected to provide a split view of both fields of view simultaneously.
- See also: microscope
- compensating eyepiece
- An eyepiece designed to help correct for chromatic aberration not entirely corrected for by the objective lens.
- See also: eyepiece, chromatic aberration, lateral chromatic aberration
- compensator
- An optical component used to introduce an (adjustable) optical path length difference (retardation) between the normal components (eigenpolarizations) of a polarized light wave. A wave plate usually introduces a fixed optical path difference.
- See also: retardation, wave plate, polarized light microscopy, birefringence
- complex pupil function
- see pupil function
- compound microscope
- Microscope designs using two or more sets of lenses (e.g., objective lens and eyepiece) to form an image of the object.
- See also: microscope
- computational microscopy
- Microscopy techniques where the final image is not acquired directly but digitally reconstructed from the raw data.
- See also: Fourier ptychographic microscopy, light field microscopy, single molecule localization microscopy, structured illumination microscopy
- condenser
- An optical component consisting of one or more lenses that is used to optimally illuminate the object.
- See also: condenser aperture, optical train
- condenser aperture
- Aperture of the condenser lens system and by extension the illumination optics. It is located in a conjugate aperture plane and an adjustable condenser aperture stop can be used to control its diameter.
- Synonyms: illuminating aperture
- See also: condenser, aperture, aperture stop, aperture plane, condenser aperture stop
- condenser aperture diaphragm
- see condenser aperture stop
- condenser aperture stop
- An adjustable aperture stop located at the condenser aperture that controls its diameter, varying the numerical aperture and depth of field of illumination.
- Synonyms: condenser aperture diaphragm
- See also: condenser, condenser aperture, aperture stop, illuminating aperture
- confocal
- In optics this term generally refers to features occurring in conjugate focal (confocal) planes. However, this term is also commonly used to refer to confocal microscopy given the importance of the confocality of the image with the pinhole aperture(s).
- See also: confocal microscopy
- confocal laser scanning microscopy (CLSM)
- A technique in which an image is formed point-by-point as a focused laser spot is scanned across a sample and emitted light is read by a point detector. Importantly, emitted light is passed through a physical pinhole that blocks out of focus light from reaching the detector to enable optical sectioning.
- See also: confocal microscopy, optical sectioning, confocal
- confocal microscopy
- Scanned illumination with a fine pattern (e.g., diffraction-limited point) and detection through an aperture mask matching the illumination pattern in a conjugate field plane, which rejects out-of-focus light.
- See also: confocal, confocal volume, confocal theta microscopy, array-scanning confocal microscopy, spinning disk confocal microscopy, optical sectioning
- confocal point-spread function
- The point-spread function (PSF) of a point-scanning confocal microscopy system, which may be expressed as the square of the Intensity PSF in an ideal system with infinitely small detection aperture.
- See also: confocal microscopy, point-spread function, intensity point-spread function
- confocal scanner unit (CSU)
- The landmark series of spinning disk confocal microscopy instruments manufactured by the Yokogawa Electric Corporation, including the CSU-X1, CSU-W1, and CSU-W1 SoRa.
- See also: confocal microscopy, spinning disk confocal microscopy, Nipkow disk, array-scanning confocal microscopy
- confocal theta microscopy
- A type of confocal microscopy that uses one objective for illumination and a second objective oriented orthogonal to the illumination axis for detection to realize an isotropic point-spread function. This technique shares several similarities with light sheet microscopy.
- See also: confocal microscopy, light sheet fluorescence microscopy
- confocal volume
- Related to the confocal point-spread function (PSF), it is the smallest discrete volume that can be detected in a confocal system, usually on the order of femtoliters with high NA objectives.
- See also: confocal microscopy, confocal point-spread function, fluorescence correlation spectroscopy, voxel
- conjugate planes
- Geometric optics reveals two sets of conjugate planes in a typical optical train - the aperture planes (illumination conjugate set) and the field planes (image-forming conjugate set). Planes in each set are simultaneously in focus and can be viewed superimposed.
- See also: optical train, conjugate points, geometric optics, aperture plane, field plane
- conjugate points
- In geometric optics, a given object point and the corresponding image point imaged by a lens or lens system.
- See also: geometric optics, conjugate planes, optical train
- conoscopic figure
- see phase telescope
- conoscopic interference pattern
- The interference pattern generated in the back focal plane of the objective when using polarized light microscopy.
- Synonyms: conoscopic figure
- See also: conoscopy, polarized light microscopy, polarized light, back focal plane
- conoscopy
- The practice of observing the conoscopic interference pattern, usually for measuring crystal orientation and birefringence and performed using a Bertrand lens or phase telescope.
- See also: conoscopic interference pattern, polarized light microscopy, Bertrand lens, phase telescope
- contrast
- Difference between signal levels of given image features - most often the difference in intensity.
- See also: contrasting technique
- contrast transfer function (CTF)
- An empirical measure of image contrast based on the imaging of a periodic line grating, it is functionally similar to the modulation transfer function (MTF).
- See also: modulation transfer function, optical transfer function, phase transfer function
- contrasting technique
- A general classification for microscopy methods that introduce/detect contrast in the final image.
- Synonyms: imaging modality
- See also: contrast
- cooling stage
- A type of microscope stage that is integrated with a device for precisely cooling the specimen. Such stages may also be capable of specimen warming.
- See also: stage
- correction
- Approaches for compensating for the effects of optical aberrations.
- See also: aberration
- correction class
- The relative level of aberration correction in objective lenses, usually divided into three classes: achromat (lowest), fluor/semi-apochromat (middle), and apochromat (highest).
- See also: achromat objective, fluorite objective, apochromat objective, objective lens
- correction collar
- A rotatable collar on an objective lens that adjusts the position of a lens or lens system to correct for spherical aberration induced by unexpected changes in optical path length (usually due to variability in coverslip thickness).
- See also: auto correction collar, spherical aberration, aberration, coverslip, coverslip correction, objective lens
- cover glass
- see coverslip
- cover slip
- see coverslip
- coverglass
- see coverslip
- coverslip
- A thin and flat piece of glass commonly used to cover slide-based preparations. Different shapes, widths, and thicknesses are available.
- Synonyms: cover glass, coverglass, cover slip
- See also: correction collar, coverslip correction
- coverslip correction
- When an objective lens is corrected for the presence of a glass coverslip in the optical path. This is usually designated on the objective barrel following tube length. 0.17 mm is most common and corresponds to the thickness of a typical #1.5 coverslip. Objectives may also feature a coverslip correction collar.
- See also: coverslip, correction collar, free working distance
- critical illumination
- Illumination of the object by focusing the image of the light source directly superimposed on it, providing a high level of brightness over a small field.
- Synonyms: source-focused illumination, Nelsonian illumination
- See also: Köhler illumination
- crossed polarizers
- In a polarized light microscope, when the polarizer axis is aligned in one direction, usually East-West (E-W) and the analyzer in an orthogonal one (usually N-S).
- See also: polarized light microscopy, extinction, polarized light, birefringence, analyzer
- crystal optics
- The field of optics concerned with the behavior of light in anisotropic materials, usually crystals.
- See also: polarized light microscopy, polarized light, birefringence, anisotropy
- curvature of field
- see field curvature
- curvature of image field
- see monochromatic aberrations
- cutoff frequency
- The highest spatial frequency that can be transmitted by the optical system.
- Synonyms: spatial cutoff frequency
- See also: spatial frequency, modulation transfer function, optical transfer function, amplitude transfer function, Fourier optics
