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f-number (f/#): In microscopes, it is the ratio of the focal length of the objective lens to the diameter of the entrance pupil.; Synonyms: focal ratio, f-ratio, f-stop; See also: numerical aperture, solid angle, angular aperture
f-ratio: see f-number
f-stop: see f-number
fast axis: In a birefringent material, the axis of lower refractive index and perpendicular to the slow axis. Light polarized parallel to the fast axis thus travels through the material faster compared to the slow axis.; See also: slow axis, birefringence, polarized light, compensator, optical indicatrix
fiber optic illuminator: An illuminator consisting of a light source and optics for collecting its output for transmission via a flexible end-emitting optical assembly to where the tip is positioned for object illumination.; See also: illuminator
field curvature: A simple lens focuses the image of a planar object to a spherical surface.; Synonyms: Petzval curvature, Petzval field curvature, curvature of image field, curvature of field; See also: aberration
field diaphragm: see field stop
field lens: A lens or lens system that is place at or proximal to an image plane in order to match the exit pupil of the preceding optic with the entrance pupil of the following optic, reducing vignetting.; See also: optical train
field number (FN): The diameter of the field of view, as measured at the intermediate image plane, supported by different microscope components. Objective lenses, eyepieces, and other components have their own limiting field numbers.; See also: field of view, eyepiece field number, objective lens field number
field of view (FOV): The usable diameter of the image measured at the intermediate image plane, it cannot be larger than the most limiting field number of the constituent optical components, such as the eyepiece field number and objective lens field number.; Synonyms: object field, microscope field-of-view; See also: field number, eyepiece field number, objective lens field number
field plane: One of the conjugate set of image-forming planes present in a microscope optical train.; Synonyms: image-forming planes; See also: aperture plane, conjugate planes, field stop
field stop (FS): A stop (diaphragm) located in a field plane that controls the extent of the field of view. It is often an adjustable iris diaphragm.; Synonyms: field diaphragm; See also: aperture stop, iris diaphragm, field of view, conjugate planes
filament lamp: A light source that uses a filament heated using an electric current as a black body radiator.; See also: lamp, light source, bulb
filar eyepiece: see micrometer eyepiece
filar micrometer: An eyepiece which includes reference lines or some type of reticle in the intermediate image plane and with axial position adjustable using a micrometer screw gauge.; Synonyms: filar eyepiece; See also: eyepiece, reticle
filter: In the context of signal processing and optics, its any device or computational approach for removing certain components from the signal (e.g., using an optical filter to detect only a desired spectral waveband).; See also: excitation filter, emission filter, interference filter, narrow-bandpass filter, bandpass filter, broad-bandpass filter, color conversion filter, color filter, heat filter, longpass filter, neutral density filter, polarizing filter, shortpass filter
final image: The image formed at the final image plane in the optical train, it is usually where the detector is placed.; See also: primary image, intermediate image, image, optical train
fine focus adjustment: That part of microscope mechanical focusing mechanism that allows for small step sizes of the focus along the optic axis.; Synonyms: fine focusing; See also: focus, coarse focus adjustment
fine focusing: see fine focus adjustment
finite intermediate image distance objective: Objective lens that forms an image of the object at a finite distance, as opposed to an infinity-corrected objective, where light emerges collimated from the objective and requires an additional tube lens to form the image.; Synonyms: fixed focal length objective; See also: objective lens, fixed tube length system, infinity optical system
first order compensator: see full-wave plate
first order red: In a polarized light microscope, retardation of ~550 nm between the ordinary and extraordinary ray results in a red interference color.; See also: full-wave plate, compensator
first order red compensator: see full-wave plate
first order retardation plate: see full-wave plate
first order yellow: The first interference color that becomes visible with increasing retardation between the ordinary and extraordinary rays in a polarized light microscope (~400 nm).; See also: first order red, polarized light microscope, birefringence, compensator, retardation
fixed focal length objective: see finite intermediate image distance objective
fixed tube length system: A microscope design where the objective lens forms the intermediate image at a finite distance without the use of an additional tube lens. The optical tube length has been standardized at 160 mm by the Royal Microscopical Society (RMS).; See also: finite intermediate image distance objective
flat-field objective: see plan objective
fluorescence: The emission of a photon due to relaxation of an electron from a singlet excited electronic state. It is a type of inelastic scattering.; See also: autofluorescence, fluorescence microscopy, fluorophore, inelastic scattering
fluorescence correlation microscopy (FCM): The use of fluorescence correlation spectroscopy (FCS) to construct an image using a microscope.; See also: fluorescence correlation spectroscopy, fluorescence cross-correlation spectroscopy
fluorescence correlation spectroscopy (FCS): Acquisition and analysis of fluorescence measurements at a particular point over time, often used to measure diffusion rates.; See also: fluorescence correlation microscopy, fluorescence cross-correlation microscopy
fluorescence cross-correlation microscopy: see fluorescence correlation spectroscopy
fluorescence cross-correlation spectroscopy (FCCS): Combined analysis of fluorescence correlation spectroscopy (FCS) data for spectrally-distinct fluorophores, often used to assess protein-protein interaction.; See also: fluorescence correlation microscopy, fluorescence correlation spectroscopy
fluorescence in situ hybridization (FISH): The use of fluorescently labeled single-strand oligonucleotide probes to highlight endogenous nucleic acids of interest. Traditionally, the detection of single RNA transcripts is referred to as single molecule FISH (smFISH).; See also: fluorescence, fluorescence microscopy
fluorescence lifetime imaging microscopy (FLIM): The measurement of fluorescence signal decay following excitation in an image. Can be used to distinguish spectrally-similar fluorophores. Environmental factors can also affect fluorescence lifetime.; See also: fluorescence, fluorescence microscopy, fluorophore, Förster resonance energy transfer
fluorescence microscopy: A microscope configured to excite fluorophores within a sample and subsequently form an image using the emitted fluorescence.; Synonyms: epifluorescence microscope; See also: fluorescence, fluorophore, excitation filter, emission filter, dichroic mirror
fluorescence recovery after photobleaching (FRAP): The measurement of fluorescence intensity recovery rate in a specific region following photobleaching. Often used to measure diffusion or trafficking.; See also: fluorescence, photobleaching
fluorite objective: An objective featuring glass composed of fluorite or synthetic alternatives designed to correct chromatic and spherical aberration in 2-3 wavelengths. Generally, apochromat lenses offer the best optical performance, followed by fluorite lenses, followed by achromat lenses.; Synonyms: semi-apochromat objective; See also: objectives, aberration
fluorochrome: see fluorophore
fluorophore: A system that exhibits fluorescence. Widely used types for biological imaging include fluorescent proteins (e.g., GFP, mCherry, etc.) and small molecule dyes (rhodamines, cyanines, etc.).; Synonyms: fluorochrome; See also: fluorescence, fluorescence microscopy
focal adjustment: see focusing
focal distance: see focal length
focal length: The distance from a lens at which light passing through the lens converges.; Synonyms: focal distance; See also: focal plane, focal point
focal plane: The plane orthogonal to the optical axis that is located one focal length away from a lens.; See also: focal length, focal point
focal point: The central point of the focal plane that lies on the optical axis, one focal length away from the lens. A lens or lens system typically has a front focal point (the first focal point in the direction of light travel) and a back focal point on the opposite side.; Synonyms: focus; See also: focal length, focal plane
focal ratio: see f-number
focal ray: In ray tracing, the ray traveling from the source through the front focal plane of a lens and refracted by that lens to continue traveling parallel to the optic axis.; See also: ray, ray tracing, characteristic rays, parallel ray, geometric optics, front focal plane
focal volume: A more realistic model of light convergence that accounts for diffraction and other factors. Rather than a perfect point, a lens will focus light to a blurred spot centered at the focal length of the lens.; See also: focal length, focal point, focal plane
focus: see image based autofocus
focus series: see Z stack
focusing: Use of the microscope focusing mechanism to adjust the distance between the sample and objective lens and achieve a clear image.; Synonyms: focal adjustment; See also: focusing mechanism, coarse focus adjustment, fine focus adjustment, focal point, focal plane
focusing mechanism: The mechanism by which focusing is achieved. For example, the objective lens is generally translated up or down relative to a stationary sample to enable focusing or examination of different planes across various sample depths.; See also: focus, focusing, coarse focus adjustment, fine focus adjustment
Förster resonance energy transfer (FRET): The non-radiative energy transfer from a donor fluorophore to a nearby acceptor fluorophore, used to measure molecular proximity in an ~1 - 10 nm range.. Requires an overlap between the donor emission spectrum and acceptor excitation spectrum.; See also: fluorescence, fluorophore
four-wave mixing (FWM): Process whereby interaction between light waves of two or three different frequencies (wavelengths) results in light of one or two new frequencies.; See also: coherent anti-stokes Raman scattering microscopy, stimulated raman scattering microscopy
Fourier optics: A wave-optical approach utilizing the Fourier transform of an image to convert from working in real space to working in frequency space, which affords greater computational simplicity for performing tasks such as deconvolution.; See also: Fourier transform, spatial frequency, image space, frequency space
Fourier ptychographic microscopy (FPM): A technique that provides both high resolution and a large field of view simultaneously by using coded illumination patterns to realize a high synthetic aperture. While this is also a quantitative phase microscopy technique, it doesn't require interferometry.; Synonyms: Fourier ptychography; See also: Fourier optics, Fourier transform, quantitative phase microscopy
Fourier ptychography: see Fourier ptychographic microscopy
Fourier space: see frequency space
Fourier transform (FT): An integral transform that is useful in optics for switching between working in real space and frequency space.; See also: Fourier optics, spatial frequency, image space, frequency space
frame averaging: The process of averaging multiple image frames together, finding the average intensity value at each pixel across the set of frames. This is useful for improving image quality by averaging out noise in the resultant image.; See also: averaging, line averaging, noise
free working distance (FWD): The distance between the objective surface and the closest part of the coverslip surface when the sample is in focus. In non-coverslip corrected objectives, it is the distance from the objective surface to the closest part of the object surface.; See also: working distance, focal length, coverslip correction
frequency domain: see frequency space
frequency doubling: see second harmonic generation microscopy
frequency space: A real space image of an object, which is in the spatial domain, can be subjected to a Fourier transform to yield its frequency domain representation, where the signal at each point corresponds to a spatial frequency present in the image. This frequency space image can also be converted back to a spatial domain image using a Fourier transform.; Synonyms: Fourier space, reciprocal space, spatial frequency domain, frequency domain; See also: Fourier optics, Fourier transform, image space, spatial frequency
frequency tripling: see third harmonic generation microscopy
front focal plane (FFP): The focal plane located at the front of a lens or lens system when considering the direction of light travel. The focal plane located on the other side of the lens from the front focal plane is known as the back focal plane.; See also: focal plane, back focal plane
full wave retardation plate: see full-wave plate
full-wave plate: A wave plate that introduces a full wavelength (~550 nm) phase difference between the orthogonal polarization components (eigenpolarizations), resulting in non-birefringent materials having a red color.; Synonyms: first order compensator, first order red compensator, first order retardation plate, full wave retardation plate, sensitive tint plate; See also: first order red, polarized light microscope, birefringence, compensator, retardation