Glossary

S

sample
see object
sample plane
see object plane
sampling
see undersampling
sampling rate
The measure of how often a given instrument can make a measurement. This can refer to temporal sampling (time) or spatial sampling (distance). The Nyquist sampling rate defines the minimal sampling rate to reconstruct a signal.
Synonyms: sampling
See also: Nyquist sampling
SbNa2 KCs PMT
see multi-alkali photomultiplier tube
scale bar
A visual indicator on a micrograph or figure of the actual size of a given distance.
scan rate
The rate at which the object can undergo a complete scanning cycle as part of a continuous acquisition. This is of interest to scanning microscope techniques such as confocal and multiphoton microscopies.
See also: sampling rate, scanned field, scanning, scanning microscope
scanned field
The region in the object plane that is scanned (imaged).
See also: scan rate, scanning, scanning microscope
scanning
The translation of an illumination pattern relative to a stationary object, or vice versa, in order to image a given region in the object. The pattern can be a diffraction-limited point, line, other pattern, or array thereof. Confocal and multiphoton microscopes are typically scanning techniques.
See also: raster scanning, confocal microscopy, multiphoton microscopy, point-scanning confocal microscopy, line-scanning confocal microscopy, array-scanning confocal microscopy, spinning disk confocal microscopy
scanning microscope
A microscope imaging strategy that assembles an image via scanning, including confocal or multiphoton point-scanning, line-scanning, spinning disk, and others.
Synonyms: scanning optical microscope
See also: point-scanning confocal microscopy, array-scanning confocal microscopy, spinning disk confocal microscopy, line-scanning confocal microscopy, laser scanning microscope
scanning near-field microscope
see near-field scanning optical microscopy
scanning optical microscope
see scanning microscope
scanning stage
A motorized stage capable of precise translation of the sample.
See also: stage scanning
scattering
In the context of optics, scattering refers to different physical phenomena that somehow alter the trajectory of electromagnetic radiation. The two main classifications of scattering are elastic scattering and inelastic scattering.
See also: elastic scattering, inelastic scattering, Rayleigh scattering, Mie scattering, Raman scattering, Brillouin scattering, fluorescence
scientific complementary metal-oxide-semiconductor detector (sCMOS)
One of the main image sensor designs. Each photodiode (pixel) has its own amplifier and digitizer, unlike charge-coupled device (CCD) sensors, avoiding issues with charge transfer. sCMOS detectors feature small pixels, large pixel arrays, fast readout speeds, and a wide dynamic range. Back-thinned sCMOS sensors can have peak quantum efficiency in excess of 95%.
See also: camera, charge coupled device, electron multiplying charge coupled device, detector, area detector
screen
A device used to display an image. This can be a computer monitor, an integrated screen on a microscope, or a mobile device such as a tablet.
second harmonic generation microscopy (SHG)
An non-linear optics methodology where two lower energy photons are up-converted to half the wavelength (i.e. double the frequency) of an excitation laser. This phenomenon is able to occur in non-centrosymmetric materials with a specific orientation. Collagen, microtubules, and other biomolecules create usable SHG signals.
Synonyms: frequency doubling
See also: non-linear optics, third harmonic generation microscopy
second order blue
One of the six colors in the second order of interference colors. The other colors in the second order are violet, green, yellow, orange, and red.
See also: interference, interference colors, polarized light microscopy, birefringence, Michel Lévy chart
selective plane illumination microscopy
see light sheet fluorescence microscopy
semi-apochromat objective
see fluorite objective
sensitive tint plate
see full-wave plate
shading correction
A post-processing analysis step typically used to correct for vignetting in the image, resulting in a flatter, more even image. This technique is especially useful when performing image stitching, which reduces stitching artifacts.
shearing interference
An interference pattern that can check collimation in a light source by observing the primary and secondary reflections of a shear plate onto a surface. The shearing interference produced can aid in adjusting the light so it is properly collimated.
shortpass filter
An optical filter which transmits incident light with shorter wavelengths, and reflects incident light with longer wavelengths.
Synonyms: dichroic, hot mirror
silicon photomultiplier (SiPM)
A type of photodetector that can detect single photons, constructed with an array of avalanche photodiodes.
See also: detector
silicone immersion objective
An objective lens designed for use with silicone oil as the immersion medium. This provides optimal optical performance when imaging samples with a refractive index of ~1.41, which closely matches different biological features. These objectives are designed for use with glass coverslips and popular for organoids, 3D cell cultures, tissue samples, and more.
See also: immersion objective, objective lens, immersion medium, mounting medium, coverslip, refractive index
simple microscope
A single double-convex lens with a short focal length. Examples of this instrument include a magnifying glass or reading lens.
See also: microscope, optical train, ray tracing
single element detector
see point detector
single molecule localization microscopy (SMLM)
A family of super-resolution methods leveraging different approaches for spatiotemporal separation of the emission from single molecules, allowing for localization of their centroid position. Acquisition of a large number of image frames provides enough localizations for creation of a composite super-resolution reconstruction.
Synonyms: localization microscopy, pointillist microscopy
See also: DNA-PAINT, photoactivated localization microscopy, stochastic optical reconstruction microscopy
single pixel photon counter array
see single-photon avalanche diode array
single-beam gradient force trap
see optical tweezers
single-mode fiber
A laser fiber which carries light of only one transverse mode, which is coherent.
See also: laser, multi-mode fiber
single-photon avalanche diode array (SPAD)
An array detector composed of individual avalanche photodiodes which provide single-photon sensitivity. SPAD arrays provide a powerful option for super-resolution image scanning microscopy (ISM) detection using otherwise traditional point-scanning confocal and multiphoton microscopy systems.
Synonyms: single pixel photon counter array
See also: image scanning microscopy, area detector
slide
A thin, transparent (usually glass) surface that is used to mount a specimen onto for imaging.
See also: coverslip
slide scanning
see whole slide imaging
slit-scanning
see line-scanning confocal microscopy
slow axis
In a Wave Plate, the slow axis is the axis with the longest optical path length (highest refractive index). It is perpendicular to the fast axis.
See also: fast axis, wave plate, birefringence, retardation
small-angle approximation
see paraxial approximation
Snell–Descartes law
see Snell's law
Snell's law
This law relates the angle of incidence (1) of light traveling in a medium of given refractive index (n1) to its angle of refraction (2) as it enters a medium of different refractive index (n2) as: n1  sin(1) = n2  sin(2)
Synonyms: law of refraction, Snell–Descartes law, ibn-Sahl law
See also: refraction, refractive index, ordinary ray
software development kit (SDK)
A collection of software development tools in one installable package.
software-triggered acquisition
An acquisition mode where a camera or imaging detector is activated using a software command or program. This can be done sequentially to perform timelapse or multi-point image acquisition at high speeds.
See also: hardware-triggered acquisition
solid angle
A three-dimensional (3D) angular volume that can be thought of as the 3D equivalent of the numerical aperture (NA) of the system. In the context of microscopy and using cone-like illumination/detection, the solid angle can be estimated as the square of NA multiplied by pi.
See also: numerical aperture, f-number, angular aperture
source
see light source
source-focused illumination
see critical illumination
sparkle
see hot pixel
spatial cutoff frequency
see cutoff frequency
spatial frequency
The Fourier transform of a real space image yields its frequency space representation, where low spatial frequencies correspond to coarse image features and high spatial frequencies to fine features.
See also: cutoff frequency, Fourier optics, Fourier transform, frequency space
spatial frequency domain
see frequency space
spatial light modulator (SLM)
Optical components capable of somehow modifying an incident wavefront in a controlled manner. Types of spatial light modulators include the digital micromirror device (DMD) and liquid crystal on silicon (LCoS).
See also: digital micromirror device
spatial resolution
see resolved distance
spatial transcriptomics
A molecular profiling method that measures gene activity in a tissue sample, mapping where activity is occurring.
spatially coherent illumination
An illumination mode where the incident light has a high degree of coherence, as opposed to partially-coherent or incoherent illumination. If the detected light is also highly coherent, then it is a coherent imaging system.
Synonyms: coherent
See also: temporally coherent illumination, coherence, coherent imaging system, incoherent imaging system
specimen
An animal, plant, piece of a mineral, etc., that is the subject of microscopic observation.
Synonyms: sample
See also: object
specimen plane
see object plane
specimen scanning
see stage scanning
spectral imaging microscopy
A microscopy technique where emission light from a multitude of fluorophores is mathematically unmixed, usually by taking a sequence of images with varying wavelengths of illumination and/or detection wavebands. This technique is also useful for identifying and removing autofluorescence from the image.
See also: fluorophore, fluorescence, confocal microscopy
spherical aberration
An optical aberration where light from a spherical lens is focused onto separate axial positions depending on the position of the ray relative to the center.
See also: aberration, coma
spherical wave
A wavefront of light that propagates in a sphere away from a point source in 3D space.
See also: wave, wavefront, plane wave
spherochromatism
see chromatic aberration
spinning disk confocal microscopy (SDCM)
An array-scanning confocal microscopy method that typically uses a Nipkow disk with hundreds of pinholes arranged in spirals that are rotated at high speed to sample the object in parallel and build the image. It is a high-speed approach and still provides a high degree of optical sectioning.
Synonyms: Nipkow disk confocal microscopy
See also: Nipkow disk, confocal microscopy, array-scanning confocal microscopy, confocal, pinhole
spot-scanning
see point-scanning
spring-loaded objective
An objective with a spring loaded component in the front lens assembly, which prevents damage to the objective caused by accidental "crashing" into a specimen, cover glass or other microscope component.
See also: objective lens
stage
A core component of a light microscope, where a specimen is placed and observed via the microscope objective. Many microscope stages are now motorized to allow for precise movement, many times controlled by external software.
See also: centering stage, cooling stage, gliding stage, heating stage, levelling stage, mechanical stage, rotating stage, scanning stage, universal stage
stage clip
A small, usually metallic clip used to secure specimens to a microscope stage.
See also: stage
stage micrometer
A microscope calibration slide with precisely spaced markings.
See also: stage
stage scanning
An image scanning technique where the stage is rapidly moved while the optics are kept stationary. This technique is an alternative to raster scanning of the illumination spot, for example.
Synonyms: specimen scanning
See also: raster scanning
stand
see microscope base
stereomicroscope
A light microscope which utilizes separate optical paths for each eyepiece, with a slight angle between the observation directions. This allows for stereo observation, where the object has a more three-dimensional appearance.
See also: Greenough stereomicroscope, common main objective stereomicroscope
stimulated emission depletion microscopy (STED)
A super-resolution technique using a donut-shaped depletion beam and typical Gaussian-shaped excitation beam in an overlapped configuration. The depletion beam is used to prevent fluorophores from fluorescing via the phenomenon of stimulated emission depletion. The non-linear response of fluorophores to increasing depletion beam intensity makes it possible to excite fluorescence from a sub-diffraction limited area at the center of the overlaid beams.
See also: super-resolution
stimulated raman scattering microscopy (SRS)
A microscopy technique based on the principle of SRS spectroscopy, where a pump and probe (Stokes) beam are combined to probe specific vibrational transitions. SRS is resonantly enhanced compared to spontaneous Raman scattering using only a pump beam.
See also: Raman microscopy, Raman scattering, coherent anti-stokes Raman scattering microscopy
stitching
see image stitching
stochastic optical reconstruction microscopy (STORM)
A super-resolution microscopy technique employing photoswitchable small-molecule fluorescent dyes for spatiotemporal isolation of single emission events. As with other single molecule localization microscopies, STORM enhances resolution via localization centroid position of each emission profile over numerous image frames.
See also: DNA-PAINT, photoactivated localization microscopy, single molecule localization microscopy, super-resolution
stop
A stop that is placed in an image or aperture plane to control the diameter of the field of view or the numerical aperture, respectively. It may be an iris diaphragm.
Synonyms: diaphragm
See also: iris diaphragm, field stop, aperture stop, illuminated field stop, illuminating aperture stop
strain-free
A designation for a specialized type of objective lens designed specifically for polarized light microscopy. Since strain in glass can induce changes in polarized light as it passes through, strain-free objectives are essential for microscopy applications depending on polarized light.
See also: polarized light, polarized light microscopy
stray light
Unwanted light rays that can negatively impact the performance of a light microscope, usually resulting from unplanned reflection or scattering somewhere along the optical train.
See also: scattering, optical train
structured illumination microscopy (SIM)
Using beam interference to create a high-frequency illumination patterns, high spatial frequency (diffraction-limited) object features outside of the passband of the system can be down-modulated via frequency mixing into the passband, and computationally identified and restored to their correct position in post-processing to realize super-resolution.
Synonyms: super-resolution structured illumination microscopy
See also: super-resolution, image scanning microscopy
stuck pixels
see hot pixel
substage
An component of a light microscope located beneath the stage, which supports condensers, stops, and other accessories.
See also: condenser
substage condenser
A condenser that is located beneath the microscope stage, typically on an upright microscope. Inverted microscopes typically have the condenser placed above the stage.
See also: substage, condenser, upright microscope
super fluor objective
CFI Super Fluor Series objective lenses provide the highest level of ultra-violet transmission, high numerical aperture, and chromatic aberration correction consistent with other fluor/semi-apo type objectives. Thanks to high transmission below 340 nm, Super Fluor objectives are well-suited for dyes such as Fura-2.
See also: objective lens, fluorite objective
super-long working distance objective (SLWD)
A class of objectives which support a longer working distance compared to standard, long working distance (LWD), or extra-long working distance (ELWD) objectives.
See also: long working distance objective, extra-long working distance objective
super-resolution (SR)
A designation for microscope-based imaging methods that overcome the Diffraction limit of conventional microscopes, and typically by a factor of at least ~2X. Some conventional techniques, such as confocal microscopy, can provide lateral resolution improvement of ~1.4X under correct conditions - sometimes referred to as "enhanced resolution."
Synonyms: nanoscopy
See also: structured illumination microscopy, single molecule localization microscopy, stimulated emission depletion microscopy, expansion microscopy, image scanning microscopy
super-resolution objective
An objective designed for use in super-resolution applications. These objectives typically have some of the highest numerical apertures available, and are highly corrected for chromatic and spherical aberrations. They may also be optimized for use with very high power laser illumination.
See also: super-resolution, objective lens
super-resolution structured illumination microscopy
see structured illumination microscopy
superposition principle
A mathematical principle stating that, for all linear systems, the net response caused by two or more stimuli is the sum of the responses that would have been caused by each stimulus individually. This can be applied to constructive and destructive wave interference.
See also: interference
swing-out top lens condenser
A substage condenser with an optional additional lens that increases the numerical aperture (NA) while decreasing the illuminated field of view, typically used at higher magnifications.
See also: condenser, field of view, numerical aperture