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Microscopy glossary & taxonomy
Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions?
Mary Chitty MSLS  mchitty@healthtech.com
Last revised January 09, 2020

Technologies map  This glossary is a sub-category of Molecular Imaging  Related glossaries include Cell & Tissue technologies

atomic force microscopy:  A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical  position is recorded as a spring attached to the probe rises and falls in response to peaks and  valleys on the surface. These deflections produce a topographic map of the sample. MeSH, 1995

Coherent Anti-Stokes Raman Scattering CARS  microscopy:  Allows researchers to localize specific types of molecules inside living cells without artificial dyes or genetic modifications. CARS builds on Raman spectroscopy, which chemists have used for decades to create fingerprints for specific molecules.  [Dan Ferber "New CARS could drive cell biology" Biophysical Society, Day 2 Report, Feb. 25, 2002] BioMedNet http://news.bmn.com/conferences/list/view?
fileyear=2002&fileacronyn=BPS&fileday=day2&pagefile=story_2.html

confocal microscopy: A light microscopic technique in which only a small spot is illuminated and observed at a time. An image is constructed through point- by- point scanning of the field in this manner. Light sources may be conventional or laser, and fluorescence or transmitted observations  are possible. MeSH, 1995

Used for fluorescence detection. Related term: scanning technology.

Confocal Scanning Laser Scanning Microscopy CLSM: See under laser scanning microscopy

cryoelectron microscopy: Cell technologies

electron microscopy:  Visual and photographic microscopy in which electron beams with wavelengths thousands of times shorter than visible light are used in place of light, thereby allowing much greater magnification.  MeSH

In high-resolution electron microscopy one can begin to do ``crystallography without crystals'', averaging thousands of images of single molecules or other assemblies to reveal near atomic level structure. These methods demand intense computing hardware, software and algorithm development. Opportunities in Molecular Biomedicine in the Era of  Teraflop Computing:  March 3 & 4, 1999, Rockville, MD,  NIH Resource for Macromolecular Modeling and Bioinformatics;  Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign Molecular Biomedicine in the Era of Teraflop Computing - DDDAS.org  Narrower term: transmission electron microscopy (TEM).

evanescent wave: See under Total Internal Reflectance Fluorescence Microscopy

FLIM Fluorescence Lifetime Imaging Microscopy:  Wikipedia https://en.wikipedia.org/wiki/Fluorescence-lifetime_imaging_microscopy

fluorescence microscopy:  Microscopy of specimens stained with fluorescent dye (usually fluorescein  isothiocyanate) or of naturally fluorescent materials, which emit light when exposed to ultraviolet or blue light. Immunofluorescence microscopy utilizes antibodies that are labeled with fluorescent dye. [MeSH]Narrower terms: Laser Fluorescence Microscopy LFM, multi- photon excitation fluorescence microscopy,  Total Internal Reflectance Fluorescence Microscopy TIR-FM
Fluorescence Microscopy, National High Field Magnetic Lab, Florida State Univ. US http://micro.magnet.fsu.edu/primer/techniques/fluorescence/fluorhome.html

immuno-electron microscopy: Microscopy in which the samples are first stained immunocytochemically and then examined using an electron microscope. Immunoelectron microscopy is used extensively in diagnostic virology as part of very sensitive immunoassays. MeSH 1991 

ion microscopy:  Use of the Secondary Ion Mass Spectrometry SIMS technique to obtain micrographs of the elemental (or isotopic) distribution at the surface of a sample with a spatial resolution of 2 mm or better.  IUPAC Compendium

lasers: An optical source that emits photons in a coherent beam. Light Amplification by Stimulated Emission of Radiation (LASER) is brought about using devices that transform light of varying frequencies into a single intense, nearly nondivergent beam of monochromatic radiation. Lasers operate in the infrared, visible, ultraviolet, or X-ray regions of the spectrum.  MeSH Year introduced: 1965(1963)

Laser Fluorescence Microscopy LFM: The development of new probe technologies, such as quantum dots and high-resolution laser fluorescence microscopy, allow real- time observations of molecular interactions and trafficking within living cells. These tools enable individual members of a population to be examined, identified, and quantitatively compared within cellular sub- populations and substructures. [NIGMS, NICDC, NHGRI, Single Molecule Detection and Manipulation, Feb. 12, 2001] http://grants.nih.gov/grants/guide/pa-files/PA-01-050.html  Related term: two photon excitation Broader term: fluorescence microscopy

laser scanning microscopy: There are two major forms of laser scanning microscopy, namely confocal laser scanning microscopy (CLSM) and multiphoton laser scanning microscopy (MPLSM). The two forms are very similar at the illumination side (as opposed to the detection side). ... MPLSM is more sensitive that CLSM because all the light generated to make an image is sent directly to the photon multiplier tube. This contrasts with  CLSM where a pin hole is required to select the light from the focal plane. In CLSM there is considerable loss of signal in the optics required to direct the light to the pin hole. MPLSM gives a sharper image than CLSM because of the lack of extraneous light and improved geometry of detection. In MPLSM the photon multiplier tube can be placed very close to the specimen whereas CLSM has all the intervening optics and the pin hole. [Bruce Jenks, Dept. of Cellular Animal Physiology, Univ. of Nijmegen, Netherlands] http://www.sci.kun.nl/celanphy/Bruce%20web/scanning%20microscopy.htm

Magnetic Resonance Force Microscopy MRFM: Wikipedia http://en.wikipedia.org/wiki/Magnetic_resonance_force_microscopy 

Magnetic Resonance Microscopy MRM: Wikipedia  https://en.wikipedia.org/wiki/Magnetic_resonance_microscopy 

microscopy: the technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye (objects that are not within the resolution range of the normal eye).[1] There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy, along with the emerging field of X-ray microscopy.  Wikipedia accessed 2018 Oct 31 https://en.wikipedia.org/wiki/Microscopy
Microscopy primer,  microscope basics, special techniques, tutorials, virtual microscopy Molecular Expressions, National High Field Magnetic Laboratory, Florida State Univ. US, Olympus America, Inc. 2003 http://micro.magnet.fsu.edu/primer/  Narrower terms: atomic force microscopy AFM, Confocal Scanning Laser Scanning Microscopy CLSM, confocal microscopy, cryoelectron microscopy, electron microscopy, fluorescence microscopy, immunoelectron microscopy, ion microscopy, Laser Fluorescence Microscopy LFM, laser scanning microscopy, Multiphoton Laser Scanning Microscopy MLSM, Magnetic Resonance Force Microscopy MRFM, multiple- photon excitation fluorescence microscopy, Near- field Scanning Optical Microscopy NSOM, Scanning Electron Microscopy SEM, Scanning Transmission Electron Microscopy STEM, Scanning Tunneling Microscopy STM, scanning probe microscopy, Surface Plasmon Resonance microscopy, Total Internal Reflectance Fluorescence Microscopy TIR-FM, Transmission Electron Microscopy TEM, two- photon Laser Fluorescence Microscopy, virtual microscopy

multiple- photon excitation fluorescence microscopy: A technique that uses non- linear optical effects to achieve optical sectioning. ... Advantages of multiphoton imaging: Optical sections may be obtained from deeper within a tissue that can be achieved by confocal or wide- field imaging. There are three main reasons for this: the excitation source is not attenuated by absorption by fluorophore above the plane of focus longer excitation wavelengths suffer less scattering  fluorescence signal is not degraded by scattering from within the sample as it is not imaged. [Laboratory for Optical and Computational Instrumentation, Univ. of Wisconsin Madison, 1999]  http://www.loci.wisc.edu/multiphoton/mp.html  Related terms: two photon, three photon

multiphoton fluorescence microscopy: Fluorescence microscopy utilizing multiple low- energy photons to produce the excitation event of the fluorophore. Multiphoton microscopes have a simplified optical path in the emission side due to the lack of an emission pinhole, which is necessary with normal confocal microscopes. Ultimately this allows spatial isolation of the excitation event, enabling deeper imaging into optically thick tissue, while restricting photobleaching and photoxicity to the area being imaged. MeSH 2003

Near-field Scanning Optical Microscopy NSOM:  Permits examination of highly localized extracellular, membrane, or intracellular chemical composition, fluorescence lifetime, and anisotropy (a sensitive monitor of interacting systems) measurements. NSOM achieves sub- optical resolution, in the 100 - 200 nm range by passing light through a small aperture. Two- photon excitation has been employed in NSOM. [National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999]   

optical microscopy OM: See under Magnetic Resonance Microscopy MRM

Scanning Electron Microscopy SEM: Any analytical technique which involves the generation and evaluation of secondary electrons (and to a lesser extent back scattered electrons) by a finely focused electron beam (typically 10 nm or less) for high resolution and high depth of field imaging.  IUPAC Compendium

Microscopy in which the object is examined directly by an electron beam scanning the specimen point- by- point, giving the surface image a three- dimensional quality. MeSH, 1972
Virtual Scanning Electron Microscopy, National High Field Magnetic Lab, Florida State Univ. US, http://micro.magnet.fsu.edu/primer/java/electronmicroscopy/magnify1/

scanning force microscopy: The scanning force microscopy (SFM), also known as atomic force microscopy (AFM), belongs to the branch of scanning probe microscopy (SPM), which comprises all microscopy techniques that form pictures of surfaces not by optical or electron-optical imaging, but due to interaction of a physical probe with the sample. Soft Matter Physics, University of Leipzig http://home.uni-leipzig.de/pwm/web/?section=introduction&page=sfm

Maps to atomic force microscopy MeSH 1995

scanning probe microscopy: Electron microscopy in which a very sharp probe is employed in  close proximity to a surface, exploiting a particular surface- related property. When this property is  local topography, the method is atomic force microscopy, and when it is local conductivity, the method is scanning tunneling microscopy. MeSH, 2000  Narrower term: scanning tunneling microscopy Related term: nanoscience Nanoscience & miniaturization glossary

Scanning Transmission Electron Microscopy STEM: A special TEM- technique in which an electron transparent sample is bombarded with a finely focused electron beam (typically of a diameter of less than 10 nm) which can be scanned across the specimen or rocked across the optical axis and transmitted secondary, backs scattered and diffracted electrons as well as the characteristic X-ray spectrum can be observed. STEM essentially provides high resolution imaging of the inner microstructure and the surface of a thin sample (or small particles), as well as the possibility of chemical and structural characterization of micrometer and sub- micrometer domains through evaluation of the X-ray spectra and the electron diffraction pattern.  IUPAC Compendium

Scanning Tunneling Microscopy STM: A type of scanning probe microscopy in which a very sharp conducting needle is swept just a few angstroms above the surface of a sample. The tiny tunneling  current that flows between the sample and the needle tip is measured, and from this are produced  three- dimensional topographs. Due to the poor electron conductivity of most biological samples,  thin metal coatings are deposited on the sample. MeSH, 1991 
Broader term: scanning probe microscopy

telemicroscope:  Any of several optical instruments that combine the functions of a telescope and microscope e.g. projecting a microscope image onto a screen. Wiktionary  https://en.wiktionary.org/wiki/telemicroscope

Total Internal Reflectance Fluorescence Microscopy TIR-FM:  Is based on the generation of an evanescent wave generated by total internal reflection at the boundary between media of differing refractive indices. The evanescent wave propagates in a direction normal to the interface for a short distance. Thus, it is useful for excitation of molecules in the vicinity of the surface- permitting membrane binding/ adsorption studies without the need to separate bulk phase ligand. Evanescent waves have been generated utilizing two- photon excitation with an accompanying decrease in the sensing depth. National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999 

Transmission Electron Microscopy TEM: Any technique in which an electron transparent sample is bombarded with an electron beam and the intensity of the transmitted electrons which is determined by scattering phenomena (electron absorption phenomena) in the interior of the sample is recorded. TEM essentially provides a high resolution image of the microstructure of a thin sample. This technique is often just called electron microscopy. The term transmission electron microscopy is however recommended for the sake of a clear distinction from other electron microscopic techniques. IUPAC Compendium  Broader term: electron microscopy, Related term: molecular distillation

Two-photon Laser Scanning Fluorescence Microscopy:   Wikipedia http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy Broader term: Laser Fluorescence Microscopy

virtual microscopy: http://virtual.itg.uiuc.edu/ 

x-ray microscopy:  Wikipedia https://en.wikipedia.org/wiki/X-ray_microscope  Useful for living cells.

Microscopy resources
Virtual Microscopy, National High Field Magnetic Lab, Florida State Univ. US http://micro.magnet.fsu.edu/primer/virtual/virtual.html  

How to look for other unfamiliar  terms

IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry.