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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. |