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Microscopy glossary & taxonomy
<%end if%> Technologies map Finding guide to terms in these glossaries Site 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] A powerful tool for studying the size and range of small forces with high spatial resolution. Traditionally, AFM has been used to record the surface topography of a sample by recording the vertical motion of the probe tip as it is scanned over a sample. With a customized probe tip, however, specific interactions between the tip and the sample surface can be measured. In this type of experiment, molecular groups that interact with the sample are added to the tip so that separating the tip from the sample deflects the cantilever- tip assembly. ... Manipulations with AFM in these studies have provided information about the structural basis for flexibility in proteins that have unusual elastic properties. In addition to making mechanical measurements, AFM has been used to observe the activity of individual proteins by measuring changes in protein positions over time. The development of carbon nanotubes for use as AFM tips is another promising approach to increasing the resolution of the method. [NIGMS, Single Molecule Detection and Manipulation Workshop "Single Molecule Fluorescence of Biomolecules and Complexes Protein Folding April 17- 18, 2000] http://www.nigms.nih.gov/news/reports/single_molecules.html#examples 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? 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 At relatively low resolutions, confocal microscopy can produce three- dimensional (3-D) images of fluorescently tagged gene products to determine their distribution in the cell during different stages of the cell cycle or under various environmental conditions. Such information allows deep insights into cell and organelle biology. Furthermore, confocal microscopy permits analysis of the cell's 3-D architecture, which cannot be achieved by conventional light microscopy. The broad goal is to visualize cellular constituents and general cytoarchitecture in a state as close to native organization as possible. Imaging Technology, DOE Genomes to Life, US http://www.doegenomestolife.org/technology/imagingtechnology.html Used for fluorescence detection. Related term: scanning technology. Confocal Scanning Laser Scanning Microscopy CLSM: See under laser scanning microscopy 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] http://www.ks.uiuc.edu/Publications/Reports/teraflop/node4.html Narrower term: transmission electron microscopy (TEM). evanescent wave: See under Total Internal Reflectance Fluorescence Microscopy FLIM Fluorescence Lifetime Imaging Microscopy: A technique in which the mean fluorescence lifetime of a chromophore is measured at each spatially resolvable element of a microscope image. The nanosecond excited- state lifetime is independent of probe concentration or light path length but dependent upon excited- state reactions such as fluorescence resonance energy transfer (FRET). These properties of fluorescence lifetimes allow exploration of the molecular environment of labelled macromolecules in the interior of cells. Imaging of fluorescence lifetimes enables biochemical reactions to be followed at each microscopically resolvable location within the cell. a technique in which the mean fluorescence lifetime of a chromophore is measured at each spatially resolvable element of a microscope image. The nanosecond excited- state lifetime is independent of probe concentration or light path length but dependent upon excited- state reactions such as fluorescence resonance energy transfer (FRET). These properties of fluorescence lifetimes allow exploration of the molecular environment of labelled macromolecules in the interior of cells. Imaging of fluorescence lifetimes enables biochemical reactions to be followed at each microscopically resolvable location within the cell. [Bastiaens, P.I. & Squire, A. Trends in Cell Biology (2) : 48- 52, Feb. 1999 http://www-db.embl-heidelberg.de:4321/emblGroups/g_lits_126.html 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 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 infrared spectromicroscopy: Synchrotron Radiation is a powerful tool in research, broadly applied in the VUV and x-ray spectral regions. The three main advantages of synchrotron radiation are: broadband characteristics, high collimation and the possibility to calculate its properties with Schwinger's equation. Synchrotron radiation can also be superior in the infrared spectral region. Electron and Optical Physics Division, NIST, Infrared SpectroMicroscopy, 2001 http://physics.nist.gov/Divisions/Div841/Gp1/infrared.html Narrower term: most-probable loss (MPL) tomography Related terms: NMR & X-ray crystallography glossary 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] 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: Confocal or optical microscopy (OM) and magnetic resonance microscopy (MRM) have developed as important tools for cellular research. MRM is noninvasive and nondestructive, and OM requires only the expression or uptake of fluorescently labeled molecules for detection. Both methods have their advantages and disadvantages. MRM provides access to several observable quantities that cannot be determined with OM alone (e.g., metabolite concentrations, chemical shifts, spin couplings, T1 and T2 relaxation times, and diffusion constants). These quantities have been related to a variety of such cellular events as tumor formation, programmed death (apoptosis), necrosis, and increased proliferation. Instruments combining OM and MRM allow live cells to be studied simultaneously using both techniques, providing a necessary link between cellular response and molecular information on proteins and other biochemicals involved in a certain cellular event. Two combined OM-MRM microscopes are under development at Pacific Northwest National Laboratory. Imaging Technology, DOE Genomes to Life, US http://www.doegenomestolife.org/technology/imagingtechnology.html 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 molecular distillation: A special method for transmission electron microscopy sample preparation. It is especially useful for immunogold labeling. This technology is being developed in the facility. [Analytical Imaging Facility, Albert Einstein College of Medicine, 2000] http://www.aecom.yu.edu/aif/instructions/EMPREP/mol_dist.htm most-probable loss (MPL) tomography: A novel method for acquiring data for electron tomography dramatically increases resolution and usable section thickness of stained samples, according to a NCMIR study published in the December 2004 issue of the Journal of Structural Biology. ... takes advantage of a new generation of energy-filtering intermediate voltage electron microscopes (IVEMs), such as NCMIR’s JEM-3200EF IVEM (300 kV). MPL tracks a narrow bandwidth of electrons during tilt series acquisition. Instead of targeting zero loss electrons, as in most energy-filtering applications. NCMIR, UCSD, US http://ncmir.ucsd.edu/Research/Highlights/2005_MPL.htm Broader term: Intermediate- high Voltage Electron Microscope IVEM 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 Multiphoton Laser Scanning Microscopy MLSM: See under laser scanning microscopy National Center for Microscopy and Imaging Research NCMIR: Imaging glossary 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 scanning force microscopy: Since its invention in 1986 by Binnig et al., scanning force microscopy has become a powerful tool for the investigation of surfaces. A great advantage of this method is the high resolution - down to the atomic scale - which can be achieved even in air and even on insulating surfaces. However, the greatest advantage is the possibility to investigate surfaces in situ in a liquid phase. Institut fur Mineralogie und Geochimie, Friedrich Schiller Universität Jena, Germany http://www.uni-koeln.de/math-nat-fak/mineral/IMGSFM.htm 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 Surface Plasmon Resonance [microscopy]:. Surface plasmons are optically stimulated by laser illumination of a metal film. These electromagnetic waves travel along the interface between the metal and a dielectric layer. The magnitude of the electromagnetic field close to the surface is extraordinarily sensitive to interface processes - in the BiaCore instrument, to receptor/ ligand interactions, which cause local refractive index changes. Since the vertical resolution of the surface plasmons extends from subnanometer to hundreds of nanometers, surface plasmon microscopy is potentially useful for the study of cell membranes, and transport and trafficking processes involving the membrane, as well as for studies of cell- nanofabricated surface interactions. [National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999] A biosensing technique in which biomolecules capable of binding to specific analytes or ligands are first immobilized on one side of a metallic film. Light is then focused on the opposite side of the film to excite the surface plasmons, that is, the oscillations of free electrons propagating along the film's surface. The refractive index of light reflecting off this surface is measured. When the immobilized biomolecules are bound by their ligands, an alteration in surface plasmons on the opposite side of the film is created which is directly proportional to the change in bound, or adsorbed, mass. Binding is measured by changes in the refractive index. The technique is used to study biomolecular interactions, such as antigen - antibody binding. MeSH, 1999 telemicroscopy: At its simplest level, telemicroscopy can mean the sharing of a static view of a microscope slide with another person via email (store-and-forward telemicroscopy). At its most sophisticated, a number of remote users may participate in examining and discussing a microscope slide using an intranet or the Internet - with control over the field-of-view, magnification and other microscope operations. Telemicroscopy depends on digital imaging for the creation of an easily-shared slide image. Remote operations depend on motorized 'robotic' microscopes, and microscope software technologies that allow network access, remote operation and security in the sharing of confidential information. Nikon Instruments http://www.nikoninstruments.com/Information-Center/Telemicroscopy 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: Soft X-ray microscopy, using X rays produced at synchrotron light sources, is an emerging biological imaging technique for the examination of intact, hydrated cells. The shorter wavelengths of X rays permit resolution 5 to 8 times better than that achieved by light microscopy, and the information obtained from the image contrast is highly quantitative in nature. Protein location can be determined at better than 50nm resolution in whole cells. Imaging Technology, DOE Genomes to Life, US http://www.doegenomestolife.org/technology/imagingtechnology.html Bibliography How to look for other unfamiliar terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
