Transmission electron microscope in the context of "Scanning transmission electron microscopy"

A microscope (from Ancient Greek μικρός (mikrós) 'small' and σκοπέω (skopéō) 'to look (at); examine, inspect') is a laboratory instrument used to examine objects that are too small to be seen by the naked eye. Microscopy is the science of investigating small objects and structures using a microscope. Microscopic means being invisible to the eye unless aided by a microscope.

There are many types of microscopes, and they may be grouped in different ways. One way is to describe the method an instrument uses to interact with a sample and produce images, either by sending a beam of light or electrons through a sample in its optical path, by detecting photon emissions from a sample, or by scanning across and a short distance from the surface of a sample using a probe. The most common microscope (and the first to be invented) is the optical microscope, which uses lenses to refract visible light that passed through a thinly sectioned sample to produce an observable image. Other major types of microscopes are the fluorescence microscope, electron microscope (both the transmission electron microscope and the scanning electron microscope) and various types of scanning probe microscopes.

Microscopy is the technical field of using microscopes to view subjects too small to be seen with the naked eye (objects that are not within the resolution range of the normal eye). There are three well-known branches of microscopy: optical, electron, and scanning probe microscopy, along with the emerging field of X-ray microscopy.

Optical microscopy and electron microscopy involve the diffraction, reflection, or refraction of electromagnetic radiation/electron beams interacting with the specimen, and the collection of the scattered radiation or another signal in order to create an image. This process may be carried out by wide-field irradiation of the sample (for example standard light microscopy and transmission electron microscopy) or by scanning a fine beam over the sample (for example confocal laser scanning microscopy and scanning electron microscopy). Scanning probe microscopy involves the interaction of a scanning probe with the surface of the object of interest. The development of microscopy revolutionized biology, gave rise to the field of histology and so remains an essential technique in the life and physical sciences. X-ray microscopy is three-dimensional and non-destructive, allowing for repeated imaging of the same sample for in situ or 4D studies, and providing the ability to "see inside" the sample being studied before sacrificing it to higher resolution techniques. A 3D X-ray microscope uses the technique of computed tomography (microCT), rotating the sample 360 degrees and reconstructing the images. CT is typically carried out with a flat panel display. A 3D X-ray microscope employs a range of objectives, e.g., from 4X to 40X, and can also include a flat panel.

Cytochemistry is the branch of cell biology dealing with the detection of cell constituents by means of biochemical analysis and visualization techniques. This is the study of the localization of cellular components through the use of staining methods. The term is also used to describe a process of identification of the biochemical content of cells. Cytochemistry is a science of localizing chemical components of cells and cell organelles on thin histological sections by using several techniques like enzyme localization, micro-incineration, micro-spectrophotometry, radioautography, cryo-electron microscopy, X-ray microanalysis by energy-dispersive X-ray spectroscopy, immunohistochemistry and cytochemistry, etc.

Ultrastructure (or ultra-structure) is the architecture of cells and biomaterials that is visible at higher magnifications than found on a standard optical light microscope. This traditionally meant the resolution and magnification range of a conventional transmission electron microscope (TEM) when viewing biological specimens such as cells, tissue, or organs. Ultrastructure can also be viewed with scanning electron microscopy and super-resolution microscopy, although TEM is a standard histology technique for viewing ultrastructure. Such cellular structures as organelles, which allow the cell to function properly within its specified environment, can be examined at the ultrastructural level.

Ultrastructure, along with molecular phylogeny, is a reliable phylogenetic way of classifying organisms. Features of ultrastructure are used industrially to control material properties and promote biocompatibility.

Kikuchi lines are patterns of electrons formed by scattering. They pair up to form bands in electron diffraction from single crystal specimens, there to serve as "roads in orientation-space" for microscopists uncertain of what they are looking at. In transmission electron microscopes, they are easily seen in diffraction from regions of the specimen thick enough for multiple scattering. Unlike diffraction spots, which blink on and off as one tilts the crystal, Kikuchi bands mark orientation space with well-defined intersections (called zones or poles) as well as paths connecting one intersection to the next.

Experimental and theoretical maps of Kikuchi band geometry, as well as their direct-space analogs e.g. bend contours, electron channeling patterns, and fringe visibility maps are increasingly useful tools in electron microscopy of crystalline and nanocrystalline materials. Because each Kikuchi line is associated with Bragg diffraction from one side of a single set of lattice planes, these lines can be labeled with the same Miller or reciprocal-lattice indices that are used to identify individual diffraction spots. Kikuchi band intersections, or zones, on the other hand are indexed with direct-lattice indices i.e. indices which represent integer multiples of the lattice basis vectors a, b and c.