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Monday, December 22, 2025

Transmission electron microscopy

A TEM image of a cluster of poliovirus. The polio virus is 30 nm in diameter.

Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a grid. An image is formed from the interaction of the electrons with the sample as the beam is transmitted through the specimen. The image is then magnified and focused onto an imaging device, such as a fluorescent screen, a layer of photographic film, or a detector such as a scintillator attached to a charge-coupled device or a direct electron detector.

Transmission electron microscopes are capable of imaging at a significantly higher resolution than light microscopes, owing to the smaller de Broglie wavelength of electrons. This enables the instrument to capture fine detail—even as small as a single column of atoms, which is thousands of times smaller than a resolvable object seen in a light microscope. Transmission electron microscopy is a major analytical method in the physical, chemical and biological sciences. TEMs find application in cancer research, virology, and materials science as well as pollution, nanotechnology and semiconductor research, but also in other fields such as paleontology and palynology.

TEM instruments have multiple operating modes including conventional imaging, scanning TEM imaging (STEM), diffraction, spectroscopy, and combinations of these. Even within conventional imaging, there are many fundamentally different ways that contrast is produced, called "image contrast mechanisms". Contrast can arise from position-to-position differences in the thickness or density ("mass-thickness contrast"), atomic number ("Z contrast", referring to the common abbreviation Z for atomic number), crystal structure or orientation ("crystallographic contrast" or "diffraction contrast"), the slight quantum-mechanical phase shifts that individual atoms produce in electrons that pass through them ("phase contrast"), the energy lost by electrons on passing through the sample ("spectrum imaging") and more. Each mechanism tells the user a different kind of information, depending not only on the contrast mechanism but on how the microscope is used—the settings of lenses, apertures, and detectors. What this means is that a TEM is capable of returning an extraordinary variety of nanometre- and atomic-resolution information, in ideal cases revealing not only where all the atoms are but what kinds of atoms they are and how they are bonded to each other. For this reason TEM is regarded as an essential tool for nanoscience in both biological and materials fields.

The first TEM was demonstrated by Max Knoll and Ernst Ruska in 1931, with this group developing the first TEM with resolution greater than that of light in 1933 and the first commercial TEM in 1939. In 1986, Ruska was awarded the Nobel Prize in physics for the development of transmission electron microscopy.

History

Initial development

The duplicate of an early TEM on display at the Deutsches Museum in Munich, Germany
A transmission electron microscope (1976)

In 1873, Ernst Abbe proposed that the ability to resolve detail in an object was limited approximately by the wavelength of the light used in imaging or a few hundred nanometres for visible light microscopes. Developments in ultraviolet (UV) microscopes, led by Köhler and Rohr, increased resolving power by a factor of two. However this required expensive quartz optics, due to the absorption of UV by glass. It was believed that obtaining an image with sub-micrometre information was not possible due to this wavelength constraint.

In 1858, Plücker observed the deflection of "cathode rays" (electrons) by magnetic fields. This effect was used by Ferdinand Braun in 1897 to build simple cathode-ray oscilloscope (CRO) measuring devices. In 1891, Eduard Riecke noticed that the cathode rays could be focused by magnetic fields, allowing for simple electromagnetic lens designs. In 1926, Hans Busch published work extending this theory and showed that the lens maker's equation could, with appropriate assumptions, be applied to electrons.

In 1928, at the Technische Hochschule in Charlottenburg (now Technische Universität Berlin), Adolf Matthias, Professor of High Voltage Technology and Electrical Installations, appointed Max Knoll to lead a team of researchers to advance the CRO design. The team consisted of several PhD students including Ernst Ruska and Bodo von Borries. The research team worked on lens design and CRO column placement, to optimize parameters to construct better CROs, and make electron optical components to generate low magnification (nearly 1:1) images. In 1931, the group successfully generated magnified images of mesh grids placed over the anode aperture. The device used two magnetic lenses to achieve higher magnifications, arguably creating the first electron microscope. In that same year, Reinhold Rudenberg, the scientific director of the Siemens company, patented an electrostatic lens electron microscope.

Improving resolution

At the time, electrons were understood to be charged particles of matter; the wave nature of electrons was not fully realized until the PhD thesis of Louis de Broglie in 1924. Knoll's research group was unaware of this publication until 1932, when they realized that the de Broglie wavelength of electrons was many orders of magnitude smaller than that for light, theoretically allowing for imaging at atomic scales. (Even for electrons with a kinetic energy of just 1 electronvolt the wavelength is already as short as 1.18 nm.) In April 1932, Ruska suggested the construction of a new electron microscope for direct imaging of specimens inserted into the microscope, rather than simple mesh grids or images of apertures. With this device successful diffraction and normal imaging of an aluminium sheet was achieved. However the magnification achievable was lower than with light microscopy. Magnifications higher than those available with a light microscope were achieved in September 1933 with images of cotton fibers quickly acquired before being damaged by the electron beam.

At this time, interest in the electron microscope had increased, with other groups, such as that of Paul Anderson and Kenneth Fitzsimmons of Washington State University and that of Albert Prebus and James Hillier at the University of Toronto, who constructed the first TEMs in North America in 1935 and 1938, respectively, continually advancing TEM design.

Research continued on the electron microscope at Siemens in 1936, where the aim of the research was the development and improvement of TEM imaging properties, particularly with regard to biological specimens. At this time electron microscopes were being fabricated for specific groups, such as the "EM1" device used at the UK National Physical Laboratory. In 1939, the first commercial electron microscope, pictured, was installed in the Physics department of IG Farben-Werke. Further work on the electron microscope was hampered by the destruction of a new laboratory constructed at Siemens by an air raid, as well as the death of two of the researchers, Heinz Müller and Friedrick Krause during World War II.

Further research

After World War II, Ruska resumed work at Siemens, where he continued to develop the electron microscope, producing the first microscope with 100k magnification. The fundamental structure of this microscope design, with multi-stage beam preparation optics, is still used in modern microscopes. The worldwide electron microscopy community advanced with electron microscopes being manufactured in Manchester UK, the USA (RCA), Germany (Siemens) and Japan (JEOL). The first international conference in electron microscopy was in Delft in 1949, with more than one hundred attendees. Later conferences included the "First" international conference in Paris, 1950 and then in London in 1954.

With the development of TEM, the associated technique of scanning transmission electron microscopy (STEM) was re-investigated and remained undeveloped until the 1970s, with Albert Crewe at the University of Chicago developing the field emission gun and adding a high quality objective lens to create the modern STEM. Using this design, Crewe demonstrated the ability to image atoms using annular dark-field imaging. Crewe and coworkers at the University of Chicago developed the cold field electron emission source and built a STEM able to visualize single heavy atoms on thin carbon substrates.

Background

Electrons

Theoretically, the maximum resolution, d, that one can obtain with a light microscope is limited by the wavelength of the photons (λ) and the numerical aperture NA of the system.

where n is the index of refraction of the medium in which the lens is working and α is the maximum half-angle of the cone of light that can enter the lens (see numerical aperture). Early twentieth century scientists theorized ways of getting around the limitations of the relatively large wavelength of visible light (wavelengths of 400–700 nanometres) by using electrons. Like all matter, electrons have both wave and particle properties (matter wave), and their wave-like properties mean that a beam of electrons can be focused and diffracted much like light can. The wavelength of electrons is related to their kinetic energy via the de Broglie equation, which says that the wavelength is inversely proportional to the momentum. Taking into account relativistic effects (as in a TEM an electron's velocity is a substantial fraction of the speed of light, c) the wavelength is

where h is the Planck constant, m0 is the rest mass of an electron and E is the kinetic energy of the accelerated electron.

Electron source

Layout of optical components in a basic TEM
Hairpin style tungsten filament on an insulating base.
Single crystal LaB6 filament

From the top down, the TEM consists of an emission source or cathode, which may be a tungsten filament, a lanthanum hexaboride (LaB6) single crystal or a field emission gun. The gun is connected to a high voltage source (typically ~100–300 kV) and emits electrons either by thermionic or field electron emission into the vacuum. In the case of a thermionic source, the electron source is mounted in a Wehnelt cylinder to provide preliminary focus of the emitted electrons into a beam while also stabilizing the current using a passive feedback circuit. A field emission source uses instead electrostatic electrodes called an extractor, a suppressor, and a gun lens, with different voltages on each, to control the electric field shape and intensity near the sharp tip. The combination of the cathode and these first electrostatic lens elements is collectively called the "electron gun". After it leaves the gun, the beam is typically accelerated until it reaches its final voltage and enters the next part of the microscope: the condenser lens system. These upper lenses of the TEM then further focus the electron beam to the desired size and location on the sample.

Manipulation of the electron beam is performed using two physical effects. The interaction of electrons with a magnetic field will cause electrons to move according to the left hand rule, thus allowing electromagnets to manipulate the electron beam. Additionally, electrostatic fields can cause the electrons to be deflected through a constant angle. Coupling of two deflections in opposing directions with a small intermediate gap allows for the formation of a shift in the beam path, allowing for beam shifting.

Optics

The lenses of a TEM are what gives it its flexibility of operating modes and ability to focus beams down to the atomic scale and magnify them to get an image. A lens is usually made of a solenoid coil nearly surrounded by ferromagnetic materials designed to concentrate the coil's magnetic field into a precise, confined shape. When an electron enters and leaves this magnetic field, it spirals around the curved magnetic field lines in a way that acts very much as an ordinary glass lens does for light—it is a converging lens. But, unlike a glass lens, a magnetic lens can very easily change its focusing power by adjusting the current passing through the coils.

Equally important to the lenses are the apertures. These are circular holes in thin strips of heavy metal. Some are fixed in size and position and play important roles in limiting x-ray generation and improving the vacuum performance. Others can be freely switched among several different sizes and have their positions adjusted. Variable apertures after the sample allow the user to select the range of spatial positions or electron scattering angles to be used in the formation of an image or a diffraction pattern.

The electron-optical system also includes deflectors and stigmators, usually made of small electromagnets. The deflectors allow the position and angle of the beam at the sample position to be independently controlled and also ensure that the beams remain near the low-aberration centers of every lens in the lens stacks. The stigmators compensate for slight imperfections and aberrations that cause astigmatism—a lens having a different focal strength in different directions.

Typically a TEM consists of three stages of lensing. The stages are the condenser lenses, the objective lenses, and the projector lenses. The condenser lenses are responsible for primary beam formation, while the objective lenses focus the beam that comes through the sample itself (in STEM scanning mode, there are also objective lenses above the sample to make the incident electron beam convergent). The projector lenses are used to expand the beam onto the phosphor screen or other imaging device, such as film. The magnification of the TEM is due to the ratio of the distances between the specimen and the objective lens' image plane. TEM optical configurations differ significantly with implementation, with manufacturers using custom lens configurations, such as in spherical aberration corrected instruments, or TEMs using energy filtering to correct electron chromatic aberration.

Reciprocity

The optical reciprocity theorem, or principle of Helmholtz reciprocity, generally holds true for elastically scattered electrons, as is often the case under standard TEM operating conditions. The theorem states that the wave amplitude at some point B as a result of electron point source A would be the same as the amplitude at A due to an equivalent point source placed at B. Simply stated, the wave function for electrons focused through any series of optical components that includes only scalar (i.e. not magnetic) fields will be exactly equivalent if the electron source and observation point are reversed. R

Reciprocity is used to understand scanning transmission electron microscopy (STEM) in the familiar context of TEM, and to obtain and interpret images using STEM.

Display and detectors

The key factors when considering electron detection include detective quantum efficiency (DQE), point spread function (PSF), modulation transfer function (MTF), pixel size and array size, noise, data readout speed, and radiation hardness.

Imaging systems in a TEM consist of a phosphor screen, which may be made of fine (10–100 μm) particulate zinc sulfide, for direct observation by the operator, and an image recording system such as photographic film, doped YAG screen coupled CCDs, or other digital detector. Typically these devices can be removed or inserted into the beam path as required. (Photograph film is no longer used.) The first report of using a Charge-Coupled Device (CCD) detector for TEM was in 1982, but the technology didn't find widespread use until the late 1990s/early 2000s. Monolithic active-pixel sensors (MAPSs) were also used in TEM. CMOS detectors, which are faster and more resistant to radiation damage than CCDs, have been used for TEM since 2005. In the early 2010s, further development of CMOS technology allowed for the detection of single electron counts ("counting mode"). These Direct Electron Detectors are available from Gatan, FEI, Quantum Detectors and Direct Electron.

Components

The electron source of the TEM is at the top, where the lensing system (4,7 and 8) focuses the beam on the specimen and then projects it onto the viewing screen (10). The beam control is on the right (13 and 14)

A TEM is composed of several components, which include a vacuum system in which the electrons travel, an electron emission source for generation of the electron stream, a series of electromagnetic lenses, as well as electrostatic plates. The latter two allow the operator to guide and manipulate the beam as required. Also required is a device to allow the insertion into, motion within, and removal of specimens from the beam path. Imaging devices are subsequently used to create an image from the electrons that exit the system.

Vacuum system

To increase the mean free path of the electron gas interaction, a standard TEM is evacuated to low pressures, typically on the order of 10−4 Pa. The need for this is twofold: first the allowance for the voltage difference between the cathode and the ground without generating an arc, and secondly to reduce the collision frequency of electrons with gas atoms to negligible levels—this effect is characterized by the mean free path. TEM components such as specimen holders and film cartridges must be routinely inserted or replaced requiring a system with the ability to re-evacuate on a regular basis. As such, TEMs are equipped with multiple pumping systems and airlocks and are not permanently vacuum sealed.

The vacuum system for evacuating a TEM to an operating pressure level consists of several stages. Initially, a low or roughing vacuum is achieved with either a rotary vane pump or diaphragm pumps setting a sufficiently low pressure to allow the operation of a turbo-molecular or diffusion pump establishing high vacuum level necessary for operations. To allow for the low vacuum pump to not require continuous operation, while continually operating the turbo-molecular pumps, the vacuum side of a low-pressure pump may be connected to chambers which accommodate the exhaust gases from the turbo-molecular pump. Sections of the TEM may be isolated by the use of pressure-limiting apertures to allow for different vacuum levels in specific areas such as a higher vacuum of 10−4 to 10−7 Pa or higher in the electron gun in high-resolution or field-emission TEMs.

High-voltage TEMs require ultra-high vacuums on the range of 10−7 to 10−9 Pa to prevent the generation of an electrical arc, particularly at the TEM cathode. As such for higher voltage TEMs a third vacuum system may operate, with the gun isolated from the main chamber either by gate valves or a differential pumping aperture – a small hole that prevents the diffusion of gas molecules into the higher vacuum gun area faster than they can be pumped out. For these very low pressures, either an ion pump or a getter material is used.

Poor vacuum in a TEM can cause several problems ranging from the deposition of gas inside the TEM onto the specimen while viewed in a process known as electron beam induced deposition to more severe cathode damages caused by electrical discharge. The use of a cold trap to adsorb sublimated gases in the vicinity of the specimen largely eliminates vacuum problems that are caused by specimen sublimation.

Specimen stage

TEM sample support mesh "grid", with ultramicrotomy sections

TEM specimen stage designs include airlocks to allow for insertion of the specimen holder into the vacuum with minimal loss of vacuum in other areas of the microscope. The specimen holders hold a standard size of sample grid or self-supporting specimen. Standard TEM grid sizes are 3.05 mm diameter, with a thickness and mesh size ranging from a few to 100 μm. The sample is placed onto the meshed area having a diameter of approximately 2.5 mm. Usual grid materials are copper, molybdenum, gold or platinum. This grid is placed into the sample holder, which is paired with the specimen stage. A wide variety of designs of stages and holders exist, depending upon the type of experiment being performed. In addition to 3.05 mm grids, 2.3 mm grids are sometimes, if rarely, used. These grids were particularly used in the mineral sciences where a large degree of tilt can be required and where specimen material may be extremely rare. Electron transparent specimens have a thickness usually less than 100 nm, but this value depends on the accelerating voltage.

Once inserted into a TEM, the sample has to be manipulated to locate the region of interest to the beam, such as in single grain diffraction, in a specific orientation. To accommodate this, the TEM stage allows movement of the sample in the XY plane, Z height adjustment, and commonly a single tilt direction parallel to the axis of side entry holders. Sample rotation may be available on specialized diffraction holders and stages. Some modern TEMs provide the ability for two orthogonal tilt angles of movement with specialized holder designs called double-tilt sample holders. Some stage designs, such as top-entry or vertical insertion stages once common for high resolution TEM studies, may simply only have X-Y translation available. The design criteria of TEM stages are complex, owing to the simultaneous requirements of mechanical and electron-optical constraints and specialized models are available for different methods.

A TEM stage is required to have the ability to hold a specimen and be manipulated to bring the region of interest into the path of the electron beam. As the TEM can operate over a wide range of magnifications, the stage must simultaneously be highly resistant to mechanical drift, with drift requirements as low as a few nm/minute while being able to move several μm/minute, with repositioning accuracy on the order of nanometres. Earlier designs of TEM accomplished this with a complex set of mechanical downgearing devices, allowing the operator to finely control the motion of the stage by several rotating rods. Modern devices may use electrical stage designs, using screw gearing in concert with stepper motors, providing the operator with a computer-based stage input, such as a joystick or trackball.

Two main designs for stages in a TEM exist, the side-entry and top entry version.[25] Each design must accommodate the matching holder to allow for specimen insertion without either damaging delicate TEM optics or allowing gas into TEM systems under vacuum.

A diagram of a single axis tilt sample holder for insertion into a TEM goniometer. Tilting of the holder is achieved by rotation of the entire goniometer

The most common is the side entry holder, where the specimen is placed near the tip of a long metal (brass or stainless steel) rod, with the specimen placed flat in a small bore. Along the rod are several polymer vacuum rings to allow for the formation of a vacuum seal of sufficient quality, when inserted into the stage. The stage is thus designed to accommodate the rod, placing the sample either in between or near the objective lens, dependent upon the objective design. When inserted into the stage, the side entry holder has its tip contained within the TEM vacuum, and the base is presented to atmosphere, the airlock formed by the vacuum rings.

Insertion procedures for side-entry TEM holders typically involve the rotation of the sample to trigger micro switches that initiate evacuation of the airlock before the sample is inserted into the TEM column.

The second design is the top-entry holder consists of a cartridge that is several cm long with a bore drilled down the cartridge axis. The specimen is loaded into the bore, possibly using a small screw ring to hold the sample in place. This cartridge is inserted into an airlock with the bore perpendicular to the TEM optic axis. When sealed, the airlock is manipulated to push the cartridge such that the cartridge falls into place, where the bore hole becomes aligned with the beam axis, such that the beam travels down the cartridge bore and into the specimen. Such designs are typically unable to be tilted without blocking the beam path or interfering with the objective lens.

Electron gun

Cross sectional diagram of an electron gun assembly, illustrating electron extraction

The electron gun is formed from several components: the filament, a biasing circuit, a Wehnelt cap, and an extraction anode. By connecting the filament to the negative component power supply, electrons can be "pumped" from the electron gun to the anode plate and the TEM column, thus completing the circuit. The gun is designed to create a beam of electrons exiting from the assembly at some given angle, known as the gun divergence semi-angle, α. By constructing the Wehnelt cylinder such that it has a higher negative charge than the filament itself, electrons that exit the filament in a diverging manner are, under proper operation, forced into a converging pattern the minimum size of which is the gun crossover diameter.

The thermionic emission current density, J, can be related to the work function of the emitting material via Richardson's law

where A is the Richardson's constant, Φ is the work function and T is the temperature of the material.

This equation shows that in order to achieve sufficient current density it is necessary to heat the emitter, taking care not to cause damage by application of excessive heat. For this reason materials with either a high melting point, such as tungsten, or those with a low work function (LaB6) are required for the gun filament. Furthermore, both lanthanum hexaboride and tungsten thermionic sources must be heated in order to achieve thermionic emission, this can be achieved by the use of a small resistive strip. To prevent thermal shock, there is often a delay enforced in the application of current to the tip, to prevent thermal gradients from damaging the filament, the delay is usually a few seconds for LaB6, and significantly lower for tungsten.

Electron lens

Diagram of a TEM split pole piece design lens

Electron lenses are designed to act in a manner emulating that of an optical lens, by focusing parallel electrons at some constant focal distance. Electron lenses may operate electrostatically or magnetically. The majority of electron lenses for TEM use electromagnetic coils to generate a convex lens. The field produced for the lens must be radially symmetrical, as deviation from the radial symmetry of the magnetic lens causes aberrations such as astigmatism, and worsens spherical and chromatic aberration. Electron lenses are manufactured from iron, iron-cobalt or nickel cobalt alloys, such as permalloy. These are selected for their magnetic properties, such as magnetic saturation, hysteresis and permeability.

The components include the yoke, the magnetic coil, the poles, the polepiece, and the external control circuitry. The pole piece must be manufactured in a very symmetrical manner, as this provides the boundary conditions for the magnetic field that forms the lens. Imperfections in the manufacture of the pole piece can induce severe distortions in the magnetic field symmetry, which induce distortions that will ultimately limit the lenses' ability to reproduce the object plane. The exact dimensions of the gap, pole piece internal diameter and taper, as well as the overall design of the lens is often performed by finite element analysis of the magnetic field, whilst considering the thermal and electrical constraints of the design.

The coils which produce the magnetic field are located within the lens yoke. The coils can contain a variable current, but typically use high voltages, and therefore require significant insulation in order to prevent short-circuiting the lens components. Thermal distributors are placed to ensure the extraction of the heat generated by the energy lost to resistance of the coil windings. The windings may be water-cooled, using a chilled water supply in order to facilitate the removal of the high thermal duty.

Apertures

Apertures are annular metallic plates, through which electrons that are further than a fixed distance from the optic axis may be excluded. These consist of a small metallic disc that is sufficiently thick to prevent electrons from passing through the disc, whilst permitting axial electrons. This permission of central electrons in a TEM causes two effects simultaneously: firstly, apertures decrease the beam intensity as electrons are filtered from the beam, which may be desired in the case of beam sensitive samples. Secondly, this filtering removes electrons that are scattered to high angles, which may be due to unwanted processes such as spherical or chromatic aberration, or due to diffraction from interaction within the sample.

Apertures are either a fixed aperture within the column, such as at the condenser lens, or are a movable aperture, which can be inserted or withdrawn from the beam path, or moved in the plane perpendicular to the beam path. Aperture assemblies are mechanical devices which allow for the selection of different aperture sizes, which may be used by the operator to trade off intensity and the filtering effect of the aperture. Aperture assemblies are often equipped with micrometers to move the aperture, required during optical calibration.

Imaging methods

Imaging methods in TEM use the information contained in the electron waves exiting from the sample to form an image. The projector lenses allow for the correct positioning of this electron wave distribution onto the viewing system. The observed intensity, I, of the image, assuming sufficiently high quality of imaging device, can be approximated as proportional to the time-averaged squared absolute value of the amplitude of the electron wavefunctions, where the wave that forms the exit beam is denoted by Ψ.

Different imaging methods therefore attempt to modify the electron waves exiting the sample in a way that provides information about the sample, or the beam itself. From the previous equation, it can be deduced that the observed image depends not only on the amplitude of beam, but also on the phase of the electrons, although phase effects may often be ignored at lower magnifications. Higher resolution imaging requires thinner samples and higher energies of incident electrons, which means that the sample can no longer be considered to be absorbing electrons (i.e., via a Beer's law effect). Instead, the sample can be modeled as an object that does not change the amplitude of the incoming electron wave function, but instead modifies the phase of the incoming wave; in this model, the sample is known as a pure phase object. For sufficiently thin specimens, phase effects dominate the image, complicating analysis of the observed intensities. To improve the contrast in the image, the TEM may be operated at a slight defocus to enhance contrast, owing to convolution by the contrast transfer function of the TEM, which would normally decrease contrast if the sample was not a weak phase object.

Schematic view of imaging and diffraction modes in TEM.

The figure on the right shows the two basic operation modes of TEM – imaging and diffraction modes. In both cases the specimen is illuminated with the parallel beam, formed by electron beam shaping with the system of Condenser lenses and Condenser aperture. After interaction with the sample, on the exit surface of the specimen two types of electrons exist – unscattered (which will correspond to the bright central beam on the diffraction pattern) and scattered electrons (which change their trajectories due to interaction with the material).

In Imaging mode, the objective aperture is inserted in a back focal plane (BFP) of the objective lens (where diffraction spots are formed). If using the objective aperture to select only the central beam, the transmitted electrons are passed through the aperture while all others are blocked, and a bright field image (BF image) is obtained. If we allow the signal from a diffracted beam, a dark field image (DF image) is received. The selected signal is magnified and projected on a screen (or on a camera) with the help of Intermediate and Projector lenses. An image of the sample is thus obtained.

In Diffraction mode, a selected area aperture may be used to determine more precisely the specimen area from which the signal will be displayed. By changing the strength of current to the intermediate lens, the diffraction pattern is projected on a screen. Diffraction is a very powerful tool for doing a cell reconstruction and crystal orientation determination.

Contrast formation

The contrast between two adjacent areas in a TEM image can be defined as the difference in the electron densities in image plane. Due to the scattering of the incident beam by the sample, the amplitude and phase of the electron wave change, which results in amplitude contrast and phase contrast, correspondingly. Most images have both contrast components.

Amplitude–contrast is obtained due to removal of some electrons before the image plane. During their interaction with the specimen some of electrons will be lost due to absorption, or due to scattering at very high angles beyond the physical limitation of microscope or are blocked by the objective aperture. While the first two losses are due to the specimen and microscope construction, the objective aperture can be used by operator to enhance the contrast.

BF and DF contrast demonstration. TEM image of polycrystalline Pt film

Figure on the right shows a TEM image (a) and the corresponding diffraction pattern (b) of Pt polycrystalline film taken without an objective aperture. In order to enhance the contrast in the TEM image the number of scattered beams as visible in the diffraction pattern should be reduced. This can be done by selecting a certain area in the back focal plane such as only the central beam or a specific diffracted beam (angle), or combinations of such beams. By intentionally selecting an objective aperture which only permits the non-diffracted beam to pass beyond the back focal plane (and onto the image plane): one creates a Bright-Field (BF) image (c), whereas if the central, non-diffracted beam is blocked: one may obtain dark-field (DF) images such as those shown in (d–e). The DF images (d–e) were obtained by selecting the diffracted beams indicated in diffraction pattern with circles (b) using an aperture at the back focal plane. Grains from which electrons are scattered into these diffraction spots appear brighter. More details about diffraction contrast formation are given further.

There are two types of amplitude contrast – mass–thickness and diffraction contrast. First, let's consider mass–thickness contrast. When the beam illuminates two neighbouring areas with low mass (or thickness) and high mass (or thickness), the heavier region scatters electrons at bigger angles. These strongly scattered electrons are blocked in BF TEM mode by objective aperture. As a result, heavier regions appear darker in BF images (have low intensity). Mass–thickness contrast is most important for non–crystalline, amorphous materials.

Diffraction contrast occurs due to a specific crystallographic orientation of a grain. In such a case the crystal is oriented in a way that there is a high probability of diffraction. Diffraction contrast provides information on the orientation of the crystals in a polycrystalline sample, as well as other information such as defects. Note that in case diffraction contrast exists, the contrast cannot be interpreted as due to mass or thickness variations.

Diffraction contrast

Transmission electron micrograph of dislocations in steel, which are faults in the structure of the crystal lattice at the atomic scale

Samples can exhibit diffraction contrast, whereby the electron beam undergoes diffraction which in the case of a crystalline sample, disperses electrons into discrete locations in the back focal plane. By the placement of apertures in the back focal plane, i.e. the objective aperture, the desired reciprocal lattice vectors can be selected (or excluded), thus only parts of the sample that are causing the electrons to scatter to the selected reflections will end up projected onto the imaging apparatus.

If the reflections that are selected do not include the unscattered beam (which will appear up at the focal point of the lens), then the image will appear dark wherever no sample scattering to the selected peak is present, as such a region without a specimen will appear dark. This is known as a dark-field image.

Modern TEMs are often equipped with specimen holders that allow the user to tilt the specimen to a range of angles in order to obtain specific diffraction conditions, and apertures placed above the specimen allow the user to select electrons that would otherwise be diffracted in a particular direction from entering the specimen.

Applications for this method include the identification of lattice defects in crystals. By carefully selecting the orientation of the sample, it is possible not just to determine the position of defects but also to determine the type of defect present. If the sample is oriented so that one particular plane is only slightly tilted away from the strongest diffracting angle (known as the Bragg Angle), any distortion of the crystal plane that locally tilts the plane to the Bragg angle will produce particularly strong contrast variations. However, defects that produce only displacement of atoms that do not tilt the crystal towards the Bragg angle (i. e. displacements parallel to the crystal plane) will produce weaker contrast.

Phase contrast

Crystal structure can also be investigated by high-resolution transmission electron microscopy (HRTEM), also known as phase contrast. When using a field emission source and a specimen of uniform thickness, the images are formed due to differences in phase of electron waves, which is caused by specimen interaction. Image formation is given by the complex modulus of the incoming electron beams. As such, the image is not only dependent on the number of electrons hitting the screen, making direct interpretation of phase contrast images slightly more complex. However this effect can be used to an advantage, as it can be manipulated to provide more information about the sample, such as in complex phase retrieval techniques.

Diffraction

Crystalline diffraction pattern from a twinned grain of FCC Austenitic steel

As previously stated, by adjusting the magnetic lenses such that the back focal plane of the lens rather than the imaging plane is placed on the imaging apparatus a diffraction pattern can be generated. For thin crystalline samples, this produces an image that consists of a pattern of dots in the case of a single crystal, or a series of rings in the case of a polycrystalline or amorphous solid material. For the single crystal case the diffraction pattern is dependent upon the orientation of the specimen and the structure of the sample illuminated by the electron beam. This image provides the investigator with information about the space group symmetries in the crystal and the crystal's orientation to the beam path. This is typically done without using any information but the position at which the diffraction spots appear and the observed image symmetries.

Diffraction patterns can have a large dynamic range, and for crystalline samples, may have intensities greater than those recordable by CCD. As such, TEMs may still be equipped with film cartridges for the purpose of obtaining these images, as the film is a single use detector.

Convergent-beam Kikuchi lines from silicon, near the [100] zone axis

Analysis of diffraction patterns beyond point-position can be complex, as the image is sensitive to a number of factors such as specimen thickness and orientation, objective lens defocus, and spherical and chromatic aberration. Although quantitative interpretation of the contrast shown in lattice images is possible, it is inherently complicated and can require extensive computer simulation and analysis, such as electron multislice analysis.

More complex behavior in the diffraction plane is also possible, with phenomena such as Kikuchi lines arising from multiple diffraction within the crystalline lattice. In convergent beam electron diffraction (CBED) where a non-parallel, i.e. converging, electron wavefront is produced by concentrating the electron beam into a fine probe at the sample surface, the interaction of the convergent beam can provide information beyond structural data such as sample thickness.

Electron energy loss spectroscopy (EELS)

Using the advanced technique of electron energy loss spectroscopy (EELS), for TEMs appropriately equipped, electrons can be separated into a spectrum based upon their velocity (which is closely related to their kinetic energy, and thus energy loss from the beam energy), using magnetic sector based devices known as EEL spectrometers. These devices allow for the selection of particular energy values, which can be associated with the way the electron has interacted with the sample. For example, different elements in a sample result in different electron energies in the beam after the sample. This normally results in chromatic aberration – however this effect can, for example, be used to generate an image which provides information on elemental composition, based upon the atomic transition during electron-electron interaction.

EELS spectrometers can often be operated in both spectroscopic and imaging modes, allowing for isolation or rejection of elastically scattered beams. As for many images inelastic scattering will include information that may not be of interest to the investigator thus reducing observable signals of interest, EELS imaging can be used to enhance contrast in observed images, including both bright field and diffraction, by rejecting unwanted components.

Three-dimensional imaging

As TEM specimen holders typically allow for the rotation of a sample by a desired angle, multiple views of the same specimen can be obtained by rotating the angle of the sample along an axis perpendicular to the beam. By taking multiple images of a single TEM sample at differing angles, typically in 1° increments, a set of images known as a "tilt series" can be collected. This methodology was proposed in the 1970s by Walter Hoppe. Under purely absorption contrast conditions, this set of images can be used to construct a three-dimensional representation of the sample.

The reconstruction is accomplished by a two-step process, first images are aligned to account for errors in the positioning of a sample; such errors can occur due to vibration or mechanical drift. Alignment methods use image registration algorithms, such as autocorrelation methods to correct these errors. Secondly, using a reconstruction algorithm, such as filtered back projection, the aligned image slices can be transformed from a set of two-dimensional images, Ij(xy), to a single three-dimensional image, Ij(xyz). This three-dimensional image is of particular interest when morphological information is required, further study can be undertaken using computer algorithms, such as isosurfaces and data slicing to analyse the data.

As TEM samples cannot typically be viewed at a full 180° rotation, the observed images typically suffer from a "missing wedge" of data, which when using Fourier-based back projection methods decreases the range of resolvable frequencies in the three-dimensional reconstruction. Mechanical refinements, such as multi-axis tilting (two tilt series of the same specimen made at orthogonal directions) and conical tomography (where the specimen is first tilted to a given fixed angle and then imaged at equal angular rotational increments through one complete rotation in the plane of the specimen grid) can be used to limit the impact of the missing data on the observed specimen morphology. Using focused ion beam milling, a new technique has been proposed which uses pillar-shaped specimen and a dedicated on-axis tomography holder to perform 180° rotation of the sample inside the pole piece of the objective lens in TEM. Using such arrangements, quantitative electron tomography without the missing wedge is possible. In addition, numerical techniques exist which can improve the collected data.

All the above-mentioned methods involve recording tilt series of a given specimen field. This inevitably results in the summation of a high dose of reactive electrons through the sample and the accompanying destruction of fine detail during recording. The technique of low-dose (minimal-dose) imaging is therefore regularly applied to mitigate this effect. Low-dose imaging is performed by deflecting illumination and imaging regions simultaneously away from the optical axis to image an adjacent region to the area to be recorded (the high-dose region). This area is maintained centered during tilting and refocused before recording. During recording the deflections are removed so that the area of interest is exposed to the electron beam only for the duration required for imaging. An improvement of this technique (for objects resting on a sloping substrate film) is to have two symmetrical off-axis regions for focusing followed by setting focus to the average of the two high-dose focus values before recording the low-dose area of interest.

Non-tomographic variants on this method, referred to as single particle analysis, use images of multiple (hopefully) identical objects at different orientations to produce the image data required for three-dimensional reconstruction. If the objects do not have significant preferred orientations, this method does not suffer from the missing data wedge (or cone) which accompany tomographic methods nor does it incur excessive radiation dosage, however it assumes that the different objects imaged can be treated as if the 3D data generated from them arose from a single stable object.

Sample preparation

A sample of cells (black) stained with osmium tetroxide and uranyl acetate embedded in epoxy resin (amber) ready for sectioning.

Sample preparation in TEM can be a complex procedure. TEM specimens should be less than 100 nanometres thick for a conventional TEM. Unlike neutron or X-ray radiation the electrons in the beam interact readily with the sample, an effect that increases roughly with atomic number squared (Z2). High quality samples will have a thickness that is comparable to the mean free path of the electrons that travel through the samples, which may be only a few tens of nanometres. Preparation of TEM specimens is specific to the material under analysis and the type of information to be obtained from the specimen.

Materials that have dimensions small enough to be electron transparent, such as powdered substances, small organisms, viruses, or nanotubes, can be quickly prepared by the deposition of a dilute sample containing the specimen onto films on support grids. Biological specimens may be embedded in resin to withstand the high vacuum in the sample chamber and to enable cutting tissue into electron transparent thin sections. The biological sample can be stained using either a negative staining material such as uranyl acetate for bacteria and viruses, or, in the case of embedded sections, the specimen may be stained with heavy metals, including osmium tetroxide. Alternately samples may be held at liquid nitrogen temperatures after embedding in vitreous ice. In material science and metallurgy the specimens can usually withstand the high vacuum, but still must be prepared as a thin foil, or etched so some portion of the specimen is thin enough for the beam to penetrate. Constraints on the thickness of the material may be limited by the scattering cross-section of the atoms from which the material is comprised.

Tissue sectioning

A diamond knife blade used for cutting ultrathin sections (typically 70 to 350 nm) for transmission electron microscopy.

Before sectioning, biological tissue is often embedded in an epoxy resin block and first trimmed using a razor blade into a trapezoidal block face. Thick sections are then cut from the block face. The thick sections are crudely stained with toluidine blue and examined for specimen and block orientation before thin sectioning. Biological tissue is then thinned to less than 100 nm on an ultramicrotome. The resin block is fractured as it passes over a glass or diamond knife edge. This method is used to obtain thin, minimally deformed samples that allow for the observation of tissue ultrastructure. Inorganic samples, such as aluminium, may also be embedded in resins and ultrathin sectioned in this way, using either coated glass, sapphire or larger angle diamond knives. To prevent charge build-up at the sample surface when viewing in the TEM, tissue samples need to be coated with a thin layer of conducting material, such as carbon.

Sample staining

A visualization of negative staining (a) and positive staining (b) of samples in transmission electron microscopy. The top row is a side profile of the sample, the bottom row shows the resulting image from the microscope.
A section of a cell of Bacillus subtilis, taken with a Tecnai T-12 TEM. The scale bar is 200 nm.

TEM samples of biological tissues need high atomic number stains to enhance contrast. The stain absorbs the beam electrons or scatters part of the electron beam which otherwise is projected onto the imaging system. Compounds of heavy metals such as osmium, lead, uranium or gold (in immunogold labelling) may be used prior to TEM observation to selectively deposit electron dense atoms in or on the sample in desired cellular or protein region. This process requires an understanding of how heavy metals bind to specific biological tissues and cellular structures.

Another form of sample staining is negative stain, where a larger amount of heavy metal stain is applied to the sample. The result is a sample with a dark background and the topological surface of the sample appearing lighter. Negative stain electron microscopy can be ideal for visualizing or forming 3D topological reconstructions of large proteins or macromolecular complexes (> 150 kDa). For smaller proteins, negative stain can be used as a screening step to find ideal sample concentration for cryogenic electron microscopy.

Mechanical milling

Mechanical polishing is also used to prepare samples for imaging on the TEM. Polishing needs to be done to a high quality, to ensure constant sample thickness across the region of interest. A diamond, or cubic boron nitride polishing compound may be used in the final stages of polishing to remove any scratches that may cause contrast fluctuations due to varying sample thickness. Even after careful mechanical milling, additional fine methods such as ion etching may be required to perform final stage thinning.

Chemical etching

Certain samples may be prepared by chemical etching, particularly metallic specimens. These samples are thinned using a chemical etchant, such as an acid, to prepare the sample for TEM observation. Devices to control the thinning process may allow the operator to control either the voltage or current passing through the specimen, and may include systems to detect when the sample has been thinned to a sufficient level of optical transparency.

Ion etching

Ion etching is a sputtering process that can remove very fine quantities of material. This is used to perform a finishing polish of specimens polished by other means. Ion etching uses an inert gas passed through an electric field to generate a plasma stream that is directed to the sample surface. Acceleration energies for gases such as argon are typically a few kilovolts. The sample may be rotated to promote even polishing of the sample surface. The sputtering rate of such methods is on the order of tens of micrometres per hour, limiting the method to only extremely fine polishing.

Ion etching by argon gas has been recently shown to be able to file down MTJ stack structures to a specific layer which has then been atomically resolved. The TEM images taken in plan view rather than cross-section reveal that the MgO layer within MTJs contains a large number of grain boundaries that may be diminishing the properties of devices.

Ion milling (FIB)

Scanning electron microscope image of a thin TEM sample milled by FIB. The thin membrane shown here is suitable for TEM examination; however, at ~300-nm thickness, it would not be suitable for high-resolution TEM without further milling.

More recently focused ion beam (FIB) methods have been used to prepare samples. FIB is a relatively new technique to prepare thin samples for TEM examination from larger specimens. Because FIB can be used to micro-machine samples very precisely, it is possible to mill very thin membranes from a specific area of interest in a sample, such as a semiconductor or metal. Unlike inert gas ion sputtering, FIB makes use of significantly more energetic gallium ions and may alter the composition or structure of the material through gallium implantation.

Nanowire assisted transfer

For a minimal introduction of stress and bending to transmission electron microscopy (TEM) samples (lamellae, thin films, and other mechanically and beam sensitive samples), when transferring inside a focused ion beam (FIB), flexible metallic nanowires can be attached to a typically rigid micromanipulator.

The main advantages of this method include a significant reduction of sample preparation time (quick welding and cutting of nanowire at low beam current), and minimization of stress-induced bending, Pt contamination, and ion beam damage. This technique is particularly suitable for in situ electron microscopy sample preparation.

Replication

Staphylococcus aureus platinum replica image shot on a TEM at 50,000x magnification.

Samples may also be replicated using cellulose acetate film, the film subsequently coated with a heavy metal such as platinum, the original film dissolved away, and the replica imaged on the TEM. Variations of the replica technique are used for both materials and biological samples. In materials science a common use is for examining the fresh fracture surface of metal alloys.

Modifications

The capabilities of the TEM can be further extended by additional stages and detectors, sometimes incorporated on the same microscope.

Scanning TEM

A TEM can be modified into a scanning transmission electron microscope (STEM) by the addition of a system that rasters a convergent beam across the sample to form the image, when combined with suitable detectors. Scanning coils are used to deflect the beam, such as by an electrostatic shift of the beam, where the beam is then collected using a current detector such as a Faraday cup, which acts as a direct electron counter. By correlating the electron count to the position of the scanning beam (known as the "probe"), the transmitted component of the beam may be measured. The non-transmitted components may be obtained either by beam tilting or by the use of annular dark field detectors.

Schematic ray diagram illustrating the optical reciprocity between TEM (left) and STEM (right). The convergence angle in TEM, , becomes the collection angle in STEM, . Image inspired by Hren et al.

Fundamentally, TEM and STEM are linked via Helmholtz reciprocity. A STEM is a TEM in which the electron source and observation point have been switched relative to the direction of travel of the electron beam. See the ray diagrams in the figure on the right. The STEM instrument effectively relies on the same optical set-up as a TEM, but operates by flipping the direction of travel of the electrons (or reversing time) during operation of a TEM. Rather than using an aperture to control detected electrons, as in TEM, a STEM uses various detectors with collection angles that may be adjusted depending on which electrons the user wants to capture.

Low-voltage electron microscope

A low-voltage electron microscope (LVEM) is operated at relatively low electron accelerating voltage between 5–25 kV. Some of these can be a combination of SEM, TEM and STEM in a single compact instrument. Low voltage increases image contrast which is especially important for biological specimens. This increase in contrast significantly reduces, or even eliminates the need to stain. Resolutions of a few nm are possible in TEM, SEM and STEM modes. The low energy of the electron beam means that permanent magnets can be used as lenses and thus a miniature column that does not require cooling can be used.

Cryo-TEM

Cryogenic transmission electron microscopy (Cryo-TEM or Cryo-EM) uses a TEM with a specimen holder capable of maintaining the specimen at liquid nitrogen or liquid helium temperatures. This allows imaging specimens prepared in vitreous ice, the preferred preparation technique for imaging individual molecules or macromolecular assemblies, imaging of vitrified solid-electrolye interfaces, and imaging of materials that are volatile in high vacuum at room temperature, such as sulfur. For many quantum materials or devices, low temperature or ultra-low temperature  is required to access phases where emergent quantum behavior occurs.

Environmental/in-situ TEM

In-situ experiments may also be conducted in TEM using differentially pumped sample chambers, or specialized holders. Types of in-situ experiments include studying nanomaterials, biological specimens, chemical reactions of molecules, liquid-phase electron microscopy, and material deformation testing.

High temperature in-situ TEM

Many phase transformations occur during heating. Additionally, coarsening and grain growth, along with other diffusion-related processes occur more rapidly at elevated temperatures, where kinetics are improved, allowing for the observation of related phenomena under transmission electron microscopy within reasonable time scales. This also allows for the observation of phenomena that occur at elevated temperatures and disappear or are not uniformly preserved in ex-situ samples.

High temperature TEM introduces various additional challenges which must be addressed in the mechanics of high temperature holders, including but not limited to drift-correction, temperature measurement, and decreased spatial resolution at the expense of more complex holders.

Sample drift in the TEM is linearly proportional to the temperature differential between the room and holder. With temperatures as high as 1500C in modern holders, samples may experience significant drift and vertical displacement (bulging), requiring continuous focus or stage adjustments, inducing resolution loss and mechanical drift. Individual labs and manufacturers have developed software coupled with advanced cooling systems to correct for thermal drift based on the predicted temperature in the sample chamber These systems often take 30 min-many hours for sample shifts to stabilize. While significant progress has been made, no universal TEM attachment has been made to account for drift at elevated temperatures.

An additional challenge of many of these specialized holders is knowing the local sample temperature. Many high temperature holders utilize a tungsten filament to locally heat the sample. Ambiguity in temperature in furnace heaters (W wire) with thermocouples arises from the thermal contact between the furnace and the TEM grid; complicated by temperature gradients along the sample caused by varying thermal conductivity with different samples and grid materials. With different holders both commercial and lab made, different methods for creating temperature calibration are available. Manufacturers like Gatan use IR pyrometry to measure temperature gradients over their entire sample. An even better method to calibrate is Raman spectroscopy which measures the local temperature of Si powder on electron transparent windows and quantitatively calibrates the IR pyrometry. These measurements have guaranteed accuracy within 5%. Research laboratories have also performed their own calibrations on commercial holders. Researchers at NIST utilized Raman spectroscopy to map the temperature profile of a sample on a TEM grid and achieve very precise measurements to enhance their research. Similarly, a research group in Germany utilized X-ray diffraction to measure slight shifts in lattice spacing caused by changes in temperature to back calculate the exact temperature in the holder. This process required careful calibration and exact TEM optics. Other examples include the use of EELS to measure local temperature using change of gas density, and resistivity changes.

Optimal resolution in a TEM is achieved when spherical aberrations are corrected with objective lens. However, due to the geometry of most TEMs, inserting large in-situ holders requires the user to compromise the objective lens and endure spherical aberrations. Therefore, there is a compromise between the width of the pole-piece gap and spatial resolution below 0.1 nm. Research groups at various institutions have tried to overcome spherical aberrations through use of monochromators to achieve 0.05 nm resolution with a 5 mm pole piece gap.

In-situ mechanical TEM

High resolution of TEM allows for monitoring the sample in question on a length scale ranging from hundreds of nanometres to several angstroms. This allows for the visualization of both elastic and plastic deformation via strain fields as well as the motion of crystallographic defects such as lattice distortions and dislocation motion. By simultaneously observing deformation phenomena and measuring mechanical response in situ, it is possible to connect nano-mechanical testing information to models that describe both the subtlety and complexity of how materials respond to stress and strain. The material properties and data accuracy obtained from such nano-mechanical tests is largely determined by the mechanical straining holder being used. Current straining holders have the ability to perform tensile tests, nano-indentation, compression tests, shear tests and bending tests on materials.

Classical mechanical holders

One of the pioneers of classical holders was Heinz G.F. Wilsdorf, who conducted a tensile test inside a TEM in 1958. In a typical experiment, electron transparent TEM samples are cut to shape and glued to a deformable grid. Advances in micromanipulators have also enabled the tensile testing of nanowires and thin films. The deformable grid attaches to the classical tensile holder which stretches the sample using a long rigid shaft attached to a worm gear box actuated by an electric motor located in a housing outside the TEM. Typically strain rates range from 10 nm/s to 10 μm/s. Custom-made holders expanding simple straining actuation have enabled bending tests using a bending holder and shear tests using a shear sample holder. The typical measured sample properties in these experiments are yield strength, elastic modulus, shear modulus, tensile strength, bending strength, and shear strength. In order to study the temperature-dependent mechanical properties of TEM samples, the holder can be cooled through a cold finger connected to a liquid nitrogen reservoir. For high temperature experiments, the TEM sample can also be heated through a miniaturized furnace or a laser that can typically reach 1000 °C.

Nano-indentation holders

Nano-Indentation holders perform a hardness test on the material in question by pressing a hard tip into a polished flat surface and measuring the applied force and the resulting displacement on the TEM sample through a change in capacitance between a reference and a movable electrostatic plate attached to the tip. The typical measured sample properties are hardness and elastic modulus. Although nano-indentation was possible since early 1980s, its investigation using a TEM was first reported in 2001 where an aluminum sample deposited on a silicon wedge was investigated. For nanoindentation experiments, TEM samples are typically shaped as wedges using a tripod polisher, H-bar window or a micro-nanopillar using focused ion beam to create enough space for a tip to be pressed at the desired electron transparent location. The indenter tips are typically flat punch-type, pyramidal, or wedge shaped elongated in the z-direction. Pyramidal tips offer high precision on the order of 10 nm but suffer from sample slip, while wedge indenters have greater contract to prevent slipping but require finite element analysis to model the transmitted stress since the high contact area with the TEM sample makes this almost a compression test.

Micro electro-mechanical systems (MEMs)

Micro Electro-Mechanical Systems (MEMs) based holders provide a cheap and customizable platform to conduct mechanical tests on previously difficult samples to work with such as micropillars, nanowires, and thin films. Passive MEMs are used as simple push to pull devices for in-situ mechanical tests. Typically, a nano-indentation holder is used to apply a pushing force at the indentation site. Using a geometry of arms, this pushing force translates to a pulling force on a pair of tensile pads to which the sample is attached. Thus, a compression applied on the outside of the MEMs translates to a tension in the central gap where the TEM sample is located. The resulting force-displacement curve needs to be corrected by performing the same test on an empty MEMs without the TEM sample to account for the stiffness of the empty MEMs. The dimensions and stiffness of the MEMs can be modified to perform tensile tests on different sized samples with different loads. To smoothen the actuation process, active MEMs have been developed with built-in actuators and sensors. These devices work by applying a stress using electrical power and measuring strain using capacitance variations. Electrostatically actuated MEMs have also been developed to accommodate very low applied forces in the 1–100 nN range.

Much of current research focuses on developing sample holders that can perform mechanical tests while creating an environmental stimulus such as temperature change, variable strain rates, and different gas environments. In addition, the emergence of high resolution detectors are allowing to monitor dislocation motion and interactions with other defects and pushing the limits of sub-nanometre strain measurements. In-situ mechanical TEM measurements are routinely coupled with other standard TEM measurements such as EELS and XEDS to reach a comprehensive understanding of the sample structure and properties.

Aberration corrected TEM

Modern research TEMs may include aberration correctors, to reduce the amount of distortion in the image. Incident beam monochromators may also be used which reduce the energy spread of the incident electron beam to less than 0.15 eV. Major aberration corrected TEM manufacturers include JEOL, Hitachi High-technologies, FEI Company, and NION.

Ultrafast and dynamic TEM

It is possible to reach temporal resolution far beyond that of the readout rate of electron detectors with the use of pulsed electrons. Pulses can be produced by either modifying the electron source to enable laser-triggered photoemission or by installation of an ultrafast beam blanker. This approach is termed ultrafast transmission electron microscopy when stroboscopic pump-probe illumination is used: an image is formed by the accumulation of many ultrashort electron pulses (typically of hundreds of femtoseconds) with a fixed time delay between the arrival of the electron pulse and the sample excitation. On the other hand, the use of single or a short sequence of electron pulses with a sufficient number of electrons to form an image from each pulse is called dynamic transmission electron microscopy. Temporal resolution down to hundreds of femtoseconds and spatial resolution comparable to that available with a Schottky field emission source is possible in ultrafast TEM. Using the Photon-gating approach, the temporal resolution in ultrafast electron microscope reaches to 30-fs allowing the imaging of ultrafast atomic and electron dynamics of matter. However, the technique can only image reversible processes that can be reproducibly triggered millions of times. Dynamic TEM can resolve irreversible processes down to tens of nanoseconds and tens of nanometres.

The technique has been pioneered at the early 2000s in laboratories in Germany (Technische Universität Berlin) and in the USA (Caltech and Lawrence Livermore National Laboratory). Ultrafast TEM and Dynamic TEM have made possible real-time investigation of numerous physical and chemical phenomena at the nanoscale.

An interesting variant of the Ultrafast Transmission Electron Microscopy technique is the Photon-Induced Near-field Electron Microscopy (PINEM). The latter is based on the inelastic coupling between electrons and photons in presence of a surface or a nanostructure. This method allows one to investigate time-varying nanoscale electromagnetic fields in an electron microscope, as well as dynamically shape the wave properties of the electron beam.

Limitations

There are a number of drawbacks to the TEM technique. Many materials require extensive sample preparation to produce a sample thin enough to be electron transparent, which makes TEM analysis a relatively time-consuming process with a low throughput of samples. The structure of the sample may also be changed during the preparation process. Also the field of view is relatively small, raising the possibility that the region analyzed may not be characteristic of the whole sample. There is potential that the sample may be damaged by the electron beam, particularly in the case of biological materials.

Resolution limits

Evolution of spatial resolution achieved with optical, transmission (TEM) and aberration-corrected electron microscopes (ACTEM).

The limit of resolution obtainable in a TEM may be described in several ways, and is typically referred to as the information limit of the microscope. One commonly used value is a cut-off value of the contrast transfer function, a function that is usually quoted in the frequency domain to define the reproduction of spatial frequencies of objects in the object plane by the microscope optics. A cut-off frequency, qmax, for the transfer function may be approximated with the following equation, where Cs is the spherical aberration coefficient and λ is the electron wavelength:

For a 200 kV microscope, with partly corrected spherical aberrations ("to the third order") and a Cs value of 1 μm, a theoretical cut-off value might be 1/qmax = 42 pm. The same microscope without a corrector would have Cs = 0.5 mm and thus a 200 pm cut-off. The spherical aberrations are suppressed to the third or fifth order in the "aberration-corrected" microscopes. Their resolution is however limited by electron source geometry and brightness and chromatic aberrations in the objective lens system.

The frequency domain representation of the contrast transfer function may often have an oscillatory nature, which can be tuned by adjusting the focal value of the objective lens. This oscillatory nature implies that some spatial frequencies are faithfully imaged by the microscope, whilst others are suppressed. By combining multiple images with different spatial frequencies, the use of techniques such as focal series reconstruction can be used to improve the resolution of the TEM in a limited manner. The contrast transfer function can, to some extent, be experimentally approximated through techniques such as Fourier transforming images of amorphous material, such as amorphous carbon.

More recently, advances in aberration corrector design have been able to reduce spherical aberrations and to achieve resolution below 0.5 ångströms (50 pm) at magnifications above 50 million times. Improved resolution allows for the imaging of lighter atoms that scatter electrons less efficiently, such as lithium atoms in lithium battery materials. The ability to determine the position of atoms within materials has made the HRTEM an indispensable tool for nanotechnology research and development in many fields, including heterogeneous catalysis and the development of semiconductor devices for electronics and photonics.

Xenobiology

From Wikipedia, the free encyclopedia

Xenobiology (XB) is a subfield of synthetic biology, the study of synthesizing and manipulating biological devices and systems. The name "xenobiology" derives from the Greek word xenos, which means "stranger, alien". Xenobiology is a form of biology that is not (yet) familiar to science and is not found in nature. In practice, it describes novel biological systems and biochemistries that differ from the canonical DNARNA-20 amino acid system (see central dogma of molecular biology). For example, instead of DNA or RNA, XB explores nucleic acid analogues, termed xeno nucleic acid (XNA) as information carriers. It also focuses on an expanded genetic code and the incorporation of non-proteinogenic amino acids, or "xeno amino acids" into proteins.

Difference between xeno-, exo-, and astro-biology

"Astro" means "star" and "exo" means "outside". Both exo- and astrobiology deal with the search for naturally evolved life in the Universe, mostly on other planets in the circumstellar habitable zone. (These are also occasionally referred to as xenobiology.) Whereas astrobiologists are concerned with the detection and analysis of life elsewhere in the Universe, xenobiology attempts to design forms of life with a different biochemistry or different genetic code than on planet Earth.

Aims

  • Xenobiology has the potential to reveal fundamental knowledge about biology and the origin of life. In order to better understand the origin of life, it is necessary to know why life evolved seemingly via an early RNA world to the DNA-RNA-protein system and its nearly universal genetic code. Was it an evolutionary "accident" or were there constraints that ruled out other types of chemistries? By testing alternative biochemical "primordial soups", it is expected to better understand the principles that gave rise to life as we know it.
  • Xenobiology is an approach to develop industrial production systems with novel capabilities by means of biopolymer engineering and pathogen resistance. The genetic code encodes in all organisms 20 canonical amino acids that are used for protein biosynthesis. In rare cases, special amino acids such as selenocysteine or pyrrolysine can be incorporated by the translational apparatus in to proteins of some organisms. Together, these 20+2 Amino Acids are known as the 22 Proteinogenic Amino Acids. By using additional amino acids from among the over 700 known to biochemistry, the capabilities of proteins may be altered to give rise to more efficient catalytical or material functions. The EC-funded project Metacode, for example, aims to incorporate metathesis (a useful catalytical function so far not known in living organisms) into bacterial cells. Another reason why XB could improve production processes lies in the possibility to reduce the risk of virus or bacteriophage contamination in cultivations since XB cells would no longer provide suitable host cells, rendering them more resistant (an approach called semantic containment)
  • Xenobiology offers the option to design a "genetic firewall", a novel biocontainment system, which may help to strengthen and diversify current bio-containment approaches. One concern with traditional genetic engineering and biotechnology is horizontal gene transfer to the environment and possible risks to human health. One major idea in XB is to design alternative genetic codes and biochemistries so that horizontal gene transfer is no longer possible. Additionally alternative biochemistry also allows for new synthetic auxotrophies. The idea is to create an orthogonal biological system that would be incompatible with natural genetic systems.

Scientific approach

In xenobiology, the aim is to design and construct biological systems that differ from their natural counterparts on one or more fundamental levels. Ideally these new-to-nature organisms would be different in every possible biochemical aspect exhibiting a very different genetic code. The long-term goal is to construct a cell that would store its genetic information not in DNA but in an alternative informational polymer consisting of xeno nucleic acids (XNA), different base pairs, using non-canonical amino acids and an altered genetic code. So far cells have been constructed that incorporate only one or two of these features.

Xeno nucleic acids (XNA)

Originally this research on alternative forms of DNA was driven by the question of how life evolved on earth and why RNA and DNA were selected by (chemical) evolution over other possible nucleic acid structures. Two hypotheses for the selection of RNA and DNA as life's backbone are either they are favored under life on Earth's conditions, or they were coincidentally present in pre-life chemistry and continue to be used now. Systematic experimental studies aiming at the diversification of the chemical structure of nucleic acids have resulted in completely novel informational biopolymers. So far a number of XNAs with new chemical backbones or leaving group of the DNA have been synthesized e.g.: hexose nucleic acid (HNA); threose nucleic acid (TNA), glycol nucleic acid (GNA) cyclohexenyl nucleic acid (CeNA). The incorporation of XNA in a plasmid, involving 3 HNA codons, has been accomplished already in 2003. This XNA is used in vivo (E coli) as template for DNA synthesis. This study, using a binary (G/T) genetic cassette and two non-DNA bases (Hx/U), was extended to CeNA, while GNA seems to be too alien at this moment for the natural biological system to be used as template for DNA synthesis. Extended bases using a natural DNA backbone could, likewise, be transliterated into natural DNA, although to a more limited extent.

Aside being used as extensions to template DNA strands, XNA activity has been tested for use as genetic catalysts. Although proteins are the most common components of cellular enzymatic activity, nucleic acids are also used in the cell to catalyze reactions. A 2015 study found several different kinds of XNA, most notably FANA (2'-fluoroarabino nucleic acids), as well as HNA, CeNA and ANA (arabino nucleic acids) could be used to cleave RNA during post-transcriptional RNA processing acting as XNA enzymes, hence the name XNAzymes. FANA XNAzymes also showed the ability to ligate DNA, RNA and XNA substrates. Although XNAzyme studies are still preliminary, this study was a step in the direction of searching for synthetic circuit components that are more efficient than those containing DNA and RNA counterparts that can regulate DNA, RNA, and their own, XNA, substrates.

Expanding the genetic alphabet

While XNAs have modified backbones, other experiments target the replacement or enlargement of the genetic alphabet of DNA with unnatural base pairs. For example, DNA has been designed that has – instead of the four standard bases A, T, G, and C – six bases A, T, G, C, and the two new ones P and Z (where Z stands for 6-Amino-5-nitro3-(l'-p-D-2'-deoxyribofuranosyl)-2(1H)-pyridone, and P stands for 2-Amino-8-(1-beta-D-2'-deoxyribofuranosyl)imidazo[1,2-a]-1,3,5-triazin-4 (8H)). In a systematic study, Leconte et al. tested the viability of 60 candidate bases (yielding potentially 3600 base pairs) for possible incorporation in the DNA.

In 2002, Hirao et al. developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions in vitro in transcription and translation toward a genetic code for protein synthesis containing a non-standard amino acid. In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription, and afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification. In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins.

In May 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA, alongside the four naturally occurring nucleotides, and by including individual artificial nucleotides in the culture media, were able to passage the bacteria 24 times; they did not create mRNA or proteins able to use the artificial nucleotides.

Novel polymerases

Neither the XNA nor the unnatural bases are recognized by natural polymerases. One of the major challenges is to find or create novel types of polymerases that will be able to replicate these new-to-nature constructs. In one case a modified variant of the HIV-reverse transcriptase was found to be able to PCR-amplify an oligonucleotide containing a third type base pair. Pinheiro et al. (2012) demonstrated that the method of polymerase evolution and design successfully led to the storage and recovery of genetic information (of less than 100bp length) from six alternative genetic polymers based on simple nucleic acid architectures not found in nature, xeno nucleic acids.

Genetic code engineering

One of the goals of xenobiology is to rewrite the genetic code. The most promising approach to change the code is the reassignment of seldom used or even unused codons. In an ideal scenario, the genetic code is expanded by one codon, thus having been liberated from its old function and fully reassigned to a non-canonical amino acid (ncAA) ("code expansion"). As these methods are laborious to implement, and some short cuts can be applied ("code engineering"), for example in bacteria that are auxotrophic for specific amino acids and at some point in the experiment are fed isostructural analogues instead of the canonical amino acids for which they are auxotrophic. In that situation, the canonical amino acid residues in native proteins are substituted with the ncAAs. Even the insertion of multiple different ncAAs into the same protein is possible. Finally, the repertoire of 20 canonical amino acids can not only be expanded, but also reduced to 19. By reassigning transfer RNA (tRNA)/aminoacyl-tRNA synthetase pairs the codon specificity can be changed. Cells endowed with such aminoacyl-[tRNA synthetases] are thus able to read [mRNA] sequences that make no sense to the existing gene expression machinery. Altering the codon: tRNA synthetases pairs may lead to the in vivo incorporation of the non-canonical amino acids into proteins. In the past reassigning codons was mainly done on a limited scale. In 2013, however, Farren Isaacs and George Church at Harvard University reported the replacement of all 321 TAG stop codons present in the genome of E. coli with synonymous TAA codons, thereby demonstrating that massive substitutions can be combined into higher-order strains without lethal effects. Following the success of this genome wide codon replacement, the authors continued and achieved the reprogramming of 13 codons throughout the genome, directly affecting 42 essential genes.

An even more radical change in the genetic code is the change of a triplet codon to a quadruplet and even quintuplet codon pioneered by Sisido in cell-free systems and by Schultz in bacteria. Finally, non-natural base pairs can be used to introduce novel amino acid in proteins.

Directed evolution

The goal of substituting DNA by XNA may also be reached by another route, namely by engineering the environment instead of the genetic modules. This approach has been successfully demonstrated by Marlière and Mutzel with the production of an E. coli strain whose DNA is composed of standard A, C and G nucleotides but has the synthetic thymine analogue 5-chlorouracil instead of thymine (T) in the corresponding positions of the sequence. These cells are then dependent on externally supplied 5-chlorouracil for growth, but otherwise they look and behave as normal E. coli. These cells, however, are currently not yet fully auxotrophic for the Xeno-base since they are still growing on thymine when this is supplied to the medium.

Biosafety

Xenobiological systems are designed to convey orthogonality to natural biological systems. A (still hypothetical) organism that uses XNA, different base pairs and polymerases and has an altered genetic code will hardly be able to interact with natural forms of life on the genetic level. Thus, these xenobiological organisms represent a genetic enclave that cannot exchange information with natural cells. Altering the genetic machinery of the cell leads to semantic containment. In analogy to information processing in IT, this safety concept is termed a "genetic firewall". The concept of the genetic firewall seems to overcome a number of limitations of previous safety systems. A first experimental evidence of the theoretical concept of the genetic firewall was achieved in 2013 with the construction of a genomically recoded organism (GRO). In this GRO all known UAG stop codons in E.coli were replaced by UAA codons, which allowed for the deletion of release factor 1 and reassignment of UAG translation function. The GRO exhibited increased resistance to T7 bacteriophage, thus showing that alternative genetic codes do reduce genetic compatibility. This GRO, however, is still very similar to its natural "parent" and cannot be regarded to have a genetic firewall. The possibility of reassigning the function of large number of triplets opens the perspective to have strains that combine XNA, novel base pairs, new genetic codes, etc. that cannot exchange any information with the natural biological world. Regardless of changes leading to a semantic containment mechanism in new organisms, any novel biochemical systems still has to undergo a toxicological screening. XNA, novel proteins, etc. might represent novel toxins, or have an allergic potential that needs to be assessed.

Governance and regulatory issues

Xenobiology might challenge the regulatory framework, as currently laws and directives deal with genetically modified organisms and do not directly mention chemically or genomically modified organisms. Taking into account that real xenobiology organisms are not expected in the next few years, policy makers do have some time at hand to prepare themselves for an upcoming governance challenge. Since 2012, the following groups have picked up the topic as a developing governance issue: policy advisers in the US, four National Biosafety Boards in Europe, the European Molecular Biology Organisation, and the European Commission's Scientific Committee on Emerging and Newly Identified Health Risks (SCENIHR) in three opinions (Definition, risk assessment methodologies and safety aspects, and risks to the environment and biodiversity related to synthetic biology and research priorities in the field of synthetic biology.)

Electron microscope

From Wikipedia, the free encyclopedia
A modern transmission electron microscope (TITAN)

An electron microscope is a microscope that uses a beam of electrons as a source of illumination. It uses electron optics that are analogous to the glass lenses of an optical light microscope to control the electron beam, for instance focusing it to produce magnified images or electron diffraction patterns. As the wavelength of an electron can be up to 100,000 times smaller than that of visible light, electron microscopes have a much higher resolution of about 0.1 nm, which compares to about 200 nm for light microscopesElectron microscope may refer to:

Additional details can be found in the above links. This article contains some general information mainly about transmission and scanning electron microscopes.

History

Many developments laid the groundwork of the electron optics used in microscopes. One significant step was the work of Hertz in 1883 who made a cathode-ray tube with electrostatic and magnetic deflection, demonstrating manipulation of the direction of an electron beam. Others were focusing of the electrons by an axial magnetic field by Emil Wiechert in 1899, improved oxide-coated cathodes which produced more electrons by Arthur Wehnelt in 1905 and the development of the electromagnetic lens in 1926 by Hans Busch. According to Dennis Gabor, the physicist Leó Szilárd tried in 1928 to convince him to build an electron microscope, for which Szilárd had filed a patent.

Reproduction of an early electron microscope constructed by Ernst Ruska in the 1930s

To this day the issue of who invented the transmission electron microscope is controversial. In 1928, at the Technische Hochschule in Charlottenburg (now Technische Universität Berlin), Adolf Matthias (Professor of High Voltage Technology and Electrical Installations) appointed Max Knoll to lead a team of researchers to advance research on electron beams and cathode-ray oscilloscopes. The team consisted of several PhD students including Ernst Ruska. In 1931, Max Knoll and Ernst Ruska successfully generated magnified images of mesh grids placed over an anode aperture. The device, a replicate of which is shown in the figure, used two magnetic lenses to achieve higher magnifications, the first electron microscope. (Max Knoll died in 1969, so did not receive a share of the 1986 Nobel prize for the invention of electron microscopes.)

Apparently independent of this effort was work at Siemens-Schuckert by Reinhold Rüdenberg. According to patent law (U.S. Patent No. 2058914 and 2070318, both filed in 1932), he is the inventor of the electron microscope, but it is not clear when he had a working instrument. He stated in a very brief article in 1932 that Siemens had been working on this for some years before the patents were filed in 1932, claiming that his effort was parallel to the university development. He died in 1961, so similar to Max Knoll, was not eligible for a share of the 1986 Nobel prize.

In the following year, 1933, Ruska and Knoll built the first electron microscope that exceeded the resolution of an optical (light) microscope. Four years later, in 1937, Siemens financed the work of Ernst Ruska and Bodo von Borries, and employed Helmut Ruska, Ernst's brother, to develop applications for the microscope, especially with biological specimens. Also in 1937, Manfred von Ardenne pioneered the scanning electron microscope. Siemens produced the first commercial electron microscope in 1938. The first North American electron microscopes were constructed in the 1930s, at the Washington State University by Anderson and Fitzsimmons  and at the University of Toronto by Eli Franklin Burton and students Cecil Hall, James Hillier, and Albert Prebus. Siemens produced a transmission electron microscope (TEM) in 1939. Although current transmission electron microscopes are capable of two million times magnification, as scientific instruments they remain similar but with improved optics.

In the 1940s, high-resolution electron microscopes were developed, enabling greater magnification and resolution. By 1965, Albert Crewe at the University of Chicago introduced the scanning transmission electron microscope using a field emission source, enabling scanning microscopes at high resolution. By the early 1980s improvements in mechanical stability as well as the use of higher accelerating voltages enabled imaging of materials at the atomic scale. In the 1980s, the field emission gun became common for electron microscopes, improving the image quality due to the additional coherence and lower chromatic aberrations. The 2000s were marked by advancements in aberration-corrected electron microscopy, allowing for significant improvements in resolution and clarity of images.

Types of electron microscopes

Transmission electron microscope (TEM)

Transmission Electron Microscope

The original form of the electron microscope, the transmission electron microscope (TEM), uses a high voltage electron beam to illuminate the specimen and create an image. An electron beam is produced by an electron gun, with the electrons typically having energies in the range 20 to 400 keV, focused by electromagnetic lenses, and transmitted through a thin specimen. When it emerges from the specimen, the electron beam carries information about the structure of the specimen that is then magnified by the lenses of the microscope. The spatial variation in this information (the "image") may be viewed by projecting the magnified electron image onto a detector. For example, the image may be viewed directly by an operator using a fluorescent viewing screen coated with a phosphor or scintillator material such as zinc sulfide. More commonly a high-resolution phosphor is coupled by means of a lens optical system or a fibre optic light-guide to the sensor of a digital camera. A different approach is to use a direct electron detector which has no scintillator, which addresses some of the limitations of scintillator-coupled cameras.

For many years the resolution of TEMs was limited by aberrations of the electron optics, primarily the spherical aberration. In most recent instruments hardware correctors can reduce spherical aberration and other aberrations, improving the resolution in high-resolution transmission electron microscopy (HRTEM) to below 0.5 angstrom (50 picometres), enabling magnifications of more than 50 million times. The ability of HRTEM to determine the positions of atoms within materials is useful for many areas of research and development.

Scanning electron microscope (SEM)

An SEM produces images by probing the specimen with a focused electron beam that is scanned across the specimen (raster scanning). When the electron beam interacts with the specimen, it loses energy and is scattered in different directions by a variety of mechanisms. These interactions lead to, among other events, emission of low-energy secondary electrons and high-energy backscattered electrons, light emission (cathodoluminescence) or X-ray emission. All of these signals carrying information about the specimen, such as the surface topography and composition. The image displayed when using an SEM shows the variation in the intensity of any of these signals as an image. In these each position in the image corresponding to a position of the beam on the specimen when the signal was generated.

TESCAN S8000X SEM

SEMs are different from TEMs in that they use electrons with much lower energy, generally below 20 keV, while TEMs generally use electrons with energies in the range of 80-300 keV. Thus, the electron sources and optics of the two microscopes have different designs, and they are normally separate instruments.

Scanning transmission electron microscope (STEM)

A STEM combines features of both a TEM and a SEM by rastering a focused incident probe across a specimen, but now mainly using the electrons which are transmitted through the sample. Many types of imaging are common to both TEM and STEM, but some such as annular dark-field imaging and other analytical techniques are much easier to perform with higher spatial resolutions in a STEM instrument. One drawback is that image data is acquired in serial rather than in parallel fashion.

Main operating modes

An image of an ant in an SEM

The most common methods of obtaining images in an electron microscope involve selecting different directions for the electrons that have been transmitted through a sample, and/or electrons of different energies. There are a very large number of methods of doing this, although not all are very common.

Secondary electrons

Electron–matter interaction volume and types of signal generated in a SEM

In a SEM the signals result from interactions of the electron beam with atoms within the sample. The most common mode is to use the secondary electrons (SE) to produce images. Secondary electrons have very low energies, on the order of 50 eV, which limits their mean free path in solid matter to a few nanometers below the sample surface. The electrons are detected by an Everhart–Thornley detector, which is a type of collector-scintillator-photomultiplier system. The signal from secondary electrons tends to be highly localized at the point of impact of the primary electron beam, making it possible to collect images of the sample surface with a resolution of better than 1 nm, and with specialized instruments at the atomic scale.

The brightness of the signal depends on the number of secondary electrons reaching the detector. If the beam enters the sample perpendicular to the surface, then the electrons come out symmetrically about the axis of the beam. As the angle of incidence increases, the interaction volume from which they cone increases and the "escape" distance from one side of the beam decreases, resulting in more secondary electrons being emitted from the sample. Thus steep surfaces and edges tend to be brighter than flat surfaces, which results in images with a well-defined, three-dimensional appearance that is similar to a reflected light image.

Backscattered electrons

Backscattered electrons (BSE) are those emitted back out from the specimen due to beam-specimen interactions where the electrons undergo elastic and inelastic scattering. They are conventionally defined as having energies from 50 eV up to the energy of the primary beam. Backscattered electrons can be used for both imaging and to form an electron backscatter diffraction (EBSD) image, the latter can be used to determine the crystallography of the specimen.

Electron backscatter diffraction pattern for (001) single crystal silicon crystals taken at 20kV using Oxford S2 detector

Heavy elements (high atomic number) backscatter electrons more strongly than light elements (low atomic number), and thus appear brighter in the image, BSE images can therefore be used to detect areas with different chemical compositions. To optimize the signal, dedicated backscattered electron detectors are positioned above the sample in a "doughnut" type arrangement, concentric with the electron beam, maximizing the solid angle of collection. BSE detectors are usually either scintillator or semiconductor types. When all parts of the detector are used to collect electrons symmetrically about the beam, atomic number contrast is produced. However, strong topographic contrast is produced by collecting back-scattered electrons from one side above the specimen using an asymmetrical, directional BSE detector; the resulting contrast appears as if there was illumination of the topography from that side. Semiconductor detectors can be made in radial segments that can be switched in or out to control the type of contrast produced and its directionality.

Diffraction contrast imaging

Diffraction contrast uses the variation in either or both the direction of diffracted electrons or their amplitude as a function of position as the contrast mechanism. It is one of the simplest ways to image in a transmission electron microscope, and widely used.

The idea is to use an objective aperture below the sample and select only one or a range of different diffracted directions, then use these to form an image. When the aperture includes the incident beam direction the images are called bright field, since in the absence of any sample the field of view would be uniformly bright. When the aperture excludes the incident beam the images are called dark field, since similarly without a sample the image would be uniformly dark. One variant of this is called weak-beam dark-field microscopy, and can be used to obtain high resolution images of defects such as dislocations.

High resolution imaging

CuTe High resolution image

In high-resolution transmission electron microscopy (also sometimes called high-resolution electron microscopy) a number of different diffracted beams are allowed through the objective aperture. These interfere, leading to images which represent the atomic structure of the material. These can include the incident beam direction, or with scanning transmission electron microscopes they typically are for a range of diffracted beams excluding the incident beam. Depending upon how thick the samples are and the aberrations of the microscope, these images can either be directly interpreted in terms of the positions of columns of atoms, or require a more careful analysis using calculations of the multiple scattering of the electrons and the effect of the contrast transfer function of the microscope.

There are many other imaging variants that can also to lead to atomic level information. Electron holography uses the interference of electrons which have been through the sample and a reference beam. 4D STEM collects diffraction data at each point using a scanning instrument, then processes them to produce different types of images.

X-ray microanalysis

EDS spectrum of the mineral crust of the vent shrimp Rimicaris exoculata Most of these peaks are K-alpha and K-beta lines. One peak is from the L shell of iron.

X-ray microanalysis is a method of obtaining local chemical information within electron microscopes of all types, although it is most commonly used in scanning instruments. When high energy electrons interact with atoms they can knock out electrons, particularly those in the inner shells and core electrons. These are then filled by valence electron, and the energy difference between the valence and core states can be converted into an x-ray which is detected by a spectrometer. The energies of these x-rays is somewhat specific to the atomic species, so local chemistry can be probed.

EELS

Experimental electron energy loss spectrum, showing the major features: zero-loss peak, plasmon peaks and core loss edge.

Similar to X-ray microanalysis, the energies of electrons which have transmitted through a sample can be analyzed and yield information ranging from details of the local electronic structure to chemical information.

Electron diffraction

Transmission electron microscopes can be used in electron diffraction mode where a map of the angles of the electrons leaving the sample is produced. The advantages of electron diffraction over X-ray crystallography are primarily in the size of the crystals. In X-ray crystallography, crystals are commonly visible by the naked eye and are generally in the hundreds of micrometers in length. In comparison, crystals for electron diffraction must be less than a few hundred nanometers in thickness, and have no lower boundary of size. Additionally, electron diffraction is done on a TEM, which can also be used to obtain other types of information, rather than requiring a separate instrument.

Variations in CBED with thickness for Si (001)

There are many variants on electron diffraction, depending upon exactly what type of illumination conditions are used. If a parallel beam is used with an aperture to limit the region exposed to the electrons then sharp diffraction features are normally observed, a technique called selected area electron diffraction. This is often the main technique used. Another common approach uses conical illumination and is called convergent beam electron diffraction (CBED). This is good for determining the symmetry of materials. A third is precession electron diffraction, where a parallel beam is spun around a large angle, producing a type of average diffraction pattern. These often have less multiple scattering.

Other electron microscope techniques

Aberration corrected instruments

Scanning transmission electron microscope equipped with a 3rd-order spherical aberration corrector

Aberration-corrected transmission electron microscopy (AC-TEM) is the general term for electron microscopes where electro optical components are introduced to reduce the aberrations that would otherwise limit the resolution of the images. Historically electron microscopes had quite severe aberrations, and until about the start of the 21st century the resolution was limited, able to image the atomic structure of materials if the atoms were far enough apart. Around the turn of the century the electron optical components were coupled with computer control of the lenses and their alignment, enabling correction of aberrations. The first demonstration of aberration correction in TEM mode was by Harald Rose and Maximilian Haider in 1998 using a hexapole corrector, and in STEM mode by Ondrej Krivanek and Niklas Dellby in 1999 using a quadrupole/octupole corrector.

As of 2025 correction of geometric aberrations is standard in many commercial electron microscopes, and they are extensively used in many different areas of science. Similar correctors have also been used at much lower energies for LEEM instruments.

Sample preparation

An insect coated in gold for viewing with a scanning electron microscope (SEM)

Samples for electron microscopes mostly cannot be observed directly. The samples need to be prepared to stabilize the sample and enhance contrast. Preparation techniques differ vastly in respect to the sample and its specific qualities to be observed as well as the specific microscope used. Details can be found in the relevant main articles listed above.

Disadvantages

JEOL transmission and scanning electron microscope made in the mid-1970s

Electron microscopes are expensive to build and maintain. Microscopes designed to achieve high resolutions must be housed in stable buildings (sometimes underground) with special services such as magnetic field canceling systems and anti vibration mounts.

The samples largely have to be viewed in vacuum, as the molecules that make up air would scatter the electrons. An exception is liquid-phase electron microscopy[60] using either a closed liquid cell or an environmental chamber, for example, in the environmental scanning electron microscope, which allows hydrated samples to be viewed in a low-pressure (up to 20 Torr or 2.7 kPa) wet environment. Various techniques for in situ electron microscopy of gaseous samples have also been developed.

Pleolipoviral virion (HRPV-6)

Samples of hydrated materials, including almost all biological specimens, have to be prepared in various ways to stabilize them, reduce their thickness (ultrathin sectioning) and increase their electron optical contrast (staining). These processes may result in artifacts, but these can usually be identified by comparing the results obtained by using radically different specimen preparation methods. Since the 1980s, analysis of cryofixed, vitrified specimens has also become increasingly used.

Many samples suffer from radiation damage which can change internal structures. This can be due to either or both radiolytic processes or ballistic, for instance with collision cascades. This can be a severe issue for biological samples.

Relationship between science and religion

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