This glossary provides definitions for electron microscopy techniques, terms and acronyms - as well as links to further information on our site. The terms are listed alphabetically, and are quick-linked to their definitions so you can easily find the information you are looking for.

Dehydration

This is the process of removing water from electron microscopy (EM) specimens. The water is generally replaced with organic solvents, such as ethanol or acetone. This happens in an intermediate step between chemical fixation and total drying for scanning electron microscopy (SEM) specimens using the critical point drying method, or between infiltration with resin and subsequent resin embedding for transmission electron microscopy (TEM) specimens.

Further information: Critical point drying technical brief (PDF) on Critical Point Drying Techniques and Advantages

Embedding

This is the infiltration of the biological tissue and similar material with wax (for light microscopy) or resin (for electron microscopy). Common embedding resins include Araldite and LR White, which can then be polymerised (by heat or UV light) into a hardened block for subsequent sectioning in an ultramicrotome and observation in a transmission electron microscope (TEM).

Environmental scanning electron microscope (ESEM)

A type of scanning electron microscope (SEM) with a specimen chamber that can be adjusted to different environmental conditions, typically to observe 'fresh' (unprocessed) material in a vacuum or to keep specimens 'wet' in order to study their equilibrium with water.

Film thickness monitor (FTM)

A film thickness monitor can be used to monitor and control the thickness of sputtered and evaporated metal films. A gold-coated quartz crystal is mounted in the vacuum chamber of the coating system, ideally close to the specimen or substrate. The quartz crystal is made to oscillate at a defined frequency, using an externally-mounted oscillator. As metal is deposited on the quartz crystal, the frequency of oscillation alters and the change is converted to a digital (eg LED) display on the monitoring unit.

Film thickness monitors are available for use with most of our coating systems and cryo preparation systems.

Further information: Film Thickness Monitors

Fixation (chemical fixation)

A general term for the process of chemically preserving specimens at a moment in time. Fixation prevents further deterioration, so that the specimen appears as close as possible to what it would be like in its original living state.

In chemical fixation for electron microscopy (EM), glutaraldehyde is widely used to crosslink protein molecules within biological specimens, and osmium tetroxide to preserve lipid content.

NB: Cryo-preservation is increasingly being used to overcome the many artefacts associated with chemical fixation.

Further information: Cryo-SEM Preparation Techniques and Advantages

Freeze-fracture-etch

Freeze-fracture-etch generally refers to a transmission electron microscopy (TEM) preparation method requiring specialist instrumentation. It can also form part of the preparation protocol for cryo-SEM, although for surface observation fracturing it is not required.

TEM freeze-fracture preparation is useful for observing specimens such as lipid membranes and their associated proteins. The fresh tissue or a cell suspension is rapidly frozen and then fractured while maintained at a low temperature. The fractured surface is generally 'etched' (sublimated) by increasing the temperature to about -95°C for a few minutes to allow some surface ice sublime to reveal microscopic details. For scanning electron microscopy (SEM), the specimen is now ready for imaging.

For TEM, the specimen can then be shadowed with evaporated platinum (Pt) at low angle (about 6°). Carbon (C) is then evaporated perpendicular to the surface plane to improve stability of the replica coating. The specimen is allowed to return to room temperature and pressure, and then the 'shadowed' metal replica of the fracture surface is removed from the underlying biological material by careful chemical digestion, normally using a bleach solution. The floating replica is thoroughly washed, carefully picked up on a TEM grid and viewed in a TEM.

Due to the improvements in the performance and resolution of SEMs and associated cryo-preparation systems, this technology has taken over many of the applications that were previously only possible with TEM freeze-fracture replication techniques.

Further information: Cryo-SEM Preparation Systems

Freeze drying

Freeze drying will reduce the distortion that occurs when a 'wet' scanning electron microscopy (SEM) or transmission electron microscopy (TEM) specimen dries by normal (room temperature) evaporation. Distortion is caused by large surface tension forces present when passing from a liquid to a gas phase. In the case of biological specimens, this means passing from liquid water to water vapour. If, however, the specimen is frozen and maintained in a frozen state under vacuum, frozen water can be removed by careful sublimation. This avoids the gas stage and thereby reduces specimen distortion.

Our product range includes both peltier-cooled and liquid nitrogen-cooled bench-top freeze dryers, specifically designed for electron microscopy (EM) specimen preparation. Alternative preparation techniques for SEM include critical point drying and cryo-SEM. Cryo preparation is the optimal technique as it allows observation with the specimen water in situ.

Further information: Freeze Dryers for Sample Preparation

Glow discharge

Electric glow discharge is a type of plasma formed by passing a current at 100V to several kV through a gas at low pressure (ie in a vacuum system). The main application of glow discharge in electron microscopy (EM) is to convert naturally hydrophobic ('water-hating') carbon-coated transmission electron microscopy (TEM) support grids into a hydrophilic ('water-loving') condition. This treatment allows the collection of ultra-thin TEM resin sections from the water bath of an ultramicrotome.

Glow discharge systems can be stand-alone units (eg the SC7620, Q150R, Q150T and Q300 series with optional attachment) or add-ons to larger vacuum evaporators (eg the K975X).

NB: Glow discharges are sometimes considered to be 'imperfect' plasmas and cannot be used to plasma etch or plasma ash specimens – their use mainly being confined to altering surface energies, not the removal of bulk material.

Further information: Glow Discharge Systems

Gold coater

A common name for a sputter coater used for coating scanning electron microscopy (SEM) specimens with thin layers of gold (Au). Historically, gold was the most common metal used for SEM coating applications. However, as the stability and resolving power of SEMs has increased over the years, a wider range of sputter target materials with smaller grain sizes have been used. These include platinum (Pt), chromium (Cr) and iridium (Ir). An alloy of gold/palladium (Au/Pd), often 80:20, is commonly used instead of gold as it gives a film with a smaller grain size.

Also see: Magnetron sputtering and Sputter coating
Further information: Sputter Coaters and SEM/TEM Carbon Coaters

High vacuum

Defined as a vacuum with a pressure between 10^-3mbar and 10^-7mbar.

Iridium sputter coating

Sputtering with iridium (Ir) is increasingly popular for high resolution sputter coating of field emission scanning electron microscopy (FE-SEM) specimens, because iridium will produce films with very small grain structure and it is a non-oxidising metal. It is increasingly preferred to chromium (Cr) as a coating material for FE-SEM. Iridium-coated specimens can be stored at atmospheric pressure, compared to chromium - which readily oxidises on contact with air.

Also see: Chromium sputter coating
Further information: Comparative sputtering of iridium and other materials (PDF) on Sputter Coating Techniques and Advantages and Q150T Turbo-Pumped Sputter Coater/Carbon Coater