The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
PERSON:Daniel Schober
definition
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
A synonym type for describing abbreviations or initalisms
NASA is an word acronym for the US National Aeronautics and Space Administration because the acronym is pronounced. FBI is an initialism (also known as alphabetism) for the US Federal Bureau of Investigation since the letters are pronounced one at a time. JPEG is an acronym for Joint Photographic Experts Group but does not count as a word acronym nor an initialism since it is mixed how it is pronounced.
A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
Examples of a Contributor include a person, an organization, or a service. Typically, the name of a Contributor should be used to indicate the entity.
Contributor
An entity responsible for making contributions to the resource.
Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
Creator
An entity primarily responsible for making the resource.
Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
Description
An account of the resource.
Date Issued
Date of formal issuance (e.g., publication) of the resource.
License
A legal document giving official permission to do something with the resource.
Title
A name given to the resource.
In current practice, this term is used primarily with literal values; however, there are important uses with non-literal values as well. As of December 2007, the DCMI Usage Board is leaving this range unspecified pending an investigation of options.
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
has_broad_synonym
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
has exact synonym
has_exact_synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
has_narrow_synonym
An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
has related synonym
has_related_synonym
Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL
has_synonym
example
An example of the use of a concept.
note
A general note, for any purpose.
This property may be used directly, or as a super-property for more specific note types.
scope note
A note that helps to clarify the meaning and/or the use of a concept.
The EM Glossary is a widespread community effort to harmonize terminology in the electron and ion microscopies. It is created in a not-for profit collaboration between academic and non-university research institutions including domain and metadata experts. It provides harmonized terminology for application level semantic artifacts to source from and align with.
Azocar Guzman, A., Brendike-Mannix, O., Hofmann, V. (2024), Electron Microscopy Glossary, https://purls.helmholtz-metadaten.de/emg/
Scattering during which electrons of an incident beam are scattered by a specimen, such that some of the scattered particles leave the specimen via the incident surface again.
Ludwig Reimer, Scanning Electron Microscopy - Physics of Image Formation and Microanalysis (ISBN 978-3-642-08372-3) - pages 57ff
We note that electrons can be backscattered inside the sample but not leave it via the surface. Therefore the definition is limited to "some" electrons.
Scattering which results in scattered electrons with an absolute scattering angle larger than 90 degrees.
Here we decided to differentiate backscattering and forwardscattering purely based on angle of the particle trajectory relative to the incident beam. We are aware that, in some instances, particles that fall under the here established definitions for backscattering as well as forwardscattering, might be referred as backscattered.
Scattering which results in scattered electrons with an absolute scattering angle smaller than 90 degrees.
Here we decided to differentiate backscattering and forwardscattering purely based on the particle trajectory angle relative to the incident beam.
The potential difference between anode and cathode.
The acceleration voltage adds kinetic energy to the particles of the beam.
A group of particles which move, on average, in a common direction.
In an electron microscope particles are originally emitted by a particle source and intended to interact with a sample or a detector. The definition here should be differentiated from particles moving due to electrochemical gradient (i.e. in diffusion of liquids). Due to the wave-particle duality, a beam can also be considered as a series of waves propagating in a common direction.
Electrical current which flows along the beam path.
The value of beam current varies along the beam axis. The points at which the beam current is measured varies between instruments and manufacturers. Beam current is always measured with respect to ground.
Path which the beam flows along defined by the optical components of the instrument.
Distance which is present between the specimen surface and the detector plane.
Camera length depends on the optical setup and it is ideally determined from calibration measurements using known samples, e.g., gold on carbon.
Historically the term camera length was used in TEM, however more recently there have been innovative applications in SEM, see publications provided under examples provided in this class.
This definition applies to the experimental technique of Fraunhofer far field diffraction. In diffraction mode the quantity camera length is used to qualify the level of magnification of the diffraction pattern onto the detector. Note that the camera length may by altered by the addition of lenses in the beam transforming the physical quantity in a virtual one.
A monochromatic beam which consists of waves that have a defined phase relationship.
This definition refers to partial waves.
The angle which is given by the semi-opening angle of the cone in a convergent beam.
The convergence angle of a beam is of high relevance in both SEM and TEM as it impacts a variety of image properties. It is affected by the focusing strength of the beam forming lens and can be reduced by inserting apertures into the beam path.
A beam which is conically shaped such that its cross section is decreased to form a disc of least confusion.
To manipulate the direction and intensity of beam particles a lens is required. Using an aperture may decrease the cross section of a beam but will not serve to create a convergent beam. A convergent beam is typically characterised through the semi-opening angle of its cone typically termed convergence angle.
A physical phenomenon during which the direction and intensity of a propagating wave is changed due to interaction with matter having structure dimensions in the order of the wavelength.
Due to the wave-particle dualism, a beam of sub-atomic particles (e.g. electrons) can be diffracted.
The term "matter" used in this definition is meant to represent crystalline as well as amorphous matter (e.g. gases or objects). Diffraction might be regarded as a specific type of elastic scattering. Diffracted waves are coherent and can interfere, forming diffraction patterns.
The terms scattering and diffraction are used to describe the same phenomenon from different perspectives. From the view of a particle, people tend to speak of scattering, while from the view of waves and the related patterns, people speak of diffraction.
A pattern which consists of spatial intensity modulation generated by diffraction.
For practical purposes we do not distinguish here between the physical phenomenon of a diffraction pattern, and the experimental recording of a diffraction pattern, although we realize that these are indeed separate concepts. A diffraction pattern is commonly recorded as an image. Changing the geometry and/or the orientation of the detector will directly influence the pattern detected.
A cross section of a beam at which the beam has the smallest spatial extent.
Time period during which the beam remains at one position.
Dynamic refocusing which keeps the electron probe focused on the surface of a tilted sample.
Implementation strongly depends on the microscope and its control software.
Information about dynamic focus correction may help others to understand the quality of an experiment.
Relevant when an area is scanned which extends off-(tilt) axis. An automatic change of the electron optics to keep the sample in focus.
A workflow to keep the specimen in focus by automatic means.
To achieve experimental reproducibility this workflow should be described in detail.
Scattering during which the particle that is scattered does not change its energy.
Diffraction may be seen as a type of elastic scattering. The change in energy mentioned in the definition depends on the measurable energy loss within an electron microscope. A physical definition of elastic scattering is, when the state of the system (probe and target) remain unchanged.
Electron diffraction which primarily involves backscattered electrons from a solid sample.
Electron backscatter diffraction (EBSD) is primarily used in Scanning Electron Microscopy (SEM). The term EBSD might be understood differently based on community and due to the differences in concepts of "TEM_backscattering" and "SEM_backscattering".
A diffraction pattern which is generated by electron backscatter diffraction.
Electron Backscatter Diffraction Pattern
Diffraction which is based on a propagating electron wave.
A diffraction pattern which is generated from electron diffraction.
The part of the beam which interacts with the sample.
Often electron probe is used to describe a point where the beam is focused. It is commonly used in connection with focused beams.
Electrical current which is released from the source.
Emission current is a device- and component-dependent numerical property that can be monitored over time to evaluate e.g. service life and wear of a source. It is not cross-vendor or cross-device comparable.
Voltage which is utilised to create an electric field that draws particles from the source.
Extraction voltage is applied to Schottky and Cold Field Emission electron sources, but not to thermionic emitters. The purpose of applying an extraction voltage is to help emit electrons from inside the source material to overcome the work function and be emitted. Gallium liquid metal ion sources also use an extraction voltage to produce ions. Higher extraction voltages will lead to higher beam currents.
Electrical current which flows through the source.
This is typically used for heating a source and supplies the emission current. Higher filament currents will result in higher beam currents.
Time period during which the beam moves from the final position of one scan line to the starting position of the subsequent scan line.
Flyback time is commonly associated with rectangular scan patterns and often described in metadata from vendors as such. A typical geometrical primitive for rectangular scans are lines. Flyback time may be considered a specific instance of wait time, however some instruments might still be able to acquire data during flyback time which is why it is defined separately in this artefact.
Distance which lies between the principal plane of the lens and the focal point along the optical axis.
A beam consisting of parallel rays converges into one point for positive focal lengths. The focal length is an inherent property of a lens.
Plane which is perpendicular to the optical axis and includes the focal point.
Point which is defined by the intersection of the optical axis and the backwards extrapolated path of a ray that (1) is tending towards infinity, (2) was parallel to the optical axis in the incident beam, and (3) that was deflected by an electron lens.
https://www.iso.org/obp/ui/#iso:std:iso:15932:ed-1:v1:en 2.1.4
https://www.iso.org/obp/ui/#iso:std:iso:22493:ed-2:v1:en 3.1.4
The here given definition applies to electromagnetic lenses and is a more general definition compared to those typically given in classical optics. The focal point is an inherent property of a lens. Definition only holds if the (virtual) source is "at infinity", meaning very far away as compared to the focal length of the objective lens. This is for an ideal lens, in the reality there might be aberrations affecting the beam profile at the focal point.
A convergent beam which originates from a coherent beam and whose cross section is decreased to the physically smallest possible disc of least confusion.
The terms focused beam and convergent beam are colloquially often used almost interchangeably. Here we differentiate these terms by pointing to focused beams being used with the intention to direct the beam to the physically smallest possible area.
Time period during which the beam moves from the final position of one frame to the starting position of the subsequent frame.
Frame flyback time may be considered a specific instance of wait time, however some instruments might still be able to acquire data during frame flyback time which is why it is defined separately in this artefact.
Time period during which a frame is fully scanned.
The frame time is typically determined by a weighted sum of dwell time, move times and potentially wait time. The weighting factors are determined by the specific scan pattern.
Primary beam before it interacts with the specimen.
You can only have an incident beam in the presence of a specimen. Incident in this sense is a verb used to describe the action of the beam. Typically the beam path of an incident beam intersects with the specimen.
Scattering during which the particle that is scattered changes its energy.
The change in energy mentioned in the definition depends on the measurable energy loss within an electron microscope. A physical definition of inelastic scattering is, when the state of the system (probe and target) changes.
A beam which consists of particles of the same energy.
According to the wave particle dualism the here given definition translates also to a beam which consists of waves having the same wavelength. Note that in practice, absolute monochromaticity cannot be achieved and consequently a small energy spread always persists.
A physical part of an electron or ion microscope which is part of the electromagnetic lens and is used to amplify and shape the magnetic field used to manipulate the beam.
A given electron microscope is likely to have multiple pole pieces. However the term is commonly used to refer to the pole piece of the final optical element between the source and the specimen.
A beam which is unaltered in terms of its direction after interaction with the specimen.
The term is commonly used in diffraction experiments to describe the non-diffracted/non-scattered part of the beam after the specimen.
Electrical current which arrives at the specimen.
Area which is (1) on the specimen and (2) to be sampled during an experiment.
The region of interest might be incoherent (i.e. random walk) or consist of a set of multiple geometric coherent parts.
We recognise this definition breaks down for non-2D regions of interest. In the future we will consider defining superclass such as "volume of interest". At the moment the majority of regions of interest are 2D and this is why this is a priority term. This class could be a potential synonym to space time in EOSC ontology
A physical phenomenon during which the trajectory of a particle is changed due to interaction with matter.
The term "matter" used in this definition is meant to represent crystalline as well as amorphous matter (e.g. gases or objects). Diffraction might be regarded as a specific type of elastic scattering. The terms scattering and diffraction are used to describe the same phenomenon from different perspectives. From the view of a particle, people tend to speak of scattering, while from the view of waves and the related patterns, people speak of diffraction.
The angle which spans between the tangent of the incoming trajectory of an particle and the the tangent of the outgoing trajectory of the same particle, prior and past an instance of scattering.
A physical part of the gun from which the particles that form the beam are emitted.
The nature and the function of sources differ depending on application case and instrument.
There are different classes of ion sources.
Thermionic emitters (filament & LaB6) and field emitters are two classes of electron emission sources.
A physical entity which contains material intended to be investigated.
It should also be noted that one often probes special anomalies, such as specific locations of the parent material. Furthermore, if the properties of a specimen are assumed to be the same as they were at the time when a specimen was taken from the parental material, they still might change over time. A specimen may not be reproducible in time, e.g. it may be taken from a flowing stream or a portion of blood, no separable sampling error exists since this error is unavoidably included with the corresponding error of the estimate of the property, function being studied. The term is used across fields, i.e. in clinical, biological, geological, and materials science studies.
The terms specimen and sample are used widely interchangeable in the community. In some cases a sample might be thought of as something which is statistically representative of the parent material/sample where it was taken from while a specimen is not. However, this statistical value is not an inherent property of the sample but of the feature that was characterized. Therefore, this the relevance of this distinction depends on the application case. During discussions a large majority of contributors favoured these terms to be implemented as synonyms in this glossary.
An imaging setting which can be used during acquisition to correct perspective distortion when imaging a tilted surface or cross section.
Applied during acquisition to compensate for tilt.
As an option in a GUI it triggers a set of algorithms to apply stretching transformation on the image.
Tilt correction involves either stretching or compression along one direction or dimension of the scan area.
Tilt correction needs to be noted at data collection.
Time period in which no data are acquired.
Wait time can happen for multiple reasons. For example, the time period until a detector is ready (e.g. EDS detector is cooled down). The time period until the specimen has reached the desired state for a measurement (e.g. in-situ heating/cooling). The time period until the machine has reached the desired state (e.g. switching from high vacuum to low vacuum mode in a variable pressure SEM). Frame flyback time may also be considered a wait time.
Distance which is determined along the optical axis within the column from (1) the lower end of the final optical element between the source and the specimen stage; to (2) the point where the beam is focused.
In modern SEM and focused ion beam microscopes working distance is displayed in the user interface as a calibrated value based on the final lens excitation. For practical reasons it commonly refers to the lower end of the column instead of the lens as this gives the user an indication how much space there is between the column and the sample surface when the latter is in focus. In general, a short working distance improves resolution and signal collection for in-column detectors.
The term is frequently used in scanning electron microscopy & scanning ion microscopy.
Typically, the unit used for expressing the working distance is millimetre.
Working distance is a property of the optical system and as such independent of the position of the specimen. During regular operation, e.g. of SEM & STEM, the here mentioned point of focus will be in direct vicinity of the specimen surface.
Electron diffraction during which, in a sequential order, electrons of the incident beam are inelastically scattered, form a point source inside the specimen, and leave the specimen through Bragg diffraction.
In an experimental setup the diffraction described here will form a Kikuchi pattern which is measured to infer information about the crystal lattice of the sample.
This definition makes use of the wave-particle dualism in the sense that we use both the term scattering and diffraction in one definition.
A diffraction pattern which is generated by Kikuchi diffraction.
Electron backscatter diffraction pattern (EBSP)
A Kikuchi pattern used for further analysis typically shows seemingly parallel lines or bands on the detector plane. These are called Kikuchi lines and Kikuchi bands - please also see related classes.
Kikuchi diffraction during which electrons leave the electron-transparent sample at the side opposite to the incident beam.
Compared to EBSD, TKD has a higher spatial resolution.
In TKD a dedicated "on-axis detector" can be used to record the diffraction pattern at highest intensities and best signal-to-noise ratio.
Sometimes TKD might be referred to as "Transmission EBSD" (t-EBSD). The authors of this glossary consider this however technically wrong and deprecate the use of this terminology.
Wait time which is due to a particle detector being physically incapable of registering detector events.
This is often related to the detector specifics - because the system may be physically unable to record a particle measurement due to it being busy processing the previously detected event. In electron microscopy, it is commonly encountered when using energy dispersive x-ray detectors.
time period during which data is acquired.
camera exposure time in an EBSD measurement
time period during which image data (e.g. TEM) is acquired
time period during which spectroscopic data (e.g. EDS, EELS) is acquired
Note that acquisition time does not include time periods like flyback time or wait times.
depending on type of measurement and method the acquisition time might be interpreted differently.
Moving time during which either the position or the tilt of the beam is altered.
Moving time during which either the position or the orientation of a detector is altered.
Time period during which the position or orientation of either the beam or physical components are changed within a coordinate system of the microscope.
The physical components relevant to moving time are typically the stage, the specimen, and the retractable detectors.
Moving time during which either the position or the orientation of the sample is altered.
An array of data which represents a coherent and discrete set of time.
A 2D EBSD map containing orientation data.
A 2D EDS map with compositional information.
A single Kikuchi pattern acquired by an EBSD camera.
Any 2D image acquired with an SEM or (S)TEM.
We note that the term is widely used in different contexts (videography, photography, data recording, data analysis). Often it is used colloquially with imprecise semantic meaning. Therefore, the definition here focuses on its use within electron microscopy and we do not claim the definition to be ubiquitously applicable.
With \"coherent\" we refer to the data within a frame being in some way logically and looked at as one unit. Furthermore, we refer to discretization of time not in the sense of smallest possible discretization because data frames may be dependent on extended exposure time periods or might also represent results of processing averaged sub-frames e.g. during analyses.
Spatial volume which has negligible extent, and from where particles or radiation originate and are emitted in all directions.
In Kikuchi diffraction the term \"point source\" may be used to refer to the volume inside the non-electron transparent sample that is illuminated with the incident beam, and from which electrons are scattered into all spatial directions. More broadly, a point source might also be a volume from which photons are emitted.
Patterns of electron intensity which are (1) formed by electron diffraction, (2) appear as a geometrical feature in a Kikuchi pattern as a pair of lines limiting Kikuchi bands.
https://www.iso.org/obp/ui/en/#iso:std:iso:22493:ed-2:v1:en (section 6.5.1)
Due to the anisotropy of the source point, Kikuchi lines typically appear as a pair of excess and defect lines.
Kikuchi lines are in fact no lines but Kossel-cone cuts. More precisely they are intersections of two opposite (Kossel) cones with the detector plane. Usually the opening angle of the cones is nearly 90 deg, therefore only at low (SEM) voltages the hyperbolic character becomes recognizable, hence the term Kikuchi lines.
Kikuchi lines can can be attributed to a specific set of lattice planes.
We note that the current definition is made for plane detectors and might need to be adjusted should non-planar detectors be used.
Pattern of electron intensity which is (1) formed by electron diffraction, (2) appears as a geometrical feature in a Kikuchi pattern, (3) is an area different in intensity compared to background, and (4) is limited on each side by a Kikuchi line.
With small angle approximation the distance between a pair of Kikuchi lines is proportional to twice the Bragg angle.
The here given definition is \"unpacked\" in order to keep brevity and precision. The specifics for e.g. \"Bragg's law\" are therefore defined elsewhere in the glossary and not part of the definition here.
A condition which (1) is defined as twice the lattice spacing in a large crystal multiplied with the sine of the Bragg angle between the incident beam and a set of lattice planes, being a whole multiple of the radiation wavelength, and (2) if satisfied, may allow to relate the location of a scattering intensity maximum within a diffraction pattern to the corresponding lattice plane spacing.
Bragg's Law is a condition for constructive interference of diffracted radiation.
Bragg's law is commonly used in TEM to calculate the lattice spacing of a crystal from a diffraction pattern, most commonly zone axis or ring diffraction patterns.
We define the use of Bragg's Law for extracting information about lattice plane spacing as \"may allow to\" because in addition to Bragg's law also other conditions need to be satisfied. For example the structure factor must be non-zero.
While Bragg's Law applies to real space (or direct space), Laue condition is its equivalent in reciprocal space (or k-space).
A physical part of an electron or ion microscope which is used for signal collection.
The detector is used to provide signals that can be quantified and analysed to ultimately draw conclusions about the interaction between the incident radiation and specimen under examination.
The term signal in this definition is related to the output of the detector which may be in analogue or digital form.
A detector which is used for registering electrons.
A detector which is used for registering ions.
A detector which is used for registering photons.
A detector which is non-divisable and of finite size.
A detector pixel is typically; but not necessarily a physical element of a detector consisting of multiple, repetitively arranged detector pixels.
Event based detectors may be interpreted as one-pixel detectors, even if further analysis of their output signal allows further spatial separation of registered signals leading to electronic pixels in their output.
Note that SEM techniques often use one-pixel detectors.
Note that in Electron Backscatter Diffraction (EBSD), which uses two-dimensional detectors, it is common to group N x N neighboring pixels into "superpixels" (in a process called binning) to reduce data size or to improve signal-to-noise ratio.
Semiconductor detectors for backscattered or transmitted electrons are sometimes segmented to achieve certain contrasts. While these segments fall under the definition of detector pixel given here, they are usually not treated as such because they are essentially operated like single pixel detectors.
Data which is the smallest element of a digital image or data array.
A pixel is often thought of as rectangular; but it could have any shape. As the term pixel originated from digital images care needs to be taken when using the term in experimental science where it can be often connected to a real physical meaning.
Note that a pixel might be the result of temporal and/or spatiotemporal integration. A detector pixel represents an area over which a signal, that is projected onto the detector plane, is spatially and temporally integrated and converted into a digital image pixel value.
When recording a data frame in electron microscopy using multi-pixel detectors, the spatial ordering of pixels follows the ordering of the detector pixels. In the case of a single pixel detectors, the pixel ordering follows the beam dwell and sampling positions. A higher effective pixel density might be necessary to represent this within a typical rectangular pixel arrangement. The pixel shape typically follows from the sampling grid, hence it does not have a physical relevance.
A quantity which quantifies the number of particles transitioning through a defined area.
Dose has different relevance in different applications. In TEM and SEM discussions of dose primarily revolve around beam induced damage and preventing sample destruction. In beam lithography and focused-ion beam milling a specific dose is intended to intentionally modify a sample.
We note that for a given experiment dose may be determined by the beam current density distribution, dwell time, and illuminated area. Connected to that, care should be taken with quantification and units of dose. Dose may be described as charge per unit area or charge per unit pixel. In specific EM application, typically beam lithography and focused-ion beam milling, instrument software may offer the possibility of calculating dose as charge per unit length or particle quantity. Despite this, the physical meaning of dose will always depend on an area.
With the given term we intend to establish an umbrella class from which different, more specific sub-classes can be defined depending on application.
Measure which corresponds to the dimensions represented by one pixel.
In case of (generated) images without physical relevance, the pixel size may be arbitrary and consequently omitted.
Include reference to step size when defined
Pixel size is determined through a calibration process.
Practically pixel size may be given with different physical units - for example with a 2-dimensional length unit. In case of spatial arrays a square pixel shape is tacitly assumed in case of a 1-dimensional length unit.
The term voxel is used for three-dimensional discretizations and as such is related to pixels and pixel size.
We stress that pixel size and detector pixel size are two distinct concepts and are not synonymous. For clarity please refer back to the definitions of pixel and detector pixel.
Area which is covered by one detector pixel.
In technical documentation of detectors, detector pixel size is often simply referred to as pixel size. We stress that pixel and detector pixel are clearly distinct concepts and consequently the terms detector pixel size and pixel size are not synonymous.
The superclass area is used in the SI meaning of area - a physically measurable thing
A physical part of an electron or ion microscope which encloses a volume intended to include the specimen.
TEM sample chambers typically have a smaller volume than those used in SEM.
The sample chamber is a partially confined volume. This is because the chamber typically has valves, windows, or doors which are open to the beam, for sample exchange, or attaching measurement devices.
The sample chamber is typically under vacuum.
The pressure which is measured by a sensor for the volume within the specimen chamber.
Custom modifications of a microscope can lead to a more accurate pressure measurement. If this is the case it will typically be detailed in the methods section of a paper.
Ideally the specimen chamber pressure should be directly measured inside the chamber; often this is not possible as the value is measured by a sensor located outside the chamber, due to manufacturer design decisions. This can result in a pressure difference between the measuring sensor and the specimen.
In the case of in-situ experiments, or where a specific sample environment is used, the pressure gradient within the specimen chamber can be exploited. c.f. sample environment pressure
A physical part of an electron or ion microscope which holds the optical components of the device.
A single electron or ion microscope may have multiple columns.
It is possible to have optical components which are not contained in the column for example an EELS detector or an additional laser.
The column is a tube-like structure which allows propagation of the beam.
The exact definition of a column's boundaries may be ambiguous, for example a pole piece extending into the specimen chamber.
The pressure which is measured by a sensor within the column.
Custom modifications of a microscope can lead to a more accurate pressure measurement. If this is the case, it will typically be detailed in the methods section of a paper.
Ideally the column pressure should be directly measured inside the column; however this is often not the case and pressure is measured by a sensor located outside the column (but inside the vacuum system) due to manufacturer design decisions.
A physical part of an electron or ion microscope which contains a source and an accelerating structure to produce a beam.
Reimer, Kohl, Transmission Electron Microscopy, https://dx.doi.org/10.1007/978-0-387-34758-5
Williams, Carter, Transmission Electron Microscopy, ISBN, 978-0-387-76500-6
The pressure which is measured by a sensor within the gun.
As the gun contains multiple components, care should be taken about where exactly in the gun pressure is measured e.g. at the source.
Ideally gun pressure should be directly measured inside the gun; however this is often not the case and pressure is measured by a sensor located outside (but close to) the gun chamber due to manufacturer design decisions.
The pressure which a specimen is exposed to locally.
The sample environment pressure sensor reading may differ from the actual pressure on the sample due to the complexity of the set-up and difficulty in calibrating the pressure measurement.
This is often the case for in-situ experiments where the sample is in a special sample holder, cryo box etc with a local pressure different to that of the rest of the chamber.
We are aware that sample environment pressure is typically only considered for in-situ experiments where the pressure is different to that in the rest of the chamber.
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