Electron Microscopy Glossary
type: Ontology
version IRI: v3.0.0
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: https://orcid.org/0000-0002-3054-8734
Contributor: https://orcid.org/0000-0002-4499-0355
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
Contributor: https://orcid.org/0009-0008-6410-7217
creator: Abril Azocar Guzman
creator: Volker Hofmann
creator: Oonagh Brendike-Mannix
description: 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.
License: https://creativecommons.org/licenses/by/4.0/
prior version: https://purls.helmholtz-metadaten.de/emg/v2.0.0/
version info: v3.0.0
citation: Azocar Guzman, A., Brendike-Mannix, O., Hofmann, V. (2024), Electron Microscopy Glossary, https://purls.helmholtz-metadaten.de/emg/
creative work status: Glossary Specification
funder: Helmholtz-Gemeinschaft Deutscher Forschungszentren
funder: Nationale Forschungsdateninfrastruktur

definition
type: AnnotationProperty
IAO_0000114: IAO_0000122
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
IAO_0000116: 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.
IAO_0000117: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
IAO_0000111: definition source
IAO_0000114: IAO_0000122
definition: 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
IAO_0000117: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

abbreviation
type: AnnotationProperty
IAO_0000112: CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)
definition: A synonym type for describing abbreviations or initalisms
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/122
Contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-03-03
sub property of: SynonymTypeProperty

acronym
type: AnnotationProperty
IAO_0000112: 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.
definition: A synonym type for describing abbreviations that are a part of the full name's words, such as initialisms or alphabetisms.
IAO_0000233: https://github.com/information-artifact-ontology/ontology-metadata/issues/135
Contributor: https://orcid.org/0000-0003-4423-4370
created: 2023-11-01
sub property of: SynonymTypeProperty

Contributor
type: AnnotationProperty
range: Agent
comment: 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.
definition: An entity responsible for making contributions to the resource.

Creator
type: AnnotationProperty
sub property of: Contributor
range: Agent
comment: 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.
definition: An entity primarily responsible for making the resource.

description
type: AnnotationProperty
comment: 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.
label: Description
definition: An account of the resource.

Date Issued
type: AnnotationProperty
definition: Date of formal issuance (e.g., publication) of the resource.
range: Literal

License
type: AnnotationProperty
range: LicenseDocument
definition: A legal document giving official permission to do something with the resource.

title
type: AnnotationProperty
label: Title
definition: A name given to the resource.
note: 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.

has broad synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
label: has_broad_synonym
sub property of: has_synonym

has exact synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
label: has_exact_synonym
sub property of: has_synonym

has narrow synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
label: has_narrow_synonym
sub property of: has_synonym

has related synonym
type: AnnotationProperty
definition: 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.
IAO_0000117: http://orcid.org/0000-0001-5208-3432
label: has_related_synonym
sub property of: has_synonym

has_synonym
type: AnnotationProperty
comment: Note that this should be a super-property of hasRelatedSynonym, hasExactSynonym etc; however, we cannot state this and remain in OWL-DL

example
type: AnnotationProperty
definition: An example of the use of a concept.
sub property of: note

note
type: AnnotationProperty
definition: A general note, for any purpose.
scope note: This property may be used directly, or as a super-property for more specific note types.

scope note
type: AnnotationProperty
definition: A note that helps to clarify the meaning and/or the use of a concept.
sub property of: note

SEM Backscattering
type: Class
subclass of: Scattering
definition: 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.
definition source: Ludwig Reimer, Scanning Electron Microscopy - Physics of Image Formation and Microanalysis (ISBN 978-3-642-08372-3) - pages 57ff
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

TEM Backscattering
type: Class
subclass of: Scattering
definition: Scattering which results in scattered electrons with an absolute scattering angle larger than 90 degrees.
definition source: Ludwig Reimer, Scanning Electron Microscopy - Physics of Image Formation and Microanalysis (ISBN 978-3-642-08372-3) - pages 57ff
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

TEM Forwardscattering
type: Class
subclass of: Scattering
definition: Scattering which results in scattered electrons with an absolute scattering angle smaller than 90 degrees.
definition source: Ludwig Reimer, Scanning Electron Microscopy - Physics of Image Formation and Microanalysis (ISBN 978-3-642-08372-3) - pages 57ff
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: Here we decided to differentiate backscattering and forwardscattering purely based on the particle trajectory angle relative to the incident beam.

Acceleration Voltage
type: Class
subclass of: Thing
definition: The potential difference between anode and cathode.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: The acceleration voltage adds kinetic energy to the particles of the beam.

Beam
type: Class
subclass of: Thing
definition: A group of particles which move, on average, in a common direction.
definition source: https://en.wikipedia.org/wiki/Charged_particle_beam
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
has related synonym: charged particle beam
scope note: 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.

Beam Current
type: Class
subclass of: Thing
definition: Electrical current which flows along the beam path.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Beam Path
type: Class
subclass of: Thing
definition: Path which the beam flows along defined by the optical components of the instrument.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735

Camera Length
type: Class
subclass of: Thing
definition: Distance which is present between the specimen surface and the detector plane.
definition source: https://www.doi.org/10.1007/978-3-030-00069-1
definition source: https://www.em.tf.fau.de/2020/04/02/low-energy-electron-diffraction-lend-published-in-ultramicroscopy/
definition source: https://www.globalsino.com/EM/page3245.html
definition source: https://www.jeol.co.jp/en/words/emterms/search_result.html
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
has exact synonym: effective camera length
scope note: Camera length depends on the optical setup and it is ideally determined from calibration measurements using known samples, e.g., gold on carbon.
scope note: 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.
scope note: 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.

Coherent Beam
type: Class
subclass of: Monochromatic Beam
definition: A monochromatic beam which consists of waves that have a defined phase relationship.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: This definition refers to partial waves.

Convergence Angle
type: Class
subclass of: Thing
definition: The angle which is given by the semi-opening angle of the cone in a convergent beam.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Convergent Beam
type: Class
subclass of: Beam
definition: A beam which is conically shaped such that its cross section is decreased to form a disc of least confusion.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Diffraction
type: Class
subclass of: Thing
definition: 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.
definition source: https://doi.org/10.1016/j.jqsrt.2018.02.002
definition source: https://doi.org/10.1351/goldbook.D01711
definition source: https://en.wikipedia.org/wiki/diffraction
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-3054-8734
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
has broad synonym: scattering
scope note: Due to the wave-particle dualism, a beam of sub-atomic particles (e.g. electrons) can be diffracted.
scope note: 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.
scope note: 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.

Diffraction Pattern
type: Class
subclass of: Thing
definition: A pattern which consists of spatial intensity modulation generated by diffraction.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Disk Of Least Confusion
type: Class
subclass of: Thing
definition: A cross section of a beam at which the beam has the smallest spatial extent.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217

Dwell Time
type: Class
subclass of: Time Period
definition: Time period during which the beam remains at one position.
definition source: https://doi.org/10.1007/978-1-4939-6676-9
definition source: https://www.iso.org/obp/ui/#iso:std:iso:22493:ed-2:v1:en
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735

Dynamic Focus Correction
type: Class
subclass of: Dynamic Refocusing
definition: Dynamic refocusing which keeps the electron probe focused on the surface of a tilted sample.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
has exact synonym: Frame corrected focus
scope note: Implementation strongly depends on the microscope and its control software.
scope note: Information about dynamic focus correction may help others to understand the quality of an experiment.
scope note: Relevant when an area is scanned which extends off-(tilt) axis. An automatic change of the electron optics to keep the sample in focus.

Dynamic Refocusing
type: Class
subclass of: Thing
definition: A workflow to keep the specimen in focus by automatic means.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: To achieve experimental reproducibility this workflow should be described in detail.

Elastic Scattering
type: Class
subclass of: Scattering
definition: Scattering during which the particle that is scattered does not change its energy.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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 Backscatter Diffraction
type: Class
subclass of: Electron Diffraction
definition: Electron diffraction which primarily involves backscattered electrons from a solid sample.
definition source: https://en.wikipedia.org/wiki/Electron_backscatter_diffraction
acronym: EBSD
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has exact synonym: Backscatter Kikuchi diffraction
scope note: 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".

Electron Backscatter Diffraction Pattern
type: Class
subclass of: Diffraction Pattern
definition: A diffraction pattern which is generated by electron backscatter diffraction.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has related synonym: Kikuchi pattern

Electron Beam
type: Class
subclass of: Beam
definition: A beam which consists of electrons.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735

Electron Diffraction
type: Class
subclass of: Diffraction
definition: Diffraction which is based on a propagating electron wave.
definition source: https://en.wikipedia.org/wiki/Diffraction
definition source: https://www.sciencedirect.com/topics/chemistry/electron-diffraction#:~:text=Electron%20diffraction%20is%20a%20technique,resulting%20in%20a%20diffraction%20pattern
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217

Electron Diffraction Pattern
type: Class
subclass of: Diffraction Pattern
definition: A diffraction pattern which is generated from electron diffraction.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217

Electron Probe
type: Class
subclass of: Thing
definition: The part of the beam which interacts with the sample.
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
has related synonym: probe
scope note: Often electron probe is used to describe a point where the beam is focused. It is commonly used in connection with focused beams.

Emission Current
type: Class
subclass of: Thing
definition: Electrical current which is released from the source.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-4499-0355
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Extraction Voltage
type: Class
subclass of: Thing
definition: Voltage which is utilised to create an electric field that draws particles from the source.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-4499-0355
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Filament Current
type: Class
subclass of: Thing
definition: Electrical current which flows through the source.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: This is typically used for heating a source and supplies the emission current. Higher filament currents will result in higher beam currents.

Flyback Time
type: Class
subclass of: Time Period
definition: Time period during which the beam moves from the final position of one scan line to the starting position of the subsequent scan line.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Focal Length
type: Class
subclass of: Thing
definition: Distance which lies between the principal plane of the lens and the focal point along the optical axis.
acronym: f
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: A beam consisting of parallel rays converges into one point for positive focal lengths. The focal length is an inherent property of a lens.

Focal Plane
type: Class
subclass of: Thing
definition: Plane which is perpendicular to the optical axis and includes the focal point.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
has exact synonym: front focal plane
has related synonym: specimen plane
scope note: The plane is typically on the specimen.

Focal Point
type: Class
subclass of: Thing
definition: 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.
definition source: https://www.iso.org/obp/ui/#iso:std:iso:15932:ed-1:v1:en 2.1.4
definition source: https://www.iso.org/obp/ui/#iso:std:iso:22493:ed-2:v1:en 3.1.4
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: 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.

Focused Beam
type: Class
subclass of: Convergent Beam
definition: A convergent beam which originates from a coherent beam and whose cross section is decreased to the physically smallest possible disc of least confusion.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Frame Flyback Time
type: Class
subclass of: Time Period
definition: Time period during which the beam moves from the final position of one frame to the starting position of the subsequent frame.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Frame Time
type: Class
subclass of: Time Period
definition: Time period during which a frame is fully scanned.
definition source: https://doi.org/10.1007/978-1-4939-6676-9
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
scope note: 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.

Incident Beam
type: Class
subclass of: Primary Beam
definition: Primary beam before it interacts with the specimen.
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
has broad synonym: primary beam
scope note: 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.

Inelastic Scattering
type: Class
subclass of: Scattering
definition: Scattering during which the particle that is scattered changes its energy.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Ion Beam
type: Class
subclass of: Beam
definition: A beam which consists of ions.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735

Monochromatic Beam
type: Class
subclass of: Beam
definition: A beam which consists of particles of the same energy.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Pole Piece
type: Class
subclass of: Thing
definition: 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.
definition source: https://en.wikipedia.org/wiki/Pole_piece
definition source: https://www.jeol.co.jp/en/words/emterms/search_result.html
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: 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.

Primary Beam
type: Class
subclass of: Beam
definition: A beam which is unaltered in terms of its direction after interaction with the specimen.
definition source: https://www.iso.org/obp/ui/#iso:std:iso:15932:ed-1:v1:en
definition source: https://www.iso.org/obp/ui/#iso:std:iso:23833:ed-2:v1:en
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
has narrow synonym: incident beam
scope note: The term is commonly used in diffraction experiments to describe the non-diffracted/non-scattered part of the beam after the specimen.

Probe Current
type: Class
subclass of: Thing
definition: Electrical current which arrives at the specimen.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735

Region Of Interest
type: Class
subclass of: Thing
definition: Area which is (1) on the specimen and (2) to be sampled during an experiment.
acronym: ROI
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: The region of interest might be incoherent (i.e. random walk) or consist of a set of multiple geometric coherent parts.
scope note: 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

Scattering
type: Class
subclass of: Thing
definition: A physical phenomenon during which the trajectory of a particle is changed due to interaction with matter.
definition source: https://doi.org/10.1016/j.jqsrt.2018.02.002
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Scattering Angle
type: Class
subclass of: Thing
definition: 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.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217

Source
type: Class
subclass of: Thing
definition: A physical part of the gun from which the particles that form the beam are emitted.
definition source: https://cmrf.research.uiowa.edu/scanning-electron-microscopy
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
has broad synonym: gun
has exact synonym: emission source
example: LaB_6 crystal
example: liquid metal Gallium
example: tungsten crystal
example: tungsten wire
scope note: The nature and the function of sources differ depending on application case and instrument.
scope note: There are different classes of ion sources.
scope note: Thermionic emitters (filament & LaB6) and field emitters are two classes of electron emission sources.

Specimen
type: Class
subclass of: Thing
definition: A physical entity which contains material intended to be investigated.
definition source: https://biolincc.nhlbi.nih.gov/glossary/
definition source: https://doi.org/10.1351/pac199062061193
definition source: https://goldbook.iupac.org/terms/view/S05809
acronym: SPEC
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
has exact synonym: sample
scope note: 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.
scope note: 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.

Tilt Correction
type: Class
subclass of: Thing
definition: An imaging setting which can be used during acquisition to correct perspective distortion when imaging a tilted surface or cross section.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: Applied during acquisition to compensate for tilt.
scope note: As an option in a GUI it triggers a set of algorithms to apply stretching transformation on the image.
scope note: Tilt correction involves either stretching or compression along one direction or dimension of the scan area.
scope note: Tilt correction needs to be noted at data collection.

Time Period
type: Class
subclass of: Thing
definition: An interval of time.
has exact synonym: epoch
has exact synonym: period

Wait Time
type: Class
subclass of: Time Period
definition: Time period in which no data are acquired.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0001-8480-4775
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1008-4530
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1418-0984
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: https://orcid.org/0000-0002-2818-5890
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6004-2304
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-8218-3116
Contributor: https://orcid.org/0000-0002-9555-7455
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0000-0003-4745-9735
has related synonym: elapsed time
scope note: 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.

Working Distance
type: Class
subclass of: Thing
definition: 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.
definition source: https://www.globalsino.com/EM/page4586.html
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-0000-4784
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2285-9329
scope note: 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.
scope note: The term is frequently used in scanning electron microscopy & scanning ion microscopy.
scope note: Typically, the unit used for expressing the working distance is millimetre.
scope note: 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.

Kikuchi Diffraction
type: Class
subclass of: Electron Diffraction
definition: 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.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
scope note: 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.
scope note: This definition makes use of the wave-particle dualism in the sense that we use both the term scattering and diffraction in one definition.

Kikuchi Pattern
type: Class
subclass of: Diffraction Pattern
definition: A diffraction pattern which is generated by Kikuchi diffraction.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has related synonym: Electron backscatter diffraction pattern (EBSP)
scope note: 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.

Transmission Kikuchi Diffraction
type: Class
subclass of: Kikuchi Diffraction
definition: Kikuchi diffraction during which electrons leave the electron-transparent sample at the side opposite to the incident beam.
abbreviation: TKD
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
scope note: Compared to EBSD, TKD has a higher spatial resolution.
scope note: In TKD a dedicated "on-axis detector" can be used to record the diffraction pattern at highest intensities and best signal-to-noise ratio.
scope note: 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.

Dead Time
type: Class
subclass of: Wait Time
definition: Wait time which is due to a particle detector being physically incapable of registering detector events.
definition source: https://www.iso.org/obp/ui/#iso:std:iso:15932:ed-1:v1:en
definition source: https://www.iso.org/obp/ui/#iso:std:iso:23833:ed-2:v1:en
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Acquisition Time
type: Class
subclass of: Time Period
definition: time period during which data is acquired.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
example: camera exposure time in an EBSD measurement
example: dwell time in SEM and STEM imaging
example: time period during which image data (e.g. TEM) is acquired
example: time period during which spectroscopic data (e.g. EDS, EELS) is acquired
scope note: Note that acquisition time does not include time periods like flyback time or wait times.
scope note: depending on type of measurement and method the acquisition time might be interpreted differently.

Beam Moving Time
type: Class
subclass of: Moving Time
definition: Moving time during which either the position or the tilt of the beam is altered.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217

Detector Moving Time
type: Class
subclass of: Moving Time
definition: Moving time during which either the position or the orientation of a detector is altered.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217

Moving Time
type: Class
subclass of: Time Period
definition: Time period during which the position or orientation of either the beam or physical components are changed within a coordinate system of the microscope.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: The physical components relevant to moving time are typically the stage, the specimen, and the retractable detectors.

Sample Moving Time
type: Class
subclass of: Moving Time
definition: Moving time during which either the position or the orientation of the sample is altered.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217

Frame
type: Class
subclass of: Thing
definition: An array of data which represents a coherent and discrete set of time.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0002-9700-4803
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
example: A 2D EBSD map containing orientation data.
example: A 2D EDS map with compositional information.
example: A single Kikuchi pattern acquired by an EBSD camera.
example: Any 2D image acquired with an SEM or (S)TEM.
scope note: 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.
scope note: 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.

Point Source
type: Class
subclass of: Thing
definition: Spatial volume which has negligible extent, and from where particles or radiation originate and are emitted in all directions.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has broad synonym: interaction volume
has broad synonym: source point
scope note: 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.

Kikuchi Lines
type: Class
subclass of: Thing
definition: 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.
definition source: https://www.iso.org/obp/ui/en/#iso:std:iso:22493:ed-2:v1:en (section 6.5.1)
definition source: https://www.jeol.com/words/emterms/20121023.015559.php
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
scope note: Due to the anisotropy of the source point, Kikuchi lines typically appear as a pair of excess and defect lines.
scope note: 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.
scope note: Kikuchi lines can can be attributed to a specific set of lattice planes.
scope note: We note that the current definition is made for plane detectors and might need to be adjusted should non-planar detectors be used.

Kikuchi Band
type: Class
subclass of: Thing
definition: 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.
definition source: https://en.wikipedia.org/wiki/Intensity_(physics)
definition source: https://en.wikipedia.org/wiki/Kikuchi_lines_(physics)
definition source: https://www.jeol.com/words/emterms/20121023.015559.php
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: https://orcid.org/0000-0003-1965-7996
scope note: With small angle approximation the distance between a pair of Kikuchi lines is proportional to twice the Bragg angle.

Bragg Diffraction
type: Class
subclass of: Electron Diffraction
definition: Diffraction which follows Bragg's law.
definition source: https://physicsopenlab.org/2018/01/18/bragg-diffraction/
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.

Bragg's Law
type: Class
subclass of: Thing
definition: 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.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7086-1901
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: Bragg's Law is a condition for constructive interference of diffracted radiation.
scope note: 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.
scope note: 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.
scope note: While Bragg's Law applies to real space (or direct space), Laue condition is its equivalent in reciprocal space (or k-space).

Detector
type: Class
subclass of: Thing
definition: A physical part of an electron or ion microscope which is used for signal collection.
definition source: https://iopscience.iop.org/article/10.1088/1742-6596/522/1/012046/pdf
definition source: https://pubmed.ncbi.nlm.nih.gov/21524337/
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
has related synonym: sensor
scope note: 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.
scope note: The term signal in this definition is related to the output of the detector which may be in analogue or digital form.

Electron Detector
type: Class
subclass of: Detector
definition: A detector which is used for registering electrons.
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix

Ion Detector
type: Class
subclass of: Detector
definition: A detector which is used for registering ions.
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix

Photon Detector
type: Class
subclass of: Detector
definition: A detector which is used for registering photons.
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix

Detector Pixel
type: Class
subclass of: Detector
definition: A detector which is non-divisable and of finite size.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has related synonym: sensor
scope note: A detector pixel is typically; but not necessarily a physical element of a detector consisting of multiple, repetitively arranged detector pixels.
scope note: 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.
scope note: Note that SEM techniques often use one-pixel detectors.
scope note: 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.
scope note: 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.

Pixel
type: Class
subclass of: Thing
definition: Data which is the smallest element of a digital image or data array.
definition source: https://en.wikipedia.org/wiki/Pixel
definition source: https://www.iso.org/obp/ui/en/#iso:std:iso:22493:ed-2:v1:en
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-1965-7996
Contributor: https://orcid.org/0009-0008-6410-7217
has narrow synonym: image pixel
scope note: 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.
scope note: 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.
scope note: 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.

Dose
type: Class
subclass of: Thing
definition: A quantity which quantifies the number of particles transitioning through a defined area.
definition source: https://doi.org/10.1016/j.ultramic.2021.113363
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: Oonagh Brendike-Mannix
scope note: 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.
scope note: 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.
scope note: With the given term we intend to establish an umbrella class from which different, more specific sub-classes can be defined depending on application.

Electron Dose
type: Class
subclass of: Dose
definition: A dose which accounts for electrons.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0002-0070-4337
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: Oonagh Brendike-Mannix

Pixel Size
type: Class
subclass of: Thing
definition: Measure which corresponds to the dimensions represented by one pixel.
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: In case of (generated) images without physical relevance, the pixel size may be arbitrary and consequently omitted.
scope note: Include reference to step size when defined
scope note: Pixel size is determined through a calibration process.
scope note: 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.
scope note: The term voxel is used for three-dimensional discretizations and as such is related to pixels and pixel size.
scope note: 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.

Detector Pixel Size
type: Class
subclass of: Thing
definition: Area which is covered by one detector pixel.
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: https://orcid.org/0000-0002-1507-9327
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-0930-082X
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.
scope note: The superclass area is used in the SI meaning of area - a physically measurable thing

Specimen Chamber
type: Class
subclass of: Thing
definition: A physical part of an electron or ion microscope which encloses a volume intended to include the specimen.
definition source: ISO22493:2014
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
has broad synonym: chamber
has exact synonym: sample chamber
scope note: TEM sample chambers typically have a smaller volume than those used in SEM.
scope note: 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.
scope note: The sample chamber is typically under vacuum.

Specimen Chamber Pressure
type: Class
subclass of: Thing
definition: The pressure which is measured by a sensor for the volume within the specimen chamber.
definition source: https://goldbook.iupac.org/terms/view/S05921
definition source: https://qudt.org/vocab/quantitykind/Pressure
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
has broad synonym: chamber pressure
has exact synonym: sample chamber pressure
scope note: 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.
scope note: 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.
scope note: 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

Column
type: Class
subclass of: Thing
definition: A physical part of an electron or ion microscope which holds the optical components of the device.
definition source: https://myscope-explore.org/3_5_electroncolumn.html
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
see also: beam current
scope note: A single electron or ion microscope may have multiple columns.
scope note: It is possible to have optical components which are not contained in the column for example an EELS detector or an additional laser.
scope note: The column is a tube-like structure which allows propagation of the beam.
scope note: The exact definition of a column's boundaries may be ambiguous, for example a pole piece extending into the specimen chamber.

Column Pressure
type: Class
subclass of: Thing
definition: The pressure which is measured by a sensor within the column.
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.
scope note: 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.

Gun
type: Class
subclass of: Thing
definition: A physical part of an electron or ion microscope which contains a source and an accelerating structure to produce a beam.
definition source: ISO22493:2024
definition source: Reimer, Kohl, Transmission Electron Microscopy, https://dx.doi.org/10.1007/978-0-387-34758-5
definition source: Williams, Carter, Transmission Electron Microscopy, ISBN, 978-0-387-76500-6
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
has exact synonym: charged particle gun
has narrow synonym: electron gun
has narrow synonym: ion gun
has narrow synonym: particle source

Gun Pressure
type: Class
subclass of: Thing
definition: The pressure which is measured by a sensor within the gun.
Contributor: https://orcid.org/0000-0001-5870-4658
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0000-0003-2534-0063
Contributor: https://orcid.org/0009-0008-6410-7217
has exact synonym: charged particle gun pressure
has narrow synonym: electron gun pressure
has narrow synonym: ion gun pressure
has narrow synonym: source pressure
scope note: As the gun contains multiple components, care should be taken about where exactly in the gun pressure is measured e.g. at the source.
scope note: 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.
scope note: 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.

Sample Environment Pressure
type: Class
subclass of: Thing
definition: The pressure which a specimen is exposed to locally.
definition source: https://sampleenvironment.github.io/secop-site/
Contributor: https://orcid.org/0000-0001-6534-4195
Contributor: https://orcid.org/0000-0002-1278-4928
Contributor: Volker Hofmann
Contributor: https://orcid.org/0000-0002-6368-2067
Contributor: https://orcid.org/0000-0002-7117-5196
Contributor: Oonagh Brendike-Mannix
Contributor: https://orcid.org/0000-0003-2285-9329
Contributor: https://orcid.org/0009-0008-6410-7217
scope note: 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.
scope note: 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.
scope note: 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.