EM_Glossary issueshttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues2024-03-25T17:14:05+01:00https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/124Bragg diffraction2024-03-25T17:14:05+01:00Volker HofmannBragg diffraction## description
during defining `Kikuchi diffraction` the term `Bragg diffraction` was identified as a required differentia and should therefore be defined here.
seeAlso: https://physicsopenlab.org/2018/01/18/bragg-diffraction/## description
during defining `Kikuchi diffraction` the term `Bragg diffraction` was identified as a required differentia and should therefore be defined here.
seeAlso: https://physicsopenlab.org/2018/01/18/bragg-diffraction/https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/123Fix camera_length.yaml2024-03-25T15:02:10+01:00Abril Azocar GuzmanFix camera_length.yamlThe sources are listed under the example key. See [here](https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/blob/main/terms/camera_length.yaml?ref_type=heads#L25)The sources are listed under the example key. See [here](https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/blob/main/terms/camera_length.yaml?ref_type=heads#L25)Volker HofmannVolker Hofmannhttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/121Improve CI pipeline2024-03-22T14:19:06+01:00Volker HofmannImprove CI pipelinethe current actions of the CI pipeline could be improved by:
- moving to a more rigorous validation of the metadata schema (i.e. in pydantics)
- automatically generating IRIs based on what is in the repo already (or some file where the ...the current actions of the CI pipeline could be improved by:
- moving to a more rigorous validation of the metadata schema (i.e. in pydantics)
- automatically generating IRIs based on what is in the repo already (or some file where the "count" is saved)
- [adding a spellchecker to check yaml files]https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/116(to be) importet terms2024-03-15T18:12:08+01:00Volker Hofmann(to be) importet terms- time period http://purl.obolibrary.org/obo/NCIT_C25616 set as "sameAs"/"EquivalentClass" as EMG:TimePeriod
-- time period http://purl.obolibrary.org/obo/NCIT_C25616 set as "sameAs"/"EquivalentClass" as EMG:TimePeriod
-https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/109[discussion] Implementation of Glossary2023-12-19T11:16:12+01:00Volker Hofmann[discussion] Implementation of GlossaryThis is to discuss the requirements for an implemented of the EMGlossary. This includes both:
- a human friendly interface for browsing
- we have implemented a web-frontend for browsing the definitions. This is open for comments towar...This is to discuss the requirements for an implemented of the EMGlossary. This includes both:
- a human friendly interface for browsing
- we have implemented a web-frontend for browsing the definitions. This is open for comments towards adaption: https://em-glossary.vercel.app/
- a machine readible and actionable artefact
This can be also be a q/a - feel free to post any thoughts comments or questions here.https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/108Electron Backscatter Diffraction (EBSD)2023-10-30T14:23:41+01:00Peter KonijnenbergElectron Backscatter Diffraction (EBSD)Sometimes referred to as Electron Backscattered Diffraction. Kikuchi diffraction in thick samples, typically strongly inclinated towards the incident beam, to characterize the microstructure at the top surface of a bulk sample.
overlap ...Sometimes referred to as Electron Backscattered Diffraction. Kikuchi diffraction in thick samples, typically strongly inclinated towards the incident beam, to characterize the microstructure at the top surface of a bulk sample.
overlap with terms in #104 and #105https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/107Transmission Kikuchi diffraction (TKD)2024-03-12T14:15:36+01:00Peter KonijnenbergTransmission Kikuchi diffraction (TKD)Sometimes referred to as transmission EBSD (t-EBSD). Kikuchi diffraction in (thin) electron transparent samples at (near) zero tilt and at relatively high acceleration voltages, to characterize the microstructure at the lower sample surf...Sometimes referred to as transmission EBSD (t-EBSD). Kikuchi diffraction in (thin) electron transparent samples at (near) zero tilt and at relatively high acceleration voltages, to characterize the microstructure at the lower sample surface in high spatial resolution.
```yaml
labels:
label_en: Transmission Kikuchi diffraction
singular:
singular_en:
plural:
plural_en:
acronyms:
acronym_en:
abbreviations:
abbreviation_en: TKD
synonyms:
exact_synonym_en:
narrow_synonym_en:
broad_synonym_en:
related_synonym_en:
iri:
definitions:
definition_en: >
is Kikuchi diffraction in electron transparent samples at approximately zero tilt.
sources:
comments:
comment_en: >
Sometimes referred to as transmission EBSD (t-EBSD). It is used to characterize the microstructure at the lower sample surface in high spatial resolution.
examples:
seeAlso:
-
contributors:
- https://orcid.org/0000-0002-1278-4928 # Peter Konijnenberg
- https://orcid.org/0000-0001-6534-4195 # Helmut Kohl
- https://orcid.org/0000-0002-7117-5196 # Markus Kühbach
- https://orcid.org/0000-0003-1965-7996 # Özlem Özkan
- https://orcid.org/0000-0002-5149-603X # Volker Hofmann
ratified: false
```https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/106Kikuchi pattern2024-03-12T14:15:39+01:00Peter KonijnenbergKikuchi pattern```yaml
label: Kikuchi pattern
narrow_synonym_en: EBSP
definition: Pattern of line pairs or bands, generated by Kikuchi diffraction, formed on a detector plane.
``````yaml
label: Kikuchi pattern
narrow_synonym_en: EBSP
definition: Pattern of line pairs or bands, generated by Kikuchi diffraction, formed on a detector plane.
```Peter KonijnenbergPeter Konijnenberghttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/105Kikuchi diffraction2024-03-12T14:15:40+01:00Peter KonijnenbergKikuchi diffractionDiffraction process in which the incident beam is scattered quasi-elastically (thermally diffuse) and incoherently first. Per set of parallel lattice planes, only specific directions in Bragg-condition can coherently channel out again. T...Diffraction process in which the incident beam is scattered quasi-elastically (thermally diffuse) and incoherently first. Per set of parallel lattice planes, only specific directions in Bragg-condition can coherently channel out again. These directions form a set of two nearly flat (Kossel) cone sectors. For Kikuchi diffraction to happen a minimum sample thickness is needed.
---
other terms in this semantic cluster:
- quasi-elastic scattering
- lattice
- lattice planes
- Bragg-condition
- flat cone /Kossel cone
Are these really EM specific terms? Are there other resources where we can source from?
---
```yaml
label: Kikuchi diffraction
definition: A process during which inelastically scattered beam particles inside the specimen are diffracted by crystal lattice planes.
```https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/103[new term] Scattering2023-09-13T10:40:28+02:00Oonagh Mannix[new term] ScatteringIdentified while working on #101 that we need to separate scattering from diffraction and have a unique definition for this.Identified while working on #101 that we need to separate scattering from diffraction and have a unique definition for this.https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/100[new term] Experiment2023-07-11T17:07:31+02:00Oonagh Mannix[new term] ExperimentWe noticed (in meeting 17/04/2023) that many of our definitions refer to an experiment (see e.g. region of interest). To ensure precision we should define what we mean by experimentWe noticed (in meeting 17/04/2023) that many of our definitions refer to an experiment (see e.g. region of interest). To ensure precision we should define what we mean by experimenthttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/99Units to be included?!2023-09-11T13:35:49+02:00Markus WollgartenUnits to be included?!Dear all,
I am little bit surprised that I did not recognize, that units are not part of the yaml files. I think this is necessary, if one wants to refer to the EM-Glossary when setting up a data structure. Just as Bernd pointed out.
C...Dear all,
I am little bit surprised that I did not recognize, that units are not part of the yaml files. I think this is necessary, if one wants to refer to the EM-Glossary when setting up a data structure. Just as Bernd pointed out.
Can't we just add a field for unit or even "typical" unit, which would refer to the typical order of magnitude.
---
**collection of terms where such additions would make sense:**
- diffraction pattern:
- unit dimension: intensity (get IRI): could be [radiant intensity](http://purl.obolibrary.org/obo/UO_0000159)?
- preferred unit: NaN
-https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/97Example EM metadata link collection2023-03-07T16:43:56+01:00Annika StruppExample EM metadata link collectionAdd / collect hyperlinks to EM metadata examples (e.g. Zenodo); e.g. FairMat examples on Zenodo with DOI
incl. vendor (software) version / build no. the example data was collected with (image acquisition)
@christophpauly
@markus.kuehbachAdd / collect hyperlinks to EM metadata examples (e.g. Zenodo); e.g. FairMat examples on Zenodo with DOI
incl. vendor (software) version / build no. the example data was collected with (image acquisition)
@christophpauly
@markus.kuehbachhttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/96[new term] stigmator (setting)2022-11-28T14:20:15+01:00Annika Strupp[new term] stigmator (setting)Discussed in dev meeting 24 Nov 2022. May not be relevant for initial user / researcher, but may contain relevant information for data re-use (e.g. seasonal changes). Optional fact in NXem metadata model. Use case dependent.
@a.strupp: ...Discussed in dev meeting 24 Nov 2022. May not be relevant for initial user / researcher, but may contain relevant information for data re-use (e.g. seasonal changes). Optional fact in NXem metadata model. Use case dependent.
@a.strupp: Check terminology with different vendor metadata models / schemas.
Stigmator is rather generic, there are usually multiple stigmators in one machine (i.e. objective stigmator). Multiple entities of type stigmator in actual metadata record.https://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/93Check Thermo Fisher introduction to electron microscopy PDF with glossary in ...2022-11-28T13:05:16+01:00Annika StruppCheck Thermo Fisher introduction to electron microscopy PDF with glossary in chapter 7see https://assets.thermofisher.com/TFS-Assets/MSD/Handbooks/Exploring-uncharted-realms-with-electron-microscopy.pdf (i.e. chapter 7, page 39 ff) for conventional / habitual descriptions of the following terms (check box if relevant for ...see https://assets.thermofisher.com/TFS-Assets/MSD/Handbooks/Exploring-uncharted-realms-with-electron-microscopy.pdf (i.e. chapter 7, page 39 ff) for conventional / habitual descriptions of the following terms (check box if relevant for EM glossary project)
terms:
- [ ] aberration
- [ ] accelerating voltage (see #91)
- [ ] airlock
- [ ] amplitude
- [ ] amplitude contrast
- [ ] Ångström
- [ ] anode (mentioned in #16)
- [ ] aperture (mentioned in #33, #63)
- [ ] astigmatism
- [ ] atom (see #41)
- [ ] atomic number
- [ ] backscattered electrons
- [ ] binocular magnifier
- [ ] cathodoluminescence
- [ ] chromatic aberration
- [ ] column (mentioned in #16)
- [ ] condenser lens
- [ ] crystal (mentioned in #16, #76)
- [ ] detector (see #20, #22, #29, #33, #83)
- [ ] diffraction (see #67)
- [ ] diffraction contrast (see #33)
- [ ] EDX
- [ ] EELS
- [ ] electron (see e.g. #18)
- [ ] electron microscope (see e.g. #35)
- [ ] electrostatic lens (see e.g. #50)
- [ ] ESEM
- [ ] ETEM
- [ ] excitation (see #26)
- [ ] excited atom (see #26)
- [ ] FEG
- [ ] FIB (see #33)
- [ ] filament (see #16, #76)
- [ ] fluorescent screen
- [ ] focal length of a lens (see #32)
- [ ] focusing (mentioned in #85)
- [ ] goniometer
- [ ] ground state (mentioned in #26)
- [ ] ion (mentioned in e.g. #16, #26, #75)
- [ ] ion getter pump
- [ ] lattice
- [ ] lens (see #50)
- [ ] LMIS
- [ ] micrometer
- [ ] microtome
- [ ] nanometer
- [ ] oil diffusion pump
- [ ] objective lens (see #31, #50)
- [ ] phase
- [ ] phase contrast
- [ ] phase diagram
- [ ] photomultiplier
- [ ] photons (mentioned in #13, #20)
- [ ] primary electrons
- [ ] quantum
- [ ] raster (see #34)
- [ ] refraction
- [ ] refractive index
- [ ] resolving power
- [ ] resolution (mentioned in e.g. #33, #35, #36)
- [ ] scanning (mentioned in e.g. #28, #33, #34, #82)
- [ ] scintillation detector (see #20)
- [ ] secondary electrons
- [ ] SEM
- [ ] semiconductor detector (see #20)
- [ ] spectrometer (see #23)
- [ ] spectrum (see 23)
- [ ] sputter coater
- [ ] STEM (see #37)
- [ ] steradian
- [ ] TEM (see #36)
- [ ] turbomolecular pump
- [ ] vacuum (mentioned in #37)
- [ ] wavelength
- [ ] WDX
- [ ] Wehnelt cylinder
- [ ] working distance (see #11)
- [ ] X-rayshttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/92[new term] (S)EM condition2022-11-18T12:41:10+01:00Annika Strupp[new term] (S)EM condition### About this request
Investigating for potential superclass in !24 and !23 I came across "SEM condition" in https://www.ebsd.com/hints-and-tips/optimization-sem-condition (by Oxford Instruments)
Potential synonyms for **(S)EM conditio...### About this request
Investigating for potential superclass in !24 and !23 I came across "SEM condition" in https://www.ebsd.com/hints-and-tips/optimization-sem-condition (by Oxford Instruments)
Potential synonyms for **(S)EM condition**:
* instruments setting
* imaging setting
* calibration process
* calibration procedure
Things listed under **SEM conditions** on ttps://www.ebsd.com/hints-and-tips/optimization-sem-condition:
* beam energy
* beam current
* imaging settings
* variable pressure
May be related to terms:
* #51
* beam.yaml
* beam_current.yaml
* electron_beam.yaml
* acceleration_voltage.yamlAnnika StruppAnnika Strupphttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/91[refine] acceleration_voltage.yaml potential synonyms2022-12-09T12:01:26+01:00Annika Strupp[refine] acceleration_voltage.yaml potential synonymsacceleration_voltage.yaml at the moment does not contain any `synonyms:`. Multiple potential synonyms where discussed in #25. I also came across "beam energy (i.e. accelerating voltage)" in https://www.ebsd.com/hints-and-tips/optimizatio...acceleration_voltage.yaml at the moment does not contain any `synonyms:`. Multiple potential synonyms where discussed in #25. I also came across "beam energy (i.e. accelerating voltage)" in https://www.ebsd.com/hints-and-tips/optimization-sem-condition (also see snapshot attached)Annika StruppAnnika Strupphttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/88Glossary term suggestions relevant for system-health monitoring2022-10-24T18:29:17+02:00Annika StruppGlossary term suggestions relevant for system-health monitoringLink to this issue all [new term] suggestion issues related with system-health monitoring rather than with vendor- or data-interoperability.
fyi @wollgartenLink to this issue all [new term] suggestion issues related with system-health monitoring rather than with vendor- or data-interoperability.
fyi @wollgartenAnnika StruppAnnika Strupphttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/87[admin] jeol.com update: broken links2022-11-15T09:27:18+01:00Annika Strupp[admin] jeol.com update: broken linksWebsite update on https://www.jeol.com/ around Sept, Oct 2022.
No 301 redirects, hyperlinks broken. Consider, check and fix as soon as YAML files are supposed to be ratified.Website update on https://www.jeol.com/ around Sept, Oct 2022.
No 301 redirects, hyperlinks broken. Consider, check and fix as soon as YAML files are supposed to be ratified.Annika StruppAnnika Strupphttps://codebase.helmholtz.cloud/em_glossary/em_glossary/-/issues/84[new term] multimodal data acquisition2022-10-25T13:16:39+02:00Peter Konijnenberg[new term] multimodal data acquisition