2.3.3.3.109. NXem

Status:

application definition, extends NXobject

Description:

Application definition for normalized representation of electron microscopy rese ...

Application definition for normalized representation of electron microscopy research.

This application definition is a comprehensive example for a general description with which to normalize specific pieces of information and data collected within electron microscopy research.

NXem is designed to be used for documenting experiments or computer simulations in which controlled electron beams are used for studying electron-beam matter interaction to explore physical mechanisms and phenomena, or to characterize materials with an electron microscope.

Symbols:

No symbol table

Groups cited:

NXaberration, NXactuator, NXaperture, NXbeam, NXchamber, NXcite, NXcomponent, NXcoordinate_system_set, NXcoordinate_system, NXcorrector_cs, NXcrystal_structure, NXcs_profiling, NXdata, NXdetector, NXebeam_column, NXem_correlation, NXem_ebsd, NXem_eds, NXem_eels, NXem_img, NXem_msr, NXem_sim, NXentry, NXevent_data_em_set, NXevent_data_em, NXfabrication, NXibeam_column, NXidentifier, NXimage_set, NXinstrument, NXion, NXlens_em, NXmonochromator, NXprocess, NXprogram, NXpump, NXroi, NXsample, NXscanbox_em, NXsensor, NXserialized, NXsource, NXspectrum_set, NXstage_lab, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXem

@version: (optional) NX_CHAR ⤆

experiment_alias: (required) NX_CHAR

Alias which scientists can easier identify this experiment by.

experiment_description: (optional) NX_CHAR ⤆

Free-text description about the experiment. ...

Free-text description about the experiment.

Users are strongly advised to parameterize the description of their experiment by using respective groups and fields and base classes instead of writing prose into the field. The reason is that such free-text field is difficult to machine-interpret. The motivation behind keeping this field for now is to learn in how far the current base classes need extension based on user feedback.

start_time: (required) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC information included ...

ISO 8601 time code with local time zone offset to UTC information included when the microscope session started. If the application demands that time codes in this section of the application definition should only be used for specifying when the experiment was performed - and the exact duration is not relevant use this start_time field.

Often though it is useful to specify a time interval via setting both a start_time and an end_time because this enables software tools and users to collect a more detailed bookkeeping of the experiment.

Users should be aware though that even with having both time instances specified, it may not be possible to infer how long the experiment took or for how long data were acquired.

More detailed timing data over the course of the experiment have to be collected to compute this. These computations can take advantage of individual time stamps start_time and end_time in NXevent_data_em instances.

end_time: (recommended) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC included when ...

ISO 8601 time code with local time zone offset to UTC included when the microscope session ended.

See docstring of the start_time field to see how to use the start_time and end_time together.

profiling: (optional) NXcs_profiling

The configuration of the I/O writer software (e.g. `pynxtools

The configuration of the I/O writer software (e.g. pynxtools or its plugins) which was used to generate this NeXus file instance.

programID: (optional) NXprogram

A collection of all programs and libraries that are considered as relevant ...

A collection of all programs and libraries that are considered as relevant to understand with which software tools this NeXus file instance was generated. Ideally, to enable a binary recreation from the input data.

Examples include the name and version of the libraries used to write the instance. Ideally, the software which writes these NXprogram instances also includes the version of the set of NeXus classes i.e. the specific set of base classes, application definitions, and contributed definitions with which the here described concepts can be resolved.

For the pynxtools library which is used by the NOMAD research data management system, it makes sense to store e.g. the GitHub repository commit and respective submodule references used.

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

experiment_identifier: (recommended) NXidentifier ⤆

Ideally, a (globally) unique persistent identifier for referring to this exp ...

Ideally, a (globally) unique persistent identifier for referring to this experiment.

An experiment should be understood in that this can be an experiment in reality or a computer simulation because also the latter is an experiment (see the Cambridge Dictionary experiment a test done in order to find out something, eg if an idea is correct).

The identifier is usually issued by the facility, laboratory, or the principle investigator. The identifier enables to link experiments/simulations to e.g. proposals.

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

citeID: (optional) NXcite

serializedID: (optional) NXserialized

Possibility to store a collection of serialized resources associated with th ...

Possibility to store a collection of serialized resources associated with the experiment.

An example how to use this set could be to document from which files, which have been e.g. generated by software of technology partners, the information in an instance of NXem was filled with during parsing or transcoding between different formats.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

userID: (optional) NXuser ⤆

Information about persons who performed or were involved in the microscope ...

Information about persons who performed or were involved in the microscope session or simulation run.

This can be the principle investigator who performed this experiment or the student who performed simulations. Adding multiple users if relevant is recommended.

name: (optional) NX_CHAR ⤆

Given (first) name and surname.

affiliation: (optional) NX_CHAR ⤆

Name of the affiliation at the point in time when the experiment was performed.

address: (optional) NX_CHAR ⤆

Postal address of the affiliation.

email: (optional) NX_CHAR ⤆

Email address at the point in time when the experiment was performed. ...

Email address at the point in time when the experiment was performed.

Writing the most permanently used email is recommended.

telephone_number: (optional) NX_CHAR ⤆

Telephone number at the point in time when the experiment was performed.

role: (optional) NX_CHAR ⤆

User role at the point in time when the experiment was performed. ...

User role at the point in time when the experiment was performed.

Examples are technician operating the microscope, student, postdoc, principle investigator, or guest.

identifier: (optional) NXidentifier ⤆

Identifier offered by a service to report the user other than by using its ...

Identifier offered by a service to report the user other than by using its name.

Examples could be an ORCID or social media account of the user.

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

sample: (required) NXsample ⤆

A physical entity which contains material intended to be investigated. ...

A physical entity which contains material intended to be investigated. Sample and specimen are treated as de facto synonyms. Samples can be real or virtual ones.

This concept is related to term Specimen of the EMglossary standard.

type: (required) NX_CHAR ⤆

Qualifier whether the sample is a real or a virtual one. ...

Qualifier whether the sample is a real or a virtual one.

Any of these values: experiment | simulation

preparation_date: (required) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC information ...

ISO 8601 time code with local time zone offset to UTC information when the specimen was prepared.

Ideally, report the end of the preparation, i.e. the last known timestamp when the measured specimen surface was actively prepared. Ideally, this matches the last timestamp that is mentioned in the digital resource pointed to by parent_identifier.

Knowing when the specimen was exposed to e.g. specific atmosphere is especially required for environmentally sensitive material such as specimen charged with hydrogen or experiments including tracers that have a short halflife. Additional time stamps prior to preparation_date should better be placed in resources which describe but which do not pollute the description here with prose. Resolving these connected pieces of information is considered the responsibility of the research data management system not of a NeXus file.

name: (recommended) NX_CHAR ⤆

An alias used to refer to the specimen to please readability for humans.

atom_types: (required) NX_CHAR

List of comma-separated elements from the periodic table that are containe ...

List of comma-separated elements from the periodic table that are contained in the sample. If the sample substance has multiple components, all elements from each component must be included in atom_types.

The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret these from the resources pointed to by parent_identifier or walk through eventually deeply nested groups in individual data instances.

thickness: (optional) NX_NUMBER {units=NX_LENGTH}

(Measured) sample thickness. ...

(Measured) sample thickness.

The information is recorded to qualify if the beam used was likely able to shine through the specimen. For scanning electron microscopy, in many cases the specimen is typically thicker than what is illuminatable by the electron beam.

In this case the value should be set to the actual thickness of the specimen viewed for an illumination situation where the nominal surface normal of the specimen is parallel to the optical axis.

density: (optional) NX_NUMBER {units=NX_ANY}

(Measured) density of the specimen. ...

(Measured) density of the specimen.

For multi-layered specimens this field should only be used to describe the density of the excited volume. For scanning electron microscopy the usage of this field is discouraged and instead an instance of an NXinteraction_vol_em within individual NXevent_data_em instances can provide a cleaner description of the relevant details why one may wish to store the density of the specimen.

description: (optional) NX_CHAR ⤆

Discouraged free-text field to provide further detail although adding ...

Discouraged free-text field to provide further detail although adding parent_identifier and having a working research data management system should provide this contextualization.

identifier: (recommended) NXidentifier ⤆

Ideally, (globally) unique persistent identifier which distinguishes the s ...

Ideally, (globally) unique persistent identifier which distinguishes the sample from all others and especially the predecessor/origin from where that sample was cut. The terms sample and specimen are here considered as exact synonyms.

This field must not be used for an alias! Instead, use name.

In cases where multiple specimens were loaded into the microscope, the identifier has to resolve the specific sample, whose results are stored by this NXentry instance because a single NXentry should be used for the characterization of a single specimen.

Details about the specimen preparation should be stored in resources referring to parent_identifier.

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

parent_identifier: (recommended) NXidentifier

Identifier of the sample from which the sample was cut or the string *None ...

Identifier of the sample from which the sample was cut or the string None.

The purpose of this field is to support functionalities for tracking sample provenance in a research data management system.

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

coordinate_system_set: (required) NXcoordinate_system_set

Set to hold different coordinate systems conventions. ...

Set to hold different coordinate systems conventions.

Inspect the description of the NXcoordinate_system_set and NXcoordinate_system base classes how to define coordinate systems in NeXus.

COORDINATE_SYSTEM: (required) NXcoordinate_system ⤆

alias: (optional) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

origin: (required) NX_CHAR ⤆

processing_reference_frame: (recommended) NXcoordinate_system ⤆

alias: (optional) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

origin: (recommended) NX_CHAR ⤆

Location of the origin of the processing_reference_frame. ...

Location of the origin of the processing_reference_frame.

It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. Edges are interpreted by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) along respective base vector direction of the reference frame.

If any of these assumptions is not met, the user is required to explicitly state this.

Any of these values:

  • undefined

  • front_top_left

  • front_top_right

  • front_bottom_right

  • front_bottom_left

  • back_top_left

  • back_top_right

  • back_bottom_right

  • back_bottom_left

x_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing x-axis base vector of the ...

Direction of the positively pointing x-axis base vector of the processing_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

y_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing y-axis base vector of the ...

Direction of the positively pointing y-axis base vector of the processing_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

z_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing z-axis base vector of the ...

Direction of the positively pointing z-axis base vector of the processing_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

sample_reference_frame: (recommended) NXcoordinate_system ⤆

depends_on: (optional) NX_CHAR ⤆

Reference to the specifically named :ref:`NXsample` instance(s) for ...

Reference to the specifically named NXsample instance(s) for which these conventions apply (e.g. /entry1/sample1).

alias: (optional) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

origin: (recommended) NX_CHAR ⤆

Location of the origin of the sample_reference_frame. ...

Location of the origin of the sample_reference_frame.

It is assumed that regions-of-interest in this reference frame form a rectangle or cuboid. Edges are interpreted by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) along respective base vector direction of the reference frame.

If any of these assumptions is not met, the user is required to explicitly state this.

Any of these values:

  • undefined

  • front_top_left

  • front_top_right

  • front_bottom_right

  • front_bottom_left

  • back_top_left

  • back_top_right

  • back_bottom_right

  • back_bottom_left

x_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing x-axis base vector of the ...

Direction of the positively pointing x-axis base vector of the sample_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

y_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing y-axis base vector of the ...

Direction of the positively pointing y-axis base vector of the sample_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

z_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing z-axis base vector of the ...

Direction of the positively pointing z-axis base vector of the sample_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

detector_reference_frameID: (optional) NXcoordinate_system ⤆

depends_on: (optional) NX_CHAR ⤆

Reference to the specifically named :ref:`NXdetector` instance for ...

Reference to the specifically named NXdetector instance for which these conventions apply (e.g. /entry1/instrument/detector1).

alias: (optional) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

origin: (recommended) NX_CHAR ⤆

Location of the origin of the detector_reference_frame. ...

Location of the origin of the detector_reference_frame.

If the regions-of-interest forms a rectangle or cuboid, it is assumed that edges are interpreted by inspecting the direction of their outer unit normals (which point either parallel or antiparallel) along respective base vector direction of the reference frame.

If any of these assumptions is not met, the user is required to explicitly state this.

Any of these values:

  • undefined

  • front_top_left

  • front_top_right

  • front_bottom_right

  • front_bottom_left

  • back_top_left

  • back_top_right

  • back_bottom_right

  • back_bottom_left

x_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing x-axis base vector of the ...

Direction of the positively pointing x-axis base vector of the detector_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

y_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing y-axis base vector of the ...

Direction of the positively pointing y-axis base vector of the detector_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

z_direction: (recommended) NX_CHAR ⤆

Direction of the positively pointing z-axis base vector of the ...

Direction of the positively pointing z-axis base vector of the detector_reference_frame.

Any of these values:

  • undefined

  • north

  • east

  • south

  • west

  • in

  • out

measurement: (optional) NXem_msr

em_lab: (required) NXinstrument ⤆

instrument_name: (recommended) NX_CHAR ⤆

location: (recommended) NX_CHAR ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

control_programID: (required) NXprogram

Details about the control program used for operating the microscope.

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

ebeam_column: (required) NXebeam_column ⤆

chamber: (optional) NXchamber ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

electron_source: (required) NXsource ⤆

This concept is related to term `Source`_ of the EMglossary standard. ...

This concept is related to term Source of the EMglossary standard.

emitter_type: (required) NX_CHAR ⤆

probe: (required) NX_CHAR ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

lensID: (optional) NXlens_em ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

apertureID: (optional) NXaperture ⤆

fabrication: (optional) NXfabrication

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

monochromatorID: (optional) NXmonochromator ⤆

Device for improving energy resolution or reducing chromatic aberratio ...

Device for improving energy resolution or reducing chromatic aberration.

Examples are Wien, $textalpha$-, or $Omega$- energy filter or cc corrector like

type: (required) NX_CHAR

Qualitative type of the component. ...

Qualitative type of the component.

Any of these values:

  • wien

  • alfa

  • omega

  • castaing_henry

  • gatan_imaging

  • sector_analyzer

fabrication: (optional) NXfabrication

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

corrector_cs: (optional) NXcorrector_cs ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

corrector_ax: (optional) NXcomponent ⤆

Device reshaping an ellipse-shaped electron beam to a circular one. ...

Device reshaping an ellipse-shaped electron beam to a circular one.

Stigmator is an exact synonym.

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

biprism: (optional) NXcomponent ⤆

Electron biprism as it is used e.g. for electron holography.

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

phaseplateID: (optional) NXcomponent ⤆

Device that causes a change in the phase of an electron wave. ...

Device that causes a change in the phase of an electron wave.

type: (required) NX_CHAR

Qualitative type ...

Qualitative type

Any of these values: thin_film | electrostatic

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

sensorID: (optional) NXsensor ⤆

actuatorID: (optional) NXactuator ⤆

ibeam_column: (optional) NXibeam_column ⤆

chamber: (optional) NXchamber ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

ion_source: (required) NXsource ⤆

probe: (required) NXion ⤆

lensID: (optional) NXlens_em ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

apertureID: (optional) NXaperture ⤆

fabrication: (optional) NXfabrication

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

monochromatorID: (optional) NXmonochromator ⤆

Device for improving energy resolution or reducing chromatic aberratio ...

Device for improving energy resolution or reducing chromatic aberration.

Examples are Wien, $textalpha$-, or $Omega$- energy filter or cc corrector like

type: (required) NX_CHAR

Qualitative type of the component. ...

Qualitative type of the component.

Any of these values:

  • wien

  • alfa

  • omega

  • castaing_henry

  • gatan_imaging

  • sector_analyzer

fabrication: (optional) NXfabrication

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

sensorID: (optional) NXsensor ⤆

actuatorID: (optional) NXactuator ⤆

detectorID: (optional) NXdetector ⤆

fabrication: (required) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

scan_controller: (optional) NXscanbox_em ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

SENSOR: (optional) NXsensor ⤆

ACTUATOR: (optional) NXactuator ⤆

STAGE_LAB: (optional) NXstage_lab ⤆

fabrication: (optional) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

CHAMBER: (optional) NXchamber ⤆

PUMP: (optional) NXpump ⤆

event_data_em_set: (optional) NXevent_data_em_set ⤆

EVENT_DATA_EM: (optional) NXevent_data_em ⤆

start_time: (recommended) NX_DATE_TIME ⤆

end_time: (recommended) NX_DATE_TIME ⤆

IMAGE_SET: (optional) NXimage_set ⤆

PROCESS: (required) NXprocess ⤆

detector_identifier: (required) NX_CHAR ⤆

source: (recommended) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

absolute_path: (recommended) NX_CHAR ⤆

image_1d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_COMPLEX

@long_name: (required) NX_CHAR

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

image_2d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_COMPLEX

@long_name: (required) NX_CHAR

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

image_3d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_COMPLEX

@long_name: (required) NX_CHAR

axis_k: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_1d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

group_identifier: (optional) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

image_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_2d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

group_identifier: (optional) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

image_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_3d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

real: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

imag: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

magnitude: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

intensity: (optional) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

group_identifier: (optional) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

image_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_k: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

SPECTRUM_SET: (optional) NXspectrum_set ⤆

PROCESS: (required) NXprocess ⤆

detector_identifier: (required) NX_CHAR ⤆

source: (recommended) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

absolute_path: (recommended) NX_CHAR ⤆

spectrum_0d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_1d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_2d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_3d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_k: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_0d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_1d: (optional) NXdata

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_identifier: (required) NX_INT

@long_name: (required) NX_CHAR

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_2d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

stack_3d: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_INT ⤆

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

spectrum_identifier: (required) NX_INT ⤆

@long_name: (required) NX_CHAR ⤆

axis_k: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_energy: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

em_lab: (recommended) NXinstrument ⤆

ebeam_column: (required) NXebeam_column ⤆

operation_mode: (required) NX_CHAR ⤆

electron_source: (required) NXsource ⤆

This concept is related to term `Source`_ of the EMglossary standa ...

This concept is related to term Source of the EMglossary standard.

voltage: (required) NX_NUMBER ⤆

The potential difference between anode and cathode. ...

The potential difference between anode and cathode.

This concept is related to term Acceleration Voltage of the EMglossary standard.

extraction_voltage: (optional) NX_NUMBER {units=NX_VOLTAGE}

Voltage which is utilised to create an electric field that draws ...

Voltage which is utilised to create an electric field that draws particles from the source.

This concept is related to term Extraction Voltage of the EMglossary standard.

emission_current: (optional) NX_NUMBER {units=NX_CURRENT}

Electrical current which is released from the source. ...

Electrical current which is released from the source.

This concept is related to term Emission Current of the EMglossary standard.

filament_current: (optional) NX_NUMBER {units=NX_CURRENT}

Electrical current which flows through the source. ...

Electrical current which flows through the source.

This concept is related to term Filament Current of the EMglossary standard.

lensID: (optional) NXlens_em ⤆

value: (required) NX_NUMBER ⤆

apertureID: (optional) NXaperture ⤆

value: (required) NX_NUMBER {units=NX_ANY}

Relevant value from the control software. ...

Relevant value from the control software.

This is not always just the diameter of the aperture (not even in the case) of a circular aperture. Usually, it is a value that is set in the control software whereby a specific configuration of an aperture is selected by the software.

The control software of commercial microscope typically offers the user access at a high abstraction level because of which many details about the actual settings of the electrical components are typically unknown.

However, if more details are known or should be documented one should use the description field for this.

monochromatorID: (optional) NXmonochromator ⤆

Device to improve energy resolution or chromatic aberration. ...

Device to improve energy resolution or chromatic aberration.

Examples are Wien, $textalpha$-, or $Omega$- energy filter or cc corrector like

applied: (required) NX_BOOLEAN

Was the corrector used?

dispersion: (recommended) NX_NUMBER {units=NX_ANY}

Energy dispersion in e.g. µm/eV.

voltage: (recommended) NX_NUMBER {units=NX_VOLTAGE}

Corresponding voltage for that energy dispersion.

corrector_cs: (optional) NXcorrector_cs ⤆

applied: (recommended) NX_BOOLEAN ⤆

tableauID: (required) NXprocess ⤆

c_1: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

a_1: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

b_2: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

a_2: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

s_3: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

a_3: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

b_4: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

d_4: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

a_4: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

s_5: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

r_5: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

a_6: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_1_0: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_1_2_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_1_2_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_2_1_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_2_1_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_2_3_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_2_3_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3_0: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3_2_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3_2_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3_4_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_3_4_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_1_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_1_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_3_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_3_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_5_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_4_5_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_0: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_2_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_2_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_4_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_4_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_6_a: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

c_5_6_b: (optional) NXaberration ⤆

magnitude: (required) NX_NUMBER ⤆

corrector_ax: (optional) NXcomponent ⤆

Device reshaping an ellipse-shaped electron beam to a circular one ...

Device reshaping an ellipse-shaped electron beam to a circular one.

Stigmator is an exact synonym.

applied: (required) NX_BOOLEAN ⤆

Was the corrector used?

value_x: (required) NX_NUMBER {units=NX_ANY}

Descriptor for the correction strength along the first direction ...

Descriptor for the correction strength along the first direction when exact technical details are unknown or not directly controllable as the control software of the microscope does not enable or was not configured to display these values (for end users).

value_y: (required) NX_NUMBER {units=NX_ANY}

Descriptor for the correction strength along the second directio ...

Descriptor for the correction strength along the second direction when exact technical details are unknown or not directly controllable as the control software of the microscope does not enable or was not configured to display these values (for end users).

biprism: (optional) NXcomponent ⤆

phaseplateID: (optional) NXcomponent ⤆

sensorID: (optional) NXsensor ⤆

actuatorID: (optional) NXactuator ⤆

BEAM: (optional) NXbeam ⤆

This concept is related to term `Electron Beam`_ of the EMglossary ...

This concept is related to term Electron Beam of the EMglossary standard.

ibeam_column: (optional) NXibeam_column ⤆

ion_source: (required) NXsource ⤆

voltage: (required) NX_NUMBER ⤆

probe: (required) NXion ⤆

lensID: (optional) NXlens_em ⤆

value: (required) NX_NUMBER ⤆

apertureID: (optional) NXaperture ⤆

value: (required) NX_NUMBER {units=NX_ANY}

Relevant value from the control software. ...

Relevant value from the control software.

This is not always just the diameter of the aperture (not even in the case) of a circular aperture. Usually, it is a value that is set in the control software whereby a specific configuration of an aperture is selected by the software.

The control software of commercial microscope typically offers the user access at a high abstraction level because of which many details about the actual settings of the electrical components are typically unknown.

However, if more details are known or should be documented one should use the description field for this.

monochromatorID: (optional) NXmonochromator ⤆

applied: (required) NX_BOOLEAN

sensorID: (optional) NXsensor ⤆

actuatorID: (optional) NXactuator ⤆

BEAM: (optional) NXbeam ⤆

detectorID: (optional) NXdetector ⤆

mode: (required) NX_CHAR

scan_controller: (optional) NXscanbox_em

scan_schema: (required) NX_CHAR ⤆

dwell_time: (required) NX_NUMBER ⤆

SENSOR: (optional) NXsensor ⤆

ACTUATOR: (optional) NXactuator ⤆

heater: (optional) NXactuator ⤆

current: (required) NX_NUMBER {units=NX_CURRENT}

Nominal current of the heater.

voltage: (required) NX_NUMBER {units=NX_VOLTAGE}

Nominal voltage of the heater.

power: (required) NX_NUMBER {units=NX_POWER}

Nominal power of the heater.

STAGE_LAB: (optional) NXstage_lab ⤆

design: (recommended) NX_CHAR ⤆

CHAMBER: (optional) NXchamber ⤆

PUMP: (optional) NXpump ⤆

simulation: (optional) NXem_sim

roiID: (optional) NXroi

A region-of-interest analyzed either during or after the session ...

A region-of-interest analyzed either during or after the session for which specific processed data are available.

This concept is related to term Region Of Interest of the EMglossary standard.

imaging: (optional) NXem_img

imaging_mode: (required) NX_CHAR ⤆

IMAGE_SET: (optional) NXimage_set ⤆

half_angle_interval: (optional) NX_NUMBER ⤆

ebsd: (optional) NXem_ebsd

gnomonic_reference_frame: (optional) NXcoordinate_system ⤆

alias: (optional) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

origin: (required) NX_CHAR ⤆

x_direction: (required) NX_CHAR ⤆

y_direction: (required) NX_CHAR ⤆

z_direction: (required) NX_CHAR ⤆

pattern_centre: (recommended) NXprocess ⤆

x_boundary_convention: (required) NX_CHAR ⤆

x_normalization_direction: (required) NX_CHAR ⤆

y_boundary_convention: (required) NX_CHAR ⤆

y_normalization_direction: (required) NX_CHAR ⤆

measurement: (optional) NXprocess ⤆

depends_on: (required) NX_CHAR ⤆

source: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

simulation: (optional) NXprocess ⤆

depends_on: (required) NX_CHAR ⤆

source: (required) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

indexing: (optional) NXprocess ⤆

number_of_scan_points: (required) NX_UINT ⤆

indexing_rate: (recommended) NX_NUMBER ⤆

source: (optional) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

phaseID: (optional) NXcrystal_structure ⤆

number_of_scan_points: (required) NX_UINT ⤆

a_b_c: (required) NX_NUMBER ⤆

alpha_beta_gamma: (required) NX_NUMBER ⤆

space_group: (required) NX_CHAR ⤆

phase_identifier: (required) NX_INT ⤆

phase_name: (required) NX_CHAR ⤆

roi: (recommended) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

title: (required) NX_CHAR ⤆

descriptor: (required) NX_CHAR ⤆

data: (required) NX_NUMBER ⤆

axis_y: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

axis_x: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

eds: (optional) NXem_eds

indexing: (required) NXprocess ⤆

atom_types: (required) NX_CHAR ⤆

summary: (optional) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

axis_energy: (required) NX_CHAR

@long_name: (required) NX_CHAR

IMAGE_SET: (optional) NXimage_set ⤆

iupac_line_candidates: (recommended) NX_CHAR ⤆

energy_range: (required) NX_NUMBER ⤆

image_2d: (required) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

title: (optional) NX_CHAR ⤆

intensity: (required) NX_NUMBER ⤆

@units: (recommended) NX_CHAR ⤆

axis_i: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

@units: (required) NX_CHAR ⤆

axis_j: (required) NX_NUMBER ⤆

@long_name: (required) NX_CHAR ⤆

@units: (required) NX_CHAR ⤆

eels: (optional) NXem_eels

correlation: (optional) NXem_correlation

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/contributed_definitions/NXem.nxdl.xml