2.3.3.3.98. NXevent_data_em

Status:

base class (contribution), extends NXobject

Description:

Base class to store state and (meta)data of events for electron microscopy. ...

Base class to store state and (meta)data of events for electron microscopy.

Electron microscopes are dynamic. Scientists often report that microscopes perform differently across sessions. That they perform differently from one day or another. In some cases, root causes for performance differences are unclear. Users of the instrument may consider such conditions impractical, or too poor, and thus abort their session. Alternatively, users may try to bring the microscope into a state where conditions are considered better or of whatever high enough quality for starting or continuing the measurement.

Which temporal granularity is adequate to log events depends on the situation and research question. Using a model which enables a collection of events offers the most flexible way to cater for both experiments with controlled electron beams in a real microscope or the simulation of such experiments or individual aspects of such experiments.

In all these use cases it is useful to have a mechanism whereby time-dependent data of the instrument state can be stored and documented in an representation that facilitates interoperability.

NXevent_data_em represents an instance to describe and serialize flexibly whatever is considered a time interval during which the instrument is considered stable enough for allowing any working on tasks with the microscope. Examples of such tasks are the collecting of data (images and spectra) or the calibrating the instrument or individual of its components. Users may wish to take only a single scan or image and complete their microscope session thereafter. Alternatively, users are working for much longer time at the microscope, perform recalibrations in between and take several scans (of different ROIs on the specimen), or they explore the state of the microscope for service or maintenance tasks.

NXevent_data_em serves the harmonization and documentation of these cases:

  • Firstly, via a header section whose purpose is to contextualize and identify the event instance in time.

  • Secondly, via a data and metadata section where individual data

    collections can be stored in a standardized representation.

The idea of the first section, the event-based em_lab, is to document the state of the microscope as it was found during the event. The idea of the other, the NXem application-definition-based em_lab(NXinstrument) section is to keep all those data that are static in the sense that they remain the same across multiple NXevent_data_em instances. This reduces the need for having many copies of the same metadata.

We are aware of the fact that given the variety how an electron microscope is used, there is a need for a flexible and adaptive documentation system. At the same time we are also convinced though that just because one has different requirements for some specific aspect under the umbrella of settings to an electron microscope, this does not necessarily warrant that one has to cook up an own data schema.

Instead, the electron microscopy community should work towards reusing schema components as frequently as possible. This will enable that there is at all not only a value of harmonizing electron microscopy research content but also there is a technical possibility to build services around such harmonized data.

Arguably it is oftentimes tricky to specify a clear time interval when the microscope is stable enough. Take for instance the acquisition of an image or a stack of spectra. Having to deal with instabilities is a common theme in electron microscopy practice. Numerical protocols can be used during data post-processing to correct for some of the instabilities. A few exemplar references to provide an overview on the subject is available in the literature:

For specific simulation purposes, mainly in an effort to digitally repeat or simulate the experiment, it is tempting to consider dynamics of the instrument, implemented as time-dependent functional descriptions of e.g. lens excitations, beam shape functions, trajectories of groups of electrons and ions, or detector noise models. This warrants to document the time-dependent details of individual components of the microscope as is implemented in NXevent_data_em.

Symbols:

No symbol table

Groups cited:

NXimage, NXinstrument_em, NXspectrum, NXuser

Structure:

start_time: (optional) 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 snapshot time interval started. If the user wishes to specify an interval of time that the snapshot should represent during which the instrument was stable and configured using specific settings and calibrations, the start_time is the start (left bound of the time interval) while the end_time specifies the end (right bound) of the time interval.

end_time: (optional) 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 snapshot time interval ended.

identifier_event: (optional) NX_INT {units=NX_UNITLESS}

Identifier of a specific state and setting of the microscope.

identifier_sample: (optional) NX_CHAR {units=NX_UNITLESS} ⤆

The name of the sample instance under NXem/ENTRY/SAMPLE to resolve ...

The name of the sample instance under NXem/ENTRY/SAMPLE to resolve ambiguities that are explained in the docstring of NXem/ENTRY/SAMPLE.

type: (optional) NX_CHAR

Which specific event/measurement type. Examples are: ...

Which specific event/measurement type. Examples are:

  • In-lens/backscattered electron, usually has quadrants

  • Secondary_electron, image, topography, fractography, overview images

  • Backscattered_electron, image, Z or channeling contrast (ECCI)

  • Bright_field, image, TEM

  • Dark_field, image, crystal defects

  • Annular dark field, image (medium- or high-angle), TEM

  • Diffraction, image, TEM, or a comparable technique in the SEM

  • Kikuchi, image, SEM EBSD and TEM diffraction

  • X-ray spectra (point, line, surface, volume), composition EDS/EDX(S)

  • Electron energy loss spectra for points, lines, surfaces, TEM

  • Auger, spectrum, (low Z contrast element composition)

  • Cathodoluminescence (optical spectra)

  • Ronchigram, image, alignment utility specifically in TEM

  • Chamber, e.g. TV camera inside the chamber, education purposes.

This field may also be used for storing additional information about the event for which there is at the moment no other place.

In the long run such free-text field description should be avoided as they are difficult to machine-interpret. Instead, reference should be given to refactoring these descriptions into structured metadata. The reason why in this base class the field event_type is nonetheless kept is to offer a place whereby practically users may enter data for follow-up modifications to support arriving at an improved NXevent_data_em base class.

USER: (optional) NXuser

INSTRUMENT_EM: (optional) NXinstrument_em

IMAGE: (optional) NXimage

SPECTRUM: (optional) NXspectrum

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/NXevent_data_em.nxdl.xml