2.3.3.1.71. NXem_event_data

Status:

base class, 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.

Event-related (meta)data, typically measured datasets like images and spectra. To avoid repetitively storing static instrument-related metadata, the dynamic (meta)data that typically changes for each image and spectrum is split from the static (meta)data.

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.

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.

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. This is the idea behind this base class.

NXem_event_data 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 it. 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 session thereafter. Alternatively, users are working for much longer time at the instrument, 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.

NXem_event_data 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.

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 provide an overview on the subject:

For specific simulation purposes, mainly in an effort to digitally repeat or simulate the experiment (digital twin), 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 also warrants to document the time-dependent details of individual components of the microscope via the here implemented class NXem_event_data.

Symbols:

No symbol table

Groups cited:

NXem_instrument, NXimage, 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 users wish 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 to resolve ambiguities.

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 it is difficult to machine-interpret. Instead, an enumeration should be used.

USER: (optional) NXuser

EM_INSTRUMENT: (optional) NXem_instrument

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/base_classes/NXem_event_data.nxdl.xml