base class, extends NXobject


Metadata and settings of an electron microscope for scans and images.

The need for such a structuring of data is evident from the fact that electron microscopes are dynamic. Oftentimes it suffices to calibrate the instrument at the start of the session. Subsequently, data (images, spectra, etc.) can be collected. Users may wish to take only a single scan or image and complete their microscope session; however

frequently users spend much longer at the microscope, recalibrate, and take multiple data items (scans, images, spectra) each coming with own detector and on-the-fly processing settings and calibration.

For the single data item use case one may argue that the need for additional grouping is redundant. Instead, the metadata could equally be stored inside the respective groups of the top-level mandatory NXinstrument group. On the flip side, even for a session with a single image it would also not harm to nest the data.

In fact, oftentimes scientists feel that there is a need to store details about eventual drift of the specimen in its holder (if such data is available) or record changes to the lens excitations caused or apertures used. Although current microscopes are usually equipped with stabilization systems for many of the individual components, it can still be useful to store time-dependent data in detail.

Another reason if not a need for more finely granularizable options for storing time-dependent data, is that over the course of a session one may reconfigure the microscope. What is a reconfiguration? This could be the change of an aperture mode because a scientist may first collect an image with some aperture and then choose a different one. As the aperture affects the electron beam it will affect the system.

Let aside for a moment the technology and business models, an EM could be monitored (and will likely become so more in the future) for streaming out spatio-temporal details about its components, locations of objects and eventually applied stimuli and positioning of the specimen.

Some snapshot or integrated data from this stream are relevant for understanding signal genesis and electron/ion beam paths. In such a generic case it might be necessary to sync these streaming data with those intervals in time when specific measurements are taken (spectra collected, images taken, diffraction images indexed on-the-fly).

Theoretically, an instrument and specimen should be considered as dynamic. Scientists often report or feel (difficult to quantify) observations that microscopes perform differently across sessions, without sometimes being able to identify clear root causes. Users of the instrument may consider such conditions impractical and thus either abort their session or try to bring the microscope first into a state where conditions are considered stable and of high enough quality for collecting data.

In all these cases it is practical to store time-dependent data of the instrument state not in the respective instrument component groups of the top-level NXinstrument but in a sort of a log of event data. This is the idea behind the NXevent_data_em snapshot containers.

The base class requires a start time and an optional end time. The end time should be added to represent a time interval (remind the idea of the instrument state stream) during which the scientist considered the microscope (especially ebeam and specimen) as stable enough.

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, or detector noise models.

For now the preferred strategy to handle these cases is through customizations of the specific fields within NXevent_data_em instances.

Another alternative could be to sample finer, eventually dissimilarly along the time axis; however this may cause situations where an NXevent_data_em instance does not contain specific measurements (i.e. images, spectra of scientific relevance).

In this case one should better go for a customized application definition with a functional property description inside members (fields or groups) in NXevent_data_em instances or resort to a specific application definition which documents metadata for tracking explicitly electrons (with ray-tracing based descriptors/computational geometry descriptors) or tracking of wave bundles.

This perspective on more subtle time-dependent considerations of electron microscopy can be advantageous also for storing details of time-dependent additional components that are coupled to and/or synced with instrument.

Examples include cutting-edge experiments where the electron beam gets coupled/excited by e.g. lasers. In this case, the laser unit should be registered under the top-level NXinstrument section. Its spatio-temporal details could be stored inside respective groups of the NXinstrument.


No symbol table

Groups cited:

NXebeam_column, NXibeam_column, NXimage_set_em_adf, NXimage_set_em_bf, NXimage_set_em_bse, NXimage_set_em_chamber, NXimage_set_em_df, NXimage_set_em_diffrac, NXimage_set_em_ecci, NXimage_set_em_kikuchi, NXimage_set_em_ronchigram, NXimage_set_em_se, NXoptical_system_em, NXscanbox_em, NXspectrum_set_em_auger, NXspectrum_set_em_cathodolum, NXspectrum_set_em_eels, NXspectrum_set_em_xray, NXuser


start_time: (optional) NX_DATE_TIME

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 included when the snapshot time interval ended. If the user does not wish to specify a time interval, end_time should have the same value as start_time.

event_identifier: (optional) NX_CHAR

Reference to a specific state and setting of the microscope components.

event_type: (optional) NX_CHAR

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.

detector_identifier: (optional) NX_CHAR

The detector or set of detectors that was used to collect this signal. The name of the detector has to match the names used for available detectors, i.e. if the instrument has an ebsd_camera named detector, instances of NXimage_em_kikuchi should use ebsd_camera as the detector name.

IMAGE_SET_EM_SE: (optional) NXimage_set_em_se

IMAGE_SET_EM_BSE: (optional) NXimage_set_em_bse

IMAGE_SET_EM_ECCI: (optional) NXimage_set_em_ecci

IMAGE_SET_EM_BF: (optional) NXimage_set_em_bf

IMAGE_SET_EM_DF: (optional) NXimage_set_em_df

IMAGE_SET_EM_ADF: (optional) NXimage_set_em_adf

IMAGE_SET_EM_KIKUCHI: (optional) NXimage_set_em_kikuchi

IMAGE_SET_EM_DIFFRAC: (optional) NXimage_set_em_diffrac

SPECTRUM_SET_EM_XRAY: (optional) NXspectrum_set_em_xray

SPECTRUM_SET_EM_EELS: (optional) NXspectrum_set_em_eels

SPECTRUM_SET_EM_AUGER: (optional) NXspectrum_set_em_auger

SPECTRUM_SET_EM_CATHODOLUM: (optional) NXspectrum_set_em_cathodolum

IMAGE_SET_EM_RONCHIGRAM: (optional) NXimage_set_em_ronchigram

IMAGE_SET_EM_CHAMBER: (optional) NXimage_set_em_chamber

EBEAM_COLUMN: (optional) NXebeam_column

IBEAM_COLUMN: (optional) NXibeam_column

ebeam_deflector: (optional) NXscanbox_em

ibeam_deflector: (optional) NXscanbox_em

OPTICAL_SYSTEM_EM: (optional) NXoptical_system_em

USER: (optional) NXuser

Hypertext Anchors

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

NXDL Source: