NXem_nion¶
Status:
application definition, extends NXobject
Description:
Template for creating draft application definitions for storing data and metadata for experiments with scanning transmission electron microscopy with a Nion instrument.
Symbols:
No symbol table
- Groups cited:
NXaperture, NXcollection, NXcorrector_cs, NXdata, NXdetector, NXentry, NXinstrument, NXlens_em, NXnote, NXpositioner, NXprocess, NXsample, NXscanbox_em, NXsource, NXstage_lab, NXtransformations, NXuser
Structure:
ENTRY: (required) NXentry
definition: (required) NX_CHAR
Official NeXus NXDL schema to which this entry conforms.
@version: (required) NX_CHAR
Version specifier which enables documentation of modifications to the schema.
experiment_identifier: (required) NX_CHAR
Ideally, a (globally persistent) unique identifier for referring to this experiment. The identifier is usually defined/issued by the facility, laboratory, or the principle investigator. The identifier enables to link experiments to e.g. proposals.
experiment_description: (optional) NX_CHAR
Possibility for leaving a free-text description about the experiment. Users are strongly advised to detail the sample history in the respective field and fill rather as completely as possible the fields of this application definition rather than writing these details in prose into this field.
start_time: (required) NX_DATE_TIME
ISO 8601 formatted time code with local time zone offset to UTC information included when the experiment 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 - this start time field should be used. Often though it is useful to specify a time interval with specifying both start_time and end_time to allow for more detailed bookkeeping and interpretation of the experiment. The user should be aware that even with having both time instances specified it may not be advisable 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.
end_time: (recommended) NX_DATE_TIME
ISO 8601-formatted time code with local time zone offset to UTC included when the experiment ended.
program_name: (required) NX_CHAR
Commercial or otherwise given name to the program which was used to acquire/measure the dataset. Electron microscopy experiments are usually controlled/performed via commercial integrated acquisition and instrument control software. In many cases, an EM dataset is useful only if gets post-processed already during the acquisition or shortly thereafter, i.e. while the scientists is still sitting at the microscope. Many of these processes are automated, if not they virtually involve GUI interactions with the control software. Examples include collecting of diffraction pattern and on-the-fly indexing of these. These situations and tools are realized with individual NXprocess groups which can hold more details and numerical data to these processing steps. Frequently, some of these NXprocess groups are performed with (open-source) research software. Therefore, there is strictly speaking not a single program used in electron microscopy, and thus each NXprocess has its own program name and description.”
@version: (required) NX_CHAR
Ideally program version plus build number, or commit hash or description of ever persistent resources where the source code of the program and build instructions can be found so that the program can be configured ideally in such a manner that the result file is numerically recreatable in the same deterministic manner.
experiment_documentation: (optional) NXnote
Binary container for a file or a compressed collection of files which can be used to add further descriptions and details to the experiment. The container can hold e.g. a ppt, pdf, latex, txt, image, or zip archive …).
thumbnail: (recommended) NXnote
A small image that is representative of the entry. This can be an image from the dataset or a thumbnail of a spectrum. Either way it is recommended to use 640x480 pixel jpeg image. Adding a scale bar to that image is recommended but not required as the main purpose of the thumbnail is to provide e.g. thumbnail images for displaying them in data repositories.
@type: (required) NX_CHAR
operator: (required) NXuser
Contact information of at least the user of the instrument who measured this specimen or the principal investigator who performed this experiment. Adding multiple users if relevant is recommended.
name: (required) NX_CHAR
Given (first) name and surname of the user.
affiliation: (recommended) NX_CHAR
Name of the affiliation of the user at the point in time when the experiment was performed.
address: (recommended) NX_CHAR
Postal address of the affiliation.
email: (required) NX_CHAR
Email address of the user at the point in time when the experiment was performed. Given the most permanently used email is recommended.
orcid: (recommended) NX_CHAR
Globally unique identifier of the user as offers by services like ORCID or Researcher ID.
telephone_number: (recommended) NX_CHAR
(Business) (tele)phone number of the user at the point in time when the experiment was performed.
role: (recommended) NX_CHAR
Which role does the user have in the place, and at the point in time when, the experiment was performed (e.g. technician operating the microscope, student, postdoc, principal investigator, guest …).
SAMPLE: (required) NXsample
name: (required) NX_CHAR
Descriptive name or identifier with which to distinguish the specimen from all others and especially the parts from where it was cut. In cases where the specimen was e.g. site-specifically cut from samples or in cases of an instrument session during which multiple specimens are loaded, the name has to be descriptive enough to resolve which specimen was investigated and is represented by this NXentry. The user is advised to store the details how specimens were cut/prepared from samples in the sample history.
sample_history: (required) NX_CHAR
Ideally, a reference to the location of or a (globally persistent) unique identifier of e.g. another file which should document ideally as many details as possible of the material, its microstructure, and its thermo-chemo-mechanical processing/preparation history. In the case that such a detailed history of the sample/specimen is not available, use this field as a free-text description to specify a sub-set of the entire sample history, i.e. what you would consider being the key steps and relevant information about the specimen, its material, microstructure, thermo-chemo-mechanical processing state and details of the preparation.
preparation_date: (recommended) NX_DATE_TIME
ISO8601 date and time with local time zone offset to UTC included when the specimen was prepared. Ideally report the end of the preparation, i.e. the last known time the measured specimen surface was actively prepared. Knowing when the specimen was exposed to e.g. specific atmosphere is especially required for environmentally sensitive material such as hydrogen-charged specimens or experiments including tracers with a short half-time. The user is advised to include these temporal details in the sample_history.
short_title: (optional) NX_CHAR
Possibility to give an abbreviation of the specimen name field.
atom_types: (required) NX_CHAR
Use Hill’s system for listing elements of the periodic table which are inside or attached to the surface of the specimen and thus relevant from a scientific point. The purpose of the field is to offer materials database systems an opportunity to parse the relevant elements without having to interpret these from the sample history.
thickness: (recommended) NX_FLOAT {units=NX_LENGTH}
(Measured) sample thickness
DATA: (required) NXdata
Hard link to a location/locations in the hierarchy of the NeXus file where the data for default plotting are stored.
em_lab: (required) NXinstrument
Metadata and numerical data of not only the microscope but also the lab in which this microscope is located.
name: (required) NX_CHAR
Given name of the microscope, e.g. NionHermes.
location: (recommended) NX_CHAR
Geographic coordinates of the lab or the place where the instrument is installed using GEOREF geocodes ideally.
instrument_manufacturer: (required) NX_CHAR
Manufacturer of the entire instrument to enable e.g. queries in materials database systems for instrument manufacturers. Usually more technical details are needed though to specify the instrument, these should be written into instrument_model and instrument_capabilities.
instrument_model: (required) NX_CHAR
Manufacturer brand/model to enable e.g. queries about microscope models. See comments on instrument_manufacturer on how to provide further specification.
instrument_identifier: (recommended) NX_CHAR
Hardware name/serial number or hash identifier given by the manufacturer to identify the instrument.
instrument_capability: (recommended) NX_CHAR
Free-text list possibly multiple terms of functionalities which the instrument provides.
electron_gun: (required) NXsource
The source creating the electron beam.
voltage: (required) NX_FLOAT {units=NX_VOLTAGE}
Voltage relevant to compute the energy of the electrons immediately after they left the gun.
probe: (optional) NX_CHAR
Type of radiation.
Obligatory value:
electronemitter_type: (recommended) NX_CHAR
Emitter type used to create the beam.
Any of these values:
thermionic|schottky|field emissiondescription: (recommended) NX_CHAR
Ideally a reference to (another) file (ideally formatted using also an application definition) via a link, name, or a (globally persistent) unique identifier to give further details about the electron gun.
APERTURE: (optional) NXaperture
Details to individual apertures in the instrument.
name: (recommended) NX_CHAR
Given name.
model: (recommended) NX_CHAR
Given brand or model name by the manufacturer.
serial_number: (recommended) NX_CHAR
Given hardware name/serial number or hash identifier issued by the manufacturer.
manufacturer_name: (recommended) NX_CHAR
Given name of the manufacturer.
value: (required) NX_NUMBER {units=NX_ANY}
Relevant value from the control software as this is not always just the diameter of (not even in the case) of a circular aperture but a rather a value from a list of predefined ones in the control software. Which actual settings are behind these should be Details which choice was made should be explained under description.
description: (recommended) NX_CHAR
An (ideally globally persistent) unique identifier, link, or text which gives further details.
TRANSFORMATIONS: (optional) NXtransformations
Affine transformations and geometrical descriptions which detail how the aperture is placed and arranged in the microscope relative to the optical axis and beam path.
LENS_EM: (optional) NXlens_em
Details to individual lenses in the microscope.
type: (recommended) NX_CHAR
Which type describes the type of the lens closest?
Any of these values:
single
double
quadrupole
hexapole
octopolname: (required) NX_CHAR
model: (recommended) NX_CHAR
serial_number: (recommended) NX_CHAR
manufacturer_name: (recommended) NX_CHAR
description: (recommended) NX_CHAR
TRANSFORMATIONS: (optional) NXtransformations
CORRECTOR_CS: (optional) NXcorrector_cs
Details about an eventual device which corrects spherical aberrations.
has_cs_corrector: (required) NX_BOOLEAN
Does the microscope have a spherical aberration correction unit and was it used?
name: (recommended) NX_CHAR
model: (recommended) NX_CHAR
serial_number: (recommended) NX_CHAR
manufacturer_name: (recommended) NX_CHAR
description: (recommended) NX_CHAR
c_1_0: (required) NX_FLOAT {units=NX_LENGTH}
c_1_2_a: (required) NX_FLOAT {units=NX_LENGTH}
c_1_2_b: (required) NX_FLOAT {units=NX_LENGTH}
c_2_1_a: (required) NX_FLOAT {units=NX_LENGTH}
c_2_1_b: (required) NX_FLOAT {units=NX_LENGTH}
c_2_3_a: (required) NX_FLOAT {units=NX_LENGTH}
c_2_3_b: (required) NX_FLOAT {units=NX_LENGTH}
c_3_0: (required) NX_FLOAT {units=NX_LENGTH}
c_3_2_a: (required) NX_FLOAT {units=NX_LENGTH}
c_3_2_b: (required) NX_FLOAT {units=NX_LENGTH}
c_3_4_a: (required) NX_FLOAT {units=NX_LENGTH}
c_3_4_b: (required) NX_FLOAT {units=NX_LENGTH}
c_5_0: (required) NX_FLOAT {units=NX_LENGTH}
TRANSFORMATIONS: (optional) NXtransformations
STAGE_LAB: (required) NXstage_lab
design: (recommended) NX_CHAR
name: (recommended) NX_CHAR
model: (recommended) NX_CHAR
serial_number: (recommended) NX_CHAR
manufacturer_name: (recommended) NX_CHAR
description: (recommended) NX_CHAR
tilt1: (required) NX_FLOAT {units=NX_ANGLE}
Stage tilt A. Exact definition as understood by HU colleagues remains to be communicated.
tilt2: (required) NX_FLOAT {units=NX_ANGLE}
Stage tilt B. Exact definition as understood by HU colleagues remains to be communicated.
position[3]: (required) NX_FLOAT {units=NX_LENGTH}
StageOutX, Y, Z. Exact definition as understood by HU colleagues remains to be communicated.
TRANSFORMATIONS: (optional) NXtransformations
POSITIONER: (optional) NXpositioner
DETECTOR: (required) NXdetector
Description of the type of the detector e.g. CCD, scintillator, direct electron, image plate, CMOS.
name: (recommended) NX_CHAR
Given name.
model: (recommended) NX_CHAR
Given brand or model name by the manufacturer.
serial_number: (recommended) NX_CHAR
Given hardware name/serial number or hash identifier issued by the manufacturer.
manufacturer_name: (recommended) NX_CHAR
Given name of the manufacturer.
sensor_material: (recommended) NX_CHAR
bit_depth_readout: (recommended) NX_INT
number_of_cycles: (recommended) NX_INT
x_pixel_size: (recommended) NX_FLOAT {units=NX_LENGTH}
y_pixel_size: (recommended) NX_FLOAT {units=NX_LENGTH}
flatfield_applied: (required) NX_BOOLEAN
flatfield: (recommended) NX_FLOAT
exposure: (recommended) NX_NUMBER {units=NX_TIME}
description: (required) NX_CHAR
Free text option to write further details about the detector.
miscellaneous: (required) NXcollection
camera_length: (recommended) NX_FLOAT {units=NX_LENGTH}
Exact definition as understood by HU colleagues remains to be communicated.
magnification: (recommended) NX_FLOAT {units=NX_DIMENSIONLESS}
Exact definition as understood by HU colleagues remains to be communicated.
defocus: (required) NX_FLOAT {units=NX_LENGTH}
Exact definition as understood by HU colleagues and Nion remains to be communicated.
semi_convergence_angle: (required) NX_FLOAT {units=NX_ANGLE}
Details how computed needs to be confirmed by Nion.
hadf: (optional) NXprocess
program: (required) NX_CHAR
Container for reporting individually processed images with the HAADF detector ?
@version: (required) NX_CHAR
Ideally program version plus build number, or commit hash or description of ever persistent resources where the source code of the program and build instructions can be found so that the program can be configured ideally in such a manner that the result of this computational process is recreatable in the same deterministic manner.
haadf_inner_half_angle: (required) NX_FLOAT {units=NX_ANGLE}
HAADF annulus inner half angle ?
haadf_outer_half_angle: (required) NX_FLOAT {units=NX_ANGLE}
HAADF annulus outer half angle ?
SCANBOX_EM: (required) NXscanbox_em
Description of the scan box which is instructed by the microscope control software to direct the probe to controlled locations according to a scan scheme and plan.
program: (required) NX_CHAR
Commercial or otherwise given name to the program which was used to execute this analysis.
@version: (required) NX_CHAR
Ideally program version plus build number, or commit hash or description of ever persistent resources where the source code of the program and build instructions can be found so that the program can be configured ideally in such a manner that the result of this computational process is recreatable in the same deterministic manner.
calibration_style: (recommended) NX_CHAR
Remains to be discussed with colleagues which suggestions to put as enumerations.
Obligatory value:
spacecenter: (recommended) NX_NUMBER {units=NX_ANY}
Remains to be discussed with colleagues how to use and interpret this.
flyback_time: (recommended) NX_FLOAT {units=NX_TIME}
Remains to be discussed with colleagues how to use and interpret this.
field_of_view: (recommended) NX_FLOAT {units=NX_LENGTH}
Remains to be discussed with colleagues how to use and interpret this.
line_time: (recommended) NX_FLOAT {units=NX_TIME}
Remains to be discussed with colleagues how to use and interpret this.
pixel_time: (recommended) NX_FLOAT {units=NX_TIME}
Remains to be discussed with colleagues how to use and interpret this.
requested_pixel_time: (recommended) NX_FLOAT {units=NX_TIME}
Remains to be discussed with colleagues how to use and interpret this.
rotation: (recommended) NX_FLOAT {units=NX_ANGLE}
Remains to be discussed with colleagues how to use and interpret this.
ac_line_sync: (recommended) NX_BOOLEAN
Remains to be discussed with colleagues how to use and interpret this.
mag_boards: (recommended) NXcollection
Detailed settings of an internal board(s) in the scanbox device. Further information exchange/discussions with Nion is needs to elucidate what these are.
board_0_dac_0: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_1: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_10: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_11: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_2: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_3: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_4: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_5: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_6: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_7: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_8: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_dac_9: (required) NX_NUMBER {units=NX_UNITLESS}
board_0_relay: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_0: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_1: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_10: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_11: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_2: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_3: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_4: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_5: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_6: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_7: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_8: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_dac_9: (required) NX_NUMBER {units=NX_UNITLESS}
board_1_relay: (required) NX_NUMBER {units=NX_UNITLESS}
DATA: (required) NXdata
Container for holding an image (stack) taken with the HA(A) ? DF detector.
@signal: (required) NX_CHAR
@axes: (required) NX_CHAR
@xpos_indices: (required) NX_CHAR
@ypos_indices: (required) NX_CHAR
@long_name: (required) NX_CHAR
Label for the y axis.
intensity[n_x, n_y]: (required) NX_NUMBER {units=NX_UNITLESS}
Image intensity values.
xpos[n_x]: (required) NX_NUMBER {units=NX_LENGTH}
Pixel barycenter position x-coordinates.
ypos[n_y]: (required) NX_NUMBER {units=NX_LENGTH}
Pixel barycenter position y-coordinates.
Hypertext Anchors¶
Table of hypertext anchors for all groups, fields, attributes, and links defined in this class.
