.. auto-generated by dev_tools.docs.nxdl from the NXDL source base_classes/NXem_instrument.nxdl.xml -- DO NOT EDIT .. index:: ! NXem_instrument (base class) ! em_instrument (base class) see: em_instrument (base class); NXem_instrument .. _NXem_instrument: =============== NXem_instrument =============== **Status**: base class, extends :ref:`NXinstrument` **Description**: .. collapse:: Base class for instrument-related details of a real or simulated electron micros ... Base class for instrument-related details of a real or simulated electron microscope. For collecting data and experiments which are simulations of an electron microscope (or such session) use the :ref:`NXem` application definition and the :ref:`NXem_event_data` groups it provides. This base class implements the concept of :ref:`NXem` whereby (meta)data are distinguished whether these typically change during a session (dynamic) or not (static metadata). This design allows to store e.g. hardware related concepts only once instead of demanding that each image or spectrum from the session needs to be stored also with the static metadata. **Symbols**: No symbol table **Groups cited**: :ref:`NXactuator`, :ref:`NXcomponent`, :ref:`NXdetector`, :ref:`NXebeam_column`, :ref:`NXem_optical_system`, :ref:`NXfabrication`, :ref:`NXibeam_column`, :ref:`NXmanipulator`, :ref:`NXpump`, :ref:`NXsensor` .. index:: NXfabrication (base class); used in base class, NXebeam_column (base class); used in base class, NXibeam_column (base class); used in base class, NXem_optical_system (base class); used in base class, NXdetector (base class); used in base class, NXmanipulator (base class); used in base class, NXcomponent (base class); used in base class, NXpump (base class); used in base class, NXsensor (base class); used in base class, NXactuator (base class); used in base class **Structure**: .. _/NXem_instrument/name-field: .. index:: name (field) **name**: (optional) :ref:`NX_CHAR ` :ref:`⤆ ` .. collapse:: Given name of the microscope at the hosting institution. ... Given name of the microscope at the hosting institution. This is an alias. Examples could be NionHermes, Titan, JEOL, Gemini, etc. .. _/NXem_instrument/location-field: .. index:: location (field) **location**: (optional) :ref:`NX_CHAR ` .. collapse:: Location of the lab or place where the instrument is installed. ... Location of the lab or place where the instrument is installed. Using GEOREF is preferred. .. _/NXem_instrument/type-field: .. index:: type (field) **type**: (recommended) :ref:`NX_CHAR ` .. collapse:: Different types of electron microscopes exist: ... Different types of electron microscopes exist: * sem, a scanning electron microscope without focused-ion beam capabilities * fib, a scanning electron microscope with focused-ion beam capabilities irrespective whether these were used or not * tem, a transmission electron microscope NXem is one joint data model that can be used to document research that is performed with several of these types of microscopes (SEM, TEM, or FIB). The NXem data model stresses that these types of instruments despite having several differences are still all electron beamlines with which to probe electron and/or ion matter interaction and in fact in practice have many similarities in how they are used, the components, they contain, etc. This field can be used in research data management systems for enabling a categorization or tagging of experiments without having to analyze if groups like NXibeam_column are present (which would indicate type is fib) or if certain lens configurations or instrument models are used which suggests the microscope is a scanning (sem) or transmission electron microscope (tem): Any of these values: ``sem`` | ``fib`` | ``tem`` .. _/NXem_instrument/FABRICATION-group: :bolditalic:`FABRICATION`: (optional) :ref:`NXfabrication` :ref:`⤆ ` .. _/NXem_instrument/EBEAM_COLUMN-group: :bolditalic:`EBEAM_COLUMN`: (optional) :ref:`NXebeam_column` .. _/NXem_instrument/IBEAM_COLUMN-group: :bolditalic:`IBEAM_COLUMN`: (optional) :ref:`NXibeam_column` .. _/NXem_instrument/EM_OPTICAL_SYSTEM-group: :bolditalic:`EM_OPTICAL_SYSTEM`: (optional) :ref:`NXem_optical_system` .. _/NXem_instrument/DETECTOR-group: :bolditalic:`DETECTOR`: (optional) :ref:`NXdetector` :ref:`⤆ ` .. collapse:: Description of the type of the detector. ... Description of the type of the detector. Electron microscopes have typically multiple detectors. Different technologies are in use like CCD, scintillator, direct electron, CMOS, or image plate to name but a few. .. _/NXem_instrument/stageID-group: **stage**\ :bolditalic:`ID`: (optional) :ref:`NXmanipulator` .. collapse:: Stages in an electron microscope are multi-functional devices. ... Stages in an electron microscope are multi-functional devices. Stages enable experimentalists the application of controlled external stimuli on the specimen. Modern stages realize a hierarchy of components. A multi-axial tilt rotation holder is a good example where the control of each degree of freedom is technically implemented via providing instances of e.g. :ref:`NXpositioner` or :ref:`NXactuator` that achieve the rotating and positioning of the specimen. The physical process of mounting a specimen on a stage in practice often comes with an own hierarchy of fixtures to bridge e.g. length scales technically. An example from atom probe microscopy is that researchers may work with wire samples which are clipped into a larger fixing unit to enable careful specimen handling. Alternatively, a microtip is a silicon post upon which e.g. an atom probe specimen is mounted. Multiple of such microtips are then grouped into a microtip array to conveniently enable loading of multiple specimens into the instrument with fewer operations. There are further scenarios typically encountered related to mounting and locating specimens inside an electron microscope, a few examples follow: * A nanoparticle on a copper grid. The copper grid is the holder. This grid itself is fixed to a stage. * An atom probe specimen fixed in a stub. In this case the stub can be considered the holder, while the cryostat temperature control unit is a component of the stage. * For in-situ experiments with e.g. chips with read-out electronics as actuators, the chips are again placed in a larger unit. A typical example are in-situ experiments using e.g. the tools of `Protochips `_. * Other examples are (quasi) in-situ experiments where experimentalists anneal or deform the specimen via e.g. in-situ tensile testing machines which are mounted on the specimen holder. For specific details and inspiration about stages in electron microscopes: * `Holders with multiple axes `_ * `Chip-based designs `_ * `Further chip-based designs `_ * `Stages in transmission electron microscopy `_ (page 103, table 4.2) * `Further stages in transmission electron microscopy `_ (page 124ff) * `Specimens in atom probe `_ (page 47ff) * `Exemplar micro-manipulators `_ .. _/NXem_instrument/stageID/design-field: .. index:: design (field) **design**: (optional) :ref:`NX_CHAR ` .. collapse:: Principal design of the stage. ... Principal design of the stage. Exemplar terms could be side_entry, top_entry, single_tilt, quick_change, multiple_specimen, bulk_specimen, double_tilt, tilt_rotate, heating_chip, atmosphere_chip, electrical_biasing_chip, liquid_cell_chip .. _/NXem_instrument/stageID/alias-field: .. index:: alias (field) **alias**: (optional) :ref:`NX_CHAR ` .. collapse:: Free-text field to give a term how that a stage_lab at this level of the ... Free-text field to give a term how that a stage_lab at this level of the stage_lab hierarchy is commonly referred to. Examples could be stub, puck, carousel, microtip, clip, holder, etc. .. _/NXem_instrument/stageID/tilt1-field: .. index:: tilt1 (field) **tilt1**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_ANGLE `} .. collapse:: The interpretation of this tilt1 value can be contextualized via the comment ... The interpretation of this tilt1 value can be contextualized via the comment attribute. However, it is better to describe the reference frame in which the tilt is defined explicitly using instances of :ref:`NXtransformations` and respective instances of :ref:`NXcoordinate_system`. Especially when this NXem_instrument base class is used in an application definition like NXem. .. _/NXem_instrument/stageID/tilt1@comment-attribute: .. index:: comment (field attribute) **@comment**: (optional) :ref:`NX_CHAR ` Discouraged free-text field to provide details about how to interpret tilt1. .. _/NXem_instrument/stageID/tilt2-field: .. index:: tilt2 (field) **tilt2**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_ANGLE `} .. collapse:: The interpretation of this tilt2 value can be contextualized via the comment ... The interpretation of this tilt2 value can be contextualized via the comment attribute. However, it is better to describe the reference frame in which the tilt is defined explicitly using instances of :ref:`NXtransformations` and respective instances of :ref:`NXcoordinate_system`. Especially when this NXem_instrument base class is used in an application definition like NXem. .. _/NXem_instrument/stageID/tilt2@comment-attribute: .. index:: comment (field attribute) **@comment**: (optional) :ref:`NX_CHAR ` Discouraged free-text field to provide details about how to interpret tilt2. .. _/NXem_instrument/stageID/rotation-field: .. index:: rotation (field) **rotation**: (optional) :ref:`NX_NUMBER ` {units=\ :ref:`NX_ANGLE `} .. collapse:: The interpretation of this rotation value can be contextualized via the comm ... The interpretation of this rotation value can be contextualized via the comment attribute. However, it is better to describe the reference frame in which the rotation is defined explicitly using instances of :ref:`NXtransformations` and respective instances of :ref:`NXcoordinate_system`. Especially when this NXem_instrument base class is used in an application definition like NXem. .. _/NXem_instrument/stageID/rotation@comment-attribute: .. index:: comment (field attribute) **@comment**: (optional) :ref:`NX_CHAR ` Discouraged free-text field to provide details about how to interpret rotation. .. _/NXem_instrument/stageID/position-field: .. index:: position (field) **position**: (optional) :ref:`NX_NUMBER ` (Rank: 1, Dimensions: [3]) {units=\ :ref:`NX_LENGTH `} .. collapse:: The interpretation of these position values can be contextualized via the co ... The interpretation of these position values can be contextualized via the comment attribute. However, it is better to describe the reference frame in which the position values are defined explicitly using instances of :ref:`NXtransformations` and respective instances of :ref:`NXcoordinate_system`. Especially when this NXem_instrument base class is used in an application definition like NXem. .. _/NXem_instrument/nanoprobeID-group: **nanoprobe**\ :bolditalic:`ID`: (optional) :ref:`NXmanipulator` .. collapse:: In contrast to the stage, the nanoprobe is an additional manipulator that is a ... In contrast to the stage, the nanoprobe is an additional manipulator that is a specifically frequently found component of FIB/SEM instruments. A nanoprobe is used to pick up and relocated portions of the specimen that have been cut off during site-specific lift-outs and specimen preparation. .. _/NXem_instrument/gas_injector-group: **gas_injector**: (optional) :ref:`NXcomponent` .. collapse:: Gas injection systems (GIS) are components of microscopes that are equipped wi ... Gas injection systems (GIS) are components of microscopes that are equipped with focused-ion beam capabilities. The component is used to introduce reactive neutral gases to the sample surface for enhanced etching, preferential etching, or material deposition. .. _/NXem_instrument/PUMP-group: :bolditalic:`PUMP`: (optional) :ref:`NXpump` .. _/NXem_instrument/SENSOR-group: :bolditalic:`SENSOR`: (optional) :ref:`NXsensor` :ref:`⤆ ` .. _/NXem_instrument/ACTUATOR-group: :bolditalic:`ACTUATOR`: (optional) :ref:`NXactuator` :ref:`⤆ ` Hypertext Anchors ----------------- List of hypertext anchors for all groups, fields, attributes, and links defined in this class. * :ref:`/NXem_instrument/ACTUATOR-group ` * :ref:`/NXem_instrument/DETECTOR-group ` * :ref:`/NXem_instrument/EBEAM_COLUMN-group ` * :ref:`/NXem_instrument/EM_OPTICAL_SYSTEM-group ` * :ref:`/NXem_instrument/FABRICATION-group ` * :ref:`/NXem_instrument/gas_injector-group ` * :ref:`/NXem_instrument/IBEAM_COLUMN-group ` * :ref:`/NXem_instrument/location-field ` * :ref:`/NXem_instrument/name-field ` * :ref:`/NXem_instrument/nanoprobeID-group ` * :ref:`/NXem_instrument/PUMP-group ` * :ref:`/NXem_instrument/SENSOR-group ` * :ref:`/NXem_instrument/stageID-group ` * :ref:`/NXem_instrument/stageID/alias-field ` * :ref:`/NXem_instrument/stageID/design-field ` * :ref:`/NXem_instrument/stageID/position-field ` * :ref:`/NXem_instrument/stageID/rotation-field ` * :ref:`/NXem_instrument/stageID/rotation@comment-attribute ` * :ref:`/NXem_instrument/stageID/tilt1-field ` * :ref:`/NXem_instrument/stageID/tilt1@comment-attribute ` * :ref:`/NXem_instrument/stageID/tilt2-field ` * :ref:`/NXem_instrument/stageID/tilt2@comment-attribute ` * :ref:`/NXem_instrument/type-field ` **NXDL Source**: https://github.com/FAIRmat-NFDI/nexus_definitions/tree/fairmat/base_classes/NXem_instrument.nxdl.xml