2.3.3.3.14. NXapm

Status:

application definition, extends NXobject

Description:

Application definition for atom probe and field ion microscopy experiments.

Symbols:

The symbols used in the schema to specify e.g. dimensions of arrays.

p: Number of pulses collected in between start_time and end_time resolved by an instance of NXevent_data_apm. If this is not defined, p is the number of ions included in the reconstructed volume if the application definition is used to store results of an already reconstructed datasets.

n: Number of ions spatially filtered from results of the hit_finding algorithm from which an instance of a reconstructed volume has been generated. These ions get new identifier assigned in the process (the so-called evaporation_identifier). This identifier must not be confused with the pulse_identifier.

Groups cited:

NXapm_charge_state_analysis, NXapm_hit_finding, NXapm_msr, NXapm_ranging, NXapm_reconstruction, NXapm_sim, NXapm_volt_and_bowl, NXchamber, NXchemical_composition, NXcite, NXcollection, NXcoordinate_system_set, NXcoordinate_system, NXcs_filter_boolean_mask, NXcs_profiling, NXdata, NXdetector, NXentry, NXevent_data_apm_set, NXevent_data_apm, NXfabrication, NXidentifier, NXimage_set, NXinstrument, NXion, NXlens_em, NXpeak, NXprocess, NXprogram, NXpulser_apm, NXreflectron, NXroi, NXsample, NXserialized, NXsource, NXstage_lab, NXuser

Structure:

ENTRY: (required) NXentry

definition: (required) NX_CHAR ⤆

Obligatory value: NXapm

@version: (optional) NX_CHAR ⤆

run_number: (recommended) NX_CHAR

The identifier whereby the experiment is referred to in the control software ...

The identifier whereby the experiment is referred to in the control software. This is neither the specimen_name nor the experiment_identifier. For Local Electrode Atom Probe (LEAP) instruments, it is recommended to use the run_number from the proprietary software IVAS/APSuite of AMETEK/Cameca. For other instruments, such as the one from Stuttgart or Oxcart from Erlangen, or the instruments at GPM in Rouen, use the identifier which matches best conceptually to the LEAP run number. The field does not have to be required if the information is recoverable in the dataset which for LEAP instruments is the case (provided these RHIT or HITS files respectively are stored alongside a data artifact). With NXapm the RHIT or HITS can be stored as via the NXserialized group in the hit_finding algorithm section.

As a destructive microscopy technique, a run can be performed only once. It is possible, however, to interrupt a run and restart data acquisition while still using the same specimen. In this case, each evaporation run needs to be distinguished with different run numbers. We follow this habit of most atom probe groups. Such interrupted runs should be stored as individual NXentry instances in one NeXus file.

experiment_alias: (required) NX_CHAR

Either an identifier or an alias that is human-friendly so that scientists f ...

Either an identifier or an alias that is human-friendly so that scientists find that experiment again. For experiments usually this is the run_number but for simulation typically no run_numbers are issued.

experiment_description: (optional) NX_CHAR ⤆

Free-text description about the experiment. ...

Free-text description about the experiment.

Users are strongly advised to parameterize the description of their experiment by using respective groups and fields and base classes instead of writing prose into this field.

The reason is that such free-text field is difficult to machine-interpret. The motivation behind keeping this field for now is to learn in how far the current base classes need extension based on user feedback.

start_time: (required) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC information ...

ISO 8601 time code with local time zone offset to UTC information included when the atom probe session started. If the exact duration of the measurement is not relevant start_time only should be used.

Often though it is useful to specify both start_time and end_time to capture more detailed bookkeeping of the experiment. The user should be aware that even with having both dates specified, it may not be possible to infer how long the experiment took or for how long data were collected.

More detailed timing data over the course of the experiment have to be collected to compute this event chain during the experiment. For this purpose the NXevent_data_apm instance should be used.

end_time: (recommended) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC included ...

ISO 8601 time code with local time zone offset to UTC included when the atom probe session ended.

operation_mode: (required) NX_CHAR

What type of atom probe experiment is performed? This field is meant to ...

What type of atom probe experiment is performed? This field is meant to inform research data management systems to allow filtering:

  • apt are experiments where the analysis_chamber has no imaging gas. experiment with LEAP instruments are typically performed such.

  • fim are experiments where the analysis_chamber has an imaging gas, which should be specified with the atmosphere in the analysis_chamber group.

  • apt_fim should be used for combinations of the two imaging modes. few experiments of this type have been performed as this can be detrimental to LEAP systems (see S. Katnagallu et al.).

  • other should be used in combination with the user specifying details in the experiment_documentation field.

If NXapm is used for storing details about a simulation use other for now.

Any of these values: apt | fim | apt_fim | other

profiling: (optional) NXcs_profiling

The configuration of the I/O writer software (e.g. `pynxtools

The configuration of the I/O writer software (e.g. pynxtools or its plugins) which was used to generate this NeXus file instance.

programID: (optional) NXprogram

A collection of all programs and libraries which are considered relevant ...

A collection of all programs and libraries which are considered relevant to understand with which software tools this NeXus file instance was generated. Ideally, to enable a binary recreation from the input data.

Examples include the name and version of the libraries used to write the instance. Ideally, the software which writes these NXprogram instances also includes the version of the set of NeXus classes i.e. the specific set of base classes, application definitions, and contributed definitions with which the here described concepts can be resolved.

For the pynxtools library which is used by the NOMAD research data management system, it makes sense to store e.g. the GitHub repository commit and respective submodule references used.

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

experiment_identifier: (recommended) NXidentifier ⤆

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

CITE: (optional) NXcite

doi: (required) NX_CHAR ⤆

serializedID: (optional) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

USER: (recommended) NXuser ⤆

name: (optional) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

sample: (recommended) NXsample ⤆

Description of the sample from which the specimen was prepared or ...

Description of the sample from which the specimen was prepared or site-specifically cut out using e.g. a focused-ion beam instrument.

The sample group is currently a place for storing suggestions from atom probers about knowledge they have gained about the sample. There are cases where the specimen is machined further or exposed to external stimuli during the experiment. In this case, these details should not be stored under sample but suggestions should be made how this application definition can be improved.

In the future also details like how the grain_diameter was characterized, how the sample was prepared, how the material was heat-treated etc., should be stored. For this specific application definitions/schemas can be used which are then arranged and documented with a description of the workflow so that actionable graphs become instantiatable.

type: (required) NX_CHAR ⤆

A qualifier whether the sample is a real one ...

A qualifier whether the sample is a real one or a virtual one (in a computer simulation).

Any of these values: experiment | simulation

alias: (required) NX_CHAR

Given name/alias for the sample.

grain_diameter: (optional) NX_FLOAT {units=NX_LENGTH}

Qualitative information about the grain size, here specifically ...

Qualitative information about the grain size, here specifically described as the equivalent spherical diameter of an assumed average grain size for the crystal ensemble. Users of this information should be aware that although the grain diameter or radius is often referred to as grain size.

In atom probe it is possible that the specimen may contain a few crystals only. In this case the grain_diameter is not a reliable descriptor. Reporting a grain size may be useful though as it allows judging if specific features are expected to be found in the detector hit map.

grain_diameter_error: (optional) NX_FLOAT {units=NX_LENGTH}

Magnitude of the standard deviation of the grain_diameter.

heat_treatment_temperature: (optional) NX_FLOAT {units=NX_TEMPERATURE}

The temperature of the last heat treatment step before quenching. ...

The temperature of the last heat treatment step before quenching. Knowledge about this value can give an idea how the sample was heat treated. However, if a documentation of the annealing treatment as a function of time is available one should better rely on this information and have it stored alongside the NeXus file.

heat_treatment_temperature_error: (optional) NX_FLOAT {units=NX_TEMPERATURE}

Magnitude of the standard deviation of the heat_treatment_temperature.

heat_treatment_quenching_rate: (optional) NX_FLOAT {units=NX_ANY}

Rate of the last quenching step. Knowledge about this value can give ...

Rate of the last quenching step. Knowledge about this value can give an idea how the sample was heat treated. However, there are many situations where one can imagine that the scalar value for just the quenching rate is insufficient.

An example is when the sample was left in the furnace after the furnace was switched off. In this case the sample cools down with a specific rate of how this furnace cools down in the lab. Processes which in practice are often not documented.

This can be problematic though because when the furnace door was left open or the ambient temperature in the lab changed, i.e. for a series of experiments where one is conducted on a hot summer day and the next during winter this can have an effect on the evolution of the microstructure. There are many cases where this has been reported to be an QA issue in industry, e.g. think about aging aluminium samples left on the factory parking lot on a hot summer day.

heat_treatment_quenching_rate_error: (optional) NX_FLOAT {units=NX_ANY}

Magnitude of the standard deviation of the heat_treatment_quenching_rate.

description: (optional) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

chemical_composition: (recommended) NXchemical_composition

The chemical composition of the sample. Typically, it is assumed that ...

The chemical composition of the sample. Typically, it is assumed that this more macroscopic composition is representative for the material so that the composition of the typically substantially less voluminous specimen probes from the more voluminous sample.

normalization: (required) NX_CHAR

Reporting compositions as atom and weight percent yields both ...

Reporting compositions as atom and weight percent yields both dimensionless quantities but their conceptual interpretation differs. A normalization based on atom_percent counts relative to the total number of atoms which are of a particular type. By contrast, weight_percent normalization factorizes in the respective mass of the elements. Python libraries like pint are challenged by these differences as at.-% and wt.-% are both fractional quantities.

Any of these values: atom_percent | weight_percent

ionID: (required) NXion ⤆

chemical_symbol: (required) NX_CHAR

Human-readable name of the element (e.g. Fe). ...

Human-readable name of the element (e.g. Fe). Name has to be a symbol of an element from the periodic table. All symbols in the set of NXion instances inside the group chemical_composition need to be disjoint.

composition: (required) NX_FLOAT {units=NX_DIMENSIONLESS}

Composition value for the element/ion referred to under name. ...

Composition value for the element/ion referred to under name. The value is normalized based on normalization, i.e. composition is either an atom or weight percent quantity.

composition_error: (optional) NX_FLOAT {units=NX_DIMENSIONLESS}

Magnitude of the standard deviation of the composition (value).

specimen: (required) NXsample ⤆

type: (required) NX_CHAR ⤆

A qualifier whether the specimen is a real one or a virtual one. ...

A qualifier whether the specimen is a real one or a virtual one.

Any of these values: experiment | simulation

alias: (recommended) NX_CHAR

Given name an alias. Better use identifier and parent_identifier instead. ...

Given name an alias. Better use identifier and parent_identifier instead. A single NXentry should be used only for the characterization of a single specimen.

preparation_date: (recommended) NX_DATE_TIME ⤆

ISO 8601 time code with local time zone offset to UTC information ...

ISO 8601 time code with local time zone offset to UTC information 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. Ideally, this matches the last timestamp that is mentioned in the digital resource pointed to by parent_identifier.

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. Additional time stamps prior to preparation_date should better be placed in resources which describe but which do not pollute the description here with prose. Resolving these connected pieces of information is considered within the responsibility of the research data management system.

atom_types: (required) NX_CHAR

List of comma-separated elements from the periodic table that are ...

List of comma-separated elements from the periodic table that are contained in the specimen. If the specimen substance has multiple components, all elements from each component must be included in atom_types.

The purpose of the field is to offer research data management systems an opportunity to parse the relevant elements without having to interpret these from the resources pointed to by parent_identifier or walk through eventually deeply nested groups in data instances.

description: (optional) NX_CHAR ⤆

Discouraged free-text field.

is_polycrystalline: (recommended) NX_BOOLEAN

Report if the specimen is polycrystalline, in which case it ...

Report if the specimen is polycrystalline, in which case it contains a grain or phase boundary, or if the specimen is a single crystal.

is_amorphous: (recommended) NX_BOOLEAN

Report if the specimen is amorphous.

initial_radius: (recommended) NX_FLOAT {units=NX_LENGTH}

Ideally measured otherwise best elaborated guess of the initial radius of ...

Ideally measured otherwise best elaborated guess of the initial radius of the specimen.

shank_angle: (recommended) NX_FLOAT {units=NX_ANGLE}

Ideally measured otherwise best elaborated guess of the (initial) shank an ...

Ideally measured otherwise best elaborated guess of the (initial) shank angle. This is a measure of the specimen taper. Define it in such a way that the base of the specimen is modelled as a conical frustrum so that the shank angle is the (shortest) angle between the specimen space z-axis and a vector on the lateral surface of the cone.

identifier: (recommended) NXidentifier ⤆

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

parent_identifier: (recommended) NXidentifier

Identifier of the sample from which the specimen was cut or the string ...

Identifier of the sample from which the specimen was cut or the string n/a. The purpose of this field is to support functionalities for tracking sample provenance via a research data management system.

service: (required) NX_CHAR ⤆

identifier: (required) NX_CHAR ⤆

is_persistent: (required) NX_BOOLEAN ⤆

coordinate_system_set: (required) NXcoordinate_system_set

Set to hold different coordinate systems conventions. ...

Set to hold different coordinate systems conventions. Inspect the description of the NXcoordinate_system_set and NXcoordinate_system base classes how to define coordinate systems in NeXus. Specific details for application in atom probe microscopy follow.

In this research field scientists usually distinguish several Euclidean coordinate systems (CS):

  • World space; a CS specifying a local coordinate system of the planet earth which identifies into which direction gravity is pointing such that the laboratory space CS can be rotated into this world CS.

  • The laboratory space; a CS specifying the room where the instrument is located in or a physical landmark on the instrument, e.g. the direction of the transfer rod where positive is the direction how the rod has to be pushed during loading a specimen into the instrument. In summary, this CS is defined by the chassis of the instrument.

  • The specimen space; a CS affixed to either the base or the initial apex of the specimen, whose z axis points towards the detector.

  • The detector space; a CS affixed to the detector plane whose xy plane is usually in the detector and whose z axis points towards the specimen. This is a distorted space with respect to the reconstructed ion positions.

  • The reconstruction space; a CS in which the reconstructed ion positions are defined. The orientation depends on the analysis software used.

  • Eventually further coordinate systems attached to the flight path of individual ions might be defined.

In atom probe microscopy a frequently used choice for the detector space (CS) is discussed with the so-called detector space image (stack). This is a stack of two-dimensional histograms of detected ions within a predefined evaporation identifier interval. Typically, the set of ion evaporation sequence IDs is grouped into chunks.

For each chunk a histogram of the ion hit positions on the detector is computed. This leaves the possibility for inconsistency between the so-called detector space and the e.g. specimen space.

To avoid these ambiguities, instances of NXtransformations should be used.

COORDINATE_SYSTEM: (required) NXcoordinate_system ⤆

origin: (required) NX_CHAR ⤆

alias: (required) NX_CHAR ⤆

type: (required) NX_CHAR ⤆

handedness: (required) NX_CHAR ⤆

x_direction: (required) NX_CHAR ⤆

y_direction: (required) NX_CHAR ⤆

z_direction: (required) NX_CHAR ⤆

measurement: (optional) NXapm_msr

instrument: (required) NXinstrument ⤆

instrument_name: (optional) NX_CHAR ⤆

status: (required) NX_CHAR ⤆

fabrication: (required) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

identifier: (recommended) NXidentifier ⤆

reflectron: (required) NXreflectron ⤆

status: (required) NX_CHAR ⤆

fabrication: (recommended) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

local_electrode: (required) NXlens_em ⤆

name: (required) NX_CHAR ⤆

fabrication: (recommended) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

ion_detector: (recommended) NXdetector ⤆

fabrication: (recommended) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

pulser: (required) NXpulser_apm ⤆

pulse_mode: (required) NX_CHAR ⤆

fabrication: (recommended) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

sourceID: (optional) NXsource ⤆

wavelength: (required) NX_FLOAT {units=NX_WAVELENGTH} ⤆

The wavelength of the radiation emitted by the source.

fabrication: (recommended) NXfabrication ⤆

vendor: (required) NX_CHAR ⤆

model: (required) NX_CHAR ⤆

analysis_chamber: (recommended) NXchamber ⤆

flight_path: (recommended) NX_FLOAT {units=NX_LENGTH}

The space inside the atom probe along which ions pass nominally ...

The space inside the atom probe along which ions pass nominally when they leave the specimen and travel to the detector.

event_data_apm_set: (optional) NXevent_data_apm_set

event_data_apm: (recommended) NXevent_data_apm ⤆

instrument: (recommended) NXinstrument ⤆

control: (required) NXcollection ⤆

evaporation_control: (required) NX_CHAR ⤆

target_detection_rate: (required) NX_FLOAT ⤆

pulser: (required) NXpulser_apm ⤆

pulse_frequency: (required) NX_FLOAT ⤆

@logged_against: (required) NX_CHAR ⤆

pulse_fraction: (required) NX_FLOAT ⤆

@logged_against: (required) NX_CHAR ⤆

pulse_voltage: (recommended) NX_FLOAT ⤆

@logged_against: (required) NX_CHAR ⤆

standing_voltage: (required) NX_FLOAT ⤆

@logged_against: (required) NX_CHAR ⤆

SOURCE: (optional) NXsource ⤆

pulse_energy: (required) NX_FLOAT ⤆

@logged_against: (required) NX_CHAR ⤆

stage_lab: (required) NXstage_lab ⤆

base_temperature: (required) NX_FLOAT ⤆

analysis_chamber: (required) NXchamber ⤆

chamber_pressure: (required) NX_FLOAT ⤆

simulation: (optional) NXapm_sim

atom_probe: (recommended) NXroi

A region-of-interest analyzed either during or after the session for which ...

A region-of-interest analyzed either during or after the session for which specific processed data of the measured or simulated data are available.

initial_specimen: (recommended) NXimage_set

SEM or TEM image of the initial specimen i.e. ...

SEM or TEM image of the initial specimen i.e. ideally taken prior to the data acquisition.

image_2d: (required) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

real: (required) NX_NUMBER ⤆

axis_j: (required) NX_NUMBER (Rank: 1, Dimensions: [n_j]) ⤆

@long_name: (required) NX_CHAR ⤆

axis_i: (required) NX_NUMBER (Rank: 1, Dimensions: [n_i]) ⤆

@long_name: (required) NX_CHAR ⤆

raw_data: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT

programID: (optional) NXprogram

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

serialized: (recommended) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

hit_finding: (recommended) NXapm_hit_finding

sequence_index: (recommended) NX_POSINT ⤆

number_of_dld_wires: (recommended) NX_UINT ⤆

arrival_time_pairs: (optional) NX_NUMBER ⤆

hit_quality_types: (optional) NX_CHAR ⤆

hit_quality_identifier: (optional) NX_UINT ⤆

hit_positions: (recommended) NX_NUMBER (Rank: 2, Dimensions: [i, 2]) ⤆

hit_quality: (optional) NX_UINT (Rank: 1, Dimensions: [i]) ⤆

hit_multiplicity: (recommended) NX_UINT (Rank: 1, Dimensions: [i]) ⤆

programID: (optional) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

serialized: (recommended) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

hit_spatial_filtering: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT

evaporation_identifier_offset: (required) NX_INT {units=NX_UNITLESS}

Integer used to name the first pulse to know if there is an ...

Integer used to name the first pulse to know if there is an offset of the evaporation_identifier to zero.

Identifiers can be defined either implicitly or explicitly. For implicit indexing identifiers are defined on the interval \([identifier\_offset, identifier\_offset + c - 1]\).

Therefore, implicit identifier are completely defined by the value of identifier_offset and cardinality. For example if identifier run from -2 to 3 the value for identifier_offset is -2.

For explicit indexing the field identifier has to be used. Fortran-/Matlab- and C-/Python-style indexing have specific implicit identifier conventions where identifier_offset is 1 and 0 respectively.

evaporation_identifier: (required) NX_INT (Rank: 1, Dimensions: [n]) {units=NX_UNITLESS}

(Molecular) ion identifier which resolves the sequence in which ...

(Molecular) ion identifier which resolves the sequence in which the ions were evaporated but taking into account that a hit_finding and spatial_filtering was applied.

programID: (required) NXprogram

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

serialized: (optional) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

hit_filter: (recommended) NXcs_filter_boolean_mask

number_of_objects: (required) NX_UINT ⤆

bitdepth: (required) NX_UINT ⤆

mask: (required) NX_UINT ⤆

identifier: (required) NX_INT ⤆

voltage_and_bowl: (recommended) NXapm_volt_and_bowl

sequence_index: (recommended) NX_POSINT ⤆

raw_tof: (recommended) NX_FLOAT (Rank: 1, Dimensions: [n]) ⤆

calibrated_tof: (required) NX_FLOAT (Rank: 1, Dimensions: [n]) ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

serialized: (optional) NXserialized ⤆

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

mass_to_charge_conversion: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT

mass_to_charge: (required) NX_FLOAT (Rank: 1, Dimensions: [n])

programID: (required) NXprogram

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

serialized: (recommended) NXserialized

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

reconstruction: (recommended) NXapm_reconstruction

sequence_index: (recommended) NX_POSINT ⤆

parameter: (required) NX_CHAR ⤆

protocol_name: (recommended) NX_CHAR ⤆

crystallographic_calibration: (recommended) NX_CHAR ⤆

field_of_view: (recommended) NX_FLOAT ⤆

reconstructed_positions: (required) NX_FLOAT (Rank: 2, Dimensions: [n, 3]) ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

config: (recommended) NXserialized ⤆

For LEAP and IVAS/APSuite-based analyses root file which stores ...

For LEAP and IVAS/APSuite-based analyses root file which stores the settings whereby an RHIT/HITS file can be used to regenerate the reconstruction that is here referred to.

The respective RHIT/HITS file should ideally be specified in the serialized group of the hit_finding section of this application definition.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

results: (recommended) NXserialized ⤆

For LEAP and IVAS/APSuite-based analyses the resulting typically ...

For LEAP and IVAS/APSuite-based analyses the resulting typically file with the reconstructed positions and (calibrated) mass-to-charge state ratio values.

For other data collection/analysis software the data artifact which comes closest conceptually to AMETEK/Cameca’s typical file formats.

These are typically exported as a POS, ePOS, APT, ATO, ENV, or HDF5 file, which should be stored alongside this record in the research data management system.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

naive_discretization: (required) NXprocess ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

DATA: (required) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER (Rank: 3, Dimensions: [n_z, n_y, n_x]) ⤆

axis_z: (required) NX_FLOAT (Rank: 1, Dimensions: [n_z])

@long_name: (required) NX_CHAR

axis_y: (required) NX_FLOAT (Rank: 1, Dimensions: [n_y])

@long_name: (required) NX_CHAR

axis_x: (required) NX_FLOAT (Rank: 1, Dimensions: [n_x])

@long_name: (required) NX_CHAR

ranging: (recommended) NXapm_ranging

sequence_index: (recommended) NX_POSINT ⤆

maximum_number_of_atoms_per_molecular_ion: (required) NX_UINT ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

definitions: (recommended) NXserialized ⤆

The respective ranging definitions file RNG/RRNG/ENV/HDF5.

type: (required) NX_CHAR ⤆

path: (required) NX_CHAR ⤆

checksum: (required) NX_CHAR ⤆

algorithm: (required) NX_CHAR ⤆

mass_to_charge_distribution: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT ⤆

min_incr_max: (required) NX_FLOAT ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

mass_spectrum: (required) NXdata ⤆

@signal: (required) NX_CHAR ⤆

@axes: (required) NX_CHAR ⤆

@AXISNAME_indices: (required) NX_CHAR

title: (required) NX_CHAR ⤆

intensity: (required) NX_NUMBER (Rank: 1, Dimensions: [n_bins]) ⤆

@long_name: (required) NX_CHAR ⤆

axis_mass_to_charge: (required) NX_FLOAT (Rank: 1, Dimensions: [n_bins])

@long_name: (required) NX_CHAR

background_quantification: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT ⤆

background: (recommended) NX_FLOAT {units=NX_ANY}

(Out-of-sync) background levels in ppm/ns ...

(Out-of-sync) background levels in ppm/ns reported by e.g. IVAS/APSuite for LEAP systems.

mrp_value: (recommended) NX_FLOAT {units=NX_DIMENSIONLESS}

MRP, mass-resolving power, `D. Larson et al. ...

MRP, mass-resolving power, D. Larson et al. (p282, Eqs. D.7 and D.8).

mrp_mass_to_charge: (recommended) NX_FLOAT {units=NX_ANY}

MRP, at which mrp_value was specified.

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

peak_search: (recommended) NXprocess

sequence_index: (recommended) NX_POSINT ⤆

programID: (required) NXprogram

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

peakID: (optional) NXpeak

label: (recommended) NX_CHAR ⤆

description: (required) NX_CHAR

category: (recommended) NX_CHAR

Category for the peak offering a qualitative statement of the locati ...

Category for the peak offering a qualitative statement of the location of the peak in light of limited mass-resolving power that is relevant for composition quantification. See D. Larson et al. (p172) for examples of each category:

  • 0, well-separated, \(^{10}B^{+}\), \(^{28}Si^{2+}\)

  • 1, close, but can be sufficiently separated for quantification in a LEAP system, \(^{94}Mo^{3+}\), \(^{63}Cu^{2+}\)

  • 2, closely overlapping, demands better than LEAP4000X MRP can provide \(^{14}N^{+}\), \(^{28}Si^{2+}\) at different charge states

  • 3, overlapped exactly due to multi-charge molecular species, \(^{16}{O_{2}}^{2+}\), \(^{16}O^{+}\)

  • 4, overlapped, same charge state, cannot as of 2013 be discriminated with a LEAP4000X, \(^{14}{N_{2}}^{+}\), \(^{28}Si^{+}\)

  • 5, overlapped, same charge state, any expectation of resolvability, \(^{54}Cr^{2+}\), \(^{54}Fe^{2+}\)

Any of these values: 0 | 1 | 2 | 3 | 4 | 5

position: (required) NX_NUMBER

peak_identification: (recommended) NXprocess ⤆

sequence_index: (recommended) NX_POSINT ⤆

programID: (required) NXprogram ⤆

program: (required) NX_CHAR ⤆

@version: (required) NX_CHAR ⤆

ionID: (required) NXion ⤆

nuclide_hash: (required) NX_UINT ⤆

charge_state: (required) NX_INT ⤆

mass_to_charge_range: (required) NX_FLOAT

nuclide_list: (recommended) NX_UINT ⤆

name: (recommended) NX_CHAR ⤆

charge_state_analysis: (optional) NXapm_charge_state_analysis

nuclides: (required) NX_UINT ⤆

mass_to_charge_range: (required) NX_FLOAT ⤆

min_half_life: (required) NX_FLOAT ⤆

min_abundance: (required) NX_FLOAT ⤆

min_abundance_product: (required) NX_FLOAT

sacrifice_isotopic_uniqueness: (required) NX_BOOLEAN ⤆

charge_state: (required) NX_INT ⤆

nuclide_hash: (required) NX_UINT ⤆

mass: (required) NX_FLOAT ⤆

natural_abundance_product: (required) NX_FLOAT ⤆

shortest_half_life: (required) NX_FLOAT ⤆

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/NXapm.nxdl.xml