Class: Instrument

Instrument values, mostly constant across a data collection.

URI: https://w3id.org/osc-em/oscem-schemas-subtomo/:Instrument

erDiagram Instrument { string illumination string imaging string electron_source string operating_mode } QuantitySI { float valueSI string unitSI string unit float value } Microscope { string model string manufacturer } Instrument ||--|| Microscope : "microscope" Instrument ||--|| QuantitySI : "acceleration_voltage" Instrument ||--|o QuantitySI : "c2_aperture" Instrument ||--|o QuantitySI : "cs" Instrument ||--|o QuantitySI : "beam_convergence"

Slots

Name	Cardinality and Range	Description	Inheritance
microscope	1 Microscope	Microscope information	direct
illumination	1 String	Mode of illumination used during data collection	direct
imaging	1 String	Mode of imaging used during data collection	direct
electron_source	1 String	Type of electron source used in the microscope, such as FEG	direct
acceleration_voltage	1 QuantitySI	Voltage used for the electron acceleration, in kV	direct
c2_aperture	0..1 QuantitySI	C2 aperture size used in data acquisition, in µm	direct
cs	0..1 QuantitySI	Spherical aberration of the instrument, in mm	direct
operating_mode	0..1 String	Operating mode of the microscope, i	direct
beam_convergence	0..1 QuantitySI	Refers to how tightly or widely the electron beam is focused onto the sample,...	direct

Usages

used by	used in	type	used
EMDatasetTomo	instrument	range	Instrument

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/osc-em/oscem-schemas-subtomo

Mappings

Mapping Type	Mapped Value
self	https://w3id.org/osc-em/oscem-schemas-subtomo/:Instrument
native	https://w3id.org/osc-em/oscem-schemas-subtomo/:Instrument

LinkML Source

Direct

name: Instrument
description: Instrument values, mostly constant across a data collection.
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
slots:
- microscope
- illumination
- imaging
- electron_source
- acceleration_voltage
- c2_aperture
- cs
- operating_mode
- beam_convergence
slot_usage:
  microscope:
    name: microscope
    required: true
  illumination:
    name: illumination
    required: true
  imaging:
    name: imaging
    required: true
  electron_source:
    name: electron_source
    required: true
  acceleration_voltage:
    name: acceleration_voltage
    required: true
  c2_aperture:
    name: c2_aperture
    required: false
  cs:
    name: cs
    required: false
  operating_mode:
    name: operating_mode
    required: false
  beam_convergence:
    name: beam_convergence
    required: false

Induced

name: Instrument
description: Instrument values, mostly constant across a data collection.
from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
slot_usage:
  microscope:
    name: microscope
    required: true
  illumination:
    name: illumination
    required: true
  imaging:
    name: imaging
    required: true
  electron_source:
    name: electron_source
    required: true
  acceleration_voltage:
    name: acceleration_voltage
    required: true
  c2_aperture:
    name: c2_aperture
    required: false
  cs:
    name: cs
    required: false
  operating_mode:
    name: operating_mode
    required: false
  beam_convergence:
    name: beam_convergence
    required: false
attributes:
  microscope:
    name: microscope
    description: Microscope information
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: microscope
    owner: Instrument
    domain_of:
    - Instrument
    range: Microscope
    required: true
  illumination:
    name: illumination
    description: Mode of illumination used during data collection
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: illumination
    owner: Instrument
    domain_of:
    - Instrument
    range: string
    required: true
  imaging:
    name: imaging
    description: Mode of imaging used during data collection
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: imaging
    owner: Instrument
    domain_of:
    - Instrument
    range: string
    required: true
  electron_source:
    name: electron_source
    description: Type of electron source used in the microscope, such as FEG
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: electron_source
    owner: Instrument
    domain_of:
    - Instrument
    range: string
    required: true
  acceleration_voltage:
    name: acceleration_voltage
    description: Voltage used for the electron acceleration, in kV
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: acceleration_voltage
    owner: Instrument
    domain_of:
    - Instrument
    range: QuantitySI
    required: true
  c2_aperture:
    name: c2_aperture
    description: C2 aperture size used in data acquisition, in µm
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: c2_aperture
    owner: Instrument
    domain_of:
    - Instrument
    range: QuantitySI
    required: false
  cs:
    name: cs
    description: Spherical aberration of the instrument, in mm
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: cs
    owner: Instrument
    domain_of:
    - Instrument
    range: QuantitySI
    required: false
  operating_mode:
    name: operating_mode
    description: Operating mode of the microscope, i.e. "TEM", "STEM"
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: operating_mode
    owner: Instrument
    domain_of:
    - Instrument
    range: string
    required: false
  beam_convergence:
    name: beam_convergence
    description: Refers to how tightly or widely the electron beam is focused onto
      the sample, in mrad. Typically low convergence for TEM and high for STEM.
    from_schema: https://w3id.org/osc-em/oscem-schemas-subtomo
    rank: 1000
    alias: beam_convergence
    owner: Instrument
    domain_of:
    - Instrument
    range: QuantitySI
    required: false