Class: CryoEMInstrument
Cryo-EM microscope specifications
URI: lambdaber:CryoEMInstrument
classDiagram
class CryoEMInstrument
click CryoEMInstrument href "../CryoEMInstrument/"
Instrument <|-- CryoEMInstrument
click Instrument href "../Instrument/"
CryoEMInstrument : accelerating_voltage
CryoEMInstrument : autoloader_capacity
CryoEMInstrument : beamline_id
CryoEMInstrument : c2_aperture
CryoEMInstrument : cs
CryoEMInstrument : cs_corrector
CryoEMInstrument : current_status
CryoEMInstrument --> "0..1" InstrumentStatusEnum : current_status
click InstrumentStatusEnum href "../InstrumentStatusEnum/"
CryoEMInstrument : description
CryoEMInstrument : detector_dimensions
CryoEMInstrument : detector_manufacturer
CryoEMInstrument : detector_mode
CryoEMInstrument --> "0..1" DetectorModeEnum : detector_mode
click DetectorModeEnum href "../DetectorModeEnum/"
CryoEMInstrument : detector_model
CryoEMInstrument : detector_position
CryoEMInstrument : detector_technology
CryoEMInstrument --> "0..1" DetectorTechnologyEnum : detector_technology
click DetectorTechnologyEnum href "../DetectorTechnologyEnum/"
CryoEMInstrument : energy_filter_make
CryoEMInstrument : energy_filter_model
CryoEMInstrument : energy_filter_present
CryoEMInstrument : energy_filter_slit_width
CryoEMInstrument : facility_name
CryoEMInstrument --> "0..1" FacilityEnum : facility_name
click FacilityEnum href "../FacilityEnum/"
CryoEMInstrument : facility_ror
CryoEMInstrument : gunlens
CryoEMInstrument : id
CryoEMInstrument : imaging_mode
CryoEMInstrument --> "0..1" ImagingModeEnum : imaging_mode
click ImagingModeEnum href "../ImagingModeEnum/"
CryoEMInstrument : installation_date
CryoEMInstrument : instrument_category
CryoEMInstrument --> "0..1" InstrumentCategoryEnum : instrument_category
click InstrumentCategoryEnum href "../InstrumentCategoryEnum/"
CryoEMInstrument : instrument_code
CryoEMInstrument : manufacturer
CryoEMInstrument : microscope_software
CryoEMInstrument : microscope_software_version
CryoEMInstrument : model
CryoEMInstrument : objective_aperture
CryoEMInstrument : phase_plate
CryoEMInstrument : phase_plate_type
CryoEMInstrument : pixel_size_physical
CryoEMInstrument : pixel_size_physical_um
CryoEMInstrument : spotsize
CryoEMInstrument : tem_beam_diameter
CryoEMInstrument : title
Inheritance
- NamedThing
- Instrument
- CryoEMInstrument
- Instrument
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| accelerating_voltage | 0..1 Integer |
Accelerating voltage in kV | direct |
| cs_corrector | 0..1 Boolean |
Spherical aberration corrector present | direct |
| phase_plate | 0..1 Boolean |
Phase plate available | direct |
| detector_technology | 0..1 DetectorTechnologyEnum |
Generic detector technology type | direct |
| detector_manufacturer | 0..1 String |
Detector manufacturer (e | direct |
| detector_model | 0..1 String |
Detector model (e | direct |
| detector_mode | 0..1 DetectorModeEnum |
Supported or default detector operating mode | direct |
| detector_position | 0..1 String |
Physical position of detector in microscope (e | direct |
| detector_dimensions | 0..1 String |
Detector dimensions in pixels (e | direct |
| pixel_size_physical_um | 0..1 Float |
Physical pixel size of the detector in micrometers | direct |
| autoloader_capacity | 0..1 Integer |
Number of grids the autoloader can hold | direct |
| cs | 0..1 Float |
Spherical aberration (Cs) in millimeters | direct |
| c2_aperture | 0..1 Float |
C2 aperture size in micrometers | direct |
| objective_aperture | 0..1 Float |
Objective aperture size in micrometers | direct |
| phase_plate_type | 0..1 String |
Type of phase plate if present | direct |
| energy_filter_present | 0..1 Boolean |
Whether energy filter is present | direct |
| energy_filter_make | 0..1 String |
Energy filter manufacturer | direct |
| energy_filter_model | 0..1 String |
Energy filter model | direct |
| energy_filter_slit_width | 0..1 Float |
Energy filter slit width in eV | direct |
| pixel_size_physical | 0..1 Float |
Physical pixel size in micrometers | direct |
| microscope_software | 0..1 String |
Microscope control software (e | direct |
| microscope_software_version | 0..1 String |
Software version | direct |
| spotsize | 0..1 Integer |
Electron beam spot size setting | direct |
| gunlens | 0..1 Integer |
Gun lens setting | direct |
| imaging_mode | 0..1 ImagingModeEnum |
Imaging mode for electron microscopy | direct |
| tem_beam_diameter | 0..1 Float |
TEM beam diameter in micrometers | direct |
| instrument_code | 1 String |
Human-friendly facility or laboratory identifier for the instrument (e | Instrument |
| instrument_category | 0..1 InstrumentCategoryEnum |
Category distinguishing beamlines from laboratory equipment | Instrument |
| facility_name | 0..1 FacilityEnum |
Name of the research facility where the instrument is located | Instrument |
| facility_ror | 0..1 Uriorcurie |
Research Organization Registry (ROR) identifier for the facility | Instrument |
| beamline_id | 0..1 String |
Beamline identifier at synchrotron/neutron facility | Instrument |
| manufacturer | 0..1 String |
Instrument manufacturer | Instrument |
| model | 0..1 String |
Instrument model | Instrument |
| installation_date | 0..1 String |
Date of instrument installation | Instrument |
| current_status | 0..1 InstrumentStatusEnum |
Current operational status | Instrument |
| id | 1 Uriorcurie |
Globally unique identifier as an IRI or CURIE for machine processing and exte... | NamedThing |
| title | 0..1 String |
A human-readable name or title for this entity | NamedThing |
| description | 0..1 String |
A detailed textual description of this entity | NamedThing |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/lambda-ber-schema/
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | lambdaber:CryoEMInstrument |
| native | lambdaber:CryoEMInstrument |
LinkML Source
Direct
name: CryoEMInstrument
description: Cryo-EM microscope specifications
from_schema: https://w3id.org/lambda-ber-schema/
is_a: Instrument
attributes:
accelerating_voltage:
name: accelerating_voltage
description: Accelerating voltage in kV
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: integer
any_of:
- equals_number: 120
- equals_number: 200
- equals_number: 300
cs_corrector:
name: cs_corrector
description: Spherical aberration corrector present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: boolean
phase_plate:
name: phase_plate
description: Phase plate available
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: boolean
detector_technology:
name: detector_technology
description: Generic detector technology type
comments:
- Use this for technology classification (e.g., direct_electron_detector, ccd)
- See detector_manufacturer and detector_model for specific equipment details
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
- XRayInstrument
- XRFImage
range: DetectorTechnologyEnum
detector_manufacturer:
name: detector_manufacturer
description: Detector manufacturer (e.g., Gatan, ThermoFisher, DirectElectron)
comments:
- 'Examples: Gatan, ThermoFisher Scientific, DirectElectron'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
- XRayInstrument
range: string
detector_model:
name: detector_model
description: Detector model (e.g., K3, Falcon 4i, DE-64)
comments:
- 'Examples: K3 BioQuantum, Falcon 4i, DE-64'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
- XRayInstrument
- XRFImage
range: string
detector_mode:
name: detector_mode
description: Supported or default detector operating mode
comments:
- Indicates operating mode capabilities (e.g., counting, super_resolution)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
- DataCollectionStrategy
range: DetectorModeEnum
detector_position:
name: detector_position
description: Physical position of detector in microscope (e.g., post-GIF, pre-column)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
detector_dimensions:
name: detector_dimensions
description: Detector dimensions in pixels (e.g., 4096x4096, 5760x4092)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
pixel_size_physical_um:
name: pixel_size_physical_um
description: Physical pixel size of the detector in micrometers
comments:
- Hardware specification, independent of magnification
- Calibrated pixel size (Å/pixel) depends on magnification and is stored in ExperimentRun
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
autoloader_capacity:
name: autoloader_capacity
description: Number of grids the autoloader can hold
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: integer
cs:
name: cs
description: Spherical aberration (Cs) in millimeters
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
c2_aperture:
name: c2_aperture
description: C2 aperture size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
objective_aperture:
name: objective_aperture
description: Objective aperture size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
phase_plate_type:
name: phase_plate_type
description: Type of phase plate if present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
energy_filter_present:
name: energy_filter_present
description: Whether energy filter is present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: boolean
energy_filter_make:
name: energy_filter_make
description: Energy filter manufacturer
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
energy_filter_model:
name: energy_filter_model
description: Energy filter model
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
energy_filter_slit_width:
name: energy_filter_slit_width
description: Energy filter slit width in eV
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
pixel_size_physical:
name: pixel_size_physical
description: Physical pixel size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
microscope_software:
name: microscope_software
description: Microscope control software (e.g., SerialEM, EPU, Leginon)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
microscope_software_version:
name: microscope_software_version
description: Software version
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: string
spotsize:
name: spotsize
description: Electron beam spot size setting
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: integer
gunlens:
name: gunlens
description: Gun lens setting
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: integer
imaging_mode:
name: imaging_mode
description: Imaging mode for electron microscopy
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: ImagingModeEnum
tem_beam_diameter:
name: tem_beam_diameter
description: TEM beam diameter in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
domain_of:
- CryoEMInstrument
range: float
Induced
name: CryoEMInstrument
description: Cryo-EM microscope specifications
from_schema: https://w3id.org/lambda-ber-schema/
is_a: Instrument
attributes:
accelerating_voltage:
name: accelerating_voltage
description: Accelerating voltage in kV
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: accelerating_voltage
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: integer
any_of:
- equals_number: 120
- equals_number: 200
- equals_number: 300
cs_corrector:
name: cs_corrector
description: Spherical aberration corrector present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: cs_corrector
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: boolean
phase_plate:
name: phase_plate
description: Phase plate available
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: phase_plate
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: boolean
detector_technology:
name: detector_technology
description: Generic detector technology type
comments:
- Use this for technology classification (e.g., direct_electron_detector, ccd)
- See detector_manufacturer and detector_model for specific equipment details
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_technology
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
- XRayInstrument
- XRFImage
range: DetectorTechnologyEnum
detector_manufacturer:
name: detector_manufacturer
description: Detector manufacturer (e.g., Gatan, ThermoFisher, DirectElectron)
comments:
- 'Examples: Gatan, ThermoFisher Scientific, DirectElectron'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_manufacturer
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
- XRayInstrument
range: string
detector_model:
name: detector_model
description: Detector model (e.g., K3, Falcon 4i, DE-64)
comments:
- 'Examples: K3 BioQuantum, Falcon 4i, DE-64'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_model
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
- XRayInstrument
- XRFImage
range: string
detector_mode:
name: detector_mode
description: Supported or default detector operating mode
comments:
- Indicates operating mode capabilities (e.g., counting, super_resolution)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_mode
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
- DataCollectionStrategy
range: DetectorModeEnum
detector_position:
name: detector_position
description: Physical position of detector in microscope (e.g., post-GIF, pre-column)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_position
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
detector_dimensions:
name: detector_dimensions
description: Detector dimensions in pixels (e.g., 4096x4096, 5760x4092)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: detector_dimensions
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
pixel_size_physical_um:
name: pixel_size_physical_um
description: Physical pixel size of the detector in micrometers
comments:
- Hardware specification, independent of magnification
- Calibrated pixel size (Å/pixel) depends on magnification and is stored in ExperimentRun
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: pixel_size_physical_um
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
autoloader_capacity:
name: autoloader_capacity
description: Number of grids the autoloader can hold
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: autoloader_capacity
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: integer
cs:
name: cs
description: Spherical aberration (Cs) in millimeters
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: cs
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
c2_aperture:
name: c2_aperture
description: C2 aperture size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: c2_aperture
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
objective_aperture:
name: objective_aperture
description: Objective aperture size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: objective_aperture
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
phase_plate_type:
name: phase_plate_type
description: Type of phase plate if present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: phase_plate_type
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
energy_filter_present:
name: energy_filter_present
description: Whether energy filter is present
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: energy_filter_present
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: boolean
energy_filter_make:
name: energy_filter_make
description: Energy filter manufacturer
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: energy_filter_make
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
energy_filter_model:
name: energy_filter_model
description: Energy filter model
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: energy_filter_model
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
energy_filter_slit_width:
name: energy_filter_slit_width
description: Energy filter slit width in eV
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: energy_filter_slit_width
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
pixel_size_physical:
name: pixel_size_physical
description: Physical pixel size in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: pixel_size_physical
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
microscope_software:
name: microscope_software
description: Microscope control software (e.g., SerialEM, EPU, Leginon)
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: microscope_software
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
microscope_software_version:
name: microscope_software_version
description: Software version
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: microscope_software_version
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: string
spotsize:
name: spotsize
description: Electron beam spot size setting
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: spotsize
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: integer
gunlens:
name: gunlens
description: Gun lens setting
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: gunlens
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: integer
imaging_mode:
name: imaging_mode
description: Imaging mode for electron microscopy
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: imaging_mode
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: ImagingModeEnum
tem_beam_diameter:
name: tem_beam_diameter
description: TEM beam diameter in micrometers
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: tem_beam_diameter
owner: CryoEMInstrument
domain_of:
- CryoEMInstrument
range: float
instrument_code:
name: instrument_code
description: Human-friendly facility or laboratory identifier for the instrument
(e.g., 'TITAN-KRIOS-1', 'ALS-12.3.1-SIBYLS', 'RIGAKU-FR-E'). Used for local
reference and equipment tracking.
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: instrument_code
owner: CryoEMInstrument
domain_of:
- Instrument
range: string
required: true
instrument_category:
name: instrument_category
description: Category distinguishing beamlines from laboratory equipment
comments:
- Use SYNCHROTRON_BEAMLINE for synchrotron beamlines
- Use ELECTRON_MICROSCOPE for cryo-EM instruments
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: instrument_category
owner: CryoEMInstrument
domain_of:
- Instrument
range: InstrumentCategoryEnum
facility_name:
name: facility_name
description: Name of the research facility where the instrument is located
comments:
- Select from the standardized list of major synchrotron facilities
- Leave empty for laboratory-based instruments
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: facility_name
owner: CryoEMInstrument
domain_of:
- Instrument
range: FacilityEnum
facility_ror:
name: facility_ror
description: Research Organization Registry (ROR) identifier for the facility
comments:
- Persistent identifier for the facility organization
- 'Example: https://ror.org/02jbv0t02 (Lawrence Berkeley National Laboratory)'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: facility_ror
owner: CryoEMInstrument
domain_of:
- Instrument
range: uriorcurie
pattern: ^https://ror\.org/\w+$
beamline_id:
name: beamline_id
description: Beamline identifier at synchrotron/neutron facility
comments:
- Use facility-specific naming convention
- 'Examples: ''12.3.1'' (ALS), ''17-ID-1'' (NSLS-II), ''I04'' (Diamond)'
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
slot_uri: mmCIF:_diffrn_source.pdbx_synchrotron_beamline
alias: beamline_id
owner: CryoEMInstrument
domain_of:
- Instrument
range: string
manufacturer:
name: manufacturer
description: Instrument manufacturer
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: manufacturer
owner: CryoEMInstrument
domain_of:
- Instrument
range: string
model:
name: model
description: Instrument model
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: model
owner: CryoEMInstrument
domain_of:
- Instrument
range: string
installation_date:
name: installation_date
description: Date of instrument installation
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: installation_date
owner: CryoEMInstrument
domain_of:
- Instrument
range: string
current_status:
name: current_status
description: Current operational status
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: current_status
owner: CryoEMInstrument
domain_of:
- Instrument
range: InstrumentStatusEnum
id:
name: id
description: Globally unique identifier as an IRI or CURIE for machine processing
and external references. Used for linking data across systems and semantic web
integration.
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
identifier: true
alias: id
owner: CryoEMInstrument
domain_of:
- NamedThing
range: uriorcurie
required: true
title:
name: title
description: A human-readable name or title for this entity
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
slot_uri: dcterms:title
alias: title
owner: CryoEMInstrument
domain_of:
- NamedThing
range: string
description:
name: description
description: A detailed textual description of this entity
from_schema: https://w3id.org/lambda-ber-schema/
rank: 1000
alias: description
owner: CryoEMInstrument
domain_of:
- NamedThing
- AttributeGroup
range: string