SchemaDefinition
name: TomographyAdditionalFields
description: Mixin for additional fields for tomography datasets.
id: https://w3id.org/oscem-schemas/latest/tomography
imports: ./custom_types
imports: acquisition
imports: linkml:types
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  prefix prefix: types
  prefix reference: https://w3id.org/oscem-schemas/latest/custom_types
prefixes:
  prefix prefix: tomo
  prefix reference: https://w3id.org/oscem-schemas/latest/tomo
default prefix: https://w3id.org/oscem-schemas/latest/tomography/
default range: string
types: TypeDefinition
  name: string
  definition uri: https://w3id.org/linkml/String
  description: A character string
  notes: In RDF serializations, a slot with range of string is treated as a literal or type xsd:string. If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "string".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Text
  base: str
  uri: http://www.w3.org/2001/XMLSchema#string
types: TypeDefinition
  name: integer
  definition uri: https://w3id.org/linkml/Integer
  description: An integer
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "integer".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Integer
  base: int
  uri: http://www.w3.org/2001/XMLSchema#integer
types: TypeDefinition
  name: boolean
  definition uri: https://w3id.org/linkml/Boolean
  description: A binary (true or false) value
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "boolean".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Boolean
  base: Bool
  uri: http://www.w3.org/2001/XMLSchema#boolean
  repr: bool
types: TypeDefinition
  name: float
  definition uri: https://w3id.org/linkml/Float
  description: A real number that conforms to the xsd:float specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "float".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Float
  base: float
  uri: http://www.w3.org/2001/XMLSchema#float
types: TypeDefinition
  name: double
  definition uri: https://w3id.org/linkml/Double
  description: A real number that conforms to the xsd:double specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "double".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  close mappings: schema:Float
  base: float
  uri: http://www.w3.org/2001/XMLSchema#double
types: TypeDefinition
  name: decimal
  definition uri: https://w3id.org/linkml/Decimal
  description: A real number with arbitrary precision that conforms to the xsd:decimal specification
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "decimal".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  broad mappings: schema:Number
  base: Decimal
  uri: http://www.w3.org/2001/XMLSchema#decimal
types: TypeDefinition
  name: time
  definition uri: https://w3id.org/linkml/Time
  description: A time object represents a (local) time of day, independent of any particular day
  notes: URI is dateTime because OWL reasoners do not work with straight date or time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "time".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Time
  base: XSDTime
  uri: http://www.w3.org/2001/XMLSchema#time
  repr: str
types: TypeDefinition
  name: date
  definition uri: https://w3id.org/linkml/Date
  description: a date (year, month and day) in an idealized calendar
  notes: URI is dateTime because OWL reasoners don't work with straight date or time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:Date
  base: XSDDate
  uri: http://www.w3.org/2001/XMLSchema#date
  repr: str
types: TypeDefinition
  name: datetime
  definition uri: https://w3id.org/linkml/Datetime
  description: The combination of a date and time
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "datetime".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  exact mappings: schema:DateTime
  base: XSDDateTime
  uri: http://www.w3.org/2001/XMLSchema#dateTime
  repr: str
types: TypeDefinition
  name: date_or_datetime
  definition uri: https://w3id.org/linkml/DateOrDatetime
  description: Either a date or a datetime
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "date_or_datetime".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: str
  uri: https://w3id.org/linkml/DateOrDatetime
  repr: str
types: TypeDefinition
  name: uriorcurie
  definition uri: https://w3id.org/linkml/Uriorcurie
  description: a URI or a CURIE
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uriorcurie".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: URIorCURIE
  uri: http://www.w3.org/2001/XMLSchema#anyURI
  repr: str
types: TypeDefinition
  name: curie
  definition uri: https://w3id.org/linkml/Curie
  conforms to: https://www.w3.org/TR/curie/
  description: a compact URI
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "curie".
  comments: in RDF serializations this MUST be expanded to a URI
  comments: in non-RDF serializations MAY be serialized as the compact representation
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: Curie
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
types: TypeDefinition
  name: uri
  definition uri: https://w3id.org/linkml/Uri
  conforms to: https://www.ietf.org/rfc/rfc3987.txt
  description: a complete URI
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "uri".
  comments: in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  close mappings: schema:URL
  base: URI
  uri: http://www.w3.org/2001/XMLSchema#anyURI
  repr: str
types: TypeDefinition
  name: ncname
  definition uri: https://w3id.org/linkml/Ncname
  description: Prefix part of CURIE
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "ncname".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: NCName
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
types: TypeDefinition
  name: objectidentifier
  definition uri: https://w3id.org/linkml/Objectidentifier
  description: A URI or CURIE that represents an object in the model.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "objectidentifier".
  comments: Used for inheritance and type checking
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: ElementIdentifier
  uri: http://www.w3.org/ns/shex#iri
  repr: str
types: TypeDefinition
  name: nodeidentifier
  definition uri: https://w3id.org/linkml/Nodeidentifier
  description: A URI, CURIE or BNODE that represents a node in a model.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "nodeidentifier".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: NodeIdentifier
  uri: http://www.w3.org/ns/shex#nonLiteral
  repr: str
types: TypeDefinition
  name: jsonpointer
  definition uri: https://w3id.org/linkml/Jsonpointer
  conforms to: https://datatracker.ietf.org/doc/html/rfc6901
  description: A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpointer".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: str
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
types: TypeDefinition
  name: jsonpath
  definition uri: https://w3id.org/linkml/Jsonpath
  conforms to: https://www.ietf.org/archive/id/draft-goessner-dispatch-jsonpath-00.html
  description: A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
  notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "jsonpath".
  from schema: https://w3id.org/linkml/types
  imported from: linkml:types
  base: str
  uri: http://www.w3.org/2001/XMLSchema#string
  repr: str
slots: SlotDefinition
classes: ClassDefinition
metamodel version: 1.7.0
source file: tomography.yaml
source file date: 2025-12-05T16:03:40
source file size: 1580
generation date: 2025-12-05T16:06:41

TypeDefinition
name: sparqlpath
definition uri: https://w3id.org/linkml/Sparqlpath
conforms to: https://www.w3.org/TR/sparql11-query/#propertypaths
description: A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
notes: If you are authoring schemas in LinkML YAML, the type is referenced with the lower case "sparqlpath".
from schema: https://w3id.org/linkml/types
imported from: linkml:types
base: str
uri: http://www.w3.org/2001/XMLSchema#string
repr: str

name: AcquisitionTechnique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisitionTechnique
from schema: https://w3id.org/oscem-schemas/latest/acquisition
permissible values:
  text: spa
permissible values:
  text: subtomo
permissible values:
  text: env_tomo
permissible values:
  text: cellular_tomo

SlotDefinition
name: tilt_axis_angle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_axis_angle
description: The tilt axis angle of a tomography series
from schema: https://w3id.org/oscem-schemas/latest/tomography
slot uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_axis_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
range: float

SlotDefinition
name: tilt_angle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_angle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/oscem-schemas/latest/tomography
slot uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
range: TiltAngle
inlined: true
inlined as list: true

SlotDefinition
name: name
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesname
description: The name of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesname
owner: Detector
domain of: Detector
range: string

SlotDefinition
name: description
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescription
description: The description of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescription
range: string

SlotDefinition
name: manufacturer
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesmanufacturer
description: The name of the manufacturer
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmanufacturer
range: string

SlotDefinition
name: model
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmodel
owner: EnergyFilter
domain of: EnergyFilter
range: string

SlotDefinition
name: minimal
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesminimal
description: Minimal value of a given dataset property
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesminimal
owner: Range
domain of: Range
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: maximal
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesmaximal
description: Maximal value of a given dataset property
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmaximal
owner: Range
domain of: Range
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: increment
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesincrement
description: Increment between elements of a series
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesincrement
owner: Series
domain of: Series
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: width
definition uri: https://w3id.org/oscem-schemas/latest/custom_typeswidth
description: The width of a given item - unit depends on item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typeswidth
owner: ImageSize
domain of: ImageSize
range: integer

SlotDefinition
name: height
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesheight
description: The height of a given item - unit depends on item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesheight
owner: ImageSize
domain of: ImageSize
range: integer

SlotDefinition
name: x_min
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesx_min
description: minimum x
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesx_min
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: x_max
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesx_max
description: maximum x
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesx_max
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: y_min
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesy_min
description: minimum y
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesy_min
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: y_max
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesy_max
description: maximum y
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesy_max
owner: BoundingBox2D
domain of: BoundingBox2D
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: unit
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: http://example.org/UNKNOWN/qudt/hasUnit
slot uri: http://example.org/UNKNOWN/qudt/hasUnit
owner: QuantityValue
domain of: QuantityValue
range: string

SlotDefinition
name: value
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: http://example.org/UNKNOWN/qudt/hasQuantityKind
slot uri: http://example.org/UNKNOWN/qudt/hasQuantityKind
owner: QuantityValue
domain of: QuantityValue
range: float

SlotDefinition
name: descriptors
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptors
description: List of custom descriptors for user-defined key-value pairs describing how movies were obtained or any related information
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptors
range: Descriptors
multivalued: true
inlined: true
inlined as list: true

SlotDefinition
name: descriptor_name
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_name
description: Name defining the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_name
owner: Descriptor
domain of: Descriptor
range: string

SlotDefinition
name: descriptor_thing
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_thing
description: Description of the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_thing
owner: Descriptor
domain of: Descriptor
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: valueSI
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesvalueSI
description: value of a given field in respect to its SI unit
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesvalueSI
owner: QuantitySI
domain of: QuantitySI
range: float

SlotDefinition
name: unitSI
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesunitSI
description: the SI unit attached to a si value
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesunitSI
owner: QuantitySI
domain of: QuantitySI
range: string

SlotDefinition
name: technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Specifies which Acquisition subschema/class is in use.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: screen_current
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionscreen_current
description: The total electron beam current hitting the viewing screen, in nA.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionscreen_current
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: nominal_defocus
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionnominal_defocus
description: Target defocus set, min and max values in nm.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionnominal_defocus
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true
inlined as list: true

SlotDefinition
name: calibrated_defocus
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioncalibrated_defocus
description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioncalibrated_defocus
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true
inlined as list: true

SlotDefinition
name: nominal_magnification
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionnominal_magnification
description: Magnification level as indicated by the instrument, no unit
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionnominal_magnification
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: calibrated_magnification
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioncalibrated_magnification
description: Calculated magnification, no unit
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioncalibrated_magnification
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: holder
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionholder
description: Speciman holder model
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionholder
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: holder_cryogen
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionholder_cryogen
description: Type of cryogen used in the holder - if the holder is cooled seperately
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionholder_cryogen
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: temperature_range
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontemperature_range
description: Temperature during data collection, in K with min and max values.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontemperature
alias: temperature
owner: Acquisition
domain of: Acquisition
range: Range
inlined: true
inlined as list: true

SlotDefinition
name: microscope_software
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionmicroscope_software
description: Software used for instrument control,
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionmicroscope_software
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: dose_per_movie
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondose_per_movie
description: Average dose per image/movie/tilt - given in electrons per square Angstrom
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondose_per_movie
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: energy_filter
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionenergy_filter
description: Whether an energy filter was used and its specifics.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionenergy_filter
owner: Acquisition
domain of: Acquisition
range: EnergyFilter
inlined: true
inlined as list: true

SlotDefinition
name: detectors
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
owner: Acquisition
domain of: Acquisition
range: Detector
multivalued: true
inlined: true
inlined as list: true

SlotDefinition
name: used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionused
owner: ChromaticAberrationCorrector
domain of: EnergyFilter
domain of: Phaseplate
domain of: SphericalAberrationCorrector
domain of: ChromaticAberrationCorrector
range: boolean

SlotDefinition
name: image_size
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionimage_size
description: The size of the image in pixels, height and width given.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimage_size
owner: Acquisition
domain of: Acquisition
range: ImageSize
inlined: true
inlined as list: true

SlotDefinition
name: date_time
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondate_time
description: Time and date of the data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondate_time
owner: Acquisition
domain of: Acquisition
range: datetime

SlotDefinition
name: exposure_time
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionexposure_time
description: Time of data acquisition per movie/tilt - in s
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionexposure_time
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: cryogen
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioncryogen
description: Cryogen used in cooling the instrument and sample, usually nitrogen
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioncryogen
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: frames_per_movie
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionframes_per_movie
description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionframes_per_movie
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: grids_imaged
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiongrids_imaged
description: Number of grids imaged for this project - here with qualifier during this data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiongrids_imaged
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: images_generated
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionimages_generated
description: Number of images generated total for this data collection - might need a qualifier for tilt series to determine whether full series or individual tilts are counted
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimages_generated
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: binning_camera
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionbinning_camera
description: Level of binning on the images applied during data collection
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbinning_camera
owner: Acquisition
domain of: Acquisition
range: ImageSize
inlined: true
inlined as list: true

SlotDefinition
name: pixel_size
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionpixel_size
description: Pixel size, in Angstrom
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionpixel_size
owner: Acquisition
domain of: Acquisition
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: specialist_optics
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionspecialist_optics
description: Any type of special optics, such as a phaseplate
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionspecialist_optics
owner: Acquisition
domain of: Acquisition
range: SpecialistOptics
inlined: true
inlined as list: true

SlotDefinition
name: phaseplate
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionphaseplate
description: Phaseplate is a special optics device that can be used to enhance contrast
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionphaseplate
owner: SpecialistOptics
domain of: SpecialistOptics
range: Phaseplate
inlined: true
inlined as list: true

SlotDefinition
name: instrument_type
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
owner: ChromaticAberrationCorrector
domain of: Phaseplate
domain of: SphericalAberrationCorrector
domain of: ChromaticAberrationCorrector
range: string

SlotDefinition
name: spherical_aberration_corrector
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionspherical_aberration_corrector
description: Specialist device to correct for spherical aberration of the microscope lenses
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionspherical_aberration_corrector
owner: SpecialistOptics
domain of: SpecialistOptics
range: SphericalAberrationCorrector
inlined: true
inlined as list: true

SlotDefinition
name: chromatic_aberration_corrector
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionchromatic_aberration_corrector
description: Specialist device to correct for chromatic aberration of the microscope lenses
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionchromatic_aberration_corrector
owner: SpecialistOptics
domain of: SpecialistOptics
range: ChromaticAberrationCorrector
inlined: true
inlined as list: true

SlotDefinition
name: beamshift
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamshift
description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: beamtilt
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtilt
description: Another way to move the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtilt
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: imageshift
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionimageshift
description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionimageshift
owner: Acquisition
domain of: Acquisition
range: BoundingBox2D
inlined: true
inlined as list: true

SlotDefinition
name: beamtiltgroups
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtiltgroups
description: Number of Beamtilt groups present in this dataset - for optimized processing split dataset into groups of same tilt angle. Despite its name Beamshift is often used to achive this result.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbeamtiltgroups
owner: Acquisition
domain of: Acquisition
range: integer

SlotDefinition
name: gainref_flip_rotate
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiongainref_flip_rotate
description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiongainref_flip_rotate
owner: Acquisition
domain of: Acquisition
range: string

SlotDefinition
name: width_energy_filter
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionwidth_energy_filter
description: Width of the energy filter used.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionwidth_energy_filter
owner: EnergyFilter
domain of: EnergyFilter
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: mode
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionmode
description: Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionmode
owner: Detector
domain of: Detector
range: string

SlotDefinition
name: dispersion
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondispersion
description: Dispersion of an analytical detector, in eV
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondispersion
owner: Detector
domain of: Detector
range: QuantitySI
inlined: true
inlined as list: true

SlotDefinition
name: collection_angle
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioncollection_angle
description: Collection angle set, min and max values in mrad.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioncollection_angle
owner: Detector
domain of: Detector
range: Range
inlined: true
inlined as list: true

SlotDefinition
name: TiltAngle_minimal
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesminimal
description: Minimal value of a given dataset property
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: minimal
domain: TiltAngle
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesminimal
alias: minimal
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: minimal
range: QuantitySI
required: true
inlined: true
inlined as list: true

SlotDefinition
name: TiltAngle_maximal
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesmaximal
description: Maximal value of a given dataset property
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: maximal
domain: TiltAngle
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmaximal
alias: maximal
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: maximal
range: QuantitySI
required: true
inlined: true
inlined as list: true

SlotDefinition
name: TiltAngle_increment
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesincrement
description: Increment between elements of a series
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: increment
domain: TiltAngle
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesincrement
alias: increment
owner: TiltAngle
domain of: TiltAngle
is usage slot: true
usage slot name: increment
range: QuantitySI
required: true
inlined: true
inlined as list: true

SlotDefinition
name: AcquisitionTomo_tilt_axis_angle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_axis_angle
description: The tilt axis angle of a tomography series
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: tilt_axis_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_axis_angle
alias: tilt_axis_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
is usage slot: true
usage slot name: tilt_axis_angle
range: float
required: true

SlotDefinition
name: AcquisitionTomo_tilt_angle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_angle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: tilt_angle
domain: AcquisitionTomo
slot uri: https://w3id.org/oscem-schemas/latest/tomography/tilt_angle
alias: tilt_angle
owner: AcquisitionTomo
domain of: AcquisitionTomo
is usage slot: true
usage slot name: tilt_angle
range: TiltAngle
required: true
inlined: true
inlined as list: true

SlotDefinition
name: AcquisitionSubTomo_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Subtomogram averaging
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: technique
domain: AcquisitionSubTomo
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
alias: technique
owner: AcquisitionSubTomo
domain of: AcquisitionSubTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: subtomo

SlotDefinition
name: AcquisitionEnvTomo_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Environmental tomography
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: technique
domain: AcquisitionEnvTomo
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
alias: technique
owner: AcquisitionEnvTomo
domain of: AcquisitionEnvTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: env_tomo

SlotDefinition
name: AcquisitionCelTomo_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Cellular tomography
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: technique
domain: AcquisitionCelTomo
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
alias: technique
owner: AcquisitionCelTomo
domain of: AcquisitionCelTomo
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: cellular_tomo

SlotDefinition
name: QuantityValue_unit
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesunit
description: the unit of a given value
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: http://example.org/UNKNOWN/qudt/hasUnit
is a: unit
domain: QuantityValue
slot uri: http://example.org/UNKNOWN/qudt/hasUnit
alias: unit
owner: QuantityValue
domain of: QuantityValue
is usage slot: true
usage slot name: unit
range: string
required: true

SlotDefinition
name: QuantityValue_value
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesvalue
description: the value of a field with a unit
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: http://example.org/UNKNOWN/qudt/hasQuantityKind
is a: value
domain: QuantityValue
slot uri: http://example.org/UNKNOWN/qudt/hasQuantityKind
alias: value
owner: QuantityValue
domain of: QuantityValue
is usage slot: true
usage slot name: value
range: float
required: true

SlotDefinition
name: Descriptor_descriptor_name
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_name
description: Name defining the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: descriptor_name
domain: Descriptor
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_name
alias: descriptor_name
owner: Descriptor
domain of: Descriptor
is usage slot: true
usage slot name: descriptor_name
range: string
required: true

SlotDefinition
name: Descriptor_descriptor_thing
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_thing
description: Description of the descriptor
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: descriptor_thing
domain: Descriptor
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesdescriptor_thing
alias: descriptor_thing
owner: Descriptor
domain of: Descriptor
is usage slot: true
usage slot name: descriptor_thing
range: Any
inlined: true
inlined as list: true

SlotDefinition
name: Acquisition_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Specifies which Acquisition subschema/class is in use.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: technique
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
alias: technique
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: technique
range: string

SlotDefinition
name: Acquisition_detectors
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: detectors
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondetectors
alias: detectors
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: detectors
range: Detector
required: true
multivalued: true
inlined: true
inlined as list: true

SlotDefinition
name: Acquisition_date_time
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiondate_time
description: Time and date of the data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: date_time
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiondate_time
alias: date_time
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: date_time
range: datetime
required: true

SlotDefinition
name: Acquisition_binning_camera
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionbinning_camera
description: Level of binning on the images applied during data collection
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: binning_camera
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionbinning_camera
alias: binning_camera
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: binning_camera
range: ImageSize
required: true
inlined: true
inlined as list: true

SlotDefinition
name: Acquisition_pixel_size
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionpixel_size
description: Pixel size, in Angstrom
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: pixel_size
domain: Acquisition
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionpixel_size
alias: pixel_size
owner: Acquisition
domain of: Acquisition
is usage slot: true
usage slot name: pixel_size
range: QuantitySI
required: true
inlined: true
inlined as list: true

SlotDefinition
name: AcquisitionSpa_technique
definition uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
description: Single particle acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition_technique
domain: AcquisitionSpa
slot uri: https://w3id.org/oscem-schemas/latest/acquisitiontechnique
alias: technique
owner: AcquisitionSpa
domain of: AcquisitionSpa
is usage slot: true
usage slot name: technique
range: string
required: true
equals string: spa

SlotDefinition
name: EnergyFilter_used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionused
alias: used
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: EnergyFilter_model
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesmodel
description: The model of the item
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: model
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/custom_typesmodel
alias: model
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: model
range: string

SlotDefinition
name: EnergyFilter_width_energy_filter
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionwidth_energy_filter
description: Width of the energy filter used.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: width_energy_filter
domain: EnergyFilter
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionwidth_energy_filter
alias: width_energy_filter
owner: EnergyFilter
domain of: EnergyFilter
is usage slot: true
usage slot name: width_energy_filter
range: QuantitySI
required: true
inlined: true
inlined as list: true

SlotDefinition
name: Phaseplate_used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: Phaseplate
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionused
alias: used
owner: Phaseplate
domain of: Phaseplate
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: Phaseplate_instrument_type
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
description: Type of phaseplate
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: Phaseplate
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
alias: instrument_type
owner: Phaseplate
domain of: Phaseplate
is usage slot: true
usage slot name: instrument_type
range: string
required: true

SlotDefinition
name: SphericalAberrationCorrector_used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionused
alias: used
owner: SphericalAberrationCorrector
domain of: SphericalAberrationCorrector
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: SphericalAberrationCorrector_instrument_type
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: SphericalAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
alias: instrument_type
owner: SphericalAberrationCorrector
domain of: SphericalAberrationCorrector
is usage slot: true
usage slot name: instrument_type
range: string
required: true

SlotDefinition
name: ChromaticAberrationCorrector_used
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionused
description: whether a specific instrument was used during data acquisition
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: used
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/acquisitionused
alias: used
owner: ChromaticAberrationCorrector
domain of: ChromaticAberrationCorrector
is usage slot: true
usage slot name: used
range: boolean
required: true

SlotDefinition
name: ChromaticAberrationCorrector_instrument_type
definition uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
description: Details of a given specialist instrument
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: instrument_type
domain: ChromaticAberrationCorrector
slot uri: https://w3id.org/oscem-schemas/latest/acquisitioninstrument_type
alias: instrument_type
owner: ChromaticAberrationCorrector
domain of: ChromaticAberrationCorrector
is usage slot: true
usage slot name: instrument_type
range: string
required: true

ClassDefinition
name: TiltAngle
definition uri: https://w3id.org/oscem-schemas/latest/tomography/TiltAngle
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: Series
slots: TiltAngle_minimal
slots: TiltAngle_maximal
slots: TiltAngle_increment
class uri: https://w3id.org/oscem-schemas/latest/tomography/TiltAngle

ClassDefinition
name: AcquisitionTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionTomo
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: Acquisition
slots: Acquisition_technique
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
class uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionTomo

ClassDefinition
name: AcquisitionSubTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionSubTomo
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionSubTomo_technique
class uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionSubTomo

ClassDefinition
name: AcquisitionEnvTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionEnvTomo
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionEnvTomo_technique
class uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionEnvTomo

ClassDefinition
name: AcquisitionCelTomo
definition uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionCelTomo
from schema: https://w3id.org/oscem-schemas/latest/tomography
is a: AcquisitionTomo
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionTomo_tilt_axis_angle
slots: AcquisitionTomo_tilt_angle
slots: AcquisitionCelTomo_technique
class uri: https://w3id.org/oscem-schemas/latest/tomography/AcquisitionCelTomo

ClassDefinition
name: Any
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesAny
description: Any type, used as the base for type-narrowing.
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: linkml:Any
class uri: https://w3id.org/linkml/Any

ClassDefinition
name: Range
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesRange
description: A range constructed from min and max
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slots: minimal
slots: maximal
class uri: https://w3id.org/oscem-schemas/latest/custom_typesRange

ClassDefinition
name: Series
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesSeries
description: A series of numbers constructed from min, max, and increment
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: Range
slots: minimal
slots: maximal
slots: increment
class uri: https://w3id.org/oscem-schemas/latest/custom_typesSeries

ClassDefinition
name: ImageSize
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesImageSize
description: size of a 2D image (in integer units)
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slots: height
slots: width
class uri: https://w3id.org/oscem-schemas/latest/custom_typesImageSize

ClassDefinition
name: BoundingBox2D
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesBoundingBox2D
description: an axis-aligned 2D bounding box (float units)
from schema: https://w3id.org/oscem-schemas/latest/custom_types
slots: x_min
slots: x_max
slots: y_min
slots: y_max
class uri: https://w3id.org/oscem-schemas/latest/custom_typesBoundingBox2D

ClassDefinition
name: QuantityValue
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesQuantityValue
description: if a value has a unit, it should be given as a unit value pair.
from schema: https://w3id.org/oscem-schemas/latest/custom_types
mappings: qudt:quantityValue
slots: QuantityValue_unit
slots: QuantityValue_value
class uri: http://example.org/UNKNOWN/qudt/quantityValue

ClassDefinition
name: QuantitySI
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesQuantitySI
description: unit value extended to have two additional fields si_value and si_unit
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: QuantityValue
slots: QuantityValue_unit
slots: QuantityValue_value
slots: valueSI
slots: unitSI
class uri: https://w3id.org/oscem-schemas/latest/custom_typesQuantitySI

ClassDefinition
name: Descriptor
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesDescriptor
description: List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
from schema: https://w3id.org/oscem-schemas/latest/custom_types
abstract: true
slots: Descriptor_descriptor_name
slots: Descriptor_descriptor_thing
class uri: https://w3id.org/oscem-schemas/latest/custom_typesDescriptor

ClassDefinition
name: Descriptors
definition uri: https://w3id.org/oscem-schemas/latest/custom_typesDescriptors
from schema: https://w3id.org/oscem-schemas/latest/custom_types
is a: Descriptor
slots: Descriptor_descriptor_name
slots: Descriptor_descriptor_thing
class uri: https://w3id.org/oscem-schemas/latest/custom_typesDescriptors

ClassDefinition
name: Acquisition
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisition
description: General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: Acquisition_technique
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
class uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisition

ClassDefinition
name: AcquisitionSpa
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisitionSpa
from schema: https://w3id.org/oscem-schemas/latest/acquisition
is a: Acquisition
slots: screen_current
slots: nominal_defocus
slots: calibrated_defocus
slots: nominal_magnification
slots: calibrated_magnification
slots: holder
slots: holder_cryogen
slots: temperature_range
slots: microscope_software
slots: Acquisition_detectors
slots: dose_per_movie
slots: energy_filter
slots: image_size
slots: Acquisition_date_time
slots: exposure_time
slots: cryogen
slots: frames_per_movie
slots: grids_imaged
slots: images_generated
slots: Acquisition_binning_camera
slots: Acquisition_pixel_size
slots: specialist_optics
slots: beamshift
slots: beamtilt
slots: imageshift
slots: beamtiltgroups
slots: gainref_flip_rotate
slots: AcquisitionSpa_technique
class uri: https://w3id.org/oscem-schemas/latest/acquisitionAcquisitionSpa

ClassDefinition
name: EnergyFilter
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionEnergyFilter
description: A device used to filter for electrons with specific energy.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: EnergyFilter_used
slots: EnergyFilter_model
slots: EnergyFilter_width_energy_filter
class uri: https://w3id.org/oscem-schemas/latest/acquisitionEnergyFilter

ClassDefinition
name: SpecialistOptics
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionSpecialistOptics
description: Optional optics used to correct for instrument limitations.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: phaseplate
slots: spherical_aberration_corrector
slots: chromatic_aberration_corrector
class uri: https://w3id.org/oscem-schemas/latest/acquisitionSpecialistOptics

ClassDefinition
name: Phaseplate
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionPhaseplate
description: Used to modulate the phase of the electron wave.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: Phaseplate_used
slots: Phaseplate_instrument_type
class uri: https://w3id.org/oscem-schemas/latest/acquisitionPhaseplate

ClassDefinition
name: SphericalAberrationCorrector
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionSphericalAberrationCorrector
description: Special device used to correct instrument inherent spherical aberration.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: SphericalAberrationCorrector_used
slots: SphericalAberrationCorrector_instrument_type
class uri: https://w3id.org/oscem-schemas/latest/acquisitionSphericalAberrationCorrector

ClassDefinition
name: ChromaticAberrationCorrector
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionChromaticAberrationCorrector
description: Special device used to correct instrument inherent chromatic aberration.
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: ChromaticAberrationCorrector_used
slots: ChromaticAberrationCorrector_instrument_type
class uri: https://w3id.org/oscem-schemas/latest/acquisitionChromaticAberrationCorrector

ClassDefinition
name: Detector
definition uri: https://w3id.org/oscem-schemas/latest/acquisitionDetector
description: Class representing a detector
from schema: https://w3id.org/oscem-schemas/latest/acquisition
slots: name
slots: mode
slots: dispersion
slots: collection_angle
class uri: https://w3id.org/oscem-schemas/latest/acquisitionDetector