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Class: ImagingProtocol

Protocol for imaging-based assays (CBF, ASL, MCC). Captures frame rate, duration, resolution, and tracer/labeling details.

URI: soma:ImagingProtocol

 classDiagram
    class ImagingProtocol
    click ImagingProtocol href "../ImagingProtocol/"
      Protocol <|-- ImagingProtocol
        click Protocol href "../Protocol/"

      ImagingProtocol : description

      ImagingProtocol : equipment_required

      ImagingProtocol : evaporation_prevention

      ImagingProtocol : fluorescent_labeling

      ImagingProtocol : fluorescent_tracer

      ImagingProtocol : humidity_control





        ImagingProtocol --> "0..1" QuantityValue : humidity_control
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : id

      ImagingProtocol : imaging_duration





        ImagingProtocol --> "0..1" QuantityValue : imaging_duration
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : imaging_frame_rate





        ImagingProtocol --> "0..1" QuantityValue : imaging_frame_rate
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : institution

      ImagingProtocol : last_updated

      ImagingProtocol : name

      ImagingProtocol : particle_size





        ImagingProtocol --> "0..1" QuantityValue : particle_size
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : particle_tracking_method

      ImagingProtocol : protocol_author

      ImagingProtocol : protocol_type

      ImagingProtocol : protocol_version

      ImagingProtocol : publication_reference

      ImagingProtocol : quality_control_criteria

      ImagingProtocol : replicate_requirements

      ImagingProtocol : spatial_resolution





        ImagingProtocol --> "0..1" QuantityValue : spatial_resolution
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : sub_protocols





        ImagingProtocol --> "*" Protocol : sub_protocols
        click Protocol href "../Protocol/"



      ImagingProtocol : temperature_control





        ImagingProtocol --> "0..1" QuantityValue : temperature_control
        click QuantityValue href "../QuantityValue/"



      ImagingProtocol : validation_status

Inheritance

Slots

Name Cardinality and Range Description Inheritance
imaging_frame_rate 0..1
QuantityValue		 Frame rate for video/imaging acquisition (e direct
imaging_duration 0..1
QuantityValue		 Duration of imaging session direct
spatial_resolution 0..1
QuantityValue		 Spatial resolution of imaging (e direct
fluorescent_labeling 0..1
String		 Fluorescent label or tracer used direct
fluorescent_tracer 0..1
String		 Fluorescent tracer used for tracking (MCC assays) direct
evaporation_prevention 0..1
String		 Method used to prevent evaporation (e direct
particle_tracking_method 0..1
String		 Method used for tracking particles or mucus direct
temperature_control 0..1
QuantityValue		 Temperature conditions during the procedure (e direct
humidity_control 0..1
QuantityValue		 Humidity conditions during the procedure direct
particle_size 0..1
QuantityValue		 Size of tracking particles direct
protocol_type 0..1
String		 The specific type of protocol Protocol
protocol_version 0..1
String		 Version of the protocol Protocol
equipment_required *
String		 Equipment required for this protocol Protocol
sub_protocols *
Protocol		 Other protocols that are part of this protocol's workflow Protocol
quality_control_criteria 0..1
String		 Quality control acceptance criteria Protocol
replicate_requirements 0..1
Integer		 Number of replicates required Protocol
protocol_author 0..1
String		 Author of the protocol Protocol
institution 0..1
String		 Institution where protocol was developed Protocol
publication_reference 0..1
String		 Reference to protocol publication Protocol
last_updated 0..1
Date		 Date protocol was last updated Protocol
validation_status 0..1
String		 Validation status of the protocol Protocol
id 1
Uriorcurie		 A unique identifier for the entity NamedThing
name 0..1
String		 A human-readable name for the entity NamedThing
description 0..1
String		 A detailed description of the entity NamedThing

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/EHS-Data-Standards/soma

Mappings

Mapping Type Mapped Value
self soma:ImagingProtocol
native soma:ImagingProtocol

LinkML Source

Direct

name: ImagingProtocol
description: Protocol for imaging-based assays (CBF, ASL, MCC). Captures frame rate,
  duration, resolution, and tracer/labeling details.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Protocol
slots:
- imaging_frame_rate
- imaging_duration
- spatial_resolution
- fluorescent_labeling
- fluorescent_tracer
- evaporation_prevention
- particle_tracking_method
- temperature_control
- humidity_control
- particle_size

Induced

name: ImagingProtocol
description: Protocol for imaging-based assays (CBF, ASL, MCC). Captures frame rate,
  duration, resolution, and tracer/labeling details.
from_schema: https://w3id.org/EHS-Data-Standards/soma
is_a: Protocol
attributes:
  imaging_frame_rate:
    name: imaging_frame_rate
    description: Frame rate for video/imaging acquisition (e.g., 200 fps).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: imaging_frame_rate
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  imaging_duration:
    name: imaging_duration
    description: Duration of imaging session.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: imaging_duration
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  spatial_resolution:
    name: spatial_resolution
    description: Spatial resolution of imaging (e.g., 1-2 um axial resolution).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: spatial_resolution
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  fluorescent_labeling:
    name: fluorescent_labeling
    description: Fluorescent label or tracer used.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: fluorescent_labeling
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: string
  fluorescent_tracer:
    name: fluorescent_tracer
    description: Fluorescent tracer used for tracking (MCC assays).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: fluorescent_tracer
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: string
  evaporation_prevention:
    name: evaporation_prevention
    description: Method used to prevent evaporation (e.g., perfluorocarbon overlay).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: evaporation_prevention
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: string
  particle_tracking_method:
    name: particle_tracking_method
    description: Method used for tracking particles or mucus.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: particle_tracking_method
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: string
  temperature_control:
    name: temperature_control
    description: Temperature conditions during the procedure (e.g., 37C).
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: temperature_control
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  humidity_control:
    name: humidity_control
    description: Humidity conditions during the procedure.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: humidity_control
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  particle_size:
    name: particle_size
    description: Size of tracking particles.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: particle_size
    owner: ImagingProtocol
    domain_of:
    - ImagingProtocol
    range: QuantityValue
    inlined: true
  protocol_type:
    name: protocol_type
    description: The specific type of protocol. Used to designate which concrete class
      (e.g., ImagingProtocol, StainingProtocol, SpirometryProtocol, MolecularAssayProtocol)
      is instantiated for polymorphic protocol slots.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    designates_type: true
    alias: protocol_type
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protocol_version
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  equipment_required:
    name: equipment_required
    description: Equipment required for this protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: equipment_required
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
    multivalued: true
  sub_protocols:
    name: sub_protocols
    description: Other protocols that are part of this protocol's workflow. Use this
      to compose protocols from reusable steps (e.g., sample preparation, wash steps,
      fixation, post-processing). Any Protocol or Protocol subclass is valid.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: sub_protocols
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: Protocol
    multivalued: true
    inlined: true
    inlined_as_list: true
  quality_control_criteria:
    name: quality_control_criteria
    description: Quality control acceptance criteria.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: quality_control_criteria
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  replicate_requirements:
    name: replicate_requirements
    description: Number of replicates required.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: replicate_requirements
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: integer
  protocol_author:
    name: protocol_author
    description: Author of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: protocol_author
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  institution:
    name: institution
    description: Institution where protocol was developed.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: institution
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  publication_reference:
    name: publication_reference
    description: Reference to protocol publication.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: publication_reference
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  last_updated:
    name: last_updated
    description: Date protocol was last updated.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: last_updated
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: date
  validation_status:
    name: validation_status
    description: Validation status of the protocol.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    alias: validation_status
    owner: ImagingProtocol
    domain_of:
    - Protocol
    range: string
  id:
    name: id
    description: A unique identifier for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    identifier: true
    alias: id
    owner: ImagingProtocol
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: uriorcurie
    required: true
  name:
    name: name
    description: A human-readable name for the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:name
    alias: name
    owner: ImagingProtocol
    domain_of:
    - NamedThing
    - Unit
    - NamedEntity
    range: string
  description:
    name: description
    description: A detailed description of the entity.
    from_schema: https://w3id.org/EHS-Data-Standards/soma
    rank: 1000
    slot_uri: schema:description
    alias: description
    owner: ImagingProtocol
    domain_of:
    - NamedThing
    range: string