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Class: ParticlePickingParameters

Parameters specific to particle picking workflows

URI: lambdaber:ParticlePickingParameters

classDiagram class ParticlePickingParameters click ParticlePickingParameters href "../ParticlePickingParameters/" AttributeGroup <|-- ParticlePickingParameters click AttributeGroup href "../AttributeGroup/" ParticlePickingParameters : box_size ParticlePickingParameters : description ParticlePickingParameters : model_file_path ParticlePickingParameters : model_name ParticlePickingParameters : model_source ParticlePickingParameters : ncc_score ParticlePickingParameters : picking_method ParticlePickingParameters : power_score ParticlePickingParameters : threshold

Inheritance

Slots

Name Cardinality and Range Description Inheritance
picking_method 0..1
String		 Method used (manual, template_matching, deep_learning, LoG, Topaz, other) direct
box_size 0..1
Integer		 Particle box size in pixels direct
threshold 0..1
Float		 Picking threshold direct
power_score 0..1
Float		 Power score threshold direct
ncc_score 0..1
Float		 Normalized cross-correlation score threshold direct
model_name 0..1
String		 Name or identifier of the deep learning model (e direct
model_file_path 0..1
String		 Path to deep learning model file if using a local or custom trained model fil... direct
model_source 0..1
String		 Source or software associated with the model (e direct
description 0..1
String		 AttributeGroup

Usages

used by used in type used
WorkflowRun particle_picking_params range ParticlePickingParameters

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type Mapped Value
self lambdaber:ParticlePickingParameters
native lambdaber:ParticlePickingParameters

LinkML Source

Direct

name: ParticlePickingParameters
description: Parameters specific to particle picking workflows
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  picking_method:
    name: picking_method
    description: Method used (manual, template_matching, deep_learning, LoG, Topaz,
      other)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: string
  box_size:
    name: box_size
    description: Particle box size in pixels
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    - RefinementParameters
    range: integer
  threshold:
    name: threshold
    description: Picking threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: float
  power_score:
    name: power_score
    description: Power score threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: float
  ncc_score:
    name: ncc_score
    description: Normalized cross-correlation score threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: float
  model_name:
    name: model_name
    description: Name or identifier of the deep learning model (e.g., 'resnet16',
      'resnet8', 'cryolo_general'). Use this for standard pretrained models. Either
      model_name or model_file_path should be provided when using deep learning methods.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: string
  model_file_path:
    name: model_file_path
    description: Path to deep learning model file if using a local or custom trained
      model file. Use this instead of model_name when pointing to a specific file
      on disk. Either model_name or model_file_path should be provided when using
      deep learning methods.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: string
  model_source:
    name: model_source
    description: Source or software associated with the model (e.g., 'topaz', 'cryolo',
      'warp', 'custom', 'pretrained'). Helps track model provenance and should be
      provided alongside model_name or model_file_path to document which software/framework
      the model is for.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - ParticlePickingParameters
    range: string

Induced

name: ParticlePickingParameters
description: Parameters specific to particle picking workflows
from_schema: https://w3id.org/lambda-ber-schema/
is_a: AttributeGroup
attributes:
  picking_method:
    name: picking_method
    description: Method used (manual, template_matching, deep_learning, LoG, Topaz,
      other)
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: picking_method
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: string
  box_size:
    name: box_size
    description: Particle box size in pixels
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: box_size
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    - RefinementParameters
    range: integer
  threshold:
    name: threshold
    description: Picking threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: threshold
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: float
  power_score:
    name: power_score
    description: Power score threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: power_score
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: float
  ncc_score:
    name: ncc_score
    description: Normalized cross-correlation score threshold
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ncc_score
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: float
  model_name:
    name: model_name
    description: Name or identifier of the deep learning model (e.g., 'resnet16',
      'resnet8', 'cryolo_general'). Use this for standard pretrained models. Either
      model_name or model_file_path should be provided when using deep learning methods.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: model_name
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: string
  model_file_path:
    name: model_file_path
    description: Path to deep learning model file if using a local or custom trained
      model file. Use this instead of model_name when pointing to a specific file
      on disk. Either model_name or model_file_path should be provided when using
      deep learning methods.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: model_file_path
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: string
  model_source:
    name: model_source
    description: Source or software associated with the model (e.g., 'topaz', 'cryolo',
      'warp', 'custom', 'pretrained'). Helps track model provenance and should be
      provided alongside model_name or model_file_path to document which software/framework
      the model is for.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: model_source
    owner: ParticlePickingParameters
    domain_of:
    - ParticlePickingParameters
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: description
    owner: ParticlePickingParameters
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string