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Class: Micrograph

Motion-corrected micrograph derived from movie

URI: lambdaber:Micrograph

classDiagram class Micrograph click Micrograph href "../Micrograph/" Image2D <|-- Micrograph click Image2D href "../Image2D/" Micrograph : acquisition_date Micrograph : astigmatism Micrograph : astigmatism_angle Micrograph : ctf_quality_score Micrograph : defocus Micrograph : defocus_u Micrograph : defocus_v Micrograph : description Micrograph : dimensions_x Micrograph : dimensions_y Micrograph : dose Micrograph : exposure_time Micrograph : file_name Micrograph : id Micrograph : origin_movie_id Micrograph : pixel_size Micrograph : resolution_fit_limit Micrograph : title

Inheritance

Slots

Name Cardinality and Range Description Inheritance
dose 0..1
Float		 Total electron dose in e-/Angstrom^2 direct
origin_movie_id 0..1
String		 Reference to original movie file direct
defocus_u 0..1
Float		 Defocus U in micrometers direct
defocus_v 0..1
Float		 Defocus V in micrometers direct
astigmatism_angle 0..1
Float		 Astigmatism angle in degrees direct
resolution_fit_limit 0..1
Float		 Resolution fit limit in Angstroms direct
ctf_quality_score 0..1
Float		 CTF estimation quality score direct
defocus 0..1
Float		 Measured defocus in micrometers Image2D
astigmatism 0..1
Float		 Astigmatism in Angstroms Image2D
file_name 1
String		 Image file name Image
acquisition_date 0..1
String		 Date image was acquired Image
pixel_size 0..1
Float		 Final pixel size in Angstroms per pixel Image
dimensions_x 0..1
Integer		 Image width in pixels Image
dimensions_y 0..1
Integer		 Image height in pixels Image
exposure_time 0..1
Float		 Exposure time in seconds Image
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:Micrograph
native lambdaber:Micrograph

LinkML Source

Direct

name: Micrograph
description: Motion-corrected micrograph derived from movie
from_schema: https://w3id.org/lambda-ber-schema/
is_a: Image2D
slot_usage:
  pixel_size:
    name: pixel_size
    description: Final pixel size in Angstroms per pixel
  defocus:
    name: defocus
    description: Measured defocus in micrometers
  astigmatism:
    name: astigmatism
    description: Astigmatism in Angstroms
attributes:
  dose:
    name: dose
    description: Total electron dose in e-/Angstrom^2
    from_schema: https://w3id.org/lambda-ber-schema/
    domain_of:
    - Image
    - Micrograph
    range: float
  origin_movie_id:
    name: origin_movie_id
    description: Reference to original movie file
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: string
  defocus_u:
    name: defocus_u
    description: Defocus U in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: float
  defocus_v:
    name: defocus_v
    description: Defocus V in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: float
  astigmatism_angle:
    name: astigmatism_angle
    description: Astigmatism angle in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: float
  resolution_fit_limit:
    name: resolution_fit_limit
    description: Resolution fit limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: float
  ctf_quality_score:
    name: ctf_quality_score
    description: CTF estimation quality score
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    domain_of:
    - Micrograph
    range: float

Induced

name: Micrograph
description: Motion-corrected micrograph derived from movie
from_schema: https://w3id.org/lambda-ber-schema/
is_a: Image2D
slot_usage:
  pixel_size:
    name: pixel_size
    description: Final pixel size in Angstroms per pixel
  defocus:
    name: defocus
    description: Measured defocus in micrometers
  astigmatism:
    name: astigmatism
    description: Astigmatism in Angstroms
attributes:
  dose:
    name: dose
    description: Total electron dose in e-/Angstrom^2
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: dose
    owner: Micrograph
    domain_of:
    - Image
    - Micrograph
    range: float
  origin_movie_id:
    name: origin_movie_id
    description: Reference to original movie file
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: origin_movie_id
    owner: Micrograph
    domain_of:
    - Micrograph
    range: string
  defocus_u:
    name: defocus_u
    description: Defocus U in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_u
    owner: Micrograph
    domain_of:
    - Micrograph
    range: float
  defocus_v:
    name: defocus_v
    description: Defocus V in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus_v
    owner: Micrograph
    domain_of:
    - Micrograph
    range: float
  astigmatism_angle:
    name: astigmatism_angle
    description: Astigmatism angle in degrees
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: astigmatism_angle
    owner: Micrograph
    domain_of:
    - Micrograph
    range: float
  resolution_fit_limit:
    name: resolution_fit_limit
    description: Resolution fit limit in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: resolution_fit_limit
    owner: Micrograph
    domain_of:
    - Micrograph
    range: float
  ctf_quality_score:
    name: ctf_quality_score
    description: CTF estimation quality score
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: ctf_quality_score
    owner: Micrograph
    domain_of:
    - Micrograph
    range: float
  defocus:
    name: defocus
    description: Measured defocus in micrometers
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: defocus
    owner: Micrograph
    domain_of:
    - Image2D
    range: float
  astigmatism:
    name: astigmatism
    description: Astigmatism in Angstroms
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: astigmatism
    owner: Micrograph
    domain_of:
    - Image2D
    range: float
  file_name:
    name: file_name
    description: Image file name
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: file_name
    owner: Micrograph
    domain_of:
    - DataFile
    - Image
    range: string
    required: true
  acquisition_date:
    name: acquisition_date
    description: Date image was acquired
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: acquisition_date
    owner: Micrograph
    domain_of:
    - Image
    range: string
  pixel_size:
    name: pixel_size
    description: Final pixel size in Angstroms per pixel
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: pixel_size
    owner: Micrograph
    domain_of:
    - Image
    - RefinementParameters
    range: float
  dimensions_x:
    name: dimensions_x
    description: Image width in pixels
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: dimensions_x
    owner: Micrograph
    domain_of:
    - Image
    range: integer
  dimensions_y:
    name: dimensions_y
    description: Image height in pixels
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: dimensions_y
    owner: Micrograph
    domain_of:
    - Image
    range: integer
  exposure_time:
    name: exposure_time
    description: Exposure time in seconds
    from_schema: https://w3id.org/lambda-ber-schema/
    alias: exposure_time
    owner: Micrograph
    domain_of:
    - ExperimentRun
    - Image
    - ExperimentalConditions
    range: float
  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: Micrograph
    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: Micrograph
    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: Micrograph
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string