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Class: AcquisitionEnvTomo

URI: https://w3id.org/osc-em/oscem-schemas-env-tomo/:AcquisitionEnvTomo

erDiagram AcquisitionEnvTomo { string technique float tilt_axis_angle integer nominal_magnification integer calibrated_magnification string holder string holder_cryogen string microscope_software datetime date_time string cryogen integer frames_per_movie integer grids_imaged integer images_generated integer beamtiltgroups string gainref_flip_rotate } BoundingBox2D { } QuantitySI { float valueSI string unitSI string unit float value } SpecialistOptics { } ChromaticAberrationCorrector { boolean used string instrument_type } SphericalAberrationCorrector { boolean used string instrument_type } Phaseplate { boolean used string instrument_type } ImageSize { integer height integer width } EnergyFilter { boolean used string model } Detector { string name string mode } Range { } TiltAngle { } AcquisitionEnvTomo ||--|| TiltAngle : "tilt_angle" AcquisitionEnvTomo ||--|o QuantitySI : "screen_current" AcquisitionEnvTomo ||--|o Range : "nominal_defocus" AcquisitionEnvTomo ||--|o Range : "calibrated_defocus" AcquisitionEnvTomo ||--|o Range : "temperature_range" AcquisitionEnvTomo ||--}| Detector : "detectors" AcquisitionEnvTomo ||--|o QuantitySI : "dose_per_movie" AcquisitionEnvTomo ||--|o EnergyFilter : "energy_filter" AcquisitionEnvTomo ||--|o ImageSize : "image_size" AcquisitionEnvTomo ||--|o QuantitySI : "exposure_time" AcquisitionEnvTomo ||--|| ImageSize : "binning_camera" AcquisitionEnvTomo ||--|| QuantitySI : "pixel_size" AcquisitionEnvTomo ||--|o SpecialistOptics : "specialist_optics" AcquisitionEnvTomo ||--|o BoundingBox2D : "beamshift" AcquisitionEnvTomo ||--|o BoundingBox2D : "beamtilt" AcquisitionEnvTomo ||--|o BoundingBox2D : "imageshift" BoundingBox2D ||--|o QuantitySI : "x_min" BoundingBox2D ||--|o QuantitySI : "x_max" BoundingBox2D ||--|o QuantitySI : "y_min" BoundingBox2D ||--|o QuantitySI : "y_max" SpecialistOptics ||--|o Phaseplate : "phaseplate" SpecialistOptics ||--|o SphericalAberrationCorrector : "spherical_aberration_corrector" SpecialistOptics ||--|o ChromaticAberrationCorrector : "chromatic_aberration_corrector" EnergyFilter ||--|| QuantitySI : "width_energy_filter" Detector ||--|o QuantitySI : "dispersion" Detector ||--|o Range : "collection_angle" Range ||--|o QuantitySI : "minimal" Range ||--|o QuantitySI : "maximal" TiltAngle ||--|| QuantitySI : "increment" TiltAngle ||--|| QuantitySI : "minimal" TiltAngle ||--|| QuantitySI : "maximal"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
technique 1
String		 Environmental tomography direct
tilt_axis_angle 1
Float		 The tilt axis angle of a tomography series AcquisitionTomo
tilt_angle 1
TiltAngle		 The min, max and increment of the tilt angle in a tomography session AcquisitionTomo
screen_current 0..1
QuantitySI		 The total electron beam current hitting the viewing screen, in nA Acquisition
nominal_defocus 0..1
Range		 Target defocus set, min and max values in nm Acquisition
calibrated_defocus 0..1
Range		 Machine estimated defocus, min and max values in µm Acquisition
nominal_magnification 0..1
Integer		 Magnification level as indicated by the instrument, no unit Acquisition
calibrated_magnification 0..1
Integer		 Calculated magnification, no unit Acquisition
holder 0..1
String		 Speciman holder model Acquisition
holder_cryogen 0..1
String		 Type of cryogen used in the holder - if the holder is cooled seperately Acquisition
temperature_range 0..1
Range		 Temperature during data collection, in K with min and max values Acquisition
microscope_software 0..1
String		 Software used for instrument control, Acquisition
detectors 1..*
Detector		 Acquisition
dose_per_movie 0..1
QuantitySI		 Average dose per image/movie/tilt - given in electrons per square Angstrom Acquisition
energy_filter 0..1
EnergyFilter		 Whether an energy filter was used and its specifics Acquisition
image_size 0..1
ImageSize		 The size of the image in pixels, height and width given Acquisition
date_time 1
Datetime		 Time and date of the data acquisition Acquisition
exposure_time 0..1
QuantitySI		 Time of data acquisition per movie/tilt - in s Acquisition
cryogen 0..1
String		 Cryogen used in cooling the instrument and sample, usually nitrogen Acquisition
frames_per_movie 0..1
Integer		 Number of frames that on average constitute a full movie, can be a bit hard t... Acquisition
grids_imaged 0..1
Integer		 Number of grids imaged for this project - here with qualifier during this dat... Acquisition
images_generated 0..1
Integer		 Number of images generated total for this data collection - might need a qual... Acquisition
binning_camera 1
ImageSize		 Level of binning on the images applied during data collection Acquisition
pixel_size 1
QuantitySI		 Pixel size, in Angstrom Acquisition
specialist_optics 0..1
SpecialistOptics		 Any type of special optics, such as a phaseplate Acquisition
beamshift 0..1
BoundingBox2D		 Movement of the beam above the sample for data collection purposes that does ... Acquisition
beamtilt 0..1
BoundingBox2D		 Another way to move the beam above the sample for data collection purposes th... Acquisition
imageshift 0..1
BoundingBox2D		 Movement of the Beam below the image in order to shift the image on the detec... Acquisition
beamtiltgroups 0..1
Integer		 Number of Beamtilt groups present in this dataset - for optimized processing ... Acquisition
gainref_flip_rotate 0..1
String		 Whether and how you have to flip or rotate the gainref in order to align with... Acquisition

Usages

used by used in type used
EMDatasetEnv acquisition range AcquisitionEnvTomo

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/osc-em/oscem-schemas-env-tomo

Mappings

Mapping Type Mapped Value
self https://w3id.org/osc-em/oscem-schemas-env-tomo/:AcquisitionEnvTomo
native https://w3id.org/osc-em/oscem-schemas-env-tomo/:AcquisitionEnvTomo

LinkML Source

Direct

name: AcquisitionEnvTomo
from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
is_a: AcquisitionTomo
attributes:
  technique:
    name: technique
    description: Environmental tomography
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    domain_of:
    - Acquisition
    - AcquisitionGeneral
    - AcquisitionSpa
    - AcquisitionSubTomo
    - AcquisitionEnvTomo
    - AcquisitionCelTomo
    equals_string: env_tomo

Induced

name: AcquisitionEnvTomo
from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
is_a: AcquisitionTomo
attributes:
  technique:
    name: technique
    description: Environmental tomography
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    alias: technique
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    - AcquisitionGeneral
    - AcquisitionSpa
    - AcquisitionSubTomo
    - AcquisitionEnvTomo
    - AcquisitionCelTomo
    required: true
    equals_string: env_tomo
  tilt_axis_angle:
    name: tilt_axis_angle
    description: The tilt axis angle of a tomography series
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: tilt_axis_angle
    owner: AcquisitionEnvTomo
    domain_of:
    - AcquisitionTomo
    range: float
    required: true
  tilt_angle:
    name: tilt_angle
    description: The min, max and increment of the tilt angle in a tomography session.
      Unit is degree.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: tilt_angle
    owner: AcquisitionEnvTomo
    domain_of:
    - AcquisitionTomo
    range: TiltAngle
    required: true
  screen_current:
    name: screen_current
    description: The total electron beam current hitting the viewing screen, in nA.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: screen_current
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: QuantitySI
  nominal_defocus:
    name: nominal_defocus
    description: Target defocus set, min and max values in nm.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: nominal_defocus
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: Range
  calibrated_defocus:
    name: calibrated_defocus
    description: Machine estimated defocus, min and max values in µm. Has a tendency
      to be off.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: calibrated_defocus
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: Range
  nominal_magnification:
    name: nominal_magnification
    description: Magnification level as indicated by the instrument, no unit
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: nominal_magnification
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  calibrated_magnification:
    name: calibrated_magnification
    description: Calculated magnification, no unit
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: calibrated_magnification
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  holder:
    name: holder
    description: Speciman holder model
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: holder
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: string
  holder_cryogen:
    name: holder_cryogen
    description: Type of cryogen used in the holder - if the holder is cooled seperately
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: holder_cryogen
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: string
  temperature_range:
    name: temperature_range
    description: Temperature during data collection, in K with min and max values.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: temperature
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: Range
  microscope_software:
    name: microscope_software
    description: Software used for instrument control,
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: microscope_software
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: string
  detectors:
    name: detectors
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: detectors
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: Detector
    required: true
    multivalued: true
  dose_per_movie:
    name: dose_per_movie
    description: Average dose per image/movie/tilt - given in electrons per square
      Angstrom
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: dose_per_movie
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: QuantitySI
  energy_filter:
    name: energy_filter
    description: Whether an energy filter was used and its specifics.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: energy_filter
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: EnergyFilter
  image_size:
    name: image_size
    description: The size of the image in pixels, height and width given.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: image_size
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: ImageSize
  date_time:
    name: date_time
    description: Time and date of the data acquisition
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: date_time
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: datetime
    required: true
  exposure_time:
    name: exposure_time
    description: Time of data acquisition per movie/tilt - in s
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: exposure_time
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: QuantitySI
  cryogen:
    name: cryogen
    description: Cryogen used in cooling the instrument and sample, usually nitrogen
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: cryogen
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: string
  frames_per_movie:
    name: frames_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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: frames_per_movie
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  grids_imaged:
    name: grids_imaged
    description: Number of grids imaged for this project - here with qualifier during
      this data acquisition
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: grids_imaged
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  images_generated:
    name: images_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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: images_generated
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  binning_camera:
    name: binning_camera
    description: Level of binning on the images applied during data collection
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: binning_camera
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: ImageSize
    required: true
  pixel_size:
    name: pixel_size
    description: Pixel size, in Angstrom
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: pixel_size
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: QuantitySI
    required: true
  specialist_optics:
    name: specialist_optics
    description: Any type of special optics, such as a phaseplate
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: specialist_optics
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: SpecialistOptics
  beamshift:
    name: beamshift
    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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: beamshift
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: BoundingBox2D
  beamtilt:
    name: beamtilt
    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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: beamtilt
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: BoundingBox2D
  imageshift:
    name: imageshift
    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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: imageshift
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: BoundingBox2D
  beamtiltgroups:
    name: beamtiltgroups
    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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: beamtiltgroups
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: integer
  gainref_flip_rotate:
    name: gainref_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/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: gainref_flip_rotate
    owner: AcquisitionEnvTomo
    domain_of:
    - Acquisition
    range: string