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Class: Acquisition

A set of parameteres describing the data acquisition

URI: https://w3id.org/osc-em/oscem-schemas/:Acquisition

classDiagram class Acquisition click Acquisition href "../Acquisition" Acquisition : beamshift Acquisition --> "0..1" BoundingBox2D : beamshift click BoundingBox2D href "../BoundingBox2D" Acquisition : beamtilt Acquisition --> "0..1" BoundingBox2D : beamtilt click BoundingBox2D href "../BoundingBox2D" Acquisition : beamtiltgroups Acquisition : binning_camera Acquisition : calibrated_defocus Acquisition --> "0..1" Range : calibrated_defocus click Range href "../Range" Acquisition : calibrated_magnification Acquisition : cryogen Acquisition : date_time Acquisition --> "1" Any : date_time click Any href "../Any" Acquisition : detector Acquisition : detector_mode Acquisition : dose_per_movie Acquisition --> "1" QuantityValue : dose_per_movie click QuantityValue href "../QuantityValue" Acquisition : energy_filter Acquisition --> "0..1" EnergyFilter : energy_filter click EnergyFilter href "../EnergyFilter" Acquisition : exposure_time Acquisition --> "0..1" QuantityValue : exposure_time click QuantityValue href "../QuantityValue" Acquisition : frames_per_movie Acquisition : gainref_flip_rotate Acquisition : grids_imaged Acquisition : holder Acquisition : holder_cryogen Acquisition : image_size Acquisition --> "0..1" ImageSize : image_size click ImageSize href "../ImageSize" Acquisition : images_generated Acquisition : imageshift Acquisition --> "0..1" BoundingBox2D : imageshift click BoundingBox2D href "../BoundingBox2D" Acquisition : microscope_software Acquisition : nominal_defocus Acquisition --> "0..1" Range : nominal_defocus click Range href "../Range" Acquisition : nominal_magnification Acquisition : pixel_size Acquisition --> "1" QuantityValue : pixel_size click QuantityValue href "../QuantityValue" Acquisition : specialist_optics Acquisition --> "0..1" SpecialistOptics : specialist_optics click SpecialistOptics href "../SpecialistOptics" Acquisition : temperature_range Acquisition --> "0..1" Range : temperature_range click Range href "../Range"

Slots

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

Usages

used by used in type used
EMDataset acquisition range Acquisition

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Acquisition
description: A set of parameteres describing the data acquisition
from_schema: https://w3id.org/osc-em/oscem-schemas
slots:
- nominal_defocus
- calibrated_defocus
- nominal_magnification
- calibrated_magnification
- holder
- holder_cryogen
- temperature_range
- microscope_software
- detector
- detector_mode
- dose_per_movie
- energy_filter
- image_size
- date_time
- exposure_time
- cryogen
- frames_per_movie
- grids_imaged
- images_generated
- binning_camera
- pixel_size
- specialist_optics
- beamshift
- beamtilt
- imageshift
- beamtiltgroups
- gainref_flip_rotate
slot_usage:
  detector:
    name: detector
    required: true
  dose_per_movie:
    name: dose_per_movie
    required: true
  date_time:
    name: date_time
    required: true
  binning_camera:
    name: binning_camera
    required: true
  pixel_size:
    name: pixel_size
    required: true

Induced

name: Acquisition
description: A set of parameteres describing the data acquisition
from_schema: https://w3id.org/osc-em/oscem-schemas
slot_usage:
  detector:
    name: detector
    required: true
  dose_per_movie:
    name: dose_per_movie
    required: true
  date_time:
    name: date_time
    required: true
  binning_camera:
    name: binning_camera
    required: true
  pixel_size:
    name: pixel_size
    required: true
attributes:
  nominal_defocus:
    name: nominal_defocus
    description: Target defocus set, min and max values in µm.
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: nominal_defocus
    owner: Acquisition
    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
    rank: 1000
    alias: calibrated_defocus
    owner: Acquisition
    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
    rank: 1000
    alias: nominal_magnification
    owner: Acquisition
    domain_of:
    - Acquisition
    range: integer
  calibrated_magnification:
    name: calibrated_magnification
    description: Calculated magnification, no unit
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: calibrated_magnification
    owner: Acquisition
    domain_of:
    - Acquisition
    range: integer
  holder:
    name: holder
    description: Speciman holder model
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: holder
    owner: Acquisition
    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
    rank: 1000
    alias: holder_cryogen
    owner: Acquisition
    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
    rank: 1000
    alias: temperature
    owner: Acquisition
    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
    rank: 1000
    alias: microscope_software
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
  detector:
    name: detector
    description: Make and model of the detector used
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: detector
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
    required: true
  detector_mode:
    name: detector_mode
    description: Operating mode of the detector
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: detector_mode
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
  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
    rank: 1000
    alias: dose_per_movie
    owner: Acquisition
    domain_of:
    - Acquisition
    range: QuantityValue
    required: true
  energy_filter:
    name: energy_filter
    description: Wether an energy filter was used and its specifics.
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: energy_filter
    owner: Acquisition
    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
    rank: 1000
    alias: image_size
    owner: Acquisition
    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
    rank: 1000
    alias: date_time
    owner: Acquisition
    domain_of:
    - Acquisition
    range: Any
    required: true
    any_of:
    - range: datetime
    - range: date
  exposure_time:
    name: exposure_time
    description: Time of data acquisition per movie/tilt - in s
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: exposure_time
    owner: Acquisition
    domain_of:
    - Acquisition
    range: QuantityValue
  cryogen:
    name: cryogen
    description: Cryogen used in cooling the instrument and sample, usually nitrogen
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: cryogen
    owner: Acquisition
    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
    rank: 1000
    alias: frames_per_movie
    owner: Acquisition
    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
    rank: 1000
    alias: grids_imaged
    owner: Acquisition
    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
    rank: 1000
    alias: images_generated
    owner: Acquisition
    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
    rank: 1000
    alias: binning_camera
    owner: Acquisition
    domain_of:
    - Acquisition
    range: float
    required: true
  pixel_size:
    name: pixel_size
    description: Pixel size, in Angstrom
    from_schema: https://w3id.org/osc-em/oscem-schemas
    rank: 1000
    alias: pixel_size
    owner: Acquisition
    domain_of:
    - Acquisition
    range: QuantityValue
    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
    rank: 1000
    alias: specialist_optics
    owner: Acquisition
    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
    rank: 1000
    alias: beamshift
    owner: Acquisition
    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
    rank: 1000
    alias: beamtilt
    owner: Acquisition
    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
    rank: 1000
    alias: imageshift
    owner: Acquisition
    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
    rank: 1000
    alias: beamtiltgroups
    owner: Acquisition
    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
    rank: 1000
    alias: gainref_flip_rotate
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string