Class: Acquisition

A set of parameteres describing the data acquisition

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

erDiagram Acquisition { AcquisitionTechnique technique 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 { } Acquisition ||--|o QuantitySI : "screen_current" Acquisition ||--|o Range : "nominal_defocus" Acquisition ||--|o Range : "calibrated_defocus" Acquisition ||--|o Range : "temperature_range" Acquisition ||--}| Detector : "detectors" Acquisition ||--|o QuantitySI : "dose_per_movie" Acquisition ||--|o EnergyFilter : "energy_filter" Acquisition ||--|o ImageSize : "image_size" Acquisition ||--|o QuantitySI : "exposure_time" Acquisition ||--|| ImageSize : "binning_camera" Acquisition ||--|| QuantitySI : "pixel_size" Acquisition ||--|o SpecialistOptics : "specialist_optics" Acquisition ||--|o BoundingBox2D : "beamshift" Acquisition ||--|o BoundingBox2D : "beamtilt" Acquisition ||--|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"

Inheritance

Acquisition

Slots

Name	Cardinality and Range	Description	Inheritance
technique	1 AcquisitionTechnique	Specifies which Acquisition subschema/class is in use	direct
screen_current	0..1 QuantitySI	The total electron beam current hitting the viewing screen, in nA	direct
nominal_defocus	0..1 Range	Target defocus set, min and max values in nm	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
detectors	1..* Detector		direct
dose_per_movie	0..1 QuantitySI	Average dose per image/movie/tilt - given in electrons per square Angstrom	direct
energy_filter	0..1 EnergyFilter	Whether 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 Datetime	Time and date of the data acquisition	direct
exposure_time	0..1 QuantitySI	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 ImageSize	Level of binning on the images applied during data collection	direct
pixel_size	1 QuantitySI	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

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/:Acquisition
native	https://w3id.org/osc-em/oscem-schemas-env-tomo/:Acquisition

LinkML Source

Direct

name: Acquisition
description: A set of parameteres describing the data acquisition
from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
slots:
- technique
- screen_current
- nominal_defocus
- calibrated_defocus
- nominal_magnification
- calibrated_magnification
- holder
- holder_cryogen
- temperature_range
- microscope_software
- detectors
- 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:
  technique:
    name: technique
    required: true
  detectors:
    name: detectors
    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-env-tomo
slot_usage:
  technique:
    name: technique
    required: true
  detectors:
    name: detectors
    required: true
  date_time:
    name: date_time
    required: true
  binning_camera:
    name: binning_camera
    required: true
  pixel_size:
    name: pixel_size
    required: true
attributes:
  technique:
    name: technique
    description: Specifies which Acquisition subschema/class is in use.
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: technique
    owner: Acquisition
    domain_of:
    - Acquisition
    - AcquisitionGeneral
    - AcquisitionSpa
    - AcquisitionSubTomo
    - AcquisitionEnvTomo
    - AcquisitionCelTomo
    range: AcquisitionTechnique
    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: Acquisition
    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: 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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    rank: 1000
    alias: microscope_software
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string
  detectors:
    name: detectors
    from_schema: https://w3id.org/osc-em/oscem-schemas-env-tomo
    rank: 1000
    alias: detectors
    owner: Acquisition
    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: Acquisition
    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: 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-env-tomo
    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-env-tomo
    rank: 1000
    alias: date_time
    owner: Acquisition
    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: Acquisition
    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: 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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    rank: 1000
    alias: binning_camera
    owner: Acquisition
    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: Acquisition
    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: 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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    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-env-tomo
    rank: 1000
    alias: gainref_flip_rotate
    owner: Acquisition
    domain_of:
    - Acquisition
    range: string