acquisitionAcquisition
type: NodeShape
closed: true
description: General acquisition covering materials science and other use cases. For specialized techniques, use the appropriate subclass (AcquisitionSpa for single particle, or tomography subclasses).
ignored properties: type
ignored properties: tilt axis angle
ignored properties: tilt angle
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 17
  path: acquisitionframes per movie
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionimageshift
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionimages generated
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitionenergy filter
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionnominal defocus
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 5
  path: acquisitioncalibrated magnification
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 11
  path: acquisitiondose per movie
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 14
  path: acquisitiondate time
property:
  datatype: string
  description: Specifies which Acquisition subschema/class is in use.
  max count: 1
  node kind: Literal
  order: 0
  path: acquisitiontechnique
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionscreen current
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 4
  path: acquisitionnominal magnification
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitionimage size
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionholder
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 16
  path: acquisitioncryogen
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiondetectors
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 8
  path: acquisitiontemperature range
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionbeamtilt
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitionholder cryogen
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 21
  path: acquisitionpixel size
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncalibrated defocus
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 27
  path: acquisitiongainref flip rotate
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionbeamshift
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 26
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionmicroscope software
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionspecialist optics
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitiongrids imaged
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionexposure time
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 20
  path: acquisitionbinning camera

acquisitionAcquisitionSpa
type: NodeShape
closed: true
ignored properties: type
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionbeamtilt
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncalibrated defocus
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionholder
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 5
  path: acquisitioncalibrated magnification
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitionenergy filter
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionimages generated
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitionimage size
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitiongrids imaged
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 14
  path: acquisitiondate time
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 26
  path: acquisitionbeamtiltgroups
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionexposure time
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionnominal defocus
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 16
  path: acquisitioncryogen
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionbeamshift
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 21
  path: acquisitionpixel size
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 27
  path: acquisitiongainref flip rotate
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 4
  path: acquisitionnominal magnification
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 20
  path: acquisitionbinning camera
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 17
  path: acquisitionframes per movie
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionimageshift
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionscreen current
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitionholder cryogen
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 8
  path: acquisitiontemperature range
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 11
  path: acquisitiondose per movie
property:
  datatype: string
  description: Single particle acquisition
  in: spa
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitiontechnique
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionspecialist optics
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiondetectors
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionmicroscope software

custom typesDescriptor
type: NodeShape
closed: false
description: List of custom descriptors for user-defined key-value pairs describing how micrographs were obtained or any related information
ignored properties: type
property:
  class: Any
  description: Description of the descriptor
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesdescriptor thing
property:
  datatype: string
  description: Name defining the descriptor
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: custom typesdescriptor name

custom typesDescriptors
type: NodeShape
closed: true
ignored properties: type
property:
  class: Any
  description: Description of the descriptor
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesdescriptor thing
property:
  datatype: string
  description: Name defining the descriptor
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: custom typesdescriptor name

custom typesSeries
type: NodeShape
closed: true
description: A series of numbers constructed from min, max, and increment
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesmaximal
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesminimal
property:
  class: custom typesQuantitySI
  description: Increment between elements of a series
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesincrement

AcquisitionCelTomo
type: NodeShape
closed: true
ignored properties: type
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionholder cryogen
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  datatype: string
  description: Cellular tomography
  in: cellular_tomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie

AcquisitionEnvTomo
type: NodeShape
closed: true
ignored properties: type
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  datatype: string
  description: Environmental tomography
  in: env_tomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder

AcquisitionSubTomo
type: NodeShape
closed: true
ignored properties: type
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  datatype: integer
  description: Magnification level as indicated by the instrument, no unit
  max count: 1
  node kind: Literal
  order: 6
  path: acquisitionnominal magnification
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: custom typesBoundingBox2D
  description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 27
  path: acquisitionimageshift
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  datatype: string
  description: Subtomogram averaging
  in: subtomo
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter

AcquisitionTomo
type: NodeShape
closed: true
ignored properties: type
property:
  class: custom typesBoundingBox2D
  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.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 26
  path: acquisitionbeamtilt
property:
  class: custom typesQuantitySI
  description: Pixel size, in Angstrom
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 23
  path: acquisitionpixel size
property:
  class: custom typesRange
  description: Temperature during data collection, in K with min and max values.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 10
  path: acquisitiontemperature range
property:
  datatype: dateTime
  description: Time and date of the data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 16
  path: acquisitiondate time
property:
  class: TiltAngle
  description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: tilt angle
property:
  datatype: integer
  description: Calculated magnification, no unit
  max count: 1
  node kind: Literal
  order: 7
  path: acquisitioncalibrated magnification
property:
  datatype: string
  description: Type of cryogen used in the holder - if the holder is cooled seperately
  max count: 1
  node kind: Literal
  order: 9
  path: acquisitionholder cryogen
property:
  datatype: string
  description: Cryogen used in cooling the instrument and sample, usually nitrogen
  max count: 1
  node kind: Literal
  order: 18
  path: acquisitioncryogen
property:
  class: acquisitionDetector
  min count: 1
  node kind: BlankNodeOrIRI
  order: 12
  path: acquisitiondetectors
property:
  class: acquisitionEnergyFilter
  description: Whether an energy filter was used and its specifics.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 14
  path: acquisitionenergy filter
property:
  datatype: float
  description: The tilt axis angle of a tomography series
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: tilt axis angle
property:
  class: custom typesImageSize
  description: The size of the image in pixels, height and width given.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 15
  path: acquisitionimage size
property:
  class: acquisitionSpecialistOptics
  description: Any type of special optics, such as a phaseplate
  max count: 1
  node kind: BlankNodeOrIRI
  order: 24
  path: acquisitionspecialist optics
property:
  datatype: integer
  description: Number of frames that on average constitute a full movie, can be a bit hard to define for some detectors
  max count: 1
  node kind: Literal
  order: 19
  path: acquisitionframes per movie
property:
  class: custom typesQuantitySI
  description: Time of data acquisition per movie/tilt - in s
  max count: 1
  node kind: BlankNodeOrIRI
  order: 17
  path: acquisitionexposure time
property:
  datatype: integer
  description: Number of grids imaged for this project - here with qualifier during this data acquisition
  max count: 1
  node kind: Literal
  order: 20
  path: acquisitiongrids imaged
property:
  class: custom typesImageSize
  description: Level of binning on the images applied during data collection
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 22
  path: acquisitionbinning camera
property:
  class: custom typesQuantitySI
  description: Average dose per image/movie/tilt - given in electrons per square Angstrom
  max count: 1
  node kind: BlankNodeOrIRI
  order: 13
  path: acquisitiondose per movie
property:
  datatype: string
  description: Speciman holder model
  max count: 1
  node kind: Literal
  order: 8
  path: acquisitionholder
property:
  datatype: integer
  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
  max count: 1
  node kind: Literal
  order: 21
  path: acquisitionimages generated
property:
  class: custom typesBoundingBox2D
  description: Movement of the beam above the sample for data collection purposes that does not require movement of the stage. Given in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 25
  path: acquisitionbeamshift
property:
  class: custom typesRange
  description: Target defocus set, min and max values in nm.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 4
  path: acquisitionnominal defocus
property:
  datatype: string
  description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
  max count: 1
  node kind: Literal
  order: 29
  path: acquisitiongainref flip rotate
property:
  class: custom typesRange
  description: Machine estimated defocus, min and max values in µm. Has a tendency to be off.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 5
  path: acquisitioncalibrated defocus
property:
  datatype: string
  description: Software used for instrument control,
  max count: 1
  node kind: Literal
  order: 11
  path: acquisitionmicroscope software
property:
  datatype: integer
  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.
  max count: 1
  node kind: Literal
  order: 28
  path: acquisitionbeamtiltgroups
property:
  datatype: string
  description: Specifies which Acquisition subschema/class is in use.
  max count: 1
  node kind: Literal
  order: 2
  path: acquisitiontechnique
property:
  class: custom typesQuantitySI
  description: The total electron beam current hitting the viewing screen, in nA.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitionscreen current

quantityValue
type: NodeShape
closed: true
description: if a value has a unit, it should be given as a unit value pair.
ignored properties: type
ignored properties: custom typesunitSI
ignored properties: custom typesvalueSI
property:
  datatype: float
  description: the value of a field with a unit
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: hasQuantityKind
property:
  datatype: string
  description: the unit of a given value
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: hasUnit

acquisitionChromaticAberrationCorrector
type: NodeShape
closed: true
description: Special device used to correct instrument inherent chromatic aberration.
ignored properties: type
property:
  datatype: string
  description: Details of a given specialist instrument
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused

acquisitionPhaseplate
type: NodeShape
closed: true
description: Used to modulate the phase of the electron wave.
ignored properties: type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: Type of phaseplate
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type

acquisitionSphericalAberrationCorrector
type: NodeShape
closed: true
description: Special device used to correct instrument inherent spherical aberration.
ignored properties: type
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: Details of a given specialist instrument
  max count: 1
  min count: 1
  node kind: Literal
  order: 1
  path: acquisitioninstrument type

Any
type: NodeShape
closed: true
description: Any type, used as the base for type-narrowing.
ignored properties: type

TiltAngle
type: NodeShape
closed: true
description: The min, max and increment of the tilt angle in a tomography session. Unit is degree.
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Increment between elements of a series
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesincrement
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesminimal
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesmaximal

acquisitionDetector
type: NodeShape
closed: true
description: Class representing a detector
ignored properties: type
property:
  class: custom typesRange
  description: Collection angle set, min and max values in mrad.
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: acquisitioncollection angle
property:
  datatype: string
  description: Mode of the detector, e.g. "counting", "ScanningDetector", "ImagingDetector", etc.
  max count: 1
  node kind: Literal
  order: 1
  path: acquisitionmode
property:
  class: custom typesQuantitySI
  description: Dispersion of an analytical detector, in eV
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitiondispersion
property:
  datatype: string
  description: The name of the item
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesname

acquisitionEnergyFilter
type: NodeShape
closed: true
description: A device used to filter for electrons with specific energy.
ignored properties: type
property:
  class: custom typesQuantitySI
  description: Width of the energy filter used.
  max count: 1
  min count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionwidth energy filter
property:
  datatype: boolean
  description: whether a specific instrument was used during data acquisition
  max count: 1
  min count: 1
  node kind: Literal
  order: 0
  path: acquisitionused
property:
  datatype: string
  description: The model of the item
  max count: 1
  node kind: Literal
  order: 1
  path: custom typesmodel

acquisitionSpecialistOptics
type: NodeShape
closed: true
description: Optional optics used to correct for instrument limitations.
ignored properties: type
property:
  class: acquisitionSphericalAberrationCorrector
  description: Specialist device to correct for spherical aberration of the microscope lenses
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: acquisitionspherical aberration corrector
property:
  class: acquisitionChromaticAberrationCorrector
  description: Specialist device to correct for chromatic aberration of the microscope lenses
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: acquisitionchromatic aberration corrector
property:
  class: acquisitionPhaseplate
  description: Phaseplate is a special optics device that can be used to enhance contrast
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: acquisitionphaseplate

custom typesImageSize
type: NodeShape
closed: true
description: size of a 2D image (in integer units)
ignored properties: type
property:
  datatype: integer
  description: The width of a given item - unit depends on item
  max count: 1
  node kind: Literal
  order: 1
  path: custom typeswidth
property:
  datatype: integer
  description: The height of a given item - unit depends on item
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesheight

custom typesBoundingBox2D
type: NodeShape
closed: true
description: an axis-aligned 2D bounding box (float units)
ignored properties: type
property:
  class: custom typesQuantitySI
  description: minimum y
  max count: 1
  node kind: BlankNodeOrIRI
  order: 2
  path: custom typesy min
property:
  class: custom typesQuantitySI
  description: maximum x
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesx max
property:
  class: custom typesQuantitySI
  description: maximum y
  max count: 1
  node kind: BlankNodeOrIRI
  order: 3
  path: custom typesy max
property:
  class: custom typesQuantitySI
  description: minimum x
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesx min

custom typesRange
type: NodeShape
closed: true
description: A range constructed from min and max
ignored properties: type
ignored properties: custom typesincrement
property:
  class: custom typesQuantitySI
  description: Maximal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 1
  path: custom typesmaximal
property:
  class: custom typesQuantitySI
  description: Minimal value of a given dataset property
  max count: 1
  node kind: BlankNodeOrIRI
  order: 0
  path: custom typesminimal

custom typesQuantitySI
type: NodeShape
closed: true
description: unit value extended to have two additional fields si_value and si_unit
ignored properties: type
property:
  datatype: string
  description: the SI unit attached to a si value
  max count: 1
  node kind: Literal
  order: 1
  path: custom typesunitSI
property:
  datatype: float
  description: the value of a field with a unit
  max count: 1
  min count: 1
  node kind: Literal
  order: 3
  path: hasQuantityKind
property:
  datatype: float
  description: value of a given field in respect to its SI unit
  max count: 1
  node kind: Literal
  order: 0
  path: custom typesvalueSI
property:
  datatype: string
  description: the unit of a given value
  max count: 1
  min count: 1
  node kind: Literal
  order: 2
  path: hasUnit

class: custom typesBoundingBox2D
description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
max count: 1
node kind: BlankNodeOrIRI
order: 27
path: acquisitionimageshift

datatype: string
description: Whether and how you have to flip or rotate the gainref in order to align with your acquired images
max count: 1
node kind: Literal
order: 29
path: acquisitiongainref flip rotate

datatype: string
description: Cryogen used in cooling the instrument and sample, usually nitrogen
max count: 1
node kind: Literal
order: 18
path: acquisitioncryogen

datatype: string
description: Type of cryogen used in the holder - if the holder is cooled seperately
max count: 1
node kind: Literal
order: 9
path: acquisitionholder cryogen

datatype: string
description: Type of cryogen used in the holder - if the holder is cooled seperately
max count: 1
node kind: Literal
order: 9
path: acquisitionholder cryogen

datatype: integer
description: Number of grids imaged for this project - here with qualifier during this data acquisition
max count: 1
node kind: Literal
order: 20
path: acquisitiongrids imaged

class: custom typesBoundingBox2D
description: Movement of the Beam below the image in order to shift the image on the detector. Given in µm.
max count: 1
node kind: BlankNodeOrIRI
order: 27
path: acquisitionimageshift

datatype: integer
description: Magnification level as indicated by the instrument, no unit
max count: 1
node kind: Literal
order: 6
path: acquisitionnominal magnification