CETMDEntities

metamodel version: 1.7.0

version: 0.0.1

Schema for cryoET geometry

Classes

• AcquisitionMetadataMixin - Metadata concerning the acquisition process.
• Alignment - The tomographic alignment for a tilt series.
• Annotation - A primitive annotation.
  • PointMatrixSet2D - A set of 2D points with an associated rotation matrix.
  • PointMatrixSet3D - A set of 3D points with an associated rotation matrix.
  • PointSet2D - A set of 2D point annotations.
  • PointSet3D - A set of 3D point annotations.
  • PointVectorSet2D - A set of 2D points with an associated direction vector.
  • PointVectorSet3D - A set of 3D points with an associated direction vector.
  • ProbabilityMap2D - An annotation image with real-valued labels.
  • ProbabilityMap3D - An annotation volume with real-valued labels.
  • SegmentationMask2D - An annotation image with categorical labels.
  • SegmentationMask3D - An annotation volume with categorical labels.
  • TriMesh - A mesh annotation.
• Average - A particle averaging experiment.
• Axis - An axis in a coordinate system
• AxisNameMapping - Axis name to Axis name mapping
• CTFMetadata - A set of CTF patameters for an image.
• CoordMetaMixin - Coordinate system mixins for annotations.
• CoordinateSystem - A coordinate system
• CoordinateTransformation - A coordinate transformation
  • Affine - An affine transformation
  • Identity - The identity transformation
  • MapAxis - Axis permutation transformation
  • Scale - A scaling transformation
  • Sequence - A sequence of transformations
    • ProjectionAlignment - The tomographic alignment for a single projection.
  • Translation - A translation transformation
• Dataset - A dataset
• Image2D - A 2D image.
  • DefectFile - A detector defect file.
  • GainFile - A gain reference file.
  • MovieFrame - An individual movie frame
  • ProjectionImage - A projection image.
    • SubProjectionImage - A croppecd projection image.
• Image3D - A 3D image.
  • ParticleMap - A 3D particle density map.
  • Tomogram - A 3D tomogram.
• ImageStack2D - A stack of 2D images.
• ImageStack3D - A stack of 3D images.
• MovieStack - A stack of movie frames.
• MovieStackCollection - A collection of movie stacks using the same gain and defect files.
• MovieStackSeries - A group of movie stacks that belong to a single tilt series.
• Region - Raw data (movie stacks) and derived data (tilt series, tomograms, annotations) from a single region of a specimen.
• TiltSeries - A stack of projection images.

Mixins

Slots

• accumulated_dose - The pre-exposure up to this image in e-/A^2
• ➞affine - The affine matrix
• ➞type - The type of transformation
• ➞projection_alignments - alignment for a specific projection
• ➞annotations - The annotations
• ➞name - The name of the averaging experiment.
• ➞particle_maps - The particle maps
• ➞axis1_name - The type of transformation
• ➞axis2_name - The mapping of the axis names
• ➞axis_type
• ➞axis_unit
• ➞name
• axis_name - The name of the axis
• axis_type - The type of axis
• axis_unit - The unit of the axis
• ➞axes - The axes of the coordinate system
• ➞name - The name of the coordinate system
• ➞input - The source coordinate system name
• ➞name - The name of the coordinate transformation
• ➞output - The target coordinate system name
• ➞type - The type of transformation
• coordinate_systems - Named coordinate systems for this entity
• coordinate_transformations - Named coordinate systems for this entity
• ctf_metadata - A set of CTF patameters for an image.
• ➞averages - The averages in the dataset
• ➞name - The name of the dataset
• ➞regions - The regions in the dataset
• defocus_angle - Estimated angle of astigmatism.
• defocus_u - Estimated defocus U for this image in Angstrom, underfocus positive.
• defocus_v - Estimated defocus V for this image in Angstrom, underfocus positive.
• depth - The depth of the image (z-axis) in pixels
• height - The height of the image (y-axis) in pixels
• ➞type - The type of transformation
• ➞images - The images in the stack
• ➞images - The images in the stack
• ➞mapAxis - The permutation of the axes
• ➞type - The type of transformation
• matrix2D - Rotation matrix associated with a point on a 2D image (Nx2x2).
• matrix3D - Rotation matrix associated with a point on a 3D image (Nx3x3).
• ➞DefectFile - The defect file for the movie stacks
• ➞GainFile - The gain file for the movie stacks
• ➞movie_stacks - The movie stacks in the collection
• ➞stacks - The movie stacks.
• ➞images - The movie frames in the stack
• ➞path
• nominal_tilt_angle - The tilt angle reported by the microscope
• origin2D - Location on a 2D image (Nx2).
• origin3D - Location on a 3D image (Nx3).
• particle_index - Index of a particle inside a tomogram.
• path - Path to a file.
• ➞input - The source coordinate system name
• ➞output - The target coordinate system name
• ➞sequence - The sequence of transformations
• ➞alignments - The alignments
• ➞annotations - The annotations for this region
• ➞movie_stack_collections - The movie stack
• ➞tilt_series - The tilt series
• ➞tomograms - The tomograms
• ➞scale - The scaling vector
• ➞type - The type of transformation
• section - 0-based section index to the entity inside a stack.
• ➞sequence - The sequence of transformations
• ➞type - The type of transformation
• ➞images - The projections in the stack
• ➞path
• translation2D - Offset from the origin of a point on a 2D image (Nx2).
• translation3D - Offset from the origin of a point on a 3D image (Nx3).
• ➞translation - The translation vector
• ➞type - The type of transformation
• vector2D - Orientation vector associated with a point on a 2D image (Nx2).
• vector3D - Orientation vector associated with a point on a 3D image (Nx3).
• width - The width of the image (x-axis) in pixels

Enums

• AxisType - The type of axis
• TransformationType

Subsets

Types

Built in

• Bool
• Curie
• Decimal
• ElementIdentifier
• NCName
• NodeIdentifier
• URI
• URIorCURIE
• XSDDate
• XSDDateTime
• XSDTime
• float
• int
• str

Defined

• Boolean (Bool) - A binary (true or false) value
• Curie (Curie) - a compact URI
• Date (XSDDate) - a date (year, month and day) in an idealized calendar
• DateOrDatetime (str) - Either a date or a datetime
• Datetime (XSDDateTime) - The combination of a date and time
• Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
• Double (float) - A real number that conforms to the xsd:double specification
• Float (float) - A real number that conforms to the xsd:float specification
• Integer (int) - An integer
• Jsonpath (str) - A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
• Jsonpointer (str) - A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
• Ncname (NCName) - Prefix part of CURIE
• Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
• Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
• Sparqlpath (str) - A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
• String (str) - A character string
• Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
• Uri (URI) - a complete URI
• Uriorcurie (URIorCURIE) - a URI or a CURIE