ome_types.model

Classes

AffineTransform

A matrix used to transform the shape.

Annotation

An annotation from which all others are ultimately derived.

AnnotationRef

The AnnotationRef element is a reference to an element derived from the CommonAnnotation element.

Arc

The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe.

BasicAnnotation

An abstract Basic Annotation from which some others are derived.

BinData

The contents of this element are base64-encoded.

BinaryFile

Describes a binary file.

BooleanAnnotation

A simple boolean annotation of type xsd:boolean

Channel

There must be one per channel in the Image, even for a single-plane image.

ChannelRef

ChannelRef.

CommentAnnotation

A simple comment annotation

Dataset

An element specifying a collection of images that are always processed together.

DatasetRef

The DatasetRef element refers to a Dataset by specifying the Dataset ID attribute.

Detector

The type of detector used to capture the image.

DetectorSettings

This holds the setting applied to a detector as well as a reference to the detector.

Dichroic

The dichromatic beamsplitter or dichroic mirror used for this filter combination.

DichroicRef

DichroicRef.

DoubleAnnotation

A simple numerical annotation of type xsd:double

Ellipse

A simple ellipse object.

Experiment

This element describes the type of experiment.

ExperimentRef

ExperimentRef.

Experimenter

This element describes a person who performed an imaging experiment.

ExperimenterGroup

The ExperimenterGroupID is required.

ExperimenterGroupRef

This empty element has a reference (the ExperimenterGroup ID attribute) to a ExperimenterGroup defined within OME.

ExperimenterRef

This empty element has a required Experimenter ID and an optional DocumentID attribute which refers to one of the Experimenters defined within OME.

External

Describes a file location.

Filament

The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen.

FileAnnotation

A file object annotation

Filter

A filter is either an excitation or emission filters.

FilterRef

FilterRef.

FilterSet

Filter set manufacturer specification

FilterSetRef

FilterSetRef.

Folder

An element specifying a possibly heterogeneous collection of data.

FolderRef

The FolderRef element refers to a Folder by specifying the Folder ID attribute.

GenericExcitationSource

The GenericExcitationSource element is used to represent a source as a collection of key/value pairs, stored in a Map.

Image

This element describes the actual image and its meta-data.

ImageRef

The ImageRef element is a reference to an Image element.

ImagingEnvironment

This describes the environment that the biological sample was in during the experiment.

Instrument

This element describes the instrument used to capture the Image.

InstrumentRef

This empty element can be used (via the required Instrument ID attribute) to refer to an Instrument defined within OME.

Label

The text label.

Laser

Laser types are specified using two attributes - the Type and the LaserMedium.

Leader

Contact information for a ExperimenterGroup leader specified using a reference to an Experimenter element defined elsewhere in the document.

LightEmittingDiode

The LightEmittingDiode element is used to describe various kinds of LED lamps.

LightPath

A description of the light path

LightSource

The lightsource for the instrument.

LightSourceGroup

alias of ome_types.model.light_source.LightSource

LightSourceSettings

LightSourceSettings.

Line

A straight line defined by it’s end points.

ListAnnotation

This annotation is a grouping object.

LongAnnotation

A simple numerical annotation of type xsd:long

ManufacturerSpec

This is the base from which many microscope components are extended.

Map

This is a Mapping of key/value pairs.

MapAnnotation

An map annotation.

Mask

The Mask ROI shape is a link to a BinData object that is a BIT mask drawn on top of the image as an ROI.

MicrobeamManipulation

Defines a microbeam operation type and the region of the image it was applied to.

MicrobeamManipulationRef

MicrobeamManipulationRef.

Microscope

The microscope’s manufacturer specification.

NumericAnnotation

An abstract Numeric Annotation from which some others are derived.

OME

The OME element is a container for all information objects accessible by OME.

Objective

A description of the microscope’s objective lens.

ObjectiveSettings

This holds the setting applied to an objective as well as a reference to the objective.

Pixels

Pixels is going to be removed in the future, but it is still required.

Plane

The Plane object holds microscope stage and image timing data for a given channel/z-section/timepoint.

Plate

This element identifies microtiter plates within a screen.

PlateAcquisition

PlateAcquisition is used to describe a single acquisition run for a plate.

Point

Point.

Polygon

The Polygon defines closed shapes formed of straight lines.

Polyline

The Polyline defines open shapes formed of straight lines.

Project

The Project ID is required.

ProjectRef

There may be one or more of these in a Dataset.

Pump

The Pump element is a reference to a LightSource.

ROI

A four dimensional ‘Region of Interest’.

ROIRef

ROIRef.

Reagent

Reagent is used to describe a chemical or some other physical experimental parameter.

ReagentRef

ReagentRef.

Rectangle

A simple rectangle object.

Reference

Reference is an empty complex type that is contained and extended by all the *Ref elements and also the Settings Complex Type Each *Ref element defines an attribute named ID of simple type *ID and no other information Each simple type *ID is restricted to the base type LSID with an appropriate pattern

Rights

The rights holder of this data and the rights held.

Screen

The Screen element is a grouping for Plates.

Settings

Settings is an empty complex type that is contained and extended by all the *Settings elements Each *Settings element defines an attribute named ID of simple type *ID and the other information that is needed.

Shape

The shape element contains a single specific ROI shape and links that to any channels, and a timepoint and a z-section.

ShapeGroup

alias of ome_types.model.shape.Shape

StageLabel

The StageLabel is used to specify a name and position for a stage position in the microscope’s reference frame.

StructuredAnnotations

An unordered collection of annotation attached to objects in the OME data model.

TagAnnotation

A tag annotation (represents a tag or a tagset)

TermAnnotation

A ontology term annotation

TextAnnotation

An abstract Text Annotation from which some others are derived.

TiffData

This described the location of the pixel data in a tiff file.

TimestampAnnotation

A date/time annotation of type xsd:dateTime

TransmittanceRange

This records the range of wavelengths that are transmitted by the filter.

TypeAnnotation

An abstract Type Annotation from which some others are derived.

Well

A Well is a component of the Well/Plate/Screen construct to describe screening applications.

WellSample

WellSample is an individual image that has been captured within a Well.

WellSampleRef

The WellSampleRef element is a reference to a WellSample element.

XMLAnnotation

An general xml annotation.