The OME element is a container for all information objects accessible by OME. These information objects include descriptions of the imaging experiments and the people who perform them, descriptions of the microscope, the resulting images and how they were acquired, the analyses performed on those images, and the analysis results themselves. An OME file may contain any or all of this information. With the creation of the Metadata Only Companion OME-XML and Binary Only OME-TIFF files the top level OME node has changed slightly. It can EITHER: Contain all the previously expected elements OR: Contain a single BinaryOnly element that points at its Metadata Only Companion OME-XML file.
This is the name of the creating application of the OME-XMLand preferably its full version.e.g "CompanyName, SoftwareName, V2.6.3456"This is optional but we hope it will be set by applicationswriting out OME-XML from scratch.
This unique identifier is used to keep track of multi part files. It allows the links between files to survive renaming. While OPTIONAL in the general case this is REQUIRED in a MetadataOnly Companion to a collection of BinaryOnly files.
Source
<xsd:element name="OME"><!-- top level definition --><xsd:annotation><xsd:documentation>The OME element is a container for all information objects accessible by OME. These information objects include descriptions of the imaging experiments and the people who perform them, descriptions of the microscope, the resulting images and how they were acquired, the analyses performed on those images, and the analysis results themselves. An OME file may contain any or all of this information. With the creation of the Metadata Only Companion OME-XML and Binary Only OME-TIFF files the top level OME node has changed slightly. It can EITHER: Contain all the previously expected elements OR: Contain a single BinaryOnly element that points at its Metadata Only Companion OME-XML file.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="Rights" minOccurs="0" maxOccurs="1"/><xsd:choice><!-- Either: standard expected elements --><xsd:sequence><xsd:element ref="Project" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Dataset" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Experiment" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="SPW:Plate" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="SPW:Screen" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Experimenter" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="ExperimenterGroup" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Instrument" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Image" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="SA:StructuredAnnotations" minOccurs="0" maxOccurs="1"/><xsd:element ref="ROI:ROI" minOccurs="0" maxOccurs="unbounded"/></xsd:sequence><!-- Or: Single BinaryOnly element --><xsd:element name="BinaryOnly" minOccurs="1" maxOccurs="1"><xsd:annotation><xsd:documentation>Pointer to an external metadata file. If this element is present, then no other metadata may be present in this file, i.e. this file is a place-holder.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="MetadataFile" type="xsd:string" use="required"><xsd:annotation><xsd:documentation>Filename of the OME-XML metadata file for this binary data. If the file cannot be found, a search can be performed based on the UUID.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="required"><xsd:annotation><xsd:documentation>The unique identifier of another OME-XML block whose metadata describes the binary data in this file. This UUID is considered authoritative regardless of mismatches in the filename.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element><!-- End of MetadataOnly Element --></xsd:choice></xsd:sequence><xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="optional"><xsd:annotation><xsd:documentation>This unique identifier is used to keep track of multi part files. It allows the links between files to survive renaming. While OPTIONAL in the general case this is REQUIRED in a MetadataOnly Companion to a collection of BinaryOnly files.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Creator" type="xsd:string" use="optional"><xsd:annotation><xsd:documentation>This is the name of the creating application of the OME-XML and preferably its full version. e.g "CompanyName, SoftwareName, V2.6.3456" This is optional but we hope it will be set by applications writing out OME-XML from scratch.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType><!-- Unique IDs --><xsd:key name="ChannelIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="DatasetIDKey"><xsd:selector xpath="OME:Dataset"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="DetectorIDKey"><xsd:selector xpath="OME:Instrument/OME:Detector"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="DichroicIDKey"><xsd:selector xpath="OME:Instrument/OME:Dichroic"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ExperimentIDKey"><xsd:selector xpath="OME:Experiment"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ExperimenterIDKey"><xsd:selector xpath="OME:Experimenter"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="FilterIDKey"><xsd:selector xpath="OME:Instrument/OME:Filter"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="FilterSetIDKey"><xsd:selector xpath="OME:Instrument/OME:FilterSet"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ExperimenterGroupIDKey"><xsd:selector xpath="OME:ExperimenterGroup"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ImageIDKey"><xsd:selector xpath="OME:Image"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="InstrumentIDKey"><xsd:selector xpath="OME:Instrument"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="LightSourceIDKey"><xsd:selector xpath="OME:Instrument/OME:LightSource"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="MicrobeamManipulationIDKey"><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ObjectiveIDKey"><xsd:selector xpath="OME:Instrument/OME:Objective"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="PixelsIDKey"><xsd:selector xpath="OME:Image/OME:Pixels"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="PlateIDKey"><xsd:selector xpath="SPW:Plate"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ProjectIDKey"><xsd:selector xpath="OME:Project"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ReagentIDKey"><xsd:selector xpath="SPW:Screen/SPW:Reagent"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ScreenAcquisitionIDKey"><xsd:selector xpath="SPW:Screen/SPW:ScreenAcquisition"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ScreenIDKey"><xsd:selector xpath="SPW:Screen"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="WellIDKey"><xsd:selector xpath="SPW:Plate/SPW:Well"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="WellSampleIDKey"><xsd:selector xpath="SPW:Plate/SPW:Well/SPW:WellSample"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ROIIDKey"><xsd:selector xpath="ROI:ROI"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="ShapeIDKey"><xsd:selector xpath="ROI:ROI/ROI:Union/ROI:Shape"/><xsd:field xpath="@ID"/></xsd:key><xsd:key name="AnnotationIDKey"><xsd:selector xpath="SA:StructuredAnnotations/*"/><xsd:field xpath="@ID"/></xsd:key><!-- Unique references --><xsd:key name="WellSampleImageRefIDKey"><xsd:selector xpath="SPW:Plate/SPW:Well/SPW:WellSample/OME:ImageRef"/><xsd:field xpath="@ID"/></xsd:key><!-- Valid references --><xsd:keyref name="DatasetExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:Dataset/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="DatasetExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey"><xsd:selector xpath="OME:Dataset/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="DatasetProjectIDKeyRef" refer="OME:ProjectIDKey"><xsd:selector xpath="OME:Dataset/OME:ProjectRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimentExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:Experiment/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimentMicrobeamManipulationExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimentMicrobeamManipulationLightSourceSettingsLightSourceIDKeyRef" refer="OME:LightSourceIDKey"><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/OME:LightSourceSettings"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimenterExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey"><xsd:selector xpath="OME:Experimenter/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimenterGroupContactExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:ExperimenterGroup/OME:Contact"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimenterGroupLeaderExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:ExperimenterGroup/OME:Leader"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageDatasetIDKeyRef" refer="OME:DatasetIDKey"><xsd:selector xpath="OME:Image/OME:DatasetRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:Image/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageExperimentIDKeyRef" refer="OME:ExperimentIDKey"><xsd:selector xpath="OME:Image/OME:ExperimentRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey"><xsd:selector xpath="OME:Image/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageInstrumentIDKeyRef" refer="OME:InstrumentIDKey"><xsd:selector xpath="OME:Image/OME:InstrumentRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageMicrobeamManipulationIDKeyRef" refer="OME:MicrobeamManipulationIDKey"><xsd:selector xpath="OME:Image/OME:MicrobeamManipulationRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageObjectiveSettingsObjectiveIDKeyRef" refer="OME:ObjectiveIDKey"><xsd:selector xpath="OME:Image/OME:ObjectiveSettings"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelDetectorSettingsDetectorIDKeyRef" refer="OME:DetectorIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:DetectorSettings"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelFilterSetIDKeyRef" refer="OME:FilterSetIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:FilterSetRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightPathExcitationFilterIDKeyRef" refer="OME:FilterIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:ExcitationFilterPath/OME:FilterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightPathExcitationDichroicIDKeyRef" refer="OME:DichroicIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:ExcitationFilterPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightPathDichroicIDKeyRef" refer="OME:DichroicIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightPathEmissionFilterIDKeyRef" refer="OME:FilterIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:EmissionFilterPath/OME:FilterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightPathEmissionDichroicIDKeyRef" refer="OME:DichroicIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightPath/OME:EmissionFilterPath/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImagePixelsChannelLightSourceSettingsLightSourceIDKeyRef" refer="OME:LightSourceIDKey"><xsd:selector xpath="OME:Image/OME:Pixels/OME:Channel/OME:LightSourceSettings"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="InstrumentFilterSetExcitationFilterIDKeyRef" refer="OME:FilterIDKey"><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:ExcitationFilterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="InstrumentFilterSetDichroicIDKeyRef" refer="OME:DichroicIDKey"><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:DichroicRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="InstrumentFilterSetEmissionFilterIDKeyRef" refer="OME:FilterIDKey"><xsd:selector xpath="OME:Instrument/OME:FilterSet/OME:EmissionFilterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="InstrumentLightSourceLaserPumpLightSourceIDKey" refer="OME:LightSourceIDKey"><xsd:selector xpath="OME:Instrument/OME:LightSource/OME:Laser/OME:Pump"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="PlateScreenIDKeyRef" refer="OME:ScreenIDKey"><xsd:selector xpath="SPW:Plate/SPW:ScreenRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="PlateWellReagentIDKeyRef" refer="OME:ReagentIDKey"><xsd:selector xpath="SPW:Plate/SPW:Well/SPW:ReagentRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="PlateWellWellSampleImageIDKeyRef" refer="OME:ImageIDKey"><xsd:selector xpath="SPW:Plate/SPW:Well/SPW:WellSample/SPW:ImageRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ProjectExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="OME:Project/OME:ExperimenterRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ProjectExperimenterGroupIDKeyRef" refer="OME:ExperimenterGroupIDKey"><xsd:selector xpath="OME:Project/OME:ExperimenterGroupRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ScreenPlateIDKeyRef" refer="OME:PlateIDKey"><xsd:selector xpath="SPW:Screen/SPW:PlateRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ScreenScreenAcquisitionWellSampleIDKeyRef" refer="OME:WellSampleIDKey"><xsd:selector xpath="SPW:Screen/SPW:ScreenAcquisition/SPW:WellSampleRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ExperimentMicrobeamManipulationROIIDKeyRef" refer="OME:ROIIDKey"><xsd:selector xpath="OME:Experiment/OME:MicrobeamManipulation/ROI:ROIRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="ImageROIIDKeyRef" refer="OME:ROIIDKey"><xsd:selector xpath="OME:Image/ROI:ROIRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="AnnotationRefAnnotationIDKeyRef" refer="OME:AnnotationIDKey"><xsd:selector xpath=".//SA:AnnotationRef"/><xsd:field xpath="@ID"/></xsd:keyref><xsd:keyref name="AnnotationAnnotatorExperimenterIDKeyRef" refer="OME:ExperimenterIDKey"><xsd:selector xpath="SA:StructuredAnnotations/*"/><xsd:field xpath="@Annotator"/></xsd:keyref></xsd:element>
<xsd:element name="Rights"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Rights</plural></xsdfu></xsd:appinfo><xsd:documentation>The rights holder of this data and the rights held.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="RightsHolder" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>The rights holder for this data. [plane text multi-line string] e.g. "Copyright (C) 2002-2013 Open Microscopy Environment"</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element name="RightsHeld" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>The rights held by the rights holder. [plane text multi-line string] e.g. "All rights reserved" or "Creative Commons Attribution 3.0 Unported License"</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element></xsd:sequence></xsd:complexType></xsd:element>
The rights holder for this data. [plane text multi-line string]e.g. "Copyright (C) 2002-2013 Open Microscopy Environment"
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="RightsHolder" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>The rights holder for this data. [plane text multi-line string] e.g. "Copyright (C) 2002-2013 Open Microscopy Environment"</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
The rights held by the rights holder. [plane text multi-line string] e.g. "All rights reserved" or "Creative Commons Attribution 3.0 Unported License"
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="RightsHeld" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>The rights held by the rights holder. [plane text multi-line string] e.g. "All rights reserved" or "Creative Commons Attribution 3.0 Unported License"</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
The Project ID is required.Datasets can be grouped into projects using a many-to-many relationship.A Dataset may belong to one or more Projects by including one or more ProjectRef elements which refer to Project IDs.Projects do not directly contain images - only by virtue of containing datasets, which themselves contain images.
<xsd:element name="Project"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Projects</plural></xsdfu></xsd:appinfo><xsd:documentation>The Project ID is required. Datasets can be grouped into projects using a many-to-many relationship. A Dataset may belong to one or more Projects by including one or more ProjectRef elements which refer to Project IDs. Projects do not directly contain images - only by virtue of containing datasets, which themselves contain images.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the project. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="ExperimenterGroupRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="DatasetRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="Name" use="optional" type="xsd:string"/><xsd:attribute name="ID" use="required" type="ProjectID"/></xsd:complexType></xsd:element>
A description for the project. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the project. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
<xsd:element name="ExperimenterRef"><!-- top level definition --><xsd:annotation><xsd:documentation>This empty element has a required Experimenter ID and an optional DocumentID attribute which refers to one of the Experimenters defined within OME.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="ExperimenterID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
<xsd:element name="ExperimenterGroupRef"><!-- top level definition --><xsd:annotation><xsd:documentation>This empty element has a reference (the ExperimenterGroup ID attribute) to a ExperimenterGroup defined within OME.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="ExperimenterGroupID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
The DatasetRef element refers to a Dataset by specifying the Dataset ID attribute.One or more DatasetRef elements may be listed within the Image element to specify what Datasetsthe Image belongs to.
<xsd:element name="DatasetRef"><!-- top level definition --><xsd:annotation><xsd:documentation>The DatasetRef element refers to a Dataset by specifying the Dataset ID attribute. One or more DatasetRef elements may be listed within the Image element to specify what Datasets the Image belongs to.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="DatasetID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
An element specifying a collection of images that are always processed together.Images can belong to more than one Dataset, and a Dataset may contain more than one Image.Images contain one or more DatasetRef elements to specify what datasets they belong to.Once a Dataset has been processed in any way, its collection of images cannot be altered.The ExperimenterRef and ExperimenterGroupRef elements specify the person and group this Dataset belongs to.Projects may contain one or more Datasets, and Datasets may belong to one or more Projects.This relationship is specified by listing DatasetRef elements within the Project element.
A name for the dataset that is suitable be presented to the user.
Source
<xsd:element name="Dataset"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Datasets</plural></xsdfu></xsd:appinfo><xsd:documentation>An element specifying a collection of images that are always processed together. Images can belong to more than one Dataset, and a Dataset may contain more than one Image. Images contain one or more DatasetRef elements to specify what datasets they belong to. Once a Dataset has been processed in any way, its collection of images cannot be altered. The ExperimenterRef and ExperimenterGroupRef elements specify the person and group this Dataset belongs to. Projects may contain one or more Datasets, and Datasets may belong to one or more Projects. This relationship is specified by listing DatasetRef elements within the Project element.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the dataset. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="ExperimenterGroupRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="ImageRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="Name" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A name for the dataset that is suitable be presented to the user.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="ID" use="required" type="DatasetID"/></xsd:complexType></xsd:element>
A description for the dataset. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the dataset. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
<xsd:element name="ImageRef"><!-- top level definition --><xsd:annotation><xsd:documentation>The ImageRef element is a reference to a OME:Image element.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="ImageID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
This element describes the type of experiment. The required Type attribute must contain one or more entries from the following list:FP FRET Time-lapse 4-D+ Screen Immunocytochemistry FISH Electrophysiology Ion-Imaging Colocalization PGI/DocumentationFRAP Photoablation Optical-Trapping Photoactivation Fluorescence-Lifetime Spectral-Imaging OtherFP refers to fluorescent proteins, PGI/Documentation is not a 'data' image.The optional Description element may contain free text to further describe the experiment.
<xsd:element name="Experiment"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Experiments</plural></xsdfu></xsd:appinfo><xsd:documentation>This element describes the type of experiment. The required Type attribute must contain one or more entries from the following list: FP FRET Time-lapse 4-D+ Screen Immunocytochemistry FISH Electrophysiology Ion-Imaging Colocalization PGI/Documentation FRAP Photoablation Optical-Trapping Photoactivation Fluorescence-Lifetime Spectral-Imaging Other FP refers to fluorescent proteins, PGI/Documentation is not a 'data' image. The optional Description element may contain free text to further describe the experiment.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the experiment. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>This is a link to the Experimenter who conducted the experiment</xsd:documentation></xsd:annotation></xsd:element><xsd:element ref="MicrobeamManipulation" minOccurs="0" maxOccurs="unbounded"/></xsd:sequence><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>A term to describe the type of experiment.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:list><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="FP"/><xsd:enumeration value="FRET"/><!-- Förster resonance energy transfer, also known as fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) --><xsd:enumeration value="TimeLapse"/><!-- Time-lapse microscopy (microphotography, photomicrography) --><xsd:enumeration value="FourDPlus"/><xsd:enumeration value="Screen"/><xsd:enumeration value="Immunocytochemistry"/><xsd:enumeration value="Immunofluorescence"/><xsd:enumeration value="FISH"/><!-- Fluorescent in situ hybridization --><xsd:enumeration value="Electrophysiology"/><xsd:enumeration value="IonImaging"/><xsd:enumeration value="Colocalization"/><xsd:enumeration value="PGIDocumentation"/><xsd:enumeration value="FluorescenceLifetime"/><!-- Fluorescence lifetime imaging (FLIM) --><xsd:enumeration value="SpectralImaging"/><xsd:enumeration value="Photobleaching"/><xsd:enumeration value="SPIM"/><!-- Selective or Single Plane Illumination Microscopy --><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:list></xsd:simpleType></xsd:attribute><xsd:attribute name="ID" use="required" type="ExperimentID"/></xsd:complexType></xsd:element>
A description for the experiment. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the experiment. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
Defines a microbeam operation type and the region of the image it was applied to.The LightSourceRef element is a reference to a LightSource specified in the Instrument element which was used for a technique other than illumination forthe purpose of imaging. For example, a laser used for photobleaching.
<xsd:element name="MicrobeamManipulation"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>MicrobeamManipulations</plural></xsdfu></xsd:appinfo><xsd:documentation>Defines a microbeam operation type and the region of the image it was applied to. The LightSourceRef element is a reference to a LightSource specified in the Instrument element which was used for a technique other than illumination for the purpose of imaging. For example, a laser used for photobleaching.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the Microbeam Manipulation. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ROI:ROIRef" minOccurs="1" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="1" maxOccurs="1"/><xsd:element ref="LightSourceSettings" minOccurs="0" maxOccurs="unbounded"/></xsd:sequence><xsd:attribute name="ID" use="required" type="MicrobeamManipulationID"/><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>The type of manipulation performed.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:list><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="FRAP"/><!-- Fluorescence recovery after photobleaching --><xsd:enumeration value="FLIP"/><!-- Fluorescence Loss in Photobleaching --><xsd:enumeration value="InverseFRAP"/><!-- iFRAP, inverse FRAP --><xsd:enumeration value="Photoablation"/><xsd:enumeration value="Photoactivation"/><xsd:enumeration value="Uncaging"/><xsd:enumeration value="OpticalTrapping"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:list></xsd:simpleType></xsd:attribute></xsd:complexType></xsd:element>
A description for the Microbeam Manipulation. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the Microbeam Manipulation. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
The Wavelength of the light source. nanometres[nm]
Source
<xsd:element name="LightSourceSettings"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>LightSourceSettingsCombinations</plural></xsdfu></xsd:appinfo></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Settings"><xsd:attribute name="ID" use="required" type="LightSourceID"/><xsd:attribute name="Attenuation" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>The Attenuation of the light source [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Wavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The Wavelength of the light source. nanometres[nm]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
This element describes a person who performed an imaging experiment.This person may also be a user of the OME system, in which case the UserName element contains their login name.Experimenters may belong to one or more groups which are specified using one or more ExperimenterGroupRef elements.
A person's InstitutionThe organizing structure that people belong to other than groups. A university, or company, etc.We do not specify a department element, and do not mean for Institution to be used in this way.We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed locationand of being more recognizable than a group of experimenters. [plain text string]
This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]
Source
<xsd:element name="Experimenter"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Experimenters</plural><global/></xsdfu></xsd:appinfo><xsd:documentation>This element describes a person who performed an imaging experiment. This person may also be a user of the OME system, in which case the UserName element contains their login name. Experimenters may belong to one or more groups which are specified using one or more ExperimenterGroupRef elements.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="ID" use="required" type="ExperimenterID"/><xsd:attribute name="FirstName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>First name, sometime called christian name or given name or forename. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="MiddleName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>Any other names. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="LastName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A person's last name sometimes called surname or family name. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Email" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A person's email address. [valid email address as string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Institution" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A person's Institution The organizing structure that people belong to other than groups. A university, or company, etc. We do not specify a department element, and do not mean for Institution to be used in this way. We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed location and of being more recognizable than a group of experimenters. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="UserName" use="optional" type="xsd:string"><xsd:annotation><xsd:appinfo><xsdfu><unique/></xsdfu></xsd:appinfo><xsd:documentation>This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
The ExperimenterGroupID is required.Information should ideally be specified for at least one Leader as a contact for the group.The Leaders are themselves Experimenters.
<xsd:element name="ExperimenterGroup"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>ExperimenterGroups</plural><global/></xsdfu></xsd:appinfo><xsd:documentation>The ExperimenterGroupID is required. Information should ideally be specified for at least one Leader as a contact for the group. The Leaders are themselves Experimenters.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the group. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/><childordered/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="Leader" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="Name" use="optional" type="xsd:string"><xsd:annotation><xsd:appinfo><xsdfu><unique/></xsdfu></xsd:appinfo></xsd:annotation></xsd:attribute><xsd:attribute name="ID" use="required" type="ExperimenterGroupID"/></xsd:complexType></xsd:element>
A description for the group. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the group. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
<xsd:element name="Leader"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Leaders</plural></xsdfu></xsd:appinfo><xsd:documentation>Contact information for a ExperimenterGroup leader specified using a reference to an Experimenter element defined elsewhere in the document.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="ExperimenterID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
This element describes the instrument used to capture the Image.It is primarily a container for manufacturer's model and catalognumbers for the Microscope, LightSource, Detector, Objective andFilters components.The Objective element contains the additional elements LensNA and Magnification.The Filters element can be composed either of separate excitation,emission filters and a dichroic mirror or a single filter set.Within the Image itself, a reference is made to this one Filter element.There may be multiple light sources, detectors, objectives and filters on a microscope.Each of these has their own ID attribute, which can be referred to from Channel.It is understood that the light path configuration can be differentfor each channel, but cannot be different for each timepoint oreach plane of an XYZ stack.
<xsd:element name="Instrument"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Instruments</plural></xsdfu></xsd:appinfo><xsd:documentation>This element describes the instrument used to capture the Image. It is primarily a container for manufacturer's model and catalog numbers for the Microscope, LightSource, Detector, Objective and Filters components. The Objective element contains the additional elements LensNA and Magnification. The Filters element can be composed either of separate excitation, emission filters and a dichroic mirror or a single filter set. Within the Image itself, a reference is made to this one Filter element. There may be multiple light sources, detectors, objectives and filters on a microscope. Each of these has their own ID attribute, which can be referred to from Channel. It is understood that the light path configuration can be different for each channel, but cannot be different for each timepoint or each plane of an XYZ stack.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="Microscope" minOccurs="0" maxOccurs="1"/><xsd:element ref="LightSource" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Detector" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Objective" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="FilterSet" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Filter" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="Dichroic" minOccurs="0" maxOccurs="unbounded"/></xsd:sequence><xsd:attribute name="ID" use="required" type="InstrumentID"/></xsd:complexType></xsd:element>
The lightsource for the instrument. An instrument may have several light sources.The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'.Each of the light source types has its own Type attribute to further differentiate the light source(eg, Nd-YAG for Laser or Hg for Arc).
A LightSource ID must be specified for each light source, and the individuallight sources can be referred to by their LightSource IDs (eg from Channel).
The serial number of the component. [plain text string]
Source
<xsd:element name="LightSource"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>LightSources</plural><abstractproprietary/></xsdfu></xsd:appinfo><xsd:documentation>The lightsource for the instrument. An instrument may have several light sources. The type of lightsource is specified by one of the child-elements which are 'Laser', 'Filament', 'Arc' or 'LightEmittingDiode'. Each of the light source types has its own Type attribute to further differentiate the light source (eg, Nd-YAG for Laser or Hg for Arc).</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="ManufacturerSpec"><xsd:choice minOccurs="1" maxOccurs="1"><xsd:element ref="Laser" minOccurs="1" maxOccurs="1"/><xsd:element ref="Filament" minOccurs="1" maxOccurs="1"/><xsd:element ref="Arc" minOccurs="1" maxOccurs="1"/><xsd:element ref="LightEmittingDiode" minOccurs="1" maxOccurs="1"/></xsd:choice><xsd:attribute name="ID" use="required" type="LightSourceID"><xsd:annotation><xsd:documentation>A LightSource ID must be specified for each light source, and the individual light sources can be referred to by their LightSource IDs (eg from Channel).</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Power" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The light-source power. units milliwatts[mW]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
<xsd:element name="Laser"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Lasers</plural></xsdfu></xsd:appinfo><xsd:documentation>Laser types are specified using two attributes - the Type and the LaserMedium.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="Pump" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>The Laser element may contain a Pump sub-element which refers to a LightSource used as a laser pump.</xsd:documentation></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>Type is the general category of laser.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Excimer"/><xsd:enumeration value="Gas"/><xsd:enumeration value="MetalVapor"/><xsd:enumeration value="SolidState"/><xsd:enumeration value="Dye"/><xsd:enumeration value="Semiconductor"/><xsd:enumeration value="FreeElectron"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="LaserMedium" use="optional"><xsd:annotation><xsd:documentation>The Medium attribute specifies the actual lasing medium for a given laser type.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><!-- MetalVaporLaserMedia --><xsd:enumeration value="Cu"/><xsd:enumeration value="Ag"/><!-- ExcimerLaserMedia --><xsd:enumeration value="ArFl"/><xsd:enumeration value="ArCl"/><xsd:enumeration value="KrFl"/><xsd:enumeration value="KrCl"/><xsd:enumeration value="XeFl"/><xsd:enumeration value="XeCl"/><xsd:enumeration value="XeBr"/><!-- GasLaserMedia --><xsd:enumeration value="N"/><xsd:enumeration value="Ar"/><xsd:enumeration value="Kr"/><xsd:enumeration value="Xe"/><xsd:enumeration value="HeNe"/><xsd:enumeration value="HeCd"/><xsd:enumeration value="CO"/><xsd:enumeration value="CO2"/><xsd:enumeration value="H2O"/><xsd:enumeration value="HFl"/><!-- SolidStateLaserMedia --><xsd:enumeration value="NdGlass"/><xsd:enumeration value="NdYAG"/><xsd:enumeration value="ErGlass"/><xsd:enumeration value="ErYAG"/><xsd:enumeration value="HoYLF"/><xsd:enumeration value="HoYAG"/><xsd:enumeration value="Ruby"/><xsd:enumeration value="TiSapphire"/><xsd:enumeration value="Alexandrite"/><!-- DyeLaserMedia --><xsd:enumeration value="Rhodamine6G"/><xsd:enumeration value="CoumarinC30"/><!-- SemiconductorLaserMedia --><xsd:enumeration value="GaAs"/><xsd:enumeration value="GaAlAs"/><!-- FreeElectronLaserMedia --><xsd:enumeration value="EMinus"/><!-- OtherLaserMedia --><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="Wavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The Wavelength of the laser in nanometres[nm]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="FrequencyMultiplication" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>FrequencyMultiplication that may be specified. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Tuneable" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>Whether or not the laser is Tuneable [flag]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Pulse" use="optional"><xsd:annotation><xsd:documentation>The Pulse mode of the laser.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="CW"/><xsd:enumeration value="Single"/><xsd:enumeration value="QSwitched"/><xsd:enumeration value="Repetitive"/><xsd:enumeration value="ModeLocked"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="PockelCell" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>If true the laser has a PockelCell to rotate the polarization of the beam. [flag]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="RepetitionRate" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The is the rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'. hertz[Hz]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
<xsd:element name="Pump"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Pumps</plural></xsdfu></xsd:appinfo><xsd:documentation>The Pump element is a reference to a LightSource. It is used within the Laser element to specify the light source for the laser's pump (if any).</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="LightSourceID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen.The Power of the Filament is now stored in the LightSource.
<xsd:element name="Filament"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Filaments</plural></xsdfu></xsd:appinfo><xsd:documentation>The Filament element is used to describe various kinds of filament bulbs such as Incadescent or Halogen. The Power of the Filament is now stored in the LightSource.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>The type of filament.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Incandescent"/><xsd:enumeration value="Halogen"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute></xsd:complexType></xsd:element>
<xsd:element name="Arc"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Arcs</plural></xsdfu></xsd:appinfo><xsd:documentation>The Arc element is used to describe various kinds of Arc lamps - Hg, Xe, HgXe. The Power of the Arc is now stored in the LightSource.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>The type of Arc lamp.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Hg"/><xsd:enumeration value="Xe"/><xsd:enumeration value="HgXe"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute></xsd:complexType></xsd:element>
The LightEmittingDiode element is used to describe various kinds of LED lamps. As the LightEmittingDiode is inside a LightSource it already has available the values from ManufacturerSpec (Manufacturer, Model, SerialNumber, LotNumber) And the values from LightSource which includes Power in milliwatts We have looked at extending this element but have had a problem producing a generic solution. Possible attributes talked about adding include: Power in lumens - but this is complicated by multi-channel devices like CoolLED where each channel's power is different Wavelength Range - not a simple value so would require multiple attributes or a child element Angle of Projection - this would be further affected by the optics used for filtering the naked LED or that combine power from multiple devices These values are further affected if you over-drive the LED resulting in a more complex system Another issue is that LED's may not be used directly for illumination but as drivers for secondary emissions from doped fiber optics. This would require the fiber optics to be modeled. Thanks to Paul Goodwin of Applied Precision of information about this topic.
<xsd:element name="LightEmittingDiode"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>LightEmittingDiodes</plural></xsdfu></xsd:appinfo><xsd:documentation>The LightEmittingDiode element is used to describe various kinds of LED lamps. As the LightEmittingDiode is inside a LightSource it already has available the values from ManufacturerSpec (Manufacturer, Model, SerialNumber, LotNumber) And the values from LightSource which includes Power in milliwatts We have looked at extending this element but have had a problem producing a generic solution. Possible attributes talked about adding include: Power in lumens - but this is complicated by multi-channel devices like CoolLED where each channel's power is different Wavelength Range - not a simple value so would require multiple attributes or a child element Angle of Projection - this would be further affected by the optics used for filtering the naked LED or that combine power from multiple devices These values are further affected if you over-drive the LED resulting in a more complex system Another issue is that LED's may not be used directly for illumination but as drivers for secondary emissions from doped fiber optics. This would require the fiber optics to be modeled. Thanks to Paul Goodwin of Applied Precision of information about this topic.</xsd:documentation></xsd:annotation></xsd:element>
The type of detector used to capture the image. The Detector ID can be used as a reference within the Channel element in the Image element. The values stored in Detector represent the fixed values, variable values modified during the acquisition go in DetectorSettings Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.
Gain applied to the detector signal.This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}
The fixed Zoom for a detector. [units:none] {used:PMT}
Source
<xsd:element name="Detector"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Detectors</plural></xsdfu></xsd:appinfo><xsd:documentation>The type of detector used to capture the image. The Detector ID can be used as a reference within the Channel element in the Image element. The values stored in Detector represent the fixed values, variable values modified during the acquisition go in DetectorSettings Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="ManufacturerSpec"><xsd:attribute name="Gain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Detector Gain for this detector, as a float. [units:none] {used:CCD,EMCCD,PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Voltage" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Voltage of the detector (e.g. PMT voltage) as a float. volts[V] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Offset" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Detector Offset. [units:none] {used:CCD,EMCCD}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Zoom" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The fixed Zoom for a detector. [units:none] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="AmplificationGain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>Gain applied to the detector signal. This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="ID" use="required" type="DetectorID"/><xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>The Type of detector. E.g. CCD, PMT, EMCCD etc.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="CCD"/><!-- Charge-Coupled Device --><xsd:enumeration value="IntensifiedCCD"/><xsd:enumeration value="AnalogVideo"/><xsd:enumeration value="PMT"/><!-- Photomultiplier tube --><xsd:enumeration value="Photodiode"/><xsd:enumeration value="Spectroscopy"/><xsd:enumeration value="LifetimeImaging"/><xsd:enumeration value="CorrelationSpectroscopy"/><xsd:enumeration value="FTIR"/><!-- Fourier transform infrared spectroscopy --><xsd:enumeration value="EMCCD"/><!-- Electron Multiplying Charge Coupled Device --><xsd:enumeration value="APD"/><!-- Avalanche Photodiode --><xsd:enumeration value="CMOS"/><!-- complementary metal oxide semiconductor --><xsd:enumeration value="EBCCD"/><!-- electron-bombarded charge-coupled device --><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
A description of the microscope's objective lens.Required elements include the lens numerical aperture,and the magnification, both of which a floatingpoint (real) numbers.The values are those that are fixed for a particularobjective: either because it has been manufactured tothis specification or the value has been measured onthis particular objective.Correction: This is the type of correction coating applied to this lens.Immersion: This is the types of immersion medium the lens is designed towork with. It is not the same as 'Medium' in ObjectiveRef (asingle type) as here Immersion can have compound values like 'Multi'.LensNA: The numerical aperture of the lens (as a float)NominalMagnification: The specified magnification e.g. x10CalibratedMagnification: The measured magnification e.g. x10.3WorkingDistance: WorkingDistance of the lens. The Units are microns[µm].
The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none]Note: The type of this has been changed from int to float to allowthe specification of additional lenses e.g. 0.5X lens
The working distance of the lens expressed as a floating point (real) number. Units are microns[µm].
Source
<xsd:element name="Objective"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Objectives</plural></xsdfu></xsd:appinfo><xsd:documentation>A description of the microscope's objective lens. Required elements include the lens numerical aperture, and the magnification, both of which a floating point (real) numbers. The values are those that are fixed for a particular objective: either because it has been manufactured to this specification or the value has been measured on this particular objective. Correction: This is the type of correction coating applied to this lens. Immersion: This is the types of immersion medium the lens is designed to work with. It is not the same as 'Medium' in ObjectiveRef (a single type) as here Immersion can have compound values like 'Multi'. LensNA: The numerical aperture of the lens (as a float) NominalMagnification: The specified magnification e.g. x10 CalibratedMagnification: The measured magnification e.g. x10.3 WorkingDistance: WorkingDistance of the lens. The Units are microns[µm].</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="ManufacturerSpec"><xsd:attribute name="ID" use="required" type="ObjectiveID"/><xsd:attribute name="Correction" use="optional"><xsd:annotation><xsd:documentation>The correction applied to the lens</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="UV"/><xsd:enumeration value="PlanApo"/><xsd:enumeration value="PlanFluor"/><xsd:enumeration value="SuperFluor"/><xsd:enumeration value="VioletCorrected"/><xsd:enumeration value="Achro"/><xsd:enumeration value="Achromat"/><xsd:enumeration value="Fluor"/><xsd:enumeration value="Fl"/><xsd:enumeration value="Fluar"/><xsd:enumeration value="Neofluar"/><xsd:enumeration value="Fluotar"/><xsd:enumeration value="Apo"/><xsd:enumeration value="PlanNeofluar"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="Immersion" use="optional"><xsd:annotation><xsd:documentation>The immersion medium the lens is designed for</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Oil"/><xsd:enumeration value="Water"/><xsd:enumeration value="WaterDipping"/><xsd:enumeration value="Air"/><xsd:enumeration value="Multi"/><xsd:enumeration value="Glycerol"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="LensNA" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The numerical aperture of the lens expressed as a floating point (real) number. Expected range 0.02 - 1.5 [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="NominalMagnification" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none] Note: The type of this has been changed from int to float to allow the specification of additional lenses e.g. 0.5X lens</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="CalibratedMagnification" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="WorkingDistance" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The working distance of the lens expressed as a floating point (real) number. Units are microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Iris" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>Records whether or not the objective was fitted with an Iris. [flag]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
A filter is either an excitation or emission filters.There should be one filter element specified per wavelength in the image.The channel number associated with a filter set is specified in Channel.It is based on the FilterSpec type, so has the required attributes Manufacturer, Model, and LotNumber.It may also contain a Type attribute which may be set to'LongPass', 'ShortPass', 'BandPass', 'MultiPass','Dichroic', 'NeutralDensity', 'Tuneable' or 'Other'.It can be associated with an optional FilterWheel - Note: this is not the same as a FilterSet
A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]
<xsd:element name="Filter"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Filters</plural></xsdfu></xsd:appinfo><xsd:documentation>A filter is either an excitation or emission filters. There should be one filter element specified per wavelength in the image. The channel number associated with a filter set is specified in Channel. It is based on the FilterSpec type, so has the required attributes Manufacturer, Model, and LotNumber. It may also contain a Type attribute which may be set to 'LongPass', 'ShortPass', 'BandPass', 'MultiPass', 'Dichroic', 'NeutralDensity', 'Tuneable' or 'Other'. It can be associated with an optional FilterWheel - Note: this is not the same as a FilterSet</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="ManufacturerSpec"><xsd:sequence><xsd:element ref="TransmittanceRange" minOccurs="0" maxOccurs="1"/></xsd:sequence><xsd:attribute name="Type" use="optional"><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Dichroic"/><xsd:enumeration value="LongPass"/><xsd:enumeration value="ShortPass"/><xsd:enumeration value="BandPass"/><xsd:enumeration value="MultiPass"/><xsd:enumeration value="NeutralDensity"/><xsd:enumeration value="Tuneable"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="FilterWheel" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="ID" use="required" type="FilterID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
The amount of light the filter transmits at a maximum [units:none]A fraction, as a value from 0.0 to 1.0.
Source
<xsd:element name="TransmittanceRange"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>TransmittanceRanges</plural></xsdfu></xsd:appinfo><xsd:documentation>This records the range of wavelengths that are transmitted by the filter. It also records the maximum amount of light transmitted.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="CutIn" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units: nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="CutOut" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units: nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="CutInTolerance" use="optional" type="NonNegativeInt"><xsd:annotation><xsd:documentation>CutInTolerance Units: nanometres[nm],</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="CutOutTolerance" use="optional" type="NonNegativeInt"><xsd:annotation><xsd:documentation>CutOutTolerance Units: nanometres[nm],</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Transmittance" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
The serial number of the component. [plain text string]
Source
<xsd:element name="Dichroic"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Dichroics</plural></xsdfu></xsd:appinfo><xsd:documentation>The dichromatic beamsplitter or dichroic mirror used for this filter combination.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="ManufacturerSpec"><xsd:attribute name="ID" use="required" type="DichroicID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
This element describes the actual image and its meta-data. The elements that are references (ending in Ref or Settings) refer to elements defined outside of the Image element. Ref elements are simple links, while Settings elements are links with additional values. If any of the required Image attributes or elements are missing, its guaranteed to be an invalid document. The required attributes and elements are ID and Pixels. ExperimenterRef is required for all Images with well formed LSIDs. ImageType is a vendor-specific designation of the type of image this is. Examples of ImageType include 'STK', 'SoftWorx', etc. The Name attributes are in all cases the name of the element instance. In this case, the name of the image, not necessarily the filename. Physical size of pixels are microns[µm].
<xsd:element name="Image"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Images</plural></xsdfu></xsd:appinfo><xsd:documentation>This element describes the actual image and its meta-data. The elements that are references (ending in Ref or Settings) refer to elements defined outside of the Image element. Ref elements are simple links, while Settings elements are links with additional values. If any of the required Image attributes or elements are missing, its guaranteed to be an invalid document. The required attributes and elements are ID and Pixels. ExperimenterRef is required for all Images with well formed LSIDs. ImageType is a vendor-specific designation of the type of image this is. Examples of ImageType include 'STK', 'SoftWorx', etc. The Name attributes are in all cases the name of the element instance. In this case, the name of the image, not necessarily the filename. Physical size of pixels are microns[µm].</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="AcquisitionDate" minOccurs="0" maxOccurs="1" type="xsd:dateTime"><xsd:annotation><xsd:documentation>The acquisition date of the Image. The element contains a string in the ISO 8601 dateTime format (i.e. 1988-04-07T18:39:09)</xsd:documentation></xsd:annotation></xsd:element><xsd:element ref="ExperimenterRef" minOccurs="0" maxOccurs="1"/><xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the image. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element><xsd:element ref="ExperimentRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="ExperimenterGroupRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="InstrumentRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="ObjectiveSettings" minOccurs="0" maxOccurs="1"/><xsd:element ref="ImagingEnvironment" minOccurs="0" maxOccurs="1"/><xsd:element ref="StageLabel" minOccurs="0" maxOccurs="1"/><xsd:element ref="Pixels" minOccurs="1" maxOccurs="1"/><xsd:element ref="ROI:ROIRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="MicrobeamManipulationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="ID" use="required" type="ImageID"/><xsd:attribute name="Name" use="optional" type="xsd:string"/></xsd:complexType></xsd:element>
The acquisition date of the Image.The element contains a string in the ISO 8601 dateTime format (i.e. 1988-04-07T18:39:09)
Diagram
Type
xsd:dateTime
Properties
content
simple
minOccurs
0
maxOccurs
1
Source
<xsd:element name="AcquisitionDate" minOccurs="0" maxOccurs="1" type="xsd:dateTime"><xsd:annotation><xsd:documentation>The acquisition date of the Image. The element contains a string in the ISO 8601 dateTime format (i.e. 1988-04-07T18:39:09)</xsd:documentation></xsd:annotation></xsd:element>
A description for the image. [plane text multi-line string]
Diagram
Type
restriction of xsd:string
Properties
content
simple
minOccurs
0
maxOccurs
1
Facets
whiteSpace
preserve
Source
<xsd:element name="Description" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>A description for the image. [plane text multi-line string]</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:whiteSpace value="preserve"/></xsd:restriction></xsd:simpleType></xsd:element>
<xsd:element name="InstrumentRef"><!-- top level definition --><xsd:annotation><xsd:documentation>This empty element can be used (via the required Instrument ID attribute) to refer to an Instrument defined within OME.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="InstrumentID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
The RefractiveIndex is that of the immersion medium. This isa ratio so it also unit-less. [units:none]
Source
<xsd:element name="ObjectiveSettings"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>ObjectiveSettingsCombinations</plural></xsdfu></xsd:appinfo><xsd:documentation>This holds the setting applied to an objective as well as a reference to the objective. The ID is the objective used in this case.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Settings"><xsd:attribute name="ID" use="required" type="ObjectiveID"/><xsd:attribute name="CorrectionCollar" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The CorrectionCollar is normally an adjustable ring on the objective. Each has an arbitrary scale on it so the values is unit-less. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Medium" use="optional"><xsd:simpleType><xsd:annotation><xsd:documentation>A description of a Medium used for the lens. The Medium is the actual immersion medium used in this case.</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:string"><xsd:enumeration value="Air"/><xsd:enumeration value="Oil"/><xsd:enumeration value="Water"/><xsd:enumeration value="Glycerol"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="RefractiveIndex" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The RefractiveIndex is that of the immersion medium. This is a ratio so it also unit-less. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
<xsd:element name="ImagingEnvironment"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>ImagingEnvironments</plural></xsdfu></xsd:appinfo><xsd:documentation>This describes the environment that the biological sample was in during the experiment.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="Temperature" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Temperature is in Celsius[°C].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="AirPressure" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>AirPressure is in millibars[mbar].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Humidity" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>Humidity around the sample [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="CO2Percent" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>Carbon Dioxide concentration around the sample [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
The Z position of the stage label. [units are in the microscope reference frame]
Source
<xsd:element name="StageLabel"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>StageLabels</plural></xsdfu></xsd:appinfo><xsd:documentation>The StageLabel is used to specify a name and position for a stage position in the microscope's reference frame.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="Name" use="required" type="xsd:string"/><xsd:attribute name="X" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The X position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Y" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Y position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Z" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Z position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
Pixels is going to be removed in the future, but it is still required. This is just notice that the contents of Pixels will be moved up to Image in a future release. This is because there has only been 1 Pixels object in each Image for some time. The concept of multiple Pixels sets for one Image failed to take off. It is therefore redundant. The Image will be unreadable if any of the required Pixel attributes are missing. The Pixels themselves can be stored within the OME-XML compressed by plane, and encoded in Base64. Or the Pixels may be stored in TIFF format. The Pixels element should contain a list of BinData or TiffData, each containing a single plane of pixels. These Pixels elements, when read in document order, must produce a 5-D pixel array of the size specified in this element, and in the dimension order specified by 'DimensionOrder'. All of the values in the Pixels object when present should match the same value stored in any associated TIFF format (e.g. SizeX should be the same). Where there is a mismatch our readers will take the value from the TIFF structure as overriding the value in the OME-XML. This is simply a pragmatic decision as it increases the likelihood of reading data from a slightly incorrect file.
This is true if the pixels data was written in BigEndian order. If this value is present it should match the value used in BinData or TiffData. If it does not a reader should honour the value used in the BinData or TiffData. This values is useful for MetadataOnly files and is to allow for future storage solutions.
The number of bits within the type storing each pixel that are significant.e.g. you can store 12 bit data within a 16 bit type.This does not reduce the storage requirements but can be a useful indicatorwhen processing or viewing the image data.
TimeIncrement is used for time series that have a globaltiming specification instead of per-timepoint timing info.For example in a video stream. The unit is seconds[s].
The variable type used to represent each pixel in the image.
Source
<xsd:element name="Pixels"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Pixels</plural></xsdfu></xsd:appinfo><xsd:documentation>Pixels is going to be removed in the future, but it is still required. This is just notice that the contents of Pixels will be moved up to Image in a future release. This is because there has only been 1 Pixels object in each Image for some time. The concept of multiple Pixels sets for one Image failed to take off. It is therefore redundant. The Image will be unreadable if any of the required Pixel attributes are missing. The Pixels themselves can be stored within the OME-XML compressed by plane, and encoded in Base64. Or the Pixels may be stored in TIFF format. The Pixels element should contain a list of BinData or TiffData, each containing a single plane of pixels. These Pixels elements, when read in document order, must produce a 5-D pixel array of the size specified in this element, and in the dimension order specified by 'DimensionOrder'. All of the values in the Pixels object when present should match the same value stored in any associated TIFF format (e.g. SizeX should be the same). Where there is a mismatch our readers will take the value from the TIFF structure as overriding the value in the OME-XML. This is simply a pragmatic decision as it increases the likelihood of reading data from a slightly incorrect file.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="Channel" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><ordered/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:choice minOccurs="1" maxOccurs="1"><xsd:element ref="BIN:BinData" minOccurs="1" maxOccurs="unbounded"/><xsd:element ref="TiffData" minOccurs="1" maxOccurs="unbounded"/><xsd:element ref="MetadataOnly" minOccurs="1" maxOccurs="1"/></xsd:choice><xsd:element ref="Plane" minOccurs="0" maxOccurs="unbounded"/><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="ID" use="required" type="PixelsID"/><xsd:attribute name="DimensionOrder" use="required"><xsd:annotation><xsd:documentation>The order in which the individual planes of data are interleaved.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="XYZCT"/><xsd:enumeration value="XYZTC"/><xsd:enumeration value="XYCTZ"/><xsd:enumeration value="XYCZT"/><xsd:enumeration value="XYTCZ"/><xsd:enumeration value="XYTZC"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="Type" use="required" type="PixelType"><xsd:annotation><xsd:documentation>The variable type used to represent each pixel in the image.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SignificantBits" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The number of bits within the type storing each pixel that are significant. e.g. you can store 12 bit data within a 16 bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the image data.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Interleaved" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>How the channels are arranged within the data block: true if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="BigEndian" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>This is true if the pixels data was written in BigEndian order. If this value is present it should match the value used in BinData or TiffData. If it does not a reader should honour the value used in the BinData or TiffData. This values is useful for MetadataOnly files and is to allow for future storage solutions.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SizeX" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SizeY" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SizeZ" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SizeC" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SizeT" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PhysicalSizeX" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PhysicalSizeY" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PhysicalSizeZ" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="TimeIncrement" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>TimeIncrement is used for time series that have a global timing specification instead of per-timepoint timing info. For example in a video stream. The unit is seconds[s].</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
There must be one per channel in the Image, even for a single-plane image.And information about how each of them was acquired is stored in the various optional *Ref elements. Each Logical Channel is composed of one or moreChannelComponents. For example, an entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrumconstituting a ChannelComponent of the FTIR Logical Channel. An RGB image where the Red, Green and Blue components do not reflect discrete probes but areinstead the output of a color camera would be treated similarly - one Logical channel with three ChannelComponents in this case.The total number of ChannelComponents for a set of pixels must equal SizeC.The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', 'Oblique', or 'NonLinear'.The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence:Name -> Fluor -> EmissionWavelength -> ChannelComponent/Index.
A color used to render this channel - encoded as RGBAThe default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value)NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.
The NDfilter attribute is used to specify the combined effect of any neutral density filters used. [units optical density expressed as a PercentFraction]
The number of samples the detector takes to form each pixel value. [units:none]Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings
Source
<xsd:element name="Channel"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Channels</plural></xsdfu></xsd:appinfo><xsd:documentation>There must be one per channel in the Image, even for a single-plane image. And information about how each of them was acquired is stored in the various optional *Ref elements. Each Logical Channel is composed of one or more ChannelComponents. For example, an entire spectrum in an FTIR experiment may be stored in a single Logical Channel with each discrete wavenumber of the spectrum constituting a ChannelComponent of the FTIR Logical Channel. An RGB image where the Red, Green and Blue components do not reflect discrete probes but are instead the output of a color camera would be treated similarly - one Logical channel with three ChannelComponents in this case. The total number of ChannelComponents for a set of pixels must equal SizeC. The IlluminationType attribute is a string enumeration which may be set to 'Transmitted', 'Epifluorescence', 'Oblique', or 'NonLinear'. The user interface logic for labeling a given channel for the user should use the first existing attribute in the following sequence: Name -> Fluor -> EmissionWavelength -> ChannelComponent/Index.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element ref="LightSourceSettings" minOccurs="0" maxOccurs="1"/><xsd:element ref="DetectorSettings" minOccurs="0" maxOccurs="1"/><xsd:element ref="FilterSetRef" minOccurs="0" maxOccurs="1"/><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element><xsd:element ref="LightPath" minOccurs="0" maxOccurs="1"/></xsd:sequence><xsd:attribute name="ID" use="required" type="ChannelID"/><xsd:attribute name="Name" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A name for the channel that is suitable be presented to the user.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SamplesPerPixel" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The number of samples the detector takes to form each pixel value. [units:none] Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="IlluminationType" use="optional"><xsd:annotation><xsd:documentation>The method of illumination used to capture the channel.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Transmitted"/><xsd:enumeration value="Epifluorescence"/><xsd:enumeration value="Oblique"/><xsd:enumeration value="NonLinear"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="PinholeSize" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The optional PinholeSize attribute allows specifying adjustable pin hole diameters for confocal microscopes (units microns[µm]).</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="AcquisitionMode" use="optional"><xsd:annotation><xsd:documentation>AcquisitionMode describes the type of microscopy performed for each channel</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="WideField"/><xsd:enumeration value="LaserScanningConfocalMicroscopy"/><!-- CLSM or LSCM --><xsd:enumeration value="SpinningDiskConfocal"/><xsd:enumeration value="SlitScanConfocal"/><xsd:enumeration value="MultiPhotonMicroscopy"/><!-- laser scanning multiphoton microscopy (LSMM), two photon microscopy --><xsd:enumeration value="StructuredIllumination"/><xsd:enumeration value="SingleMoleculeImaging"/><xsd:enumeration value="TotalInternalReflection"/><xsd:enumeration value="FluorescenceLifetime"/><xsd:enumeration value="SpectralImaging"/><xsd:enumeration value="FluorescenceCorrelationSpectroscopy"/><xsd:enumeration value="NearFieldScanningOpticalMicroscopy"/><!-- NSOM --><xsd:enumeration value="SecondHarmonicGenerationImaging"/><!-- Second harmonic imaging microscopy (SHIM) --><xsd:enumeration value="PALM"/><!-- photo-activated localization microscopy, photo-activation localization microscopy --><xsd:enumeration value="STORM"/><!-- stochastic optical reconstruction microscopy --><xsd:enumeration value="STED"/><!-- stimulated emission depletion --><xsd:enumeration value="TIRF"/><!-- total internal reflection fluorescence (TIRFM) --><xsd:enumeration value="FSM"/><!-- Fluorescence speckle microscopy --><xsd:enumeration value="LCM"/><!-- Laser capture microdissection --><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="ContrastMethod" use="optional"><xsd:annotation><xsd:documentation>ContrastMethod describes the technique used to achieve contrast for each channel</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Brightfield"/><xsd:enumeration value="Phase"/><xsd:enumeration value="DIC"/><!-- Differential Interference Contrast --><xsd:enumeration value="HoffmanModulation"/><!-- Hoffman Modulation Contrast (HMC) --><xsd:enumeration value="ObliqueIllumination"/><xsd:enumeration value="PolarizedLight"/><!-- Polarization Microscopy --><xsd:enumeration value="Darkfield"/><!-- Dark Field Imaging --><xsd:enumeration value="Fluorescence"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="ExcitationWavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>Excitation wavelength of excitation for a particular channel, in nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="EmissionWavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>Emission wavelength of excitation for a particular channel, in nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Fluor" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The Fluor attribute is used for fluorescence images. This is the name of the fluorophore used to produce this channel [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="NDFilter" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The NDfilter attribute is used to specify the combined effect of any neutral density filters used. [units optical density expressed as a PercentFraction]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PockelCellSetting" use="optional" type="xsd:int"><xsd:annotation><xsd:documentation>The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Color" use="optional" type="Color" default="-1"><xsd:annotation><xsd:documentation>A color used to render this channel - encoded as RGBA The default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value) NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
This holds the setting applied to a detector as well as a reference to the detector. The ID is the detector used in this case. The values stored in DetectorSettings represent the variable values, fixed values not modified during the acquisition go in Detector. Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.
The speed at which the detector can count pixels. {used:CCD,EMCCD}Units of ReadOutRate is MHz. This is the bytes per second thatcan be read from the detector (like a baud rate). megahertz[MHz]
The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}
Source
<xsd:element name="DetectorSettings"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>DetectorSettingsCombinations</plural></xsdfu></xsd:appinfo><xsd:documentation>This holds the setting applied to a detector as well as a reference to the detector. The ID is the detector used in this case. The values stored in DetectorSettings represent the variable values, fixed values not modified during the acquisition go in Detector. Each attribute now has an indication of what type of detector it applies to. This is preparatory work for cleaning up and possibly splitting this object into sub-types.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Settings"><xsd:attribute name="ID" use="required" type="DetectorID"/><xsd:attribute name="Offset" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Offset of the detector. [units none] {used:CCD,EMCCD}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Gain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Gain of the detector. [units:none] {used:CCD,EMCCD,PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Voltage" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Voltage of the detector. volts[V] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Zoom" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="ReadOutRate" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The speed at which the detector can count pixels. {used:CCD,EMCCD} Units of ReadOutRate is MHz. This is the bytes per second that can be read from the detector (like a baud rate). megahertz[MHz]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Binning" use="optional"><xsd:annotation><xsd:documentation>Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="1x1"/><xsd:enumeration value="2x2"/><xsd:enumeration value="4x4"/><xsd:enumeration value="8x8"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute><xsd:attribute name="Integration" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>This is the number of sequential frames that get averaged, to improve the signal-to-noise ratio. [units:none] {used:CCD,EMCCD}</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosingPixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFFfile, unless an IFD is specified, in which case the default is 1. [units:none]
Source
<xsd:element name="TiffData"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>TiffDataBlocks</plural></xsdfu></xsd:appinfo><xsd:documentation>This described the location of the pixel data in a tiff file.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:element name="UUID" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>This must be used when the IFDs are located in another file. Note: It is permissible for this to be self referential.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:simpleContent><xsd:extension base="UniversallyUniqueIdentifier"><xsd:attribute name="FileName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>This can be used when the IFDs are located in another file. The / (forward slash) is used as the path separator. A relative path is recommended. However an absolute path can be specified. Default is to use the file the ome-xml data has been pulled from. Note: It is permissible for this to be self referential. The file image1.tiff may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:simpleContent></xsd:complexType></xsd:element></xsd:sequence><xsd:attribute name="IFD" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the IFD(s) for which this element is applicable. Indexed from 0. Default is 0 (the first IFD). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="FirstZ" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the Z position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first Z position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="FirstT" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the T position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first T position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="FirstC" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the C position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first C position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PlaneCount" use="optional" type="NonNegativeInt"><xsd:annotation><xsd:documentation>Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF file, unless an IFD is specified, in which case the default is 1. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
This can be used when the IFDs are located in another file.The / (forward slash) is used as the path separator.A relative path is recommended. However an absolute path can be specified.Default is to use the file the ome-xml data has been pulled from.Note: It is permissible for this to be self referential. The file image1.tiffmay contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"
Source
<xsd:element name="UUID" minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>This must be used when the IFDs are located in another file. Note: It is permissible for this to be self referential.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:simpleContent><xsd:extension base="UniversallyUniqueIdentifier"><xsd:attribute name="FileName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>This can be used when the IFDs are located in another file. The / (forward slash) is used as the path separator. A relative path is recommended. However an absolute path can be specified. Default is to use the file the ome-xml data has been pulled from. Note: It is permissible for this to be self referential. The file image1.tiff may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"</xsd:documentation></xsd:annotation></xsd:attribute></xsd:extension></xsd:simpleContent></xsd:complexType></xsd:element>
<xsd:element name="MetadataOnly"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>MetadataOnlyMarkers</plural></xsdfu></xsd:appinfo><xsd:documentation>This place holder means there is on pixel data in this file.</xsd:documentation></xsd:annotation></xsd:element>
The Z-section this plane is for. [units:none]This is numbered from 0.
Source
<xsd:element name="Plane"><!-- top level definition --><xsd:annotation><xsd:appinfo><xsdfu><plural>Planes</plural></xsdfu></xsd:appinfo><xsd:documentation>The Plane object holds microscope stage and image timing data for a given channel/z-section/timepoint.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:sequence><xsd:choice minOccurs="0" maxOccurs="1"><xsd:annotation><xsd:documentation>This optional element is a hash of the plane's image data. It is a choice between all the support hash types. Currently the only method supported is SHA1.</xsd:documentation></xsd:annotation><xsd:element name="HashSHA1" type="Hex40" minOccurs="1" maxOccurs="1"/></xsd:choice><xsd:element ref="SA:AnnotationRef" minOccurs="0" maxOccurs="unbounded"><xsd:annotation><xsd:appinfo><xsdfu><manytomany/></xsdfu></xsd:appinfo></xsd:annotation></xsd:element></xsd:sequence><xsd:attribute name="TheZ" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The Z-section this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="TheT" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The timepoint this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="TheC" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The channel this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="DeltaT" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>Units are seconds since the beginning of the experiment [s]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="ExposureTime" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>Units are seconds [s]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PositionX" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The X position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PositionY" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Y position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="PositionZ" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Z position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
The unique identifier of another OME-XMLblock whose metadata describes the binary data in this file.This UUID is considered authoritative regardless ofmismatches in the filename.
Source
<xsd:element name="BinaryOnly" minOccurs="1" maxOccurs="1"><xsd:annotation><xsd:documentation>Pointer to an external metadata file. If this element is present, then no other metadata may be present in this file, i.e. this file is a place-holder.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:attribute name="MetadataFile" type="xsd:string" use="required"><xsd:annotation><xsd:documentation>Filename of the OME-XML metadata file for this binary data. If the file cannot be found, a search can be performed based on the UUID.</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="required"><xsd:annotation><xsd:documentation>The unique identifier of another OME-XML block whose metadata describes the binary data in this file. This UUID is considered authoritative regardless of mismatches in the filename.</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType></xsd:element>
There may be one or more of these in a Dataset.This empty element has a required Project ID attribute that refers to Projects defined within the OME element.
<xsd:element name="ProjectRef"><!-- top level definition --><xsd:annotation><xsd:documentation>There may be one or more of these in a Dataset. This empty element has a required Project ID attribute that refers to Projects defined within the OME element.</xsd:documentation></xsd:annotation><xsd:complexType><xsd:complexContent><xsd:extension base="Reference"><xsd:attribute name="ID" use="required" type="ProjectID"/></xsd:extension></xsd:complexContent></xsd:complexType></xsd:element>
Reference is an empty complex type that is contained and extended by all the *Ref elements and also the Settings Complex TypeEach *Ref element defines an attribute named ID of simple type *ID and no other informationEach simple type *ID is restricted to the base type LSID with an appropriate pattern
<xsd:complexType name="Reference"><xsd:annotation><xsd:appinfo><xsdfu><abstract/></xsdfu></xsd:appinfo><xsd:documentation>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</xsd:documentation></xsd:annotation></xsd:complexType>
<xsd:simpleType name="LSID"><xsd:annotation><xsd:documentation>Either LSID or internal consistent IDs for the file See: http://www.openmicroscopy.org/site/support/file-formats/working-with-ome-xml/id-and-lsid</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:string"><xsd:pattern value="(urn:lsid:([\w\-\.]+\.[\w\-\.]+)+:\S+:\S+)|(\S+:\S+)"/></xsd:restriction></xsd:simpleType>
Settings is an empty complex type that is contained and extended by all the *Settings elementsEach *Settings element defines an attribute named ID of simple type *ID and the other information that is needed.Each simple type *ID is restricted to the base type LSID with an appropriate pattern
<xsd:complexType name="Settings"><xsd:annotation><xsd:appinfo><xsdfu><abstract/></xsdfu></xsd:appinfo><xsd:documentation>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. Each simple type *ID is restricted to the base type LSID with an appropriate pattern</xsd:documentation></xsd:annotation><xsd:complexContent><xsd:extension base="Reference"></xsd:extension></xsd:complexContent></xsd:complexType>
<xsd:simpleType name="PercentFraction"><xsd:annotation><xsd:documentation>A simple type that restricts the value to a float between 0 and 1 (inclusive).</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:float"><xsd:maxInclusive value="1.0"/><xsd:minInclusive value="0.0"/></xsd:restriction></xsd:simpleType>
<xsd:simpleType name="PositiveInt"><xsd:annotation><xsd:documentation>A simple type that restricts the value to an integer between 1 and 2,147,483,647 (inclusive).</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:int"><xsd:minInclusive value="1"/></xsd:restriction></xsd:simpleType>
<xsd:simpleType name="NonNegativeInt"><xsd:annotation><xsd:documentation>A simple type that restricts the value to an integer between 0 and 2,147,483,647 (inclusive).</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:int"><xsd:minInclusive value="0"/></xsd:restriction></xsd:simpleType>
A simple type that identifies itself as a Color, the value is an integer between -2,147,483,648 and 2,147,483,647 (inclusive).The value is a signed 32 bit encoding of RGBA so "-1" is #FFFFFFFF or solid white.NOTE: Prior to the 2012-06 schema the default values were incorrect and produced a transparent red not solid white.
<xsd:simpleType name="Color"><xsd:annotation><xsd:documentation>A simple type that identifies itself as a Color, the value is an integer between -2,147,483,648 and 2,147,483,647 (inclusive). The value is a signed 32 bit encoding of RGBA so "-1" is #FFFFFFFF or solid white. NOTE: Prior to the 2012-06 schema the default values were incorrect and produced a transparent red not solid white.</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:int"></xsd:restriction></xsd:simpleType>
This is the base from which many microscope components are extended. E.g Objective, Filter etc.Provides attributes for recording common properties of these components such as Manufacturer name, Model etc,all of which are optional.
The serial number of the component. [plain text string]
Source
<xsd:complexType name="ManufacturerSpec"><xsd:annotation><xsd:appinfo><xsdfu><abstract/></xsdfu></xsd:appinfo><xsd:documentation>This is the base from which many microscope components are extended. E.g Objective, Filter etc. Provides attributes for recording common properties of these components such as Manufacturer name, Model etc, all of which are optional.</xsd:documentation></xsd:annotation><xsd:attribute name="Manufacturer" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The manufacturer of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="Model" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The Model of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="SerialNumber" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The serial number of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute><xsd:attribute name="LotNumber" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The lot number of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute></xsd:complexType>
<xsd:simpleType name="NonNegativeLong"><xsd:annotation><xsd:documentation>A simple type that restricts the value to an integer between 0 and 9223372036854775807 (inclusive).</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:long"><xsd:minInclusive value="0"/></xsd:restriction></xsd:simpleType>
This is a unique ID for the file but does not conform to the ID pattern used in the rest of the file.The rest of the IDs are either an full LSID or an internal ID which is a string that is simply unique in this file.As the UniversallyUniqueIdentifier is used from outside this file to identify it having the same ID in another file could cause problems.A UUID is 32 hexadecimal digits, in 5 groups, 8-4-4-4-12, separated by hyphense.g. urn:uuid:3e450fae-b8f2-4d35-aa54-702168b2487fThere are methods to generate these in most modern languages.http://www.ietf.org/rfc/rfc4122.txt
<xsd:simpleType name="UniversallyUniqueIdentifier"><xsd:annotation><xsd:documentation>This is a unique ID for the file but does not conform to the ID pattern used in the rest of the file. The rest of the IDs are either an full LSID or an internal ID which is a string that is simply unique in this file. As the UniversallyUniqueIdentifier is used from outside this file to identify it having the same ID in another file could cause problems. A UUID is 32 hexadecimal digits, in 5 groups, 8-4-4-4-12, separated by hyphens e.g. urn:uuid:3e450fae-b8f2-4d35-aa54-702168b2487f There are methods to generate these in most modern languages. http://www.ietf.org/rfc/rfc4122.txt</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:anyURI"><xsd:pattern value="(urn:uuid:[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{4}-[0-9a-fA-F]{12})"/></xsd:restriction></xsd:simpleType>
<xsd:simpleType name="PositiveFloat"><xsd:annotation><xsd:documentation>A simple type that restricts the value to a float between >0 and max 32-bit float {i.e. (2−2^-23) × 2^27 ≈ 3.4 × 10^38}</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:float"><xsd:minExclusive value="0.0"/></xsd:restriction></xsd:simpleType>
<xsd:attribute name="Name" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A name for the dataset that is suitable be presented to the user.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Attenuation" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>The Attenuation of the light source [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Wavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The Wavelength of the light source. nanometres[nm]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>A term to describe the type of experiment.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:list><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="FP"/><xsd:enumeration value="FRET"/><!-- Förster resonance energy transfer, also known as fluorescence resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET) --><xsd:enumeration value="TimeLapse"/><!-- Time-lapse microscopy (microphotography, photomicrography) --><xsd:enumeration value="FourDPlus"/><xsd:enumeration value="Screen"/><xsd:enumeration value="Immunocytochemistry"/><xsd:enumeration value="Immunofluorescence"/><xsd:enumeration value="FISH"/><!-- Fluorescent in situ hybridization --><xsd:enumeration value="Electrophysiology"/><xsd:enumeration value="IonImaging"/><xsd:enumeration value="Colocalization"/><xsd:enumeration value="PGIDocumentation"/><xsd:enumeration value="FluorescenceLifetime"/><!-- Fluorescence lifetime imaging (FLIM) --><xsd:enumeration value="SpectralImaging"/><xsd:enumeration value="Photobleaching"/><xsd:enumeration value="SPIM"/><!-- Selective or Single Plane Illumination Microscopy --><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:list></xsd:simpleType></xsd:attribute>
<xsd:attribute name="FirstName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>First name, sometime called christian name or given name or forename. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="MiddleName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>Any other names. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="LastName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A person's last name sometimes called surname or family name. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
A person's InstitutionThe organizing structure that people belong to other than groups. A university, or company, etc.We do not specify a department element, and do not mean for Institution to be used in this way.We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed locationand of being more recognizable than a group of experimenters. [plain text string]
<xsd:attribute name="Institution" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A person's Institution The organizing structure that people belong to other than groups. A university, or company, etc. We do not specify a department element, and do not mean for Institution to be used in this way. We simply wish to say XXX at YYY. Where YYY has a better chance of being tied to a geographically fixed location and of being more recognizable than a group of experimenters. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="UserName" use="optional" type="xsd:string"><xsd:annotation><xsd:appinfo><xsdfu><unique/></xsdfu></xsd:appinfo><xsd:documentation>This is the username of the experimenter (in a 'unix' or 'database' sense). [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Manufacturer" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The manufacturer of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Model" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The Model of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SerialNumber" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The serial number of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="LotNumber" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The lot number of the component. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>Type is the general category of laser.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Excimer"/><xsd:enumeration value="Gas"/><xsd:enumeration value="MetalVapor"/><xsd:enumeration value="SolidState"/><xsd:enumeration value="Dye"/><xsd:enumeration value="Semiconductor"/><xsd:enumeration value="FreeElectron"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="Wavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The Wavelength of the laser in nanometres[nm]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="FrequencyMultiplication" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>FrequencyMultiplication that may be specified. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Tuneable" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>Whether or not the laser is Tuneable [flag]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PockelCell" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>If true the laser has a PockelCell to rotate the polarization of the beam. [flag]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="RepetitionRate" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The is the rate in Hz at which the laser pulses if the Pulse type is 'Repetitive'. hertz[Hz]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Type" use="optional"><xsd:annotation><xsd:documentation>The type of filament.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Incandescent"/><xsd:enumeration value="Halogen"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
A LightSource ID must be specified for each light source, and the individuallight sources can be referred to by their LightSource IDs (eg from Channel).
<xsd:attribute name="ID" use="required" type="LightSourceID"><xsd:annotation><xsd:documentation>A LightSource ID must be specified for each light source, and the individual light sources can be referred to by their LightSource IDs (eg from Channel).</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Gain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Detector Gain for this detector, as a float. [units:none] {used:CCD,EMCCD,PMT}</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Voltage" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Voltage of the detector (e.g. PMT voltage) as a float. volts[V] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute>
Gain applied to the detector signal.This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}
<xsd:attribute name="AmplificationGain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>Gain applied to the detector signal. This is the electronic gain (as apposed to the inherent gain) that is set for the detector. [units:none] {used:EMCCD#EMGain}</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Immersion" use="optional"><xsd:annotation><xsd:documentation>The immersion medium the lens is designed for</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Oil"/><xsd:enumeration value="Water"/><xsd:enumeration value="WaterDipping"/><xsd:enumeration value="Air"/><xsd:enumeration value="Multi"/><xsd:enumeration value="Glycerol"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="LensNA" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The numerical aperture of the lens expressed as a floating point (real) number. Expected range 0.02 - 1.5 [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none]Note: The type of this has been changed from int to float to allowthe specification of additional lenses e.g. 0.5X lens
<xsd:attribute name="NominalMagnification" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The magnification of the lens as specified by the manufacturer - i.e. '60' is a 60X lens. [units:none] Note: The type of this has been changed from int to float to allow the specification of additional lenses e.g. 0.5X lens</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="CalibratedMagnification" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The magnification of the lens as measured by a calibration process- i.e. '59.987' for a 60X lens. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="WorkingDistance" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The working distance of the lens expressed as a floating point (real) number. Units are microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Iris" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>Records whether or not the objective was fitted with an Iris. [flag]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="CutIn" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>CutIn is the wavelength below which there is less than 50% transmittance for a filter. Units: nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="CutOut" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>CutOut is the wavelength above which there is less than 50% transmittance for a filter. Units: nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Transmittance" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>The amount of light the filter transmits at a maximum [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute>
A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]
<xsd:attribute name="FilterWheel" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A filter 'wheel' in OME can refer to any arrangement of filters in a filter holder of any shape. It could, for example, be a filter slider. [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="CorrectionCollar" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The CorrectionCollar is normally an adjustable ring on the objective. Each has an arbitrary scale on it so the values is unit-less. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Medium" use="optional"><xsd:simpleType><xsd:annotation><xsd:documentation>A description of a Medium used for the lens. The Medium is the actual immersion medium used in this case.</xsd:documentation></xsd:annotation><xsd:restriction base="xsd:string"><xsd:enumeration value="Air"/><xsd:enumeration value="Oil"/><xsd:enumeration value="Water"/><xsd:enumeration value="Glycerol"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="RefractiveIndex" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The RefractiveIndex is that of the immersion medium. This is a ratio so it also unit-less. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Temperature" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Temperature is in Celsius[°C].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="AirPressure" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>AirPressure is in millibars[mbar].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Humidity" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>Humidity around the sample [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="CO2Percent" use="optional" type="PercentFraction"><xsd:annotation><xsd:documentation>Carbon Dioxide concentration around the sample [units:none] A fraction, as a value from 0.0 to 1.0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="X" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The X position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Y" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Y position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Z" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Z position of the stage label. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Gain" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Gain of the detector. [units:none] {used:CCD,EMCCD,PMT}</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Voltage" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Voltage of the detector. volts[V] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Zoom" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Zoom or "Confocal Zoom" or "Scan Zoom" for a detector. [units:none] {used:PMT}</xsd:documentation></xsd:annotation></xsd:attribute>
The speed at which the detector can count pixels. {used:CCD,EMCCD}Units of ReadOutRate is MHz. This is the bytes per second thatcan be read from the detector (like a baud rate). megahertz[MHz]
<xsd:attribute name="ReadOutRate" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The speed at which the detector can count pixels. {used:CCD,EMCCD} Units of ReadOutRate is MHz. This is the bytes per second that can be read from the detector (like a baud rate). megahertz[MHz]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Binning" use="optional"><xsd:annotation><xsd:documentation>Represents the number of pixels that are combined to form larger pixels. {used:CCD,EMCCD}</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="1x1"/><xsd:enumeration value="2x2"/><xsd:enumeration value="4x4"/><xsd:enumeration value="8x8"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="Integration" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>This is the number of sequential frames that get averaged, to improve the signal-to-noise ratio. [units:none] {used:CCD,EMCCD}</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Name" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>A name for the channel that is suitable be presented to the user.</xsd:documentation></xsd:annotation></xsd:attribute>
The number of samples the detector takes to form each pixel value. [units:none]Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings
<xsd:attribute name="SamplesPerPixel" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The number of samples the detector takes to form each pixel value. [units:none] Note: This is not the same as "Frame Averaging" - see Integration in DetectorSettings</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="IlluminationType" use="optional"><xsd:annotation><xsd:documentation>The method of illumination used to capture the channel.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="Transmitted"/><xsd:enumeration value="Epifluorescence"/><xsd:enumeration value="Oblique"/><xsd:enumeration value="NonLinear"/><xsd:enumeration value="Other"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="ExcitationWavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>Excitation wavelength of excitation for a particular channel, in nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="EmissionWavelength" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>Emission wavelength of excitation for a particular channel, in nanometres[nm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Fluor" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>The Fluor attribute is used for fluorescence images. This is the name of the fluorophore used to produce this channel [plain text string]</xsd:documentation></xsd:annotation></xsd:attribute>
The NDfilter attribute is used to specify the combined effect of any neutral density filters used. [units optical density expressed as a PercentFraction]
<xsd:attribute name="NDFilter" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The NDfilter attribute is used to specify the combined effect of any neutral density filters used. [units optical density expressed as a PercentFraction]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PockelCellSetting" use="optional" type="xsd:int"><xsd:annotation><xsd:documentation>The PockelCellSetting used for this channel. This is the amount the polarization of the beam is rotated by. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
A color used to render this channel - encoded as RGBAThe default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value)NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.
<xsd:attribute name="Color" use="optional" type="Color" default="-1"><xsd:annotation><xsd:documentation>A color used to render this channel - encoded as RGBA The default value "-1" is #FFFFFFFF so solid white (it is a signed 32 bit value) NOTE: Prior to the 2012-06 schema the default value was incorrect and produced a transparent red not solid white.</xsd:documentation></xsd:annotation></xsd:attribute>
This can be used when the IFDs are located in another file.The / (forward slash) is used as the path separator.A relative path is recommended. However an absolute path can be specified.Default is to use the file the ome-xml data has been pulled from.Note: It is permissible for this to be self referential. The file image1.tiffmay contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"
<xsd:attribute name="FileName" use="optional" type="xsd:string"><xsd:annotation><xsd:documentation>This can be used when the IFDs are located in another file. The / (forward slash) is used as the path separator. A relative path is recommended. However an absolute path can be specified. Default is to use the file the ome-xml data has been pulled from. Note: It is permissible for this to be self referential. The file image1.tiff may contain ome-xml data that has FilePath="image1.tiff" or "./image1.tiff"</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="IFD" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the IFD(s) for which this element is applicable. Indexed from 0. Default is 0 (the first IFD). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="FirstZ" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the Z position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first Z position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="FirstT" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the T position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first T position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="FirstC" type="NonNegativeInt" default="0" use="optional"><xsd:annotation><xsd:documentation>Gives the C position of the image plane at the specified IFD. Indexed from 0. Default is 0 (the first C position). [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosingPixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFFfile, unless an IFD is specified, in which case the default is 1. [units:none]
<xsd:attribute name="PlaneCount" use="optional" type="NonNegativeInt"><xsd:annotation><xsd:documentation>Gives the number of IFDs affected. Dimension order of IFDs is given by the enclosing Pixels element's DimensionOrder attribute. Default is the number of IFDs in the TIFF file, unless an IFD is specified, in which case the default is 1. [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="TheZ" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The Z-section this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="TheT" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The timepoint this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="TheC" use="required" type="NonNegativeInt"><xsd:annotation><xsd:documentation>The channel this plane is for. [units:none] This is numbered from 0.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="DeltaT" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>Units are seconds since the beginning of the experiment [s]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PositionX" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The X position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PositionY" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Y position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PositionZ" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>The Z position of the stage. [units are in the microscope reference frame]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="DimensionOrder" use="required"><xsd:annotation><xsd:documentation>The order in which the individual planes of data are interleaved.</xsd:documentation></xsd:annotation><xsd:simpleType><xsd:restriction base="xsd:string"><xsd:enumeration value="XYZCT"/><xsd:enumeration value="XYZTC"/><xsd:enumeration value="XYCTZ"/><xsd:enumeration value="XYCZT"/><xsd:enumeration value="XYTCZ"/><xsd:enumeration value="XYTZC"/></xsd:restriction></xsd:simpleType></xsd:attribute>
<xsd:attribute name="Type" use="required" type="PixelType"><xsd:annotation><xsd:documentation>The variable type used to represent each pixel in the image.</xsd:documentation></xsd:annotation></xsd:attribute>
The number of bits within the type storing each pixel that are significant.e.g. you can store 12 bit data within a 16 bit type.This does not reduce the storage requirements but can be a useful indicatorwhen processing or viewing the image data.
<xsd:attribute name="SignificantBits" use="optional" type="PositiveInt"><xsd:annotation><xsd:documentation>The number of bits within the type storing each pixel that are significant. e.g. you can store 12 bit data within a 16 bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the image data.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="Interleaved" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>How the channels are arranged within the data block: true if channels are stored RGBRGBRGB...; false if channels are stored RRR...GGG...BBB...</xsd:documentation></xsd:annotation></xsd:attribute>
This is true if the pixels data was written in BigEndian order. If this value is present it should match the value used in BinData or TiffData. If it does not a reader should honour the value used in the BinData or TiffData. This values is useful for MetadataOnly files and is to allow for future storage solutions.
<xsd:attribute name="BigEndian" use="optional" type="xsd:boolean"><xsd:annotation><xsd:documentation>This is true if the pixels data was written in BigEndian order. If this value is present it should match the value used in BinData or TiffData. If it does not a reader should honour the value used in the BinData or TiffData. This values is useful for MetadataOnly files and is to allow for future storage solutions.</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SizeX" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SizeY" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SizeZ" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SizeC" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="SizeT" use="required" type="PositiveInt"><xsd:annotation><xsd:documentation>Dimensional size of pixel data array [units:none]</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PhysicalSizeX" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PhysicalSizeY" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="PhysicalSizeZ" use="optional" type="PositiveFloat"><xsd:annotation><xsd:documentation>Physical size of a pixel in microns[µm].</xsd:documentation></xsd:annotation></xsd:attribute>
TimeIncrement is used for time series that have a globaltiming specification instead of per-timepoint timing info.For example in a video stream. The unit is seconds[s].
<xsd:attribute name="TimeIncrement" use="optional" type="xsd:float"><xsd:annotation><xsd:documentation>TimeIncrement is used for time series that have a global timing specification instead of per-timepoint timing info. For example in a video stream. The unit is seconds[s].</xsd:documentation></xsd:annotation></xsd:attribute>
<xsd:attribute name="MetadataFile" type="xsd:string" use="required"><xsd:annotation><xsd:documentation>Filename of the OME-XML metadata file for this binary data. If the file cannot be found, a search can be performed based on the UUID.</xsd:documentation></xsd:annotation></xsd:attribute>
The unique identifier of another OME-XMLblock whose metadata describes the binary data in this file.This UUID is considered authoritative regardless ofmismatches in the filename.
<xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="required"><xsd:annotation><xsd:documentation>The unique identifier of another OME-XML block whose metadata describes the binary data in this file. This UUID is considered authoritative regardless of mismatches in the filename.</xsd:documentation></xsd:annotation></xsd:attribute>
This unique identifier is used to keep track of multi part files. It allows the links between files to survive renaming. While OPTIONAL in the general case this is REQUIRED in a MetadataOnly Companion to a collection of BinaryOnly files.
<xsd:attribute name="UUID" type="UniversallyUniqueIdentifier" use="optional"><xsd:annotation><xsd:documentation>This unique identifier is used to keep track of multi part files. It allows the links between files to survive renaming. While OPTIONAL in the general case this is REQUIRED in a MetadataOnly Companion to a collection of BinaryOnly files.</xsd:documentation></xsd:annotation></xsd:attribute>
This is the name of the creating application of the OME-XMLand preferably its full version.e.g "CompanyName, SoftwareName, V2.6.3456"This is optional but we hope it will be set by applicationswriting out OME-XML from scratch.
<xsd:attribute name="Creator" type="xsd:string" use="optional"><xsd:annotation><xsd:documentation>This is the name of the creating application of the OME-XML and preferably its full version. e.g "CompanyName, SoftwareName, V2.6.3456" This is optional but we hope it will be set by applications writing out OME-XML from scratch.</xsd:documentation></xsd:annotation></xsd:attribute>
