OMEXMLMetadataImpl (Bio-Formats API)

java.lang.Object
- loci.formats.ome.AbstractOMEXMLMetadata
- - loci.formats.ome.OMEXMLMetadataImpl

All Implemented Interfaces:

IMetadata, MetadataRetrieve, MetadataStore, OMEXMLMetadata
```
public class OMEXMLMetadataImpl
extends AbstractOMEXMLMetadata
```
A metadata store implementation for constructing and manipulating OME-XML DOMs for the current version of OME-XML. It requires the ome.xml.model package to compile (part of ome-xml.jar).
Source code:

Trac, Gitweb

Author:

Curtis Rueden ctrueden at wisc.edu, Melissa Linkert linkert at wisc.edu

Field Summary
- Fields inherited from class loci.formats.ome.AbstractOMEXMLMetadata
  LOGGER, SCHEMA, XSI_NS

Constructor Summary

Constructors
Constructor and Description

OMEXMLMetadataImpl()

Constructors
Constructor and Description
`OMEXMLMetadataImpl()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`createRoot()`
`String`	`dumpXML()` Dumps the given OME-XML DOM tree to a string.
`String`	`getArcID(int instrumentIndex, int lightSourceIndex)`
`String`	`getArcLotNumber(int instrumentIndex, int lightSourceIndex)`
`String`	`getArcManufacturer(int instrumentIndex, int lightSourceIndex)`
`String`	`getArcModel(int instrumentIndex, int lightSourceIndex)`
`Double`	`getArcPower(int instrumentIndex, int lightSourceIndex)`
`String`	`getArcSerialNumber(int instrumentIndex, int lightSourceIndex)`
`ArcType`	`getArcType(int instrumentIndex, int lightSourceIndex)`
`String`	`getBinaryFileFileName(int fileAnnotationIndex)`
`String`	`getBinaryFileMIMEType(int fileAnnotationIndex)`
`NonNegativeLong`	`getBinaryFileSize(int fileAnnotationIndex)`
`String`	`getBinaryOnlyMetadataFile(int metadataFileIndex)`
`String`	`getBinaryOnlyUUID(int UUIDIndex)`
`int`	`getBooleanAnnotationAnnotationCount(int booleanAnnotationIndex)`
`String`	`getBooleanAnnotationAnnotationRef(int booleanAnnotationIndex, int annotationRefIndex)`
`int`	`getBooleanAnnotationCount()`
`String`	`getBooleanAnnotationDescription(int booleanAnnotationIndex)`
`String`	`getBooleanAnnotationID(int booleanAnnotationIndex)`
`String`	`getBooleanAnnotationNamespace(int booleanAnnotationIndex)`
`Boolean`	`getBooleanAnnotationValue(int booleanAnnotationIndex)`
`AcquisitionMode`	`getChannelAcquisitionMode(int imageIndex, int channelIndex)`
`String`	`getChannelAnnotationRef(int imageIndex, int channelIndex, int annotationRefIndex)`
`int`	`getChannelAnnotationRefCount(int imageIndex, int channelIndex)`
`Color`	`getChannelColor(int imageIndex, int channelIndex)`
`ContrastMethod`	`getChannelContrastMethod(int imageIndex, int channelIndex)`
`int`	`getChannelCount(int imageIndex)`
`PositiveInteger`	`getChannelEmissionWavelength(int imageIndex, int channelIndex)`
`PositiveInteger`	`getChannelExcitationWavelength(int imageIndex, int channelIndex)`
`String`	`getChannelFilterSetRef(int imageIndex, int channelIndex)`
`String`	`getChannelFluor(int imageIndex, int channelIndex)`
`String`	`getChannelID(int imageIndex, int channelIndex)`
`IlluminationType`	`getChannelIlluminationType(int imageIndex, int channelIndex)`
`PercentFraction`	`getChannelLightSourceSettingsAttenuation(int imageIndex, int channelIndex)`
`String`	`getChannelLightSourceSettingsID(int imageIndex, int channelIndex)`
`PositiveInteger`	`getChannelLightSourceSettingsWavelength(int imageIndex, int channelIndex)`
`String`	`getChannelName(int imageIndex, int channelIndex)`
`Double`	`getChannelNDFilter(int imageIndex, int channelIndex)`
`Double`	`getChannelPinholeSize(int imageIndex, int channelIndex)`
`Integer`	`getChannelPockelCellSetting(int imageIndex, int channelIndex)`
`PositiveInteger`	`getChannelSamplesPerPixel(int imageIndex, int channelIndex)`
`int`	`getCommentAnnotationAnnotationCount(int commentAnnotationIndex)`
`String`	`getCommentAnnotationAnnotationRef(int commentAnnotationIndex, int annotationRefIndex)`
`int`	`getCommentAnnotationCount()`
`String`	`getCommentAnnotationDescription(int commentAnnotationIndex)`
`String`	`getCommentAnnotationID(int commentAnnotationIndex)`
`String`	`getCommentAnnotationNamespace(int commentAnnotationIndex)`
`String`	`getCommentAnnotationValue(int commentAnnotationIndex)`
`String`	`getDatasetAnnotationRef(int datasetIndex, int annotationRefIndex)`
`int`	`getDatasetAnnotationRefCount(int datasetIndex)`
`int`	`getDatasetCount()`
`String`	`getDatasetDescription(int datasetIndex)`
`String`	`getDatasetExperimenterGroupRef(int datasetIndex)`
`String`	`getDatasetExperimenterRef(int datasetIndex)`
`String`	`getDatasetID(int datasetIndex)`
`String`	`getDatasetImageRef(int datasetIndex, int imageRefIndex)`
`int`	`getDatasetImageRefCount(int datasetIndex)`
`String`	`getDatasetName(int datasetIndex)`
`int`	`getDatasetRefCount(int projectIndex)`
`Double`	`getDetectorAmplificationGain(int instrumentIndex, int detectorIndex)`
`int`	`getDetectorCount(int instrumentIndex)`
`Double`	`getDetectorGain(int instrumentIndex, int detectorIndex)`
`String`	`getDetectorID(int instrumentIndex, int detectorIndex)`
`String`	`getDetectorLotNumber(int instrumentIndex, int detectorIndex)`
`String`	`getDetectorManufacturer(int instrumentIndex, int detectorIndex)`
`String`	`getDetectorModel(int instrumentIndex, int detectorIndex)`
`Double`	`getDetectorOffset(int instrumentIndex, int detectorIndex)`
`String`	`getDetectorSerialNumber(int instrumentIndex, int detectorIndex)`
`Binning`	`getDetectorSettingsBinning(int imageIndex, int channelIndex)`
`Double`	`getDetectorSettingsGain(int imageIndex, int channelIndex)`
`String`	`getDetectorSettingsID(int imageIndex, int channelIndex)`
`Double`	`getDetectorSettingsOffset(int imageIndex, int channelIndex)`
`Double`	`getDetectorSettingsReadOutRate(int imageIndex, int channelIndex)`
`Double`	`getDetectorSettingsVoltage(int imageIndex, int channelIndex)`
`DetectorType`	`getDetectorType(int instrumentIndex, int detectorIndex)`
`Double`	`getDetectorVoltage(int instrumentIndex, int detectorIndex)`
`Double`	`getDetectorZoom(int instrumentIndex, int detectorIndex)`
`int`	`getDichroicCount(int instrumentIndex)`
`String`	`getDichroicID(int instrumentIndex, int dichroicIndex)`
`String`	`getDichroicLotNumber(int instrumentIndex, int dichroicIndex)`
`String`	`getDichroicManufacturer(int instrumentIndex, int dichroicIndex)`
`String`	`getDichroicModel(int instrumentIndex, int dichroicIndex)`
`String`	`getDichroicSerialNumber(int instrumentIndex, int dichroicIndex)`
`int`	`getDoubleAnnotationAnnotationCount(int doubleAnnotationIndex)`
`String`	`getDoubleAnnotationAnnotationRef(int doubleAnnotationIndex, int annotationRefIndex)`
`int`	`getDoubleAnnotationCount()`
`String`	`getDoubleAnnotationDescription(int doubleAnnotationIndex)`
`String`	`getDoubleAnnotationID(int doubleAnnotationIndex)`
`String`	`getDoubleAnnotationNamespace(int doubleAnnotationIndex)`
`Double`	`getDoubleAnnotationValue(int doubleAnnotationIndex)`
`Color`	`getEllipseFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getEllipseFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getEllipseFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getEllipseFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getEllipseFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getEllipseID(int ROIIndex, int shapeIndex)`
`LineCap`	`getEllipseLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getEllipseLocked(int ROIIndex, int shapeIndex)`
`Double`	`getEllipseRadiusX(int ROIIndex, int shapeIndex)`
`Double`	`getEllipseRadiusY(int ROIIndex, int shapeIndex)`
`Color`	`getEllipseStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getEllipseStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getEllipseStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getEllipseText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getEllipseTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getEllipseTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getEllipseTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getEllipseTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getEllipseVisible(int ROIIndex, int shapeIndex)`
`Double`	`getEllipseX(int ROIIndex, int shapeIndex)`
`Double`	`getEllipseY(int ROIIndex, int shapeIndex)`
`int`	`getExperimentCount()`
`String`	`getExperimentDescription(int experimentIndex)`
`String`	`getExperimenterAnnotationRef(int experimenterIndex, int annotationRefIndex)`
`int`	`getExperimenterAnnotationRefCount(int experimenterIndex)`
`int`	`getExperimenterCount()`
`String`	`getExperimenterEmail(int experimenterIndex)`
`String`	`getExperimenterFirstName(int experimenterIndex)`
`String`	`getExperimenterGroupAnnotationRef(int experimenterGroupIndex, int annotationRefIndex)`
`int`	`getExperimenterGroupAnnotationRefCount(int experimenterGroupIndex)`
`int`	`getExperimenterGroupCount()`
`String`	`getExperimenterGroupDescription(int experimenterGroupIndex)`
`String`	`getExperimenterGroupExperimenterRef(int experimenterGroupIndex, int experimenterRefIndex)`
`int`	`getExperimenterGroupExperimenterRefCount(int experimenterGroupIndex)`
`String`	`getExperimenterGroupID(int experimenterGroupIndex)`
`String`	`getExperimenterGroupLeader(int experimenterGroupIndex, int leaderIndex)`
`String`	`getExperimenterGroupName(int experimenterGroupIndex)`
`String`	`getExperimenterID(int experimenterIndex)`
`String`	`getExperimenterInstitution(int experimenterIndex)`
`String`	`getExperimenterLastName(int experimenterIndex)`
`String`	`getExperimenterMiddleName(int experimenterIndex)`
`String`	`getExperimenterUserName(int experimenterIndex)`
`String`	`getExperimentExperimenterRef(int experimentIndex)`
`String`	`getExperimentID(int experimentIndex)`
`ExperimentType`	`getExperimentType(int experimentIndex)`
`String`	`getFilamentID(int instrumentIndex, int lightSourceIndex)`
`String`	`getFilamentLotNumber(int instrumentIndex, int lightSourceIndex)`
`String`	`getFilamentManufacturer(int instrumentIndex, int lightSourceIndex)`
`String`	`getFilamentModel(int instrumentIndex, int lightSourceIndex)`
`Double`	`getFilamentPower(int instrumentIndex, int lightSourceIndex)`
`String`	`getFilamentSerialNumber(int instrumentIndex, int lightSourceIndex)`
`FilamentType`	`getFilamentType(int instrumentIndex, int lightSourceIndex)`
`int`	`getFileAnnotationAnnotationCount(int fileAnnotationIndex)`
`String`	`getFileAnnotationAnnotationRef(int fileAnnotationIndex, int annotationRefIndex)`
`int`	`getFileAnnotationCount()`
`String`	`getFileAnnotationDescription(int fileAnnotationIndex)`
`String`	`getFileAnnotationID(int fileAnnotationIndex)`
`String`	`getFileAnnotationNamespace(int fileAnnotationIndex)`
`int`	`getFilterCount(int instrumentIndex)`
`String`	`getFilterFilterWheel(int instrumentIndex, int filterIndex)`
`String`	`getFilterID(int instrumentIndex, int filterIndex)`
`String`	`getFilterLotNumber(int instrumentIndex, int filterIndex)`
`String`	`getFilterManufacturer(int instrumentIndex, int filterIndex)`
`String`	`getFilterModel(int instrumentIndex, int filterIndex)`
`String`	`getFilterSerialNumber(int instrumentIndex, int filterIndex)`
`int`	`getFilterSetCount(int instrumentIndex)`
`String`	`getFilterSetDichroicRef(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetEmissionFilterRef(int instrumentIndex, int filterSetIndex, int emissionFilterRefIndex)`
`int`	`getFilterSetEmissionFilterRefCount(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetExcitationFilterRef(int instrumentIndex, int filterSetIndex, int excitationFilterRefIndex)`
`int`	`getFilterSetExcitationFilterRefCount(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetID(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetLotNumber(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetManufacturer(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetModel(int instrumentIndex, int filterSetIndex)`
`String`	`getFilterSetSerialNumber(int instrumentIndex, int filterSetIndex)`
`FilterType`	`getFilterType(int instrumentIndex, int filterIndex)`
`Timestamp`	`getImageAcquisitionDate(int imageIndex)`
`String`	`getImageAnnotationRef(int imageIndex, int annotationRefIndex)`
`int`	`getImageAnnotationRefCount(int imageIndex)`
`int`	`getImageCount()`
`String`	`getImageDescription(int imageIndex)`
`String`	`getImageExperimenterGroupRef(int imageIndex)`
`String`	`getImageExperimenterRef(int imageIndex)`
`String`	`getImageExperimentRef(int imageIndex)`
`String`	`getImageID(int imageIndex)`
`String`	`getImageInstrumentRef(int imageIndex)`
`String`	`getImageMicrobeamManipulationRef(int imageIndex, int microbeamManipulationRefIndex)`
`String`	`getImageName(int imageIndex)`
`String`	`getImageROIRef(int imageIndex, int ROIRefIndex)`
`int`	`getImageROIRefCount(int imageIndex)`
`Double`	`getImagingEnvironmentAirPressure(int imageIndex)`
`PercentFraction`	`getImagingEnvironmentCO2Percent(int imageIndex)`
`PercentFraction`	`getImagingEnvironmentHumidity(int imageIndex)`
`Double`	`getImagingEnvironmentTemperature(int imageIndex)`
`int`	`getInstrumentCount()`
`String`	`getInstrumentID(int instrumentIndex)`
`Color`	`getLabelFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getLabelFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getLabelFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLabelFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getLabelFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getLabelID(int ROIIndex, int shapeIndex)`
`LineCap`	`getLabelLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getLabelLocked(int ROIIndex, int shapeIndex)`
`Color`	`getLabelStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getLabelStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getLabelStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getLabelText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLabelTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLabelTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLabelTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getLabelTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getLabelVisible(int ROIIndex, int shapeIndex)`
`Double`	`getLabelX(int ROIIndex, int shapeIndex)`
`Double`	`getLabelY(int ROIIndex, int shapeIndex)`
`PositiveInteger`	`getLaserFrequencyMultiplication(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserID(int instrumentIndex, int lightSourceIndex)`
`LaserMedium`	`getLaserLaserMedium(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserLotNumber(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserManufacturer(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserModel(int instrumentIndex, int lightSourceIndex)`
`Boolean`	`getLaserPockelCell(int instrumentIndex, int lightSourceIndex)`
`Double`	`getLaserPower(int instrumentIndex, int lightSourceIndex)`
`Pulse`	`getLaserPulse(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserPump(int instrumentIndex, int lightSourceIndex)`
`Double`	`getLaserRepetitionRate(int instrumentIndex, int lightSourceIndex)`
`String`	`getLaserSerialNumber(int instrumentIndex, int lightSourceIndex)`
`Boolean`	`getLaserTuneable(int instrumentIndex, int lightSourceIndex)`
`LaserType`	`getLaserType(int instrumentIndex, int lightSourceIndex)`
`PositiveInteger`	`getLaserWavelength(int instrumentIndex, int lightSourceIndex)`
`int`	`getLeaderCount(int experimenterGroupIndex)`
`String`	`getLightEmittingDiodeID(int instrumentIndex, int lightSourceIndex)`
`String`	`getLightEmittingDiodeLotNumber(int instrumentIndex, int lightSourceIndex)`
`String`	`getLightEmittingDiodeManufacturer(int instrumentIndex, int lightSourceIndex)`
`String`	`getLightEmittingDiodeModel(int instrumentIndex, int lightSourceIndex)`
`Double`	`getLightEmittingDiodePower(int instrumentIndex, int lightSourceIndex)`
`String`	`getLightEmittingDiodeSerialNumber(int instrumentIndex, int lightSourceIndex)`
`String`	`getLightPathDichroicRef(int imageIndex, int channelIndex)`
`String`	`getLightPathEmissionFilterRef(int imageIndex, int channelIndex, int emissionFilterRefIndex)`
`int`	`getLightPathEmissionFilterRefCount(int imageIndex, int channelIndex)`
`String`	`getLightPathExcitationFilterRef(int imageIndex, int channelIndex, int excitationFilterRefIndex)`
`int`	`getLightPathExcitationFilterRefCount(int imageIndex, int channelIndex)`
`int`	`getLightSourceCount(int instrumentIndex)`
`String`	`getLightSourceType(int instrumentIndex, int lightSourceIndex)`
`Color`	`getLineFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getLineFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getLineFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLineFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getLineFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getLineID(int ROIIndex, int shapeIndex)`
`LineCap`	`getLineLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getLineLocked(int ROIIndex, int shapeIndex)`
`Marker`	`getLineMarkerEnd(int ROIIndex, int shapeIndex)`
`Marker`	`getLineMarkerStart(int ROIIndex, int shapeIndex)`
`Color`	`getLineStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getLineStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getLineStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getLineText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLineTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLineTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getLineTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getLineTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getLineVisible(int ROIIndex, int shapeIndex)`
`Double`	`getLineX1(int ROIIndex, int shapeIndex)`
`Double`	`getLineX2(int ROIIndex, int shapeIndex)`
`Double`	`getLineY1(int ROIIndex, int shapeIndex)`
`Double`	`getLineY2(int ROIIndex, int shapeIndex)`
`int`	`getListAnnotationAnnotationCount(int listAnnotationIndex)`
`String`	`getListAnnotationAnnotationRef(int listAnnotationIndex, int annotationRefIndex)`
`int`	`getListAnnotationCount()`
`String`	`getListAnnotationDescription(int listAnnotationIndex)`
`String`	`getListAnnotationID(int listAnnotationIndex)`
`String`	`getListAnnotationNamespace(int listAnnotationIndex)`
`int`	`getLongAnnotationAnnotationCount(int longAnnotationIndex)`
`String`	`getLongAnnotationAnnotationRef(int longAnnotationIndex, int annotationRefIndex)`
`int`	`getLongAnnotationCount()`
`String`	`getLongAnnotationDescription(int longAnnotationIndex)`
`String`	`getLongAnnotationID(int longAnnotationIndex)`
`String`	`getLongAnnotationNamespace(int longAnnotationIndex)`
`Long`	`getLongAnnotationValue(int longAnnotationIndex)`
`Color`	`getMaskFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getMaskFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getMaskFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getMaskFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getMaskFontStyle(int ROIIndex, int shapeIndex)`
`Double`	`getMaskHeight(int ROIIndex, int shapeIndex)`
`String`	`getMaskID(int ROIIndex, int shapeIndex)`
`LineCap`	`getMaskLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getMaskLocked(int ROIIndex, int shapeIndex)`
`Color`	`getMaskStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getMaskStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getMaskStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getMaskText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getMaskTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getMaskTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getMaskTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getMaskTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getMaskVisible(int ROIIndex, int shapeIndex)`
`Double`	`getMaskWidth(int ROIIndex, int shapeIndex)`
`Double`	`getMaskX(int ROIIndex, int shapeIndex)`
`Double`	`getMaskY(int ROIIndex, int shapeIndex)`
`int`	`getMicrobeamManipulationCount(int experimentIndex)`
`String`	`getMicrobeamManipulationDescription(int experimentIndex, int microbeamManipulationIndex)`
`String`	`getMicrobeamManipulationExperimenterRef(int experimentIndex, int microbeamManipulationIndex)`
`String`	`getMicrobeamManipulationID(int experimentIndex, int microbeamManipulationIndex)`
`PercentFraction`	`getMicrobeamManipulationLightSourceSettingsAttenuation(int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`int`	`getMicrobeamManipulationLightSourceSettingsCount(int experimentIndex, int microbeamManipulationIndex)`
`String`	`getMicrobeamManipulationLightSourceSettingsID(int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`PositiveInteger`	`getMicrobeamManipulationLightSourceSettingsWavelength(int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`int`	`getMicrobeamManipulationRefCount(int imageIndex)`
`String`	`getMicrobeamManipulationROIRef(int experimentIndex, int microbeamManipulationIndex, int ROIRefIndex)`
`int`	`getMicrobeamManipulationROIRefCount(int experimentIndex, int microbeamManipulationIndex)`
`MicrobeamManipulationType`	`getMicrobeamManipulationType(int experimentIndex, int microbeamManipulationIndex)`
`String`	`getMicroscopeLotNumber(int instrumentIndex)`
`String`	`getMicroscopeManufacturer(int instrumentIndex)`
`String`	`getMicroscopeModel(int instrumentIndex)`
`String`	`getMicroscopeSerialNumber(int instrumentIndex)`
`MicroscopeType`	`getMicroscopeType(int instrumentIndex)`
`Double`	`getObjectiveCalibratedMagnification(int instrumentIndex, int objectiveIndex)`
`Correction`	`getObjectiveCorrection(int instrumentIndex, int objectiveIndex)`
`int`	`getObjectiveCount(int instrumentIndex)`
`String`	`getObjectiveID(int instrumentIndex, int objectiveIndex)`
`Immersion`	`getObjectiveImmersion(int instrumentIndex, int objectiveIndex)`
`Boolean`	`getObjectiveIris(int instrumentIndex, int objectiveIndex)`
`Double`	`getObjectiveLensNA(int instrumentIndex, int objectiveIndex)`
`String`	`getObjectiveLotNumber(int instrumentIndex, int objectiveIndex)`
`String`	`getObjectiveManufacturer(int instrumentIndex, int objectiveIndex)`
`String`	`getObjectiveModel(int instrumentIndex, int objectiveIndex)`
`PositiveInteger`	`getObjectiveNominalMagnification(int instrumentIndex, int objectiveIndex)`
`String`	`getObjectiveSerialNumber(int instrumentIndex, int objectiveIndex)`
`Double`	`getObjectiveSettingsCorrectionCollar(int imageIndex)`
`String`	`getObjectiveSettingsID(int imageIndex)`
`Medium`	`getObjectiveSettingsMedium(int imageIndex)`
`Double`	`getObjectiveSettingsRefractiveIndex(int imageIndex)`
`Double`	`getObjectiveWorkingDistance(int instrumentIndex, int objectiveIndex)`
`String`	`getPixelsAnnotationRef(int imageIndex, int annotationRefIndex)`
`int`	`getPixelsAnnotationRefCount(int imageIndex)`
`Boolean`	`getPixelsBinDataBigEndian(int imageIndex, int binDataIndex)`
`int`	`getPixelsBinDataCount(int imageIndex)`
`DimensionOrder`	`getPixelsDimensionOrder(int imageIndex)`
`String`	`getPixelsID(int imageIndex)`
`PositiveFloat`	`getPixelsPhysicalSizeX(int imageIndex)`
`PositiveFloat`	`getPixelsPhysicalSizeY(int imageIndex)`
`PositiveFloat`	`getPixelsPhysicalSizeZ(int imageIndex)`
`PositiveInteger`	`getPixelsSizeC(int imageIndex)`
`PositiveInteger`	`getPixelsSizeT(int imageIndex)`
`PositiveInteger`	`getPixelsSizeX(int imageIndex)`
`PositiveInteger`	`getPixelsSizeY(int imageIndex)`
`PositiveInteger`	`getPixelsSizeZ(int imageIndex)`
`Double`	`getPixelsTimeIncrement(int imageIndex)`
`PixelType`	`getPixelsType(int imageIndex)`
`String`	`getPlaneAnnotationRef(int imageIndex, int planeIndex, int annotationRefIndex)`
`int`	`getPlaneAnnotationRefCount(int imageIndex, int planeIndex)`
`int`	`getPlaneCount(int imageIndex)`
`Double`	`getPlaneDeltaT(int imageIndex, int planeIndex)`
`Double`	`getPlaneExposureTime(int imageIndex, int planeIndex)`
`String`	`getPlaneHashSHA1(int imageIndex, int planeIndex)`
`Double`	`getPlanePositionX(int imageIndex, int planeIndex)`
`Double`	`getPlanePositionY(int imageIndex, int planeIndex)`
`Double`	`getPlanePositionZ(int imageIndex, int planeIndex)`
`NonNegativeInteger`	`getPlaneTheC(int imageIndex, int planeIndex)`
`NonNegativeInteger`	`getPlaneTheT(int imageIndex, int planeIndex)`
`NonNegativeInteger`	`getPlaneTheZ(int imageIndex, int planeIndex)`
`String`	`getPlateAcquisitionAnnotationRef(int plateIndex, int plateAcquisitionIndex, int annotationRefIndex)`
`int`	`getPlateAcquisitionAnnotationRefCount(int plateIndex, int plateAcquisitionIndex)`
`int`	`getPlateAcquisitionCount(int plateIndex)`
`String`	`getPlateAcquisitionDescription(int plateIndex, int plateAcquisitionIndex)`
`Timestamp`	`getPlateAcquisitionEndTime(int plateIndex, int plateAcquisitionIndex)`
`String`	`getPlateAcquisitionID(int plateIndex, int plateAcquisitionIndex)`
`PositiveInteger`	`getPlateAcquisitionMaximumFieldCount(int plateIndex, int plateAcquisitionIndex)`
`String`	`getPlateAcquisitionName(int plateIndex, int plateAcquisitionIndex)`
`Timestamp`	`getPlateAcquisitionStartTime(int plateIndex, int plateAcquisitionIndex)`
`String`	`getPlateAcquisitionWellSampleRef(int plateIndex, int plateAcquisitionIndex, int wellSampleRefIndex)`
`String`	`getPlateAnnotationRef(int plateIndex, int annotationRefIndex)`
`int`	`getPlateAnnotationRefCount(int plateIndex)`
`NamingConvention`	`getPlateColumnNamingConvention(int plateIndex)`
`PositiveInteger`	`getPlateColumns(int plateIndex)`
`int`	`getPlateCount()`
`String`	`getPlateDescription(int plateIndex)`
`String`	`getPlateExternalIdentifier(int plateIndex)`
`NonNegativeInteger`	`getPlateFieldIndex(int plateIndex)`
`String`	`getPlateID(int plateIndex)`
`String`	`getPlateName(int plateIndex)`
`int`	`getPlateRefCount(int screenIndex)`
`NamingConvention`	`getPlateRowNamingConvention(int plateIndex)`
`PositiveInteger`	`getPlateRows(int plateIndex)`
`String`	`getPlateStatus(int plateIndex)`
`Double`	`getPlateWellOriginX(int plateIndex)`
`Double`	`getPlateWellOriginY(int plateIndex)`
`Color`	`getPointFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getPointFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getPointFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPointFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getPointFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getPointID(int ROIIndex, int shapeIndex)`
`LineCap`	`getPointLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getPointLocked(int ROIIndex, int shapeIndex)`
`Color`	`getPointStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getPointStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getPointStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getPointText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPointTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPointTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPointTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getPointTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getPointVisible(int ROIIndex, int shapeIndex)`
`Double`	`getPointX(int ROIIndex, int shapeIndex)`
`Double`	`getPointY(int ROIIndex, int shapeIndex)`
`Color`	`getPolygonFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getPolygonFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getPolygonFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolygonFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getPolygonFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getPolygonID(int ROIIndex, int shapeIndex)`
`LineCap`	`getPolygonLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getPolygonLocked(int ROIIndex, int shapeIndex)`
`String`	`getPolygonPoints(int ROIIndex, int shapeIndex)`
`Color`	`getPolygonStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getPolygonStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getPolygonStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getPolygonText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolygonTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolygonTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolygonTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getPolygonTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getPolygonVisible(int ROIIndex, int shapeIndex)`
`Color`	`getPolylineFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getPolylineFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getPolylineFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolylineFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getPolylineFontStyle(int ROIIndex, int shapeIndex)`
`String`	`getPolylineID(int ROIIndex, int shapeIndex)`
`LineCap`	`getPolylineLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getPolylineLocked(int ROIIndex, int shapeIndex)`
`Marker`	`getPolylineMarkerEnd(int ROIIndex, int shapeIndex)`
`Marker`	`getPolylineMarkerStart(int ROIIndex, int shapeIndex)`
`String`	`getPolylinePoints(int ROIIndex, int shapeIndex)`
`Color`	`getPolylineStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getPolylineStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getPolylineStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getPolylineText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolylineTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolylineTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getPolylineTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getPolylineTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getPolylineVisible(int ROIIndex, int shapeIndex)`
`String`	`getProjectAnnotationRef(int projectIndex, int annotationRefIndex)`
`int`	`getProjectAnnotationRefCount(int projectIndex)`
`int`	`getProjectCount()`
`String`	`getProjectDatasetRef(int projectIndex, int datasetRefIndex)`
`String`	`getProjectDescription(int projectIndex)`
`String`	`getProjectExperimenterGroupRef(int projectIndex)`
`String`	`getProjectExperimenterRef(int projectIndex)`
`String`	`getProjectID(int projectIndex)`
`String`	`getProjectName(int projectIndex)`
`String`	`getReagentAnnotationRef(int screenIndex, int reagentIndex, int annotationRefIndex)`
`int`	`getReagentAnnotationRefCount(int screenIndex, int reagentIndex)`
`int`	`getReagentCount(int screenIndex)`
`String`	`getReagentDescription(int screenIndex, int reagentIndex)`
`String`	`getReagentID(int screenIndex, int reagentIndex)`
`String`	`getReagentName(int screenIndex, int reagentIndex)`
`String`	`getReagentReagentIdentifier(int screenIndex, int reagentIndex)`
`Color`	`getRectangleFillColor(int ROIIndex, int shapeIndex)`
`FillRule`	`getRectangleFillRule(int ROIIndex, int shapeIndex)`
`FontFamily`	`getRectangleFontFamily(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getRectangleFontSize(int ROIIndex, int shapeIndex)`
`FontStyle`	`getRectangleFontStyle(int ROIIndex, int shapeIndex)`
`Double`	`getRectangleHeight(int ROIIndex, int shapeIndex)`
`String`	`getRectangleID(int ROIIndex, int shapeIndex)`
`LineCap`	`getRectangleLineCap(int ROIIndex, int shapeIndex)`
`Boolean`	`getRectangleLocked(int ROIIndex, int shapeIndex)`
`Color`	`getRectangleStrokeColor(int ROIIndex, int shapeIndex)`
`String`	`getRectangleStrokeDashArray(int ROIIndex, int shapeIndex)`
`Double`	`getRectangleStrokeWidth(int ROIIndex, int shapeIndex)`
`String`	`getRectangleText(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getRectangleTheC(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getRectangleTheT(int ROIIndex, int shapeIndex)`
`NonNegativeInteger`	`getRectangleTheZ(int ROIIndex, int shapeIndex)`
`AffineTransform`	`getRectangleTransform(int ROIIndex, int shapeIndex)`
`Boolean`	`getRectangleVisible(int ROIIndex, int shapeIndex)`
`Double`	`getRectangleWidth(int ROIIndex, int shapeIndex)`
`Double`	`getRectangleX(int ROIIndex, int shapeIndex)`
`Double`	`getRectangleY(int ROIIndex, int shapeIndex)`
`String`	`getROIAnnotationRef(int ROIIndex, int annotationRefIndex)`
`int`	`getROIAnnotationRefCount(int ROIIndex)`
`int`	`getROICount()`
`String`	`getROIDescription(int ROIIndex)`
`String`	`getROIID(int ROIIndex)`
`String`	`getROIName(int ROIIndex)`
`String`	`getROINamespace(int ROIIndex)`
`Object`	`getRoot()`
`String`	`getScreenAnnotationRef(int screenIndex, int annotationRefIndex)`
`int`	`getScreenAnnotationRefCount(int screenIndex)`
`int`	`getScreenCount()`
`String`	`getScreenDescription(int screenIndex)`
`String`	`getScreenID(int screenIndex)`
`String`	`getScreenName(int screenIndex)`
`String`	`getScreenPlateRef(int screenIndex, int plateRefIndex)`
`String`	`getScreenProtocolDescription(int screenIndex)`
`String`	`getScreenProtocolIdentifier(int screenIndex)`
`String`	`getScreenReagentSetDescription(int screenIndex)`
`String`	`getScreenReagentSetIdentifier(int screenIndex)`
`String`	`getScreenType(int screenIndex)`
`int`	`getShapeCount(int ROIIndex)`
`String`	`getShapeType(int roiIndex, int shapeIndex)`
`String`	`getStageLabelName(int imageIndex)`
`Double`	`getStageLabelX(int imageIndex)`
`Double`	`getStageLabelY(int imageIndex)`
`Double`	`getStageLabelZ(int imageIndex)`
`int`	`getTagAnnotationAnnotationCount(int tagAnnotationIndex)`
`String`	`getTagAnnotationAnnotationRef(int tagAnnotationIndex, int annotationRefIndex)`
`int`	`getTagAnnotationCount()`
`String`	`getTagAnnotationDescription(int tagAnnotationIndex)`
`String`	`getTagAnnotationID(int tagAnnotationIndex)`
`String`	`getTagAnnotationNamespace(int tagAnnotationIndex)`
`String`	`getTagAnnotationValue(int tagAnnotationIndex)`
`int`	`getTermAnnotationAnnotationCount(int termAnnotationIndex)`
`String`	`getTermAnnotationAnnotationRef(int termAnnotationIndex, int annotationRefIndex)`
`int`	`getTermAnnotationCount()`
`String`	`getTermAnnotationDescription(int termAnnotationIndex)`
`String`	`getTermAnnotationID(int termAnnotationIndex)`
`String`	`getTermAnnotationNamespace(int termAnnotationIndex)`
`String`	`getTermAnnotationValue(int termAnnotationIndex)`
`int`	`getTiffDataCount(int imageIndex)`
`NonNegativeInteger`	`getTiffDataFirstC(int imageIndex, int tiffDataIndex)`
`NonNegativeInteger`	`getTiffDataFirstT(int imageIndex, int tiffDataIndex)`
`NonNegativeInteger`	`getTiffDataFirstZ(int imageIndex, int tiffDataIndex)`
`NonNegativeInteger`	`getTiffDataIFD(int imageIndex, int tiffDataIndex)`
`NonNegativeInteger`	`getTiffDataPlaneCount(int imageIndex, int tiffDataIndex)`
`int`	`getTimestampAnnotationAnnotationCount(int timestampAnnotationIndex)`
`String`	`getTimestampAnnotationAnnotationRef(int timestampAnnotationIndex, int annotationRefIndex)`
`int`	`getTimestampAnnotationCount()`
`String`	`getTimestampAnnotationDescription(int timestampAnnotationIndex)`
`String`	`getTimestampAnnotationID(int timestampAnnotationIndex)`
`String`	`getTimestampAnnotationNamespace(int timestampAnnotationIndex)`
`Timestamp`	`getTimestampAnnotationValue(int timestampAnnotationIndex)`
`PositiveInteger`	`getTransmittanceRangeCutIn(int instrumentIndex, int filterIndex)`
`NonNegativeInteger`	`getTransmittanceRangeCutInTolerance(int instrumentIndex, int filterIndex)`
`PositiveInteger`	`getTransmittanceRangeCutOut(int instrumentIndex, int filterIndex)`
`NonNegativeInteger`	`getTransmittanceRangeCutOutTolerance(int instrumentIndex, int filterIndex)`
`PercentFraction`	`getTransmittanceRangeTransmittance(int instrumentIndex, int filterIndex)`
`String`	`getUUID()` Gets the UUID associated with this collection of metadata.
`String`	`getUUIDFileName(int imageIndex, int tiffDataIndex)`
`String`	`getUUIDValue(int imageIndex, int tiffDataIndex)`
`String`	`getWellAnnotationRef(int plateIndex, int wellIndex, int annotationRefIndex)`
`int`	`getWellAnnotationRefCount(int plateIndex, int wellIndex)`
`Color`	`getWellColor(int plateIndex, int wellIndex)`
`NonNegativeInteger`	`getWellColumn(int plateIndex, int wellIndex)`
`int`	`getWellCount(int plateIndex)`
`String`	`getWellExternalDescription(int plateIndex, int wellIndex)`
`String`	`getWellExternalIdentifier(int plateIndex, int wellIndex)`
`String`	`getWellID(int plateIndex, int wellIndex)`
`String`	`getWellReagentRef(int plateIndex, int wellIndex)`
`NonNegativeInteger`	`getWellRow(int plateIndex, int wellIndex)`
`String`	`getWellSampleAnnotationRef(int plateIndex, int wellIndex, int wellSampleIndex, int annotationRefIndex)`
`int`	`getWellSampleAnnotationRefCount(int plateIndex, int wellIndex, int wellSampleIndex)`
`int`	`getWellSampleCount(int plateIndex, int wellIndex)`
`String`	`getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex)`
`String`	`getWellSampleImageRef(int plateIndex, int wellIndex, int wellSampleIndex)`
`NonNegativeInteger`	`getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex)`
`Double`	`getWellSamplePositionX(int plateIndex, int wellIndex, int wellSampleIndex)`
`Double`	`getWellSamplePositionY(int plateIndex, int wellIndex, int wellSampleIndex)`
`int`	`getWellSampleRefCount(int plateIndex, int plateAcquisitionIndex)`
`Timestamp`	`getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex)`
`String`	`getWellType(int plateIndex, int wellIndex)`
`int`	`getXMLAnnotationAnnotationCount(int xmlAnnotationIndex)`
`String`	`getXMLAnnotationAnnotationRef(int XMLAnnotationIndex, int annotationRefIndex)`
`int`	`getXMLAnnotationCount()`
`String`	`getXMLAnnotationDescription(int XMLAnnotationIndex)`
`String`	`getXMLAnnotationID(int XMLAnnotationIndex)`
`String`	`getXMLAnnotationNamespace(int XMLAnnotationIndex)`
`String`	`getXMLAnnotationValue(int XMLAnnotationIndex)`
`int`	`resolveReferences()`
`void`	`setArcID(String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcModel(String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcPower(Double power, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setArcType(ArcType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setBinaryFileFileName(String fileName, int fileAnnotationIndex)`
`void`	`setBinaryFileMIMEType(String mimeType, int fileAnnotationIndex)`
`void`	`setBinaryFileSize(NonNegativeLong size, int fileAnnotationIndex)`
`void`	`setBinaryOnlyMetadataFile(String metadataFile)`
`void`	`setBinaryOnlyUUID(String uuid)`
`void`	`setBooleanAnnotationAnnotationRef(String annotation, int booleanAnnotationIndex, int annotationRefIndex)`
`void`	`setBooleanAnnotationDescription(String description, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationID(String id, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationNamespace(String namespace, int booleanAnnotationIndex)`
`void`	`setBooleanAnnotationValue(Boolean value, int booleanAnnotationIndex)`
`void`	`setChannelAcquisitionMode(AcquisitionMode acquisitionMode, int imageIndex, int channelIndex)`
`void`	`setChannelAnnotationRef(String annotation, int imageIndex, int channelIndex, int annotationRefIndex)`
`void`	`setChannelColor(Color color, int imageIndex, int channelIndex)`
`void`	`setChannelContrastMethod(ContrastMethod contrastMethod, int imageIndex, int channelIndex)`
`void`	`setChannelEmissionWavelength(PositiveInteger emissionWavelength, int imageIndex, int channelIndex)`
`void`	`setChannelExcitationWavelength(PositiveInteger excitationWavelength, int imageIndex, int channelIndex)`
`void`	`setChannelFilterSetRef(String filterSet, int imageIndex, int channelIndex)`
`void`	`setChannelFluor(String fluor, int imageIndex, int channelIndex)`
`void`	`setChannelID(String id, int imageIndex, int channelIndex)`
`void`	`setChannelIlluminationType(IlluminationType illuminationType, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsAttenuation(PercentFraction attenuation, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsID(String id, int imageIndex, int channelIndex)`
`void`	`setChannelLightSourceSettingsWavelength(PositiveInteger wavelength, int imageIndex, int channelIndex)`
`void`	`setChannelName(String name, int imageIndex, int channelIndex)`
`void`	`setChannelNDFilter(Double ndFilter, int imageIndex, int channelIndex)`
`void`	`setChannelPinholeSize(Double pinholeSize, int imageIndex, int channelIndex)`
`void`	`setChannelPockelCellSetting(Integer pockelCellSetting, int imageIndex, int channelIndex)`
`void`	`setChannelSamplesPerPixel(PositiveInteger samplesPerPixel, int imageIndex, int channelIndex)`
`void`	`setCommentAnnotationAnnotationRef(String annotation, int commentAnnotationIndex, int annotationRefIndex)`
`void`	`setCommentAnnotationDescription(String description, int commentAnnotationIndex)`
`void`	`setCommentAnnotationID(String id, int commentAnnotationIndex)`
`void`	`setCommentAnnotationNamespace(String namespace, int commentAnnotationIndex)`
`void`	`setCommentAnnotationValue(String value, int commentAnnotationIndex)`
`void`	`setDatasetAnnotationRef(String annotation, int datasetIndex, int annotationRefIndex)`
`void`	`setDatasetDescription(String description, int datasetIndex)`
`void`	`setDatasetExperimenterGroupRef(String experimenterGroup, int datasetIndex)`
`void`	`setDatasetExperimenterRef(String experimenter, int datasetIndex)`
`void`	`setDatasetID(String id, int datasetIndex)`
`void`	`setDatasetImageRef(String image, int datasetIndex, int imageRefIndex)`
`void`	`setDatasetName(String name, int datasetIndex)`
`void`	`setDetectorAmplificationGain(Double amplificationGain, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorGain(Double gain, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorID(String id, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorLotNumber(String lotNumber, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorManufacturer(String manufacturer, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorModel(String model, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorOffset(Double offset, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorSerialNumber(String serialNumber, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorSettingsBinning(Binning binning, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsGain(Double gain, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsID(String id, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsOffset(Double offset, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsReadOutRate(Double readOutRate, int imageIndex, int channelIndex)`
`void`	`setDetectorSettingsVoltage(Double voltage, int imageIndex, int channelIndex)`
`void`	`setDetectorType(DetectorType type, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorVoltage(Double voltage, int instrumentIndex, int detectorIndex)`
`void`	`setDetectorZoom(Double zoom, int instrumentIndex, int detectorIndex)`
`void`	`setDichroicID(String id, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicLotNumber(String lotNumber, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicManufacturer(String manufacturer, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicModel(String model, int instrumentIndex, int dichroicIndex)`
`void`	`setDichroicSerialNumber(String serialNumber, int instrumentIndex, int dichroicIndex)`
`void`	`setDoubleAnnotationAnnotationRef(String annotation, int doubleAnnotationIndex, int annotationRefIndex)`
`void`	`setDoubleAnnotationDescription(String description, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationID(String id, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationNamespace(String namespace, int doubleAnnotationIndex)`
`void`	`setDoubleAnnotationValue(Double value, int doubleAnnotationIndex)`
`void`	`setEllipseFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setEllipseFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setEllipseID(String id, int ROIIndex, int shapeIndex)`
`void`	`setEllipseLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setEllipseLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setEllipseRadiusX(Double radiusX, int ROIIndex, int shapeIndex)`
`void`	`setEllipseRadiusY(Double radiusY, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setEllipseStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setEllipseText(String text, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setEllipseTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setEllipseVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setEllipseX(Double x, int ROIIndex, int shapeIndex)`
`void`	`setEllipseY(Double y, int ROIIndex, int shapeIndex)`
`void`	`setExperimentDescription(String description, int experimentIndex)`
`void`	`setExperimenterAnnotationRef(String annotation, int experimenterIndex, int annotationRefIndex)`
`void`	`setExperimenterEmail(String email, int experimenterIndex)`
`void`	`setExperimenterFirstName(String firstName, int experimenterIndex)`
`void`	`setExperimenterGroupAnnotationRef(String annotation, int experimenterGroupIndex, int annotationRefIndex)`
`void`	`setExperimenterGroupDescription(String description, int experimenterGroupIndex)`
`void`	`setExperimenterGroupExperimenterRef(String experimenter, int experimenterGroupIndex, int experimenterRefIndex)`
`void`	`setExperimenterGroupID(String id, int experimenterGroupIndex)`
`void`	`setExperimenterGroupLeader(String leader, int experimenterGroupIndex, int leaderIndex)`
`void`	`setExperimenterGroupName(String name, int experimenterGroupIndex)`
`void`	`setExperimenterID(String id, int experimenterIndex)`
`void`	`setExperimenterInstitution(String institution, int experimenterIndex)`
`void`	`setExperimenterLastName(String lastName, int experimenterIndex)`
`void`	`setExperimenterMiddleName(String middleName, int experimenterIndex)`
`void`	`setExperimenterUserName(String userName, int experimenterIndex)`
`void`	`setExperimentExperimenterRef(String experimenter, int experimentIndex)`
`void`	`setExperimentID(String id, int experimentIndex)`
`void`	`setExperimentType(ExperimentType type, int experimentIndex)`
`void`	`setFilamentID(String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentModel(String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentPower(Double power, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setFilamentType(FilamentType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setFileAnnotationAnnotationRef(String annotation, int fileAnnotationIndex, int annotationRefIndex)`
`void`	`setFileAnnotationDescription(String description, int fileAnnotationIndex)`
`void`	`setFileAnnotationID(String id, int fileAnnotationIndex)`
`void`	`setFileAnnotationNamespace(String namespace, int fileAnnotationIndex)`
`void`	`setFilterFilterWheel(String filterWheel, int instrumentIndex, int filterIndex)`
`void`	`setFilterID(String id, int instrumentIndex, int filterIndex)`
`void`	`setFilterLotNumber(String lotNumber, int instrumentIndex, int filterIndex)`
`void`	`setFilterManufacturer(String manufacturer, int instrumentIndex, int filterIndex)`
`void`	`setFilterModel(String model, int instrumentIndex, int filterIndex)`
`void`	`setFilterSerialNumber(String serialNumber, int instrumentIndex, int filterIndex)`
`void`	`setFilterSetDichroicRef(String dichroic, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetEmissionFilterRef(String emissionFilter, int instrumentIndex, int filterSetIndex, int emissionFilterRefIndex)`
`void`	`setFilterSetExcitationFilterRef(String excitationFilter, int instrumentIndex, int filterSetIndex, int excitationFilterRefIndex)`
`void`	`setFilterSetID(String id, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetLotNumber(String lotNumber, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetManufacturer(String manufacturer, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetModel(String model, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterSetSerialNumber(String serialNumber, int instrumentIndex, int filterSetIndex)`
`void`	`setFilterType(FilterType type, int instrumentIndex, int filterIndex)`
`void`	`setImageAcquisitionDate(Timestamp acquisitionDate, int imageIndex)`
`void`	`setImageAnnotationRef(String annotation, int imageIndex, int annotationRefIndex)`
`void`	`setImageDescription(String description, int imageIndex)`
`void`	`setImageExperimenterGroupRef(String experimenterGroup, int imageIndex)`
`void`	`setImageExperimenterRef(String experimenter, int imageIndex)`
`void`	`setImageExperimentRef(String experiment, int imageIndex)`
`void`	`setImageID(String id, int imageIndex)`
`void`	`setImageInstrumentRef(String instrument, int imageIndex)`
`void`	`setImageMicrobeamManipulationRef(String microbeamManipulation, int imageIndex, int microbeamManipulationRefIndex)`
`void`	`setImageName(String name, int imageIndex)`
`void`	`setImageROIRef(String roi, int imageIndex, int ROIRefIndex)`
`void`	`setImagingEnvironmentAirPressure(Double airPressure, int imageIndex)`
`void`	`setImagingEnvironmentCO2Percent(PercentFraction co2Percent, int imageIndex)`
`void`	`setImagingEnvironmentHumidity(PercentFraction humidity, int imageIndex)`
`void`	`setImagingEnvironmentTemperature(Double temperature, int imageIndex)`
`void`	`setInstrumentID(String id, int instrumentIndex)`
`void`	`setLabelFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setLabelFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setLabelFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setLabelID(String id, int ROIIndex, int shapeIndex)`
`void`	`setLabelLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setLabelLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setLabelStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setLabelText(String text, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setLabelTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setLabelTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setLabelVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setLabelX(Double x, int ROIIndex, int shapeIndex)`
`void`	`setLabelY(Double y, int ROIIndex, int shapeIndex)`
`void`	`setLaserFrequencyMultiplication(PositiveInteger frequencyMultiplication, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserID(String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserLaserMedium(LaserMedium laserMedium, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserModel(String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPockelCell(Boolean pockelCell, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPower(Double power, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPulse(Pulse pulse, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserPump(String pump, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserRepetitionRate(Double repetitionRate, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserTuneable(Boolean tuneable, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserType(LaserType type, int instrumentIndex, int lightSourceIndex)`
`void`	`setLaserWavelength(PositiveInteger wavelength, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeID(String id, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeLotNumber(String lotNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeManufacturer(String manufacturer, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeModel(String model, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodePower(Double power, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightEmittingDiodeSerialNumber(String serialNumber, int instrumentIndex, int lightSourceIndex)`
`void`	`setLightPathDichroicRef(String dichroic, int imageIndex, int channelIndex)`
`void`	`setLightPathEmissionFilterRef(String emissionFilter, int imageIndex, int channelIndex, int emissionFilterRefIndex)`
`void`	`setLightPathExcitationFilterRef(String excitationFilter, int imageIndex, int channelIndex, int excitationFilterRefIndex)`
`void`	`setLineFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setLineFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setLineFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setLineFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setLineFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setLineID(String id, int ROIIndex, int shapeIndex)`
`void`	`setLineLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setLineLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setLineMarkerEnd(Marker markerEnd, int ROIIndex, int shapeIndex)`
`void`	`setLineMarkerStart(Marker markerStart, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setLineStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setLineText(String text, int ROIIndex, int shapeIndex)`
`void`	`setLineTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setLineTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setLineTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setLineTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setLineVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setLineX1(Double x1, int ROIIndex, int shapeIndex)`
`void`	`setLineX2(Double x2, int ROIIndex, int shapeIndex)`
`void`	`setLineY1(Double y1, int ROIIndex, int shapeIndex)`
`void`	`setLineY2(Double y2, int ROIIndex, int shapeIndex)`
`void`	`setListAnnotationAnnotationRef(String annotation, int listAnnotationIndex, int annotationRefIndex)`
`void`	`setListAnnotationDescription(String description, int listAnnotationIndex)`
`void`	`setListAnnotationID(String id, int listAnnotationIndex)`
`void`	`setListAnnotationNamespace(String namespace, int listAnnotationIndex)`
`void`	`setLongAnnotationAnnotationRef(String annotation, int longAnnotationIndex, int annotationRefIndex)`
`void`	`setLongAnnotationDescription(String description, int longAnnotationIndex)`
`void`	`setLongAnnotationID(String id, int longAnnotationIndex)`
`void`	`setLongAnnotationNamespace(String namespace, int longAnnotationIndex)`
`void`	`setLongAnnotationValue(Long value, int longAnnotationIndex)`
`void`	`setMaskBinData(byte[] binData, int ROIIndex, int shapeIndex)`
`void`	`setMaskFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setMaskFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setMaskFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setMaskHeight(Double height, int ROIIndex, int shapeIndex)`
`void`	`setMaskID(String id, int ROIIndex, int shapeIndex)`
`void`	`setMaskLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setMaskLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setMaskStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setMaskText(String text, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setMaskTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setMaskTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setMaskVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setMaskWidth(Double width, int ROIIndex, int shapeIndex)`
`void`	`setMaskX(Double x, int ROIIndex, int shapeIndex)`
`void`	`setMaskY(Double y, int ROIIndex, int shapeIndex)`
`void`	`setMicrobeamManipulationDescription(String description, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationExperimenterRef(String experimenter, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationID(String id, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction attenuation, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsID(String id, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationLightSourceSettingsWavelength(PositiveInteger wavelength, int experimentIndex, int microbeamManipulationIndex, int lightSourceSettingsIndex)`
`void`	`setMicrobeamManipulationROIRef(String roi, int experimentIndex, int microbeamManipulationIndex, int ROIRefIndex)`
`void`	`setMicrobeamManipulationType(MicrobeamManipulationType type, int experimentIndex, int microbeamManipulationIndex)`
`void`	`setMicroscopeLotNumber(String lotNumber, int instrumentIndex)`
`void`	`setMicroscopeManufacturer(String manufacturer, int instrumentIndex)`
`void`	`setMicroscopeModel(String model, int instrumentIndex)`
`void`	`setMicroscopeSerialNumber(String serialNumber, int instrumentIndex)`
`void`	`setMicroscopeType(MicroscopeType type, int instrumentIndex)`
`void`	`setObjectiveCalibratedMagnification(Double calibratedMagnification, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveCorrection(Correction correction, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveID(String id, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveImmersion(Immersion immersion, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveIris(Boolean iris, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveLensNA(Double lensNA, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveLotNumber(String lotNumber, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveManufacturer(String manufacturer, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveModel(String model, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveNominalMagnification(PositiveInteger nominalMagnification, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveSerialNumber(String serialNumber, int instrumentIndex, int objectiveIndex)`
`void`	`setObjectiveSettingsCorrectionCollar(Double correctionCollar, int imageIndex)`
`void`	`setObjectiveSettingsID(String id, int imageIndex)`
`void`	`setObjectiveSettingsMedium(Medium medium, int imageIndex)`
`void`	`setObjectiveSettingsRefractiveIndex(Double refractiveIndex, int imageIndex)`
`void`	`setObjectiveWorkingDistance(Double workingDistance, int instrumentIndex, int objectiveIndex)`
`void`	`setPixelsAnnotationRef(String annotation, int imageIndex, int annotationRefIndex)`
`void`	`setPixelsBinDataBigEndian(Boolean bigEndian, int imageIndex, int binDataIndex)`
`void`	`setPixelsDimensionOrder(DimensionOrder dimensionOrder, int imageIndex)`
`void`	`setPixelsID(String id, int imageIndex)`
`void`	`setPixelsPhysicalSizeX(PositiveFloat physicalSizeX, int imageIndex)`
`void`	`setPixelsPhysicalSizeY(PositiveFloat physicalSizeY, int imageIndex)`
`void`	`setPixelsPhysicalSizeZ(PositiveFloat physicalSizeZ, int imageIndex)`
`void`	`setPixelsSizeC(PositiveInteger sizeC, int imageIndex)`
`void`	`setPixelsSizeT(PositiveInteger sizeT, int imageIndex)`
`void`	`setPixelsSizeX(PositiveInteger sizeX, int imageIndex)`
`void`	`setPixelsSizeY(PositiveInteger sizeY, int imageIndex)`
`void`	`setPixelsSizeZ(PositiveInteger sizeZ, int imageIndex)`
`void`	`setPixelsTimeIncrement(Double timeIncrement, int imageIndex)`
`void`	`setPixelsType(PixelType type, int imageIndex)`
`void`	`setPlaneAnnotationRef(String annotation, int imageIndex, int planeIndex, int annotationRefIndex)`
`void`	`setPlaneDeltaT(Double deltaT, int imageIndex, int planeIndex)`
`void`	`setPlaneExposureTime(Double exposureTime, int imageIndex, int planeIndex)`
`void`	`setPlaneHashSHA1(String hashSHA1, int imageIndex, int planeIndex)`
`void`	`setPlanePositionX(Double positionX, int imageIndex, int planeIndex)`
`void`	`setPlanePositionY(Double positionY, int imageIndex, int planeIndex)`
`void`	`setPlanePositionZ(Double positionZ, int imageIndex, int planeIndex)`
`void`	`setPlaneTheC(NonNegativeInteger theC, int imageIndex, int planeIndex)`
`void`	`setPlaneTheT(NonNegativeInteger theT, int imageIndex, int planeIndex)`
`void`	`setPlaneTheZ(NonNegativeInteger theZ, int imageIndex, int planeIndex)`
`void`	`setPlateAcquisitionAnnotationRef(String annotation, int plateIndex, int plateAcquisitionIndex, int annotationRefIndex)`
`void`	`setPlateAcquisitionDescription(String description, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionEndTime(Timestamp endTime, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionID(String id, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionMaximumFieldCount(PositiveInteger maximumFieldCount, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionName(String name, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionStartTime(Timestamp startTime, int plateIndex, int plateAcquisitionIndex)`
`void`	`setPlateAcquisitionWellSampleRef(String wellSample, int plateIndex, int plateAcquisitionIndex, int wellSampleRefIndex)`
`void`	`setPlateAnnotationRef(String annotation, int plateIndex, int annotationRefIndex)`
`void`	`setPlateColumnNamingConvention(NamingConvention columnNamingConvention, int plateIndex)`
`void`	`setPlateColumns(PositiveInteger columns, int plateIndex)`
`void`	`setPlateDescription(String description, int plateIndex)`
`void`	`setPlateExternalIdentifier(String externalIdentifier, int plateIndex)`
`void`	`setPlateFieldIndex(NonNegativeInteger fieldIndex, int plateIndex)`
`void`	`setPlateID(String id, int plateIndex)`
`void`	`setPlateName(String name, int plateIndex)`
`void`	`setPlateRowNamingConvention(NamingConvention rowNamingConvention, int plateIndex)`
`void`	`setPlateRows(PositiveInteger rows, int plateIndex)`
`void`	`setPlateStatus(String status, int plateIndex)`
`void`	`setPlateWellOriginX(Double wellOriginX, int plateIndex)`
`void`	`setPlateWellOriginY(Double wellOriginY, int plateIndex)`
`void`	`setPointFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setPointFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPointFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPointFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPointFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPointID(String id, int ROIIndex, int shapeIndex)`
`void`	`setPointLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setPointLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPointStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPointText(String text, int ROIIndex, int shapeIndex)`
`void`	`setPointTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPointTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPointTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPointTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setPointVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setPointX(Double x, int ROIIndex, int shapeIndex)`
`void`	`setPointY(Double y, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPolygonFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPolygonID(String id, int ROIIndex, int shapeIndex)`
`void`	`setPolygonLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setPolygonLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPolygonPoints(String points, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPolygonStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPolygonText(String text, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPolygonTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setPolygonVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setPolylineFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setPolylineID(String id, int ROIIndex, int shapeIndex)`
`void`	`setPolylineLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setPolylineLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setPolylineMarkerEnd(Marker markerEnd, int ROIIndex, int shapeIndex)`
`void`	`setPolylineMarkerStart(Marker markerStart, int ROIIndex, int shapeIndex)`
`void`	`setPolylinePoints(String points, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setPolylineStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setPolylineText(String text, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setPolylineTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setPolylineVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setProjectAnnotationRef(String annotation, int projectIndex, int annotationRefIndex)`
`void`	`setProjectDatasetRef(String dataset, int projectIndex, int datasetRefIndex)`
`void`	`setProjectDescription(String description, int projectIndex)`
`void`	`setProjectExperimenterGroupRef(String experimenterGroup, int projectIndex)`
`void`	`setProjectExperimenterRef(String experimenter, int projectIndex)`
`void`	`setProjectID(String id, int projectIndex)`
`void`	`setProjectName(String name, int projectIndex)`
`void`	`setReagentAnnotationRef(String annotation, int screenIndex, int reagentIndex, int annotationRefIndex)`
`void`	`setReagentDescription(String description, int screenIndex, int reagentIndex)`
`void`	`setReagentID(String id, int screenIndex, int reagentIndex)`
`void`	`setReagentName(String name, int screenIndex, int reagentIndex)`
`void`	`setReagentReagentIdentifier(String reagentIdentifier, int screenIndex, int reagentIndex)`
`void`	`setRectangleFillColor(Color fillColor, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFillRule(FillRule fillRule, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontFamily(FontFamily fontFamily, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontSize(NonNegativeInteger fontSize, int ROIIndex, int shapeIndex)`
`void`	`setRectangleFontStyle(FontStyle fontStyle, int ROIIndex, int shapeIndex)`
`void`	`setRectangleHeight(Double height, int ROIIndex, int shapeIndex)`
`void`	`setRectangleID(String id, int ROIIndex, int shapeIndex)`
`void`	`setRectangleLineCap(LineCap lineCap, int ROIIndex, int shapeIndex)`
`void`	`setRectangleLocked(Boolean locked, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeColor(Color strokeColor, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeDashArray(String strokeDashArray, int ROIIndex, int shapeIndex)`
`void`	`setRectangleStrokeWidth(Double strokeWidth, int ROIIndex, int shapeIndex)`
`void`	`setRectangleText(String text, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheC(NonNegativeInteger theC, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheT(NonNegativeInteger theT, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTheZ(NonNegativeInteger theZ, int ROIIndex, int shapeIndex)`
`void`	`setRectangleTransform(AffineTransform transform, int ROIIndex, int shapeIndex)`
`void`	`setRectangleVisible(Boolean visible, int ROIIndex, int shapeIndex)`
`void`	`setRectangleWidth(Double width, int ROIIndex, int shapeIndex)`
`void`	`setRectangleX(Double x, int ROIIndex, int shapeIndex)`
`void`	`setRectangleY(Double y, int ROIIndex, int shapeIndex)`
`void`	`setROIAnnotationRef(String annotation, int ROIIndex, int annotationRefIndex)`
`void`	`setROIDescription(String description, int ROIIndex)`
`void`	`setROIID(String id, int ROIIndex)`
`void`	`setROIName(String name, int ROIIndex)`
`void`	`setROINamespace(String namespace, int ROIIndex)`
`void`	`setRoot(Object root)`
`void`	`setScreenAnnotationRef(String annotation, int screenIndex, int annotationRefIndex)`
`void`	`setScreenDescription(String description, int screenIndex)`
`void`	`setScreenID(String id, int screenIndex)`
`void`	`setScreenName(String name, int screenIndex)`
`void`	`setScreenPlateRef(String plate, int screenIndex, int plateRefIndex)`
`void`	`setScreenProtocolDescription(String protocolDescription, int screenIndex)`
`void`	`setScreenProtocolIdentifier(String protocolIdentifier, int screenIndex)`
`void`	`setScreenReagentSetDescription(String reagentSetDescription, int screenIndex)`
`void`	`setScreenReagentSetIdentifier(String reagentSetIdentifier, int screenIndex)`
`void`	`setScreenType(String type, int screenIndex)`
`void`	`setStageLabelName(String name, int imageIndex)`
`void`	`setStageLabelX(Double x, int imageIndex)`
`void`	`setStageLabelY(Double y, int imageIndex)`
`void`	`setStageLabelZ(Double z, int imageIndex)`
`void`	`setTagAnnotationAnnotationRef(String annotation, int tagAnnotationIndex, int annotationRefIndex)`
`void`	`setTagAnnotationDescription(String description, int tagAnnotationIndex)`
`void`	`setTagAnnotationID(String id, int tagAnnotationIndex)`
`void`	`setTagAnnotationNamespace(String namespace, int tagAnnotationIndex)`
`void`	`setTagAnnotationValue(String value, int tagAnnotationIndex)`
`void`	`setTermAnnotationAnnotationRef(String annotation, int termAnnotationIndex, int annotationRefIndex)`
`void`	`setTermAnnotationDescription(String description, int termAnnotationIndex)`
`void`	`setTermAnnotationID(String id, int termAnnotationIndex)`
`void`	`setTermAnnotationNamespace(String namespace, int termAnnotationIndex)`
`void`	`setTermAnnotationValue(String value, int termAnnotationIndex)`
`void`	`setTiffDataFirstC(NonNegativeInteger firstC, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataFirstT(NonNegativeInteger firstT, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataFirstZ(NonNegativeInteger firstZ, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataIFD(NonNegativeInteger ifd, int imageIndex, int tiffDataIndex)`
`void`	`setTiffDataPlaneCount(NonNegativeInteger planeCount, int imageIndex, int tiffDataIndex)`
`void`	`setTimestampAnnotationAnnotationRef(String annotation, int timestampAnnotationIndex, int annotationRefIndex)`
`void`	`setTimestampAnnotationDescription(String description, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationID(String id, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationNamespace(String namespace, int timestampAnnotationIndex)`
`void`	`setTimestampAnnotationValue(Timestamp value, int timestampAnnotationIndex)`
`void`	`setTransmittanceRangeCutIn(PositiveInteger cutIn, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutInTolerance(NonNegativeInteger cutInTolerance, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutOut(PositiveInteger cutOut, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeCutOutTolerance(NonNegativeInteger cutOutTolerance, int instrumentIndex, int filterIndex)`
`void`	`setTransmittanceRangeTransmittance(PercentFraction transmittance, int instrumentIndex, int filterIndex)`
`void`	`setUUID(String uuid)` Sets the UUID associated with this collection of metadata.
`void`	`setUUIDFileName(String fileName, int imageIndex, int tiffDataIndex)`
`void`	`setUUIDValue(String value, int imageIndex, int tiffDataIndex)`
`void`	`setWellAnnotationRef(String annotation, int plateIndex, int wellIndex, int annotationRefIndex)`
`void`	`setWellColor(Color color, int plateIndex, int wellIndex)`
`void`	`setWellColumn(NonNegativeInteger column, int plateIndex, int wellIndex)`
`void`	`setWellExternalDescription(String externalDescription, int plateIndex, int wellIndex)`
`void`	`setWellExternalIdentifier(String externalIdentifier, int plateIndex, int wellIndex)`
`void`	`setWellID(String id, int plateIndex, int wellIndex)`
`void`	`setWellReagentRef(String reagent, int plateIndex, int wellIndex)`
`void`	`setWellRow(NonNegativeInteger row, int plateIndex, int wellIndex)`
`void`	`setWellSampleAnnotationRef(String annotation, int plateIndex, int wellIndex, int wellSampleIndex, int annotationRefIndex)`
`void`	`setWellSampleID(String id, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleImageRef(String image, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleIndex(NonNegativeInteger index, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSamplePositionX(Double positionX, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSamplePositionY(Double positionY, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellSampleTimepoint(Timestamp timepoint, int plateIndex, int wellIndex, int wellSampleIndex)`
`void`	`setWellType(String type, int plateIndex, int wellIndex)`
`void`	`setXMLAnnotationAnnotationRef(String annotation, int XMLAnnotationIndex, int annotationRefIndex)`
`void`	`setXMLAnnotationDescription(String description, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationID(String id, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationNamespace(String namespace, int XMLAnnotationIndex)`
`void`	`setXMLAnnotationValue(String value, int XMLAnnotationIndex)`

Methods inherited from class loci.formats.ome.AbstractOMEXMLMetadata
booleanToInteger, doubleToInteger, integerToBoolean, integerToDouble

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail
- OMEXMLMetadataImpl
```
public OMEXMLMetadataImpl()
```

Method Detail

createRoot
```
public void createRoot()
```

getRoot
```
public Object getRoot()
```
Specified by:

getRoot in interface MetadataStore

Overrides:

getRoot in class AbstractOMEXMLMetadata

setRoot
```
public void setRoot(Object root)
```
Specified by:

setRoot in interface MetadataStore

Overrides:

setRoot in class AbstractOMEXMLMetadata

dumpXML
```
public String dumpXML()
```
Description copied from class: AbstractOMEXMLMetadata

Dumps the given OME-XML DOM tree to a string.

Specified by:

dumpXML in interface OMEXMLMetadata

Overrides:

dumpXML in class AbstractOMEXMLMetadata

Returns:
OME-XML as a string.

resolveReferences
```
public int resolveReferences()
```

getPixelsBinDataCount

public int getPixelsBinDataCount(int imageIndex)

getBooleanAnnotationAnnotationCount

public int getBooleanAnnotationAnnotationCount(int booleanAnnotationIndex)

getCommentAnnotationAnnotationCount

public int getCommentAnnotationAnnotationCount(int commentAnnotationIndex)

getDoubleAnnotationAnnotationCount

public int getDoubleAnnotationAnnotationCount(int doubleAnnotationIndex)

getFileAnnotationAnnotationCount

public int getFileAnnotationAnnotationCount(int fileAnnotationIndex)

getListAnnotationAnnotationCount

public int getListAnnotationAnnotationCount(int listAnnotationIndex)

getLongAnnotationAnnotationCount

public int getLongAnnotationAnnotationCount(int longAnnotationIndex)

getTagAnnotationAnnotationCount

public int getTagAnnotationAnnotationCount(int tagAnnotationIndex)

getTermAnnotationAnnotationCount

public int getTermAnnotationAnnotationCount(int termAnnotationIndex)

getTimestampAnnotationAnnotationCount

public int getTimestampAnnotationAnnotationCount(int timestampAnnotationIndex)

getXMLAnnotationAnnotationCount

public int getXMLAnnotationAnnotationCount(int xmlAnnotationIndex)

getLightSourceType

public String getLightSourceType(int instrumentIndex,
                        int lightSourceIndex)

getShapeType

public String getShapeType(int roiIndex,
                  int shapeIndex)

getROIAnnotationRefCount

public int getROIAnnotationRefCount(int ROIIndex)

getPlateAcquisitionAnnotationRefCount

public int getPlateAcquisitionAnnotationRefCount(int plateIndex,
                                        int plateAcquisitionIndex)

getPlateAnnotationRefCount

public int getPlateAnnotationRefCount(int plateIndex)

getExperimenterGroupAnnotationRefCount

public int getExperimenterGroupAnnotationRefCount(int experimenterGroupIndex)

getImageAnnotationRefCount

public int getImageAnnotationRefCount(int imageIndex)

getScreenAnnotationRefCount

public int getScreenAnnotationRefCount(int screenIndex)

getWellAnnotationRefCount

public int getWellAnnotationRefCount(int plateIndex,
                            int wellIndex)

getDatasetAnnotationRefCount

public int getDatasetAnnotationRefCount(int datasetIndex)

getProjectAnnotationRefCount

public int getProjectAnnotationRefCount(int projectIndex)

getReagentAnnotationRefCount

public int getReagentAnnotationRefCount(int screenIndex,
                               int reagentIndex)

getPlaneAnnotationRefCount

public int getPlaneAnnotationRefCount(int imageIndex,
                             int planeIndex)

getExperimenterAnnotationRefCount

public int getExperimenterAnnotationRefCount(int experimenterIndex)

getWellSampleAnnotationRefCount

public int getWellSampleAnnotationRefCount(int plateIndex,
                                  int wellIndex,
                                  int wellSampleIndex)

getPixelsAnnotationRefCount

public int getPixelsAnnotationRefCount(int imageIndex)

getChannelAnnotationRefCount

public int getChannelAnnotationRefCount(int imageIndex,
                               int channelIndex)

getBooleanAnnotationCount

public int getBooleanAnnotationCount()

getChannelCount

public int getChannelCount(int imageIndex)

getCommentAnnotationCount

public int getCommentAnnotationCount()

getDatasetCount
```
public int getDatasetCount()
```

getDatasetRefCount

public int getDatasetRefCount(int projectIndex)

getDetectorCount

public int getDetectorCount(int instrumentIndex)

getDichroicCount

public int getDichroicCount(int instrumentIndex)

getDoubleAnnotationCount
```
public int getDoubleAnnotationCount()
```

getLightPathEmissionFilterRefCount

public int getLightPathEmissionFilterRefCount(int imageIndex,
                                     int channelIndex)

getFilterSetEmissionFilterRefCount

public int getFilterSetEmissionFilterRefCount(int instrumentIndex,
                                     int filterSetIndex)

getLightPathExcitationFilterRefCount

public int getLightPathExcitationFilterRefCount(int imageIndex,
                                       int channelIndex)

getFilterSetExcitationFilterRefCount

public int getFilterSetExcitationFilterRefCount(int instrumentIndex,
                                       int filterSetIndex)

getExperimentCount
```
public int getExperimentCount()
```

getExperimenterCount
```
public int getExperimenterCount()
```

getExperimenterGroupCount

public int getExperimenterGroupCount()

getExperimenterGroupExperimenterRefCount

public int getExperimenterGroupExperimenterRefCount(int experimenterGroupIndex)

getFileAnnotationCount
```
public int getFileAnnotationCount()
```

getFilterCount

public int getFilterCount(int instrumentIndex)

getFilterSetCount

public int getFilterSetCount(int instrumentIndex)

getImageCount
```
public int getImageCount()
```

getDatasetImageRefCount

public int getDatasetImageRefCount(int datasetIndex)

getInstrumentCount
```
public int getInstrumentCount()
```

getLeaderCount

public int getLeaderCount(int experimenterGroupIndex)

getLightSourceCount

public int getLightSourceCount(int instrumentIndex)

getMicrobeamManipulationLightSourceSettingsCount

public int getMicrobeamManipulationLightSourceSettingsCount(int experimentIndex,
                                                   int microbeamManipulationIndex)

getListAnnotationCount
```
public int getListAnnotationCount()
```

getLongAnnotationCount
```
public int getLongAnnotationCount()
```

getMicrobeamManipulationCount

public int getMicrobeamManipulationCount(int experimentIndex)

getMicrobeamManipulationRefCount

public int getMicrobeamManipulationRefCount(int imageIndex)

getObjectiveCount

public int getObjectiveCount(int instrumentIndex)

getPlaneCount

public int getPlaneCount(int imageIndex)

getPlateCount
```
public int getPlateCount()
```

getPlateAcquisitionCount

public int getPlateAcquisitionCount(int plateIndex)

getPlateRefCount

public int getPlateRefCount(int screenIndex)

getProjectCount
```
public int getProjectCount()
```

getROICount
```
public int getROICount()
```

getImageROIRefCount

public int getImageROIRefCount(int imageIndex)

getMicrobeamManipulationROIRefCount

public int getMicrobeamManipulationROIRefCount(int experimentIndex,
                                      int microbeamManipulationIndex)

getReagentCount

public int getReagentCount(int screenIndex)

getScreenCount
```
public int getScreenCount()
```

getShapeCount

public int getShapeCount(int ROIIndex)

getTagAnnotationCount
```
public int getTagAnnotationCount()
```

getTermAnnotationCount
```
public int getTermAnnotationCount()
```

getTiffDataCount

public int getTiffDataCount(int imageIndex)

getTimestampAnnotationCount

public int getTimestampAnnotationCount()

setUUIDValue

public void setUUIDValue(String value,
                int imageIndex,
                int tiffDataIndex)

getUUIDValue

public String getUUIDValue(int imageIndex,
                  int tiffDataIndex)

getWellCount

public int getWellCount(int plateIndex)

getWellSampleCount

public int getWellSampleCount(int plateIndex,
                     int wellIndex)

getWellSampleRefCount

public int getWellSampleRefCount(int plateIndex,
                        int plateAcquisitionIndex)

getXMLAnnotationCount
```
public int getXMLAnnotationCount()
```

getPixelsBinDataBigEndian

public Boolean getPixelsBinDataBigEndian(int imageIndex,
                                int binDataIndex)

getUUID
```
public String getUUID()
```
Gets the UUID associated with this collection of metadata.

Specified by:

getUUID in interface MetadataRetrieve

Overrides:

getUUID in class AbstractOMEXMLMetadata

getArcID

public String getArcID(int instrumentIndex,
              int lightSourceIndex)

getArcLotNumber

public String getArcLotNumber(int instrumentIndex,
                     int lightSourceIndex)

getArcManufacturer

public String getArcManufacturer(int instrumentIndex,
                        int lightSourceIndex)

getArcModel

public String getArcModel(int instrumentIndex,
                 int lightSourceIndex)

getArcPower

public Double getArcPower(int instrumentIndex,
                 int lightSourceIndex)

getArcSerialNumber

public String getArcSerialNumber(int instrumentIndex,
                        int lightSourceIndex)

getArcType

public ArcType getArcType(int instrumentIndex,
                 int lightSourceIndex)

getBinaryFileFileName

public String getBinaryFileFileName(int fileAnnotationIndex)

getBinaryFileMIMEType

public String getBinaryFileMIMEType(int fileAnnotationIndex)

getBinaryFileSize

public NonNegativeLong getBinaryFileSize(int fileAnnotationIndex)

getBinaryOnlyMetadataFile

public String getBinaryOnlyMetadataFile(int metadataFileIndex)

getBinaryOnlyUUID

public String getBinaryOnlyUUID(int UUIDIndex)

getBooleanAnnotationAnnotationRef

public String getBooleanAnnotationAnnotationRef(int booleanAnnotationIndex,
                                       int annotationRefIndex)

getBooleanAnnotationDescription

public String getBooleanAnnotationDescription(int booleanAnnotationIndex)

getBooleanAnnotationID

public String getBooleanAnnotationID(int booleanAnnotationIndex)

getBooleanAnnotationNamespace

public String getBooleanAnnotationNamespace(int booleanAnnotationIndex)

getBooleanAnnotationValue

public Boolean getBooleanAnnotationValue(int booleanAnnotationIndex)

getChannelAcquisitionMode

public AcquisitionMode getChannelAcquisitionMode(int imageIndex,
                                        int channelIndex)

getChannelAnnotationRef

public String getChannelAnnotationRef(int imageIndex,
                             int channelIndex,
                             int annotationRefIndex)

getChannelColor

public Color getChannelColor(int imageIndex,
                    int channelIndex)

getChannelContrastMethod

public ContrastMethod getChannelContrastMethod(int imageIndex,
                                      int channelIndex)

getChannelEmissionWavelength

public PositiveInteger getChannelEmissionWavelength(int imageIndex,
                                           int channelIndex)

getChannelExcitationWavelength

public PositiveInteger getChannelExcitationWavelength(int imageIndex,
                                             int channelIndex)

getChannelFilterSetRef

public String getChannelFilterSetRef(int imageIndex,
                            int channelIndex)

getChannelFluor

public String getChannelFluor(int imageIndex,
                     int channelIndex)

getChannelID

public String getChannelID(int imageIndex,
                  int channelIndex)

getChannelIlluminationType

public IlluminationType getChannelIlluminationType(int imageIndex,
                                          int channelIndex)

getChannelNDFilter

public Double getChannelNDFilter(int imageIndex,
                        int channelIndex)

getChannelName

public String getChannelName(int imageIndex,
                    int channelIndex)

getChannelPinholeSize

public Double getChannelPinholeSize(int imageIndex,
                           int channelIndex)

getChannelPockelCellSetting

public Integer getChannelPockelCellSetting(int imageIndex,
                                  int channelIndex)

getChannelSamplesPerPixel

public PositiveInteger getChannelSamplesPerPixel(int imageIndex,
                                        int channelIndex)

getCommentAnnotationAnnotationRef

public String getCommentAnnotationAnnotationRef(int commentAnnotationIndex,
                                       int annotationRefIndex)

getCommentAnnotationDescription

public String getCommentAnnotationDescription(int commentAnnotationIndex)

getCommentAnnotationID

public String getCommentAnnotationID(int commentAnnotationIndex)

getCommentAnnotationNamespace

public String getCommentAnnotationNamespace(int commentAnnotationIndex)

getCommentAnnotationValue

public String getCommentAnnotationValue(int commentAnnotationIndex)

getDatasetAnnotationRef

public String getDatasetAnnotationRef(int datasetIndex,
                             int annotationRefIndex)

getDatasetDescription

public String getDatasetDescription(int datasetIndex)

getDatasetExperimenterGroupRef

public String getDatasetExperimenterGroupRef(int datasetIndex)

getDatasetExperimenterRef

public String getDatasetExperimenterRef(int datasetIndex)

getDatasetID

public String getDatasetID(int datasetIndex)

getDatasetImageRef

public String getDatasetImageRef(int datasetIndex,
                        int imageRefIndex)

getDatasetName

public String getDatasetName(int datasetIndex)

getDetectorAmplificationGain

public Double getDetectorAmplificationGain(int instrumentIndex,
                                  int detectorIndex)

getDetectorGain

public Double getDetectorGain(int instrumentIndex,
                     int detectorIndex)

getDetectorID

public String getDetectorID(int instrumentIndex,
                   int detectorIndex)

getDetectorLotNumber

public String getDetectorLotNumber(int instrumentIndex,
                          int detectorIndex)

getDetectorManufacturer

public String getDetectorManufacturer(int instrumentIndex,
                             int detectorIndex)

getDetectorModel

public String getDetectorModel(int instrumentIndex,
                      int detectorIndex)

getDetectorOffset

public Double getDetectorOffset(int instrumentIndex,
                       int detectorIndex)

getDetectorSerialNumber

public String getDetectorSerialNumber(int instrumentIndex,
                             int detectorIndex)

getDetectorType

public DetectorType getDetectorType(int instrumentIndex,
                           int detectorIndex)

getDetectorVoltage

public Double getDetectorVoltage(int instrumentIndex,
                        int detectorIndex)

getDetectorZoom

public Double getDetectorZoom(int instrumentIndex,
                     int detectorIndex)

getDetectorSettingsBinning

public Binning getDetectorSettingsBinning(int imageIndex,
                                 int channelIndex)

getDetectorSettingsGain

public Double getDetectorSettingsGain(int imageIndex,
                             int channelIndex)

getDetectorSettingsID

public String getDetectorSettingsID(int imageIndex,
                           int channelIndex)

getDetectorSettingsOffset

public Double getDetectorSettingsOffset(int imageIndex,
                               int channelIndex)

getDetectorSettingsReadOutRate

public Double getDetectorSettingsReadOutRate(int imageIndex,
                                    int channelIndex)

getDetectorSettingsVoltage

public Double getDetectorSettingsVoltage(int imageIndex,
                                int channelIndex)

getDichroicID

public String getDichroicID(int instrumentIndex,
                   int dichroicIndex)

getDichroicLotNumber

public String getDichroicLotNumber(int instrumentIndex,
                          int dichroicIndex)

getDichroicManufacturer

public String getDichroicManufacturer(int instrumentIndex,
                             int dichroicIndex)

getDichroicModel

public String getDichroicModel(int instrumentIndex,
                      int dichroicIndex)

getDichroicSerialNumber

public String getDichroicSerialNumber(int instrumentIndex,
                             int dichroicIndex)

getDoubleAnnotationAnnotationRef

public String getDoubleAnnotationAnnotationRef(int doubleAnnotationIndex,
                                      int annotationRefIndex)

getDoubleAnnotationDescription

public String getDoubleAnnotationDescription(int doubleAnnotationIndex)

getDoubleAnnotationID

public String getDoubleAnnotationID(int doubleAnnotationIndex)

getDoubleAnnotationNamespace

public String getDoubleAnnotationNamespace(int doubleAnnotationIndex)

getDoubleAnnotationValue

public Double getDoubleAnnotationValue(int doubleAnnotationIndex)

getEllipseFillColor

public Color getEllipseFillColor(int ROIIndex,
                        int shapeIndex)

getEllipseFillRule

public FillRule getEllipseFillRule(int ROIIndex,
                          int shapeIndex)

getEllipseFontFamily

public FontFamily getEllipseFontFamily(int ROIIndex,
                              int shapeIndex)

getEllipseFontSize

public NonNegativeInteger getEllipseFontSize(int ROIIndex,
                                    int shapeIndex)

getEllipseFontStyle

public FontStyle getEllipseFontStyle(int ROIIndex,
                            int shapeIndex)

getEllipseID

public String getEllipseID(int ROIIndex,
                  int shapeIndex)

getEllipseLineCap

public LineCap getEllipseLineCap(int ROIIndex,
                        int shapeIndex)

getEllipseLocked

public Boolean getEllipseLocked(int ROIIndex,
                       int shapeIndex)

getEllipseStrokeColor

public Color getEllipseStrokeColor(int ROIIndex,
                          int shapeIndex)

getEllipseStrokeDashArray

public String getEllipseStrokeDashArray(int ROIIndex,
                               int shapeIndex)

getEllipseStrokeWidth

public Double getEllipseStrokeWidth(int ROIIndex,
                           int shapeIndex)

getEllipseText

public String getEllipseText(int ROIIndex,
                    int shapeIndex)

getEllipseTheC

public NonNegativeInteger getEllipseTheC(int ROIIndex,
                                int shapeIndex)

getEllipseTheT

public NonNegativeInteger getEllipseTheT(int ROIIndex,
                                int shapeIndex)

getEllipseTheZ

public NonNegativeInteger getEllipseTheZ(int ROIIndex,
                                int shapeIndex)

getEllipseTransform

public AffineTransform getEllipseTransform(int ROIIndex,
                                  int shapeIndex)

getEllipseVisible

public Boolean getEllipseVisible(int ROIIndex,
                        int shapeIndex)

getEllipseRadiusX

public Double getEllipseRadiusX(int ROIIndex,
                       int shapeIndex)

getEllipseRadiusY

public Double getEllipseRadiusY(int ROIIndex,
                       int shapeIndex)

getEllipseX

public Double getEllipseX(int ROIIndex,
                 int shapeIndex)

getEllipseY

public Double getEllipseY(int ROIIndex,
                 int shapeIndex)

getExperimentDescription

public String getExperimentDescription(int experimentIndex)

getExperimentExperimenterRef

public String getExperimentExperimenterRef(int experimentIndex)

getExperimentID

public String getExperimentID(int experimentIndex)

getExperimentType

public ExperimentType getExperimentType(int experimentIndex)

getExperimenterAnnotationRef

public String getExperimenterAnnotationRef(int experimenterIndex,
                                  int annotationRefIndex)

getExperimenterEmail

public String getExperimenterEmail(int experimenterIndex)

getExperimenterFirstName

public String getExperimenterFirstName(int experimenterIndex)

getExperimenterID

public String getExperimenterID(int experimenterIndex)

getExperimenterInstitution

public String getExperimenterInstitution(int experimenterIndex)

getExperimenterLastName

public String getExperimenterLastName(int experimenterIndex)

getExperimenterMiddleName

public String getExperimenterMiddleName(int experimenterIndex)

getExperimenterUserName

public String getExperimenterUserName(int experimenterIndex)

getExperimenterGroupAnnotationRef

public String getExperimenterGroupAnnotationRef(int experimenterGroupIndex,
                                       int annotationRefIndex)

getExperimenterGroupDescription

public String getExperimenterGroupDescription(int experimenterGroupIndex)

getExperimenterGroupExperimenterRef

public String getExperimenterGroupExperimenterRef(int experimenterGroupIndex,
                                         int experimenterRefIndex)

getExperimenterGroupID

public String getExperimenterGroupID(int experimenterGroupIndex)

getExperimenterGroupLeader

public String getExperimenterGroupLeader(int experimenterGroupIndex,
                                int leaderIndex)

getExperimenterGroupName

public String getExperimenterGroupName(int experimenterGroupIndex)

getFilamentID

public String getFilamentID(int instrumentIndex,
                   int lightSourceIndex)

getFilamentLotNumber

public String getFilamentLotNumber(int instrumentIndex,
                          int lightSourceIndex)

getFilamentManufacturer

public String getFilamentManufacturer(int instrumentIndex,
                             int lightSourceIndex)

getFilamentModel

public String getFilamentModel(int instrumentIndex,
                      int lightSourceIndex)

getFilamentPower

public Double getFilamentPower(int instrumentIndex,
                      int lightSourceIndex)

getFilamentSerialNumber

public String getFilamentSerialNumber(int instrumentIndex,
                             int lightSourceIndex)

getFilamentType

public FilamentType getFilamentType(int instrumentIndex,
                           int lightSourceIndex)

getFileAnnotationAnnotationRef

public String getFileAnnotationAnnotationRef(int fileAnnotationIndex,
                                    int annotationRefIndex)

getFileAnnotationDescription

public String getFileAnnotationDescription(int fileAnnotationIndex)

getFileAnnotationID

public String getFileAnnotationID(int fileAnnotationIndex)

getFileAnnotationNamespace

public String getFileAnnotationNamespace(int fileAnnotationIndex)

getFilterFilterWheel

public String getFilterFilterWheel(int instrumentIndex,
                          int filterIndex)

getFilterID

public String getFilterID(int instrumentIndex,
                 int filterIndex)

getFilterLotNumber

public String getFilterLotNumber(int instrumentIndex,
                        int filterIndex)

getFilterManufacturer

public String getFilterManufacturer(int instrumentIndex,
                           int filterIndex)

getFilterModel

public String getFilterModel(int instrumentIndex,
                    int filterIndex)

getFilterSerialNumber

public String getFilterSerialNumber(int instrumentIndex,
                           int filterIndex)

getFilterType

public FilterType getFilterType(int instrumentIndex,
                       int filterIndex)

getFilterSetDichroicRef

public String getFilterSetDichroicRef(int instrumentIndex,
                             int filterSetIndex)

getFilterSetEmissionFilterRef

public String getFilterSetEmissionFilterRef(int instrumentIndex,
                                   int filterSetIndex,
                                   int emissionFilterRefIndex)

getFilterSetExcitationFilterRef

public String getFilterSetExcitationFilterRef(int instrumentIndex,
                                     int filterSetIndex,
                                     int excitationFilterRefIndex)

getFilterSetID

public String getFilterSetID(int instrumentIndex,
                    int filterSetIndex)

getFilterSetLotNumber

public String getFilterSetLotNumber(int instrumentIndex,
                           int filterSetIndex)

getFilterSetManufacturer

public String getFilterSetManufacturer(int instrumentIndex,
                              int filterSetIndex)

getFilterSetModel

public String getFilterSetModel(int instrumentIndex,
                       int filterSetIndex)

getFilterSetSerialNumber

public String getFilterSetSerialNumber(int instrumentIndex,
                              int filterSetIndex)

getImageAcquisitionDate

public Timestamp getImageAcquisitionDate(int imageIndex)

getImageAnnotationRef

public String getImageAnnotationRef(int imageIndex,
                           int annotationRefIndex)

getImageDescription

public String getImageDescription(int imageIndex)

getImageExperimentRef

public String getImageExperimentRef(int imageIndex)

getImageExperimenterGroupRef

public String getImageExperimenterGroupRef(int imageIndex)

getImageExperimenterRef

public String getImageExperimenterRef(int imageIndex)

getImageID

public String getImageID(int imageIndex)

getImageInstrumentRef

public String getImageInstrumentRef(int imageIndex)

getImageMicrobeamManipulationRef

public String getImageMicrobeamManipulationRef(int imageIndex,
                                      int microbeamManipulationRefIndex)

getImageName

public String getImageName(int imageIndex)

getImageROIRef

public String getImageROIRef(int imageIndex,
                    int ROIRefIndex)

getImagingEnvironmentAirPressure

public Double getImagingEnvironmentAirPressure(int imageIndex)

getImagingEnvironmentCO2Percent

public PercentFraction getImagingEnvironmentCO2Percent(int imageIndex)

getImagingEnvironmentHumidity

public PercentFraction getImagingEnvironmentHumidity(int imageIndex)

getImagingEnvironmentTemperature

public Double getImagingEnvironmentTemperature(int imageIndex)

getInstrumentID

public String getInstrumentID(int instrumentIndex)

getLabelFillColor

public Color getLabelFillColor(int ROIIndex,
                      int shapeIndex)

getLabelFillRule

public FillRule getLabelFillRule(int ROIIndex,
                        int shapeIndex)

getLabelFontFamily

public FontFamily getLabelFontFamily(int ROIIndex,
                            int shapeIndex)

getLabelFontSize

public NonNegativeInteger getLabelFontSize(int ROIIndex,
                                  int shapeIndex)

getLabelFontStyle

public FontStyle getLabelFontStyle(int ROIIndex,
                          int shapeIndex)

getLabelID

public String getLabelID(int ROIIndex,
                int shapeIndex)

getLabelLineCap

public LineCap getLabelLineCap(int ROIIndex,
                      int shapeIndex)

getLabelLocked

public Boolean getLabelLocked(int ROIIndex,
                     int shapeIndex)

getLabelStrokeColor

public Color getLabelStrokeColor(int ROIIndex,
                        int shapeIndex)

getLabelStrokeDashArray

public String getLabelStrokeDashArray(int ROIIndex,
                             int shapeIndex)

getLabelStrokeWidth

public Double getLabelStrokeWidth(int ROIIndex,
                         int shapeIndex)

getLabelText

public String getLabelText(int ROIIndex,
                  int shapeIndex)

getLabelTheC

public NonNegativeInteger getLabelTheC(int ROIIndex,
                              int shapeIndex)

getLabelTheT

public NonNegativeInteger getLabelTheT(int ROIIndex,
                              int shapeIndex)

getLabelTheZ

public NonNegativeInteger getLabelTheZ(int ROIIndex,
                              int shapeIndex)

getLabelTransform

public AffineTransform getLabelTransform(int ROIIndex,
                                int shapeIndex)

getLabelVisible

public Boolean getLabelVisible(int ROIIndex,
                      int shapeIndex)

getLabelX

public Double getLabelX(int ROIIndex,
               int shapeIndex)

getLabelY

public Double getLabelY(int ROIIndex,
               int shapeIndex)

getLaserID

public String getLaserID(int instrumentIndex,
                int lightSourceIndex)

getLaserLotNumber

public String getLaserLotNumber(int instrumentIndex,
                       int lightSourceIndex)

getLaserManufacturer

public String getLaserManufacturer(int instrumentIndex,
                          int lightSourceIndex)

getLaserModel

public String getLaserModel(int instrumentIndex,
                   int lightSourceIndex)

getLaserPower

public Double getLaserPower(int instrumentIndex,
                   int lightSourceIndex)

getLaserSerialNumber

public String getLaserSerialNumber(int instrumentIndex,
                          int lightSourceIndex)

getLaserFrequencyMultiplication

public PositiveInteger getLaserFrequencyMultiplication(int instrumentIndex,
                                              int lightSourceIndex)

getLaserLaserMedium

public LaserMedium getLaserLaserMedium(int instrumentIndex,
                              int lightSourceIndex)

getLaserPockelCell

public Boolean getLaserPockelCell(int instrumentIndex,
                         int lightSourceIndex)

getLaserPulse

public Pulse getLaserPulse(int instrumentIndex,
                  int lightSourceIndex)

getLaserPump

public String getLaserPump(int instrumentIndex,
                  int lightSourceIndex)

getLaserRepetitionRate

public Double getLaserRepetitionRate(int instrumentIndex,
                            int lightSourceIndex)

getLaserTuneable

public Boolean getLaserTuneable(int instrumentIndex,
                       int lightSourceIndex)

getLaserType

public LaserType getLaserType(int instrumentIndex,
                     int lightSourceIndex)

getLaserWavelength

public PositiveInteger getLaserWavelength(int instrumentIndex,
                                 int lightSourceIndex)

getLightEmittingDiodeID

public String getLightEmittingDiodeID(int instrumentIndex,
                             int lightSourceIndex)

getLightEmittingDiodeLotNumber

public String getLightEmittingDiodeLotNumber(int instrumentIndex,
                                    int lightSourceIndex)

getLightEmittingDiodeManufacturer

public String getLightEmittingDiodeManufacturer(int instrumentIndex,
                                       int lightSourceIndex)

getLightEmittingDiodeModel

public String getLightEmittingDiodeModel(int instrumentIndex,
                                int lightSourceIndex)

getLightEmittingDiodePower

public Double getLightEmittingDiodePower(int instrumentIndex,
                                int lightSourceIndex)

getLightEmittingDiodeSerialNumber

public String getLightEmittingDiodeSerialNumber(int instrumentIndex,
                                       int lightSourceIndex)

getLightPathDichroicRef

public String getLightPathDichroicRef(int imageIndex,
                             int channelIndex)

getLightPathEmissionFilterRef

public String getLightPathEmissionFilterRef(int imageIndex,
                                   int channelIndex,
                                   int emissionFilterRefIndex)

getLightPathExcitationFilterRef

public String getLightPathExcitationFilterRef(int imageIndex,
                                     int channelIndex,
                                     int excitationFilterRefIndex)

getChannelLightSourceSettingsAttenuation

public PercentFraction getChannelLightSourceSettingsAttenuation(int imageIndex,
                                                       int channelIndex)

getMicrobeamManipulationLightSourceSettingsAttenuation

public PercentFraction getMicrobeamManipulationLightSourceSettingsAttenuation(int experimentIndex,
                                                                     int microbeamManipulationIndex,
                                                                     int lightSourceSettingsIndex)

getChannelLightSourceSettingsID

public String getChannelLightSourceSettingsID(int imageIndex,
                                     int channelIndex)

getMicrobeamManipulationLightSourceSettingsID

public String getMicrobeamManipulationLightSourceSettingsID(int experimentIndex,
                                                   int microbeamManipulationIndex,
                                                   int lightSourceSettingsIndex)

getChannelLightSourceSettingsWavelength

public PositiveInteger getChannelLightSourceSettingsWavelength(int imageIndex,
                                                      int channelIndex)

getMicrobeamManipulationLightSourceSettingsWavelength

public PositiveInteger getMicrobeamManipulationLightSourceSettingsWavelength(int experimentIndex,
                                                                    int microbeamManipulationIndex,
                                                                    int lightSourceSettingsIndex)

getLineFillColor

public Color getLineFillColor(int ROIIndex,
                     int shapeIndex)

getLineFillRule

public FillRule getLineFillRule(int ROIIndex,
                       int shapeIndex)

getLineFontFamily

public FontFamily getLineFontFamily(int ROIIndex,
                           int shapeIndex)

getLineFontSize

public NonNegativeInteger getLineFontSize(int ROIIndex,
                                 int shapeIndex)

getLineFontStyle

public FontStyle getLineFontStyle(int ROIIndex,
                         int shapeIndex)

getLineID

public String getLineID(int ROIIndex,
               int shapeIndex)

getLineLineCap

public LineCap getLineLineCap(int ROIIndex,
                     int shapeIndex)

getLineLocked

public Boolean getLineLocked(int ROIIndex,
                    int shapeIndex)

getLineStrokeColor

public Color getLineStrokeColor(int ROIIndex,
                       int shapeIndex)

getLineStrokeDashArray

public String getLineStrokeDashArray(int ROIIndex,
                            int shapeIndex)

getLineStrokeWidth

public Double getLineStrokeWidth(int ROIIndex,
                        int shapeIndex)

getLineText

public String getLineText(int ROIIndex,
                 int shapeIndex)

getLineTheC

public NonNegativeInteger getLineTheC(int ROIIndex,
                             int shapeIndex)

getLineTheT

public NonNegativeInteger getLineTheT(int ROIIndex,
                             int shapeIndex)

getLineTheZ

public NonNegativeInteger getLineTheZ(int ROIIndex,
                             int shapeIndex)

getLineTransform

public AffineTransform getLineTransform(int ROIIndex,
                               int shapeIndex)

getLineVisible

public Boolean getLineVisible(int ROIIndex,
                     int shapeIndex)

getLineMarkerEnd

public Marker getLineMarkerEnd(int ROIIndex,
                      int shapeIndex)

getLineMarkerStart

public Marker getLineMarkerStart(int ROIIndex,
                        int shapeIndex)

getLineX1

public Double getLineX1(int ROIIndex,
               int shapeIndex)

getLineX2

public Double getLineX2(int ROIIndex,
               int shapeIndex)

getLineY1

public Double getLineY1(int ROIIndex,
               int shapeIndex)

getLineY2

public Double getLineY2(int ROIIndex,
               int shapeIndex)

getListAnnotationAnnotationRef

public String getListAnnotationAnnotationRef(int listAnnotationIndex,
                                    int annotationRefIndex)

getListAnnotationDescription

public String getListAnnotationDescription(int listAnnotationIndex)

getListAnnotationID

public String getListAnnotationID(int listAnnotationIndex)

getListAnnotationNamespace

public String getListAnnotationNamespace(int listAnnotationIndex)

getLongAnnotationAnnotationRef

public String getLongAnnotationAnnotationRef(int longAnnotationIndex,
                                    int annotationRefIndex)

getLongAnnotationDescription

public String getLongAnnotationDescription(int longAnnotationIndex)

getLongAnnotationID

public String getLongAnnotationID(int longAnnotationIndex)

getLongAnnotationNamespace

public String getLongAnnotationNamespace(int longAnnotationIndex)

getLongAnnotationValue

public Long getLongAnnotationValue(int longAnnotationIndex)

getMaskFillColor

public Color getMaskFillColor(int ROIIndex,
                     int shapeIndex)

getMaskFillRule

public FillRule getMaskFillRule(int ROIIndex,
                       int shapeIndex)

getMaskFontFamily

public FontFamily getMaskFontFamily(int ROIIndex,
                           int shapeIndex)

getMaskFontSize

public NonNegativeInteger getMaskFontSize(int ROIIndex,
                                 int shapeIndex)

getMaskFontStyle

public FontStyle getMaskFontStyle(int ROIIndex,
                         int shapeIndex)

getMaskID

public String getMaskID(int ROIIndex,
               int shapeIndex)

getMaskLineCap

public LineCap getMaskLineCap(int ROIIndex,
                     int shapeIndex)

getMaskLocked

public Boolean getMaskLocked(int ROIIndex,
                    int shapeIndex)

getMaskStrokeColor

public Color getMaskStrokeColor(int ROIIndex,
                       int shapeIndex)

getMaskStrokeDashArray

public String getMaskStrokeDashArray(int ROIIndex,
                            int shapeIndex)

getMaskStrokeWidth

public Double getMaskStrokeWidth(int ROIIndex,
                        int shapeIndex)

getMaskText

public String getMaskText(int ROIIndex,
                 int shapeIndex)

getMaskTheC

public NonNegativeInteger getMaskTheC(int ROIIndex,
                             int shapeIndex)

getMaskTheT

public NonNegativeInteger getMaskTheT(int ROIIndex,
                             int shapeIndex)

getMaskTheZ

public NonNegativeInteger getMaskTheZ(int ROIIndex,
                             int shapeIndex)

getMaskTransform

public AffineTransform getMaskTransform(int ROIIndex,
                               int shapeIndex)

getMaskVisible

public Boolean getMaskVisible(int ROIIndex,
                     int shapeIndex)

getMaskHeight

public Double getMaskHeight(int ROIIndex,
                   int shapeIndex)

getMaskWidth

public Double getMaskWidth(int ROIIndex,
                  int shapeIndex)

getMaskX

public Double getMaskX(int ROIIndex,
              int shapeIndex)

getMaskY

public Double getMaskY(int ROIIndex,
              int shapeIndex)

getMicrobeamManipulationDescription

public String getMicrobeamManipulationDescription(int experimentIndex,
                                         int microbeamManipulationIndex)

getMicrobeamManipulationExperimenterRef

public String getMicrobeamManipulationExperimenterRef(int experimentIndex,
                                             int microbeamManipulationIndex)

getMicrobeamManipulationID

public String getMicrobeamManipulationID(int experimentIndex,
                                int microbeamManipulationIndex)

getMicrobeamManipulationROIRef

public String getMicrobeamManipulationROIRef(int experimentIndex,
                                    int microbeamManipulationIndex,
                                    int ROIRefIndex)

getMicrobeamManipulationType

public MicrobeamManipulationType getMicrobeamManipulationType(int experimentIndex,
                                                     int microbeamManipulationIndex)

getMicroscopeLotNumber

public String getMicroscopeLotNumber(int instrumentIndex)

getMicroscopeManufacturer

public String getMicroscopeManufacturer(int instrumentIndex)

getMicroscopeModel

public String getMicroscopeModel(int instrumentIndex)

getMicroscopeSerialNumber

public String getMicroscopeSerialNumber(int instrumentIndex)

getMicroscopeType

public MicroscopeType getMicroscopeType(int instrumentIndex)

getObjectiveCalibratedMagnification

public Double getObjectiveCalibratedMagnification(int instrumentIndex,
                                         int objectiveIndex)

getObjectiveCorrection

public Correction getObjectiveCorrection(int instrumentIndex,
                                int objectiveIndex)

getObjectiveID

public String getObjectiveID(int instrumentIndex,
                    int objectiveIndex)

getObjectiveImmersion

public Immersion getObjectiveImmersion(int instrumentIndex,
                              int objectiveIndex)

getObjectiveIris

public Boolean getObjectiveIris(int instrumentIndex,
                       int objectiveIndex)

getObjectiveLensNA

public Double getObjectiveLensNA(int instrumentIndex,
                        int objectiveIndex)

getObjectiveLotNumber

public String getObjectiveLotNumber(int instrumentIndex,
                           int objectiveIndex)

getObjectiveManufacturer

public String getObjectiveManufacturer(int instrumentIndex,
                              int objectiveIndex)

getObjectiveModel

public String getObjectiveModel(int instrumentIndex,
                       int objectiveIndex)

getObjectiveNominalMagnification

public PositiveInteger getObjectiveNominalMagnification(int instrumentIndex,
                                               int objectiveIndex)

getObjectiveSerialNumber

public String getObjectiveSerialNumber(int instrumentIndex,
                              int objectiveIndex)

getObjectiveWorkingDistance

public Double getObjectiveWorkingDistance(int instrumentIndex,
                                 int objectiveIndex)

getObjectiveSettingsCorrectionCollar

public Double getObjectiveSettingsCorrectionCollar(int imageIndex)

getObjectiveSettingsID

public String getObjectiveSettingsID(int imageIndex)

getObjectiveSettingsMedium

public Medium getObjectiveSettingsMedium(int imageIndex)

getObjectiveSettingsRefractiveIndex

public Double getObjectiveSettingsRefractiveIndex(int imageIndex)

getPixelsAnnotationRef

public String getPixelsAnnotationRef(int imageIndex,
                            int annotationRefIndex)

getPixelsDimensionOrder

public DimensionOrder getPixelsDimensionOrder(int imageIndex)

getPixelsID

public String getPixelsID(int imageIndex)

getPixelsPhysicalSizeX

public PositiveFloat getPixelsPhysicalSizeX(int imageIndex)

getPixelsPhysicalSizeY

public PositiveFloat getPixelsPhysicalSizeY(int imageIndex)

getPixelsPhysicalSizeZ

public PositiveFloat getPixelsPhysicalSizeZ(int imageIndex)

getPixelsSizeC

public PositiveInteger getPixelsSizeC(int imageIndex)

getPixelsSizeT

public PositiveInteger getPixelsSizeT(int imageIndex)

getPixelsSizeX

public PositiveInteger getPixelsSizeX(int imageIndex)

getPixelsSizeY

public PositiveInteger getPixelsSizeY(int imageIndex)

getPixelsSizeZ

public PositiveInteger getPixelsSizeZ(int imageIndex)

getPixelsTimeIncrement

public Double getPixelsTimeIncrement(int imageIndex)

getPixelsType

public PixelType getPixelsType(int imageIndex)

getPlaneAnnotationRef

public String getPlaneAnnotationRef(int imageIndex,
                           int planeIndex,
                           int annotationRefIndex)

getPlaneDeltaT

public Double getPlaneDeltaT(int imageIndex,
                    int planeIndex)

getPlaneExposureTime

public Double getPlaneExposureTime(int imageIndex,
                          int planeIndex)

getPlaneHashSHA1

public String getPlaneHashSHA1(int imageIndex,
                      int planeIndex)

getPlanePositionX

public Double getPlanePositionX(int imageIndex,
                       int planeIndex)

getPlanePositionY

public Double getPlanePositionY(int imageIndex,
                       int planeIndex)

getPlanePositionZ

public Double getPlanePositionZ(int imageIndex,
                       int planeIndex)

getPlaneTheC

public NonNegativeInteger getPlaneTheC(int imageIndex,
                              int planeIndex)

getPlaneTheT

public NonNegativeInteger getPlaneTheT(int imageIndex,
                              int planeIndex)

getPlaneTheZ

public NonNegativeInteger getPlaneTheZ(int imageIndex,
                              int planeIndex)

getPlateAnnotationRef

public String getPlateAnnotationRef(int plateIndex,
                           int annotationRefIndex)

getPlateColumnNamingConvention

public NamingConvention getPlateColumnNamingConvention(int plateIndex)

getPlateColumns

public PositiveInteger getPlateColumns(int plateIndex)

getPlateDescription

public String getPlateDescription(int plateIndex)

getPlateExternalIdentifier

public String getPlateExternalIdentifier(int plateIndex)

getPlateFieldIndex

public NonNegativeInteger getPlateFieldIndex(int plateIndex)

getPlateID

public String getPlateID(int plateIndex)

getPlateName

public String getPlateName(int plateIndex)

getPlateRowNamingConvention

public NamingConvention getPlateRowNamingConvention(int plateIndex)

getPlateRows

public PositiveInteger getPlateRows(int plateIndex)

getPlateStatus

public String getPlateStatus(int plateIndex)

getPlateWellOriginX

public Double getPlateWellOriginX(int plateIndex)

getPlateWellOriginY

public Double getPlateWellOriginY(int plateIndex)

getPlateAcquisitionAnnotationRef

public String getPlateAcquisitionAnnotationRef(int plateIndex,
                                      int plateAcquisitionIndex,
                                      int annotationRefIndex)

getPlateAcquisitionDescription

public String getPlateAcquisitionDescription(int plateIndex,
                                    int plateAcquisitionIndex)

getPlateAcquisitionEndTime

public Timestamp getPlateAcquisitionEndTime(int plateIndex,
                                   int plateAcquisitionIndex)

getPlateAcquisitionID

public String getPlateAcquisitionID(int plateIndex,
                           int plateAcquisitionIndex)

getPlateAcquisitionMaximumFieldCount

public PositiveInteger getPlateAcquisitionMaximumFieldCount(int plateIndex,
                                                   int plateAcquisitionIndex)

getPlateAcquisitionName

public String getPlateAcquisitionName(int plateIndex,
                             int plateAcquisitionIndex)

getPlateAcquisitionStartTime

public Timestamp getPlateAcquisitionStartTime(int plateIndex,
                                     int plateAcquisitionIndex)

getPlateAcquisitionWellSampleRef

public String getPlateAcquisitionWellSampleRef(int plateIndex,
                                      int plateAcquisitionIndex,
                                      int wellSampleRefIndex)

getPointFillColor

public Color getPointFillColor(int ROIIndex,
                      int shapeIndex)

getPointFillRule

public FillRule getPointFillRule(int ROIIndex,
                        int shapeIndex)

getPointFontFamily

public FontFamily getPointFontFamily(int ROIIndex,
                            int shapeIndex)

getPointFontSize

public NonNegativeInteger getPointFontSize(int ROIIndex,
                                  int shapeIndex)

getPointFontStyle

public FontStyle getPointFontStyle(int ROIIndex,
                          int shapeIndex)

getPointID

public String getPointID(int ROIIndex,
                int shapeIndex)

getPointLineCap

public LineCap getPointLineCap(int ROIIndex,
                      int shapeIndex)

getPointLocked

public Boolean getPointLocked(int ROIIndex,
                     int shapeIndex)

getPointStrokeColor

public Color getPointStrokeColor(int ROIIndex,
                        int shapeIndex)

getPointStrokeDashArray

public String getPointStrokeDashArray(int ROIIndex,
                             int shapeIndex)

getPointStrokeWidth

public Double getPointStrokeWidth(int ROIIndex,
                         int shapeIndex)

getPointText

public String getPointText(int ROIIndex,
                  int shapeIndex)

getPointTheC

public NonNegativeInteger getPointTheC(int ROIIndex,
                              int shapeIndex)

getPointTheT

public NonNegativeInteger getPointTheT(int ROIIndex,
                              int shapeIndex)

getPointTheZ

public NonNegativeInteger getPointTheZ(int ROIIndex,
                              int shapeIndex)

getPointTransform

public AffineTransform getPointTransform(int ROIIndex,
                                int shapeIndex)

getPointVisible

public Boolean getPointVisible(int ROIIndex,
                      int shapeIndex)

getPointX

public Double getPointX(int ROIIndex,
               int shapeIndex)

getPointY

public Double getPointY(int ROIIndex,
               int shapeIndex)

getPolygonFillColor

public Color getPolygonFillColor(int ROIIndex,
                        int shapeIndex)

getPolygonFillRule

public FillRule getPolygonFillRule(int ROIIndex,
                          int shapeIndex)

getPolygonFontFamily

public FontFamily getPolygonFontFamily(int ROIIndex,
                              int shapeIndex)

getPolygonFontSize

public NonNegativeInteger getPolygonFontSize(int ROIIndex,
                                    int shapeIndex)

getPolygonFontStyle

public FontStyle getPolygonFontStyle(int ROIIndex,
                            int shapeIndex)

getPolygonID

public String getPolygonID(int ROIIndex,
                  int shapeIndex)

getPolygonLineCap

public LineCap getPolygonLineCap(int ROIIndex,
                        int shapeIndex)

getPolygonLocked

public Boolean getPolygonLocked(int ROIIndex,
                       int shapeIndex)

getPolygonStrokeColor

public Color getPolygonStrokeColor(int ROIIndex,
                          int shapeIndex)

getPolygonStrokeDashArray

public String getPolygonStrokeDashArray(int ROIIndex,
                               int shapeIndex)

getPolygonStrokeWidth

public Double getPolygonStrokeWidth(int ROIIndex,
                           int shapeIndex)

getPolygonText

public String getPolygonText(int ROIIndex,
                    int shapeIndex)

getPolygonTheC

public NonNegativeInteger getPolygonTheC(int ROIIndex,
                                int shapeIndex)

getPolygonTheT

public NonNegativeInteger getPolygonTheT(int ROIIndex,
                                int shapeIndex)

getPolygonTheZ

public NonNegativeInteger getPolygonTheZ(int ROIIndex,
                                int shapeIndex)

getPolygonTransform

public AffineTransform getPolygonTransform(int ROIIndex,
                                  int shapeIndex)

getPolygonVisible

public Boolean getPolygonVisible(int ROIIndex,
                        int shapeIndex)

getPolygonPoints

public String getPolygonPoints(int ROIIndex,
                      int shapeIndex)

getPolylineFillColor

public Color getPolylineFillColor(int ROIIndex,
                         int shapeIndex)

getPolylineFillRule

public FillRule getPolylineFillRule(int ROIIndex,
                           int shapeIndex)

getPolylineFontFamily

public FontFamily getPolylineFontFamily(int ROIIndex,
                               int shapeIndex)

getPolylineFontSize

public NonNegativeInteger getPolylineFontSize(int ROIIndex,
                                     int shapeIndex)

getPolylineFontStyle

public FontStyle getPolylineFontStyle(int ROIIndex,
                             int shapeIndex)

getPolylineID

public String getPolylineID(int ROIIndex,
                   int shapeIndex)

getPolylineLineCap

public LineCap getPolylineLineCap(int ROIIndex,
                         int shapeIndex)

getPolylineLocked

public Boolean getPolylineLocked(int ROIIndex,
                        int shapeIndex)

getPolylineStrokeColor

public Color getPolylineStrokeColor(int ROIIndex,
                           int shapeIndex)

getPolylineStrokeDashArray

public String getPolylineStrokeDashArray(int ROIIndex,
                                int shapeIndex)

getPolylineStrokeWidth

public Double getPolylineStrokeWidth(int ROIIndex,
                            int shapeIndex)

getPolylineText

public String getPolylineText(int ROIIndex,
                     int shapeIndex)

getPolylineTheC

public NonNegativeInteger getPolylineTheC(int ROIIndex,
                                 int shapeIndex)

getPolylineTheT

public NonNegativeInteger getPolylineTheT(int ROIIndex,
                                 int shapeIndex)

getPolylineTheZ

public NonNegativeInteger getPolylineTheZ(int ROIIndex,
                                 int shapeIndex)

getPolylineTransform

public AffineTransform getPolylineTransform(int ROIIndex,
                                   int shapeIndex)

getPolylineVisible

public Boolean getPolylineVisible(int ROIIndex,
                         int shapeIndex)

getPolylineMarkerEnd

public Marker getPolylineMarkerEnd(int ROIIndex,
                          int shapeIndex)

getPolylineMarkerStart

public Marker getPolylineMarkerStart(int ROIIndex,
                            int shapeIndex)

getPolylinePoints

public String getPolylinePoints(int ROIIndex,
                       int shapeIndex)

getProjectAnnotationRef

public String getProjectAnnotationRef(int projectIndex,
                             int annotationRefIndex)

getProjectDatasetRef

public String getProjectDatasetRef(int projectIndex,
                          int datasetRefIndex)

getProjectDescription

public String getProjectDescription(int projectIndex)

getProjectExperimenterGroupRef

public String getProjectExperimenterGroupRef(int projectIndex)

getProjectExperimenterRef

public String getProjectExperimenterRef(int projectIndex)

getProjectID

public String getProjectID(int projectIndex)

getProjectName

public String getProjectName(int projectIndex)

getROIAnnotationRef

public String getROIAnnotationRef(int ROIIndex,
                         int annotationRefIndex)

getROIDescription

public String getROIDescription(int ROIIndex)

getROIID
```
public String getROIID(int ROIIndex)
```

getROIName

public String getROIName(int ROIIndex)

getROINamespace

public String getROINamespace(int ROIIndex)

getReagentAnnotationRef

public String getReagentAnnotationRef(int screenIndex,
                             int reagentIndex,
                             int annotationRefIndex)

getReagentDescription

public String getReagentDescription(int screenIndex,
                           int reagentIndex)

getReagentID

public String getReagentID(int screenIndex,
                  int reagentIndex)

getReagentName

public String getReagentName(int screenIndex,
                    int reagentIndex)

getReagentReagentIdentifier

public String getReagentReagentIdentifier(int screenIndex,
                                 int reagentIndex)

getRectangleFillColor

public Color getRectangleFillColor(int ROIIndex,
                          int shapeIndex)

getRectangleFillRule

public FillRule getRectangleFillRule(int ROIIndex,
                            int shapeIndex)

getRectangleFontFamily

public FontFamily getRectangleFontFamily(int ROIIndex,
                                int shapeIndex)

getRectangleFontSize

public NonNegativeInteger getRectangleFontSize(int ROIIndex,
                                      int shapeIndex)

getRectangleFontStyle

public FontStyle getRectangleFontStyle(int ROIIndex,
                              int shapeIndex)

getRectangleID

public String getRectangleID(int ROIIndex,
                    int shapeIndex)

getRectangleLineCap

public LineCap getRectangleLineCap(int ROIIndex,
                          int shapeIndex)

getRectangleLocked

public Boolean getRectangleLocked(int ROIIndex,
                         int shapeIndex)

getRectangleStrokeColor

public Color getRectangleStrokeColor(int ROIIndex,
                            int shapeIndex)

getRectangleStrokeDashArray

public String getRectangleStrokeDashArray(int ROIIndex,
                                 int shapeIndex)

getRectangleStrokeWidth

public Double getRectangleStrokeWidth(int ROIIndex,
                             int shapeIndex)

getRectangleText

public String getRectangleText(int ROIIndex,
                      int shapeIndex)

getRectangleTheC

public NonNegativeInteger getRectangleTheC(int ROIIndex,
                                  int shapeIndex)

getRectangleTheT

public NonNegativeInteger getRectangleTheT(int ROIIndex,
                                  int shapeIndex)

getRectangleTheZ

public NonNegativeInteger getRectangleTheZ(int ROIIndex,
                                  int shapeIndex)

getRectangleTransform

public AffineTransform getRectangleTransform(int ROIIndex,
                                    int shapeIndex)

getRectangleVisible

public Boolean getRectangleVisible(int ROIIndex,
                          int shapeIndex)

getRectangleHeight

public Double getRectangleHeight(int ROIIndex,
                        int shapeIndex)

getRectangleWidth

public Double getRectangleWidth(int ROIIndex,
                       int shapeIndex)

getRectangleX

public Double getRectangleX(int ROIIndex,
                   int shapeIndex)

getRectangleY

public Double getRectangleY(int ROIIndex,
                   int shapeIndex)

getScreenAnnotationRef

public String getScreenAnnotationRef(int screenIndex,
                            int annotationRefIndex)

getScreenDescription

public String getScreenDescription(int screenIndex)

getScreenID

public String getScreenID(int screenIndex)

getScreenName

public String getScreenName(int screenIndex)

getScreenPlateRef

public String getScreenPlateRef(int screenIndex,
                       int plateRefIndex)

getScreenProtocolDescription

public String getScreenProtocolDescription(int screenIndex)

getScreenProtocolIdentifier

public String getScreenProtocolIdentifier(int screenIndex)

getScreenReagentSetDescription

public String getScreenReagentSetDescription(int screenIndex)

getScreenReagentSetIdentifier

public String getScreenReagentSetIdentifier(int screenIndex)

getScreenType

public String getScreenType(int screenIndex)

getStageLabelName

public String getStageLabelName(int imageIndex)

getStageLabelX

public Double getStageLabelX(int imageIndex)

getStageLabelY

public Double getStageLabelY(int imageIndex)

getStageLabelZ

public Double getStageLabelZ(int imageIndex)

getTagAnnotationAnnotationRef

public String getTagAnnotationAnnotationRef(int tagAnnotationIndex,
                                   int annotationRefIndex)

getTagAnnotationDescription

public String getTagAnnotationDescription(int tagAnnotationIndex)

getTagAnnotationID

public String getTagAnnotationID(int tagAnnotationIndex)

getTagAnnotationNamespace

public String getTagAnnotationNamespace(int tagAnnotationIndex)

getTagAnnotationValue

public String getTagAnnotationValue(int tagAnnotationIndex)

getTermAnnotationAnnotationRef

public String getTermAnnotationAnnotationRef(int termAnnotationIndex,
                                    int annotationRefIndex)

getTermAnnotationDescription

public String getTermAnnotationDescription(int termAnnotationIndex)

getTermAnnotationID

public String getTermAnnotationID(int termAnnotationIndex)

getTermAnnotationNamespace

public String getTermAnnotationNamespace(int termAnnotationIndex)

getTermAnnotationValue

public String getTermAnnotationValue(int termAnnotationIndex)

getTiffDataFirstC

public NonNegativeInteger getTiffDataFirstC(int imageIndex,
                                   int tiffDataIndex)

getTiffDataFirstT

public NonNegativeInteger getTiffDataFirstT(int imageIndex,
                                   int tiffDataIndex)

getTiffDataFirstZ

public NonNegativeInteger getTiffDataFirstZ(int imageIndex,
                                   int tiffDataIndex)

getTiffDataIFD

public NonNegativeInteger getTiffDataIFD(int imageIndex,
                                int tiffDataIndex)

getTiffDataPlaneCount

public NonNegativeInteger getTiffDataPlaneCount(int imageIndex,
                                       int tiffDataIndex)

getTimestampAnnotationAnnotationRef

public String getTimestampAnnotationAnnotationRef(int timestampAnnotationIndex,
                                         int annotationRefIndex)

getTimestampAnnotationDescription

public String getTimestampAnnotationDescription(int timestampAnnotationIndex)

getTimestampAnnotationID

public String getTimestampAnnotationID(int timestampAnnotationIndex)

getTimestampAnnotationNamespace

public String getTimestampAnnotationNamespace(int timestampAnnotationIndex)

getTimestampAnnotationValue

public Timestamp getTimestampAnnotationValue(int timestampAnnotationIndex)

getTransmittanceRangeCutIn

public PositiveInteger getTransmittanceRangeCutIn(int instrumentIndex,
                                         int filterIndex)

getTransmittanceRangeCutInTolerance

public NonNegativeInteger getTransmittanceRangeCutInTolerance(int instrumentIndex,
                                                     int filterIndex)

getTransmittanceRangeCutOut

public PositiveInteger getTransmittanceRangeCutOut(int instrumentIndex,
                                          int filterIndex)

getTransmittanceRangeCutOutTolerance

public NonNegativeInteger getTransmittanceRangeCutOutTolerance(int instrumentIndex,
                                                      int filterIndex)

getTransmittanceRangeTransmittance

public PercentFraction getTransmittanceRangeTransmittance(int instrumentIndex,
                                                 int filterIndex)

getUUIDFileName

public String getUUIDFileName(int imageIndex,
                     int tiffDataIndex)

getWellAnnotationRef

public String getWellAnnotationRef(int plateIndex,
                          int wellIndex,
                          int annotationRefIndex)

getWellColor

public Color getWellColor(int plateIndex,
                 int wellIndex)

getWellColumn

public NonNegativeInteger getWellColumn(int plateIndex,
                               int wellIndex)

getWellExternalDescription

public String getWellExternalDescription(int plateIndex,
                                int wellIndex)

getWellExternalIdentifier

public String getWellExternalIdentifier(int plateIndex,
                               int wellIndex)

getWellID

public String getWellID(int plateIndex,
               int wellIndex)

getWellReagentRef

public String getWellReagentRef(int plateIndex,
                       int wellIndex)

getWellRow

public NonNegativeInteger getWellRow(int plateIndex,
                            int wellIndex)

getWellType

public String getWellType(int plateIndex,
                 int wellIndex)

getWellSampleAnnotationRef

public String getWellSampleAnnotationRef(int plateIndex,
                                int wellIndex,
                                int wellSampleIndex,
                                int annotationRefIndex)

getWellSampleID

public String getWellSampleID(int plateIndex,
                     int wellIndex,
                     int wellSampleIndex)

getWellSampleImageRef

public String getWellSampleImageRef(int plateIndex,
                           int wellIndex,
                           int wellSampleIndex)

getWellSampleIndex

public NonNegativeInteger getWellSampleIndex(int plateIndex,
                                    int wellIndex,
                                    int wellSampleIndex)

getWellSamplePositionX

public Double getWellSamplePositionX(int plateIndex,
                            int wellIndex,
                            int wellSampleIndex)

getWellSamplePositionY

public Double getWellSamplePositionY(int plateIndex,
                            int wellIndex,
                            int wellSampleIndex)

getWellSampleTimepoint

public Timestamp getWellSampleTimepoint(int plateIndex,
                               int wellIndex,
                               int wellSampleIndex)

getXMLAnnotationAnnotationRef

public String getXMLAnnotationAnnotationRef(int XMLAnnotationIndex,
                                   int annotationRefIndex)

getXMLAnnotationDescription

public String getXMLAnnotationDescription(int XMLAnnotationIndex)

getXMLAnnotationID

public String getXMLAnnotationID(int XMLAnnotationIndex)

getXMLAnnotationNamespace

public String getXMLAnnotationNamespace(int XMLAnnotationIndex)

getXMLAnnotationValue

public String getXMLAnnotationValue(int XMLAnnotationIndex)

setPixelsBinDataBigEndian

public void setPixelsBinDataBigEndian(Boolean bigEndian,
                             int imageIndex,
                             int binDataIndex)

setMaskBinData

public void setMaskBinData(byte[] binData,
                  int ROIIndex,
                  int shapeIndex)

setUUID
```
public void setUUID(String uuid)
```
Sets the UUID associated with this collection of metadata.

Specified by:

setUUID in interface MetadataStore

Overrides:

setUUID in class AbstractOMEXMLMetadata

setArcID

public void setArcID(String id,
            int instrumentIndex,
            int lightSourceIndex)

setArcLotNumber

public void setArcLotNumber(String lotNumber,
                   int instrumentIndex,
                   int lightSourceIndex)

setArcManufacturer

public void setArcManufacturer(String manufacturer,
                      int instrumentIndex,
                      int lightSourceIndex)

setArcModel

public void setArcModel(String model,
               int instrumentIndex,
               int lightSourceIndex)

setArcPower

public void setArcPower(Double power,
               int instrumentIndex,
               int lightSourceIndex)

setArcSerialNumber

public void setArcSerialNumber(String serialNumber,
                      int instrumentIndex,
                      int lightSourceIndex)

setArcType

public void setArcType(ArcType type,
              int instrumentIndex,
              int lightSourceIndex)

setBinaryFileFileName

public void setBinaryFileFileName(String fileName,
                         int fileAnnotationIndex)

setBinaryFileMIMEType

public void setBinaryFileMIMEType(String mimeType,
                         int fileAnnotationIndex)

setBinaryFileSize

public void setBinaryFileSize(NonNegativeLong size,
                     int fileAnnotationIndex)

setBinaryOnlyMetadataFile

public void setBinaryOnlyMetadataFile(String metadataFile)

setBinaryOnlyUUID

public void setBinaryOnlyUUID(String uuid)

setBooleanAnnotationAnnotationRef

public void setBooleanAnnotationAnnotationRef(String annotation,
                                     int booleanAnnotationIndex,
                                     int annotationRefIndex)

setBooleanAnnotationDescription

public void setBooleanAnnotationDescription(String description,
                                   int booleanAnnotationIndex)

setBooleanAnnotationID

public void setBooleanAnnotationID(String id,
                          int booleanAnnotationIndex)

setBooleanAnnotationNamespace

public void setBooleanAnnotationNamespace(String namespace,
                                 int booleanAnnotationIndex)

setBooleanAnnotationValue

public void setBooleanAnnotationValue(Boolean value,
                             int booleanAnnotationIndex)

setChannelAcquisitionMode

public void setChannelAcquisitionMode(AcquisitionMode acquisitionMode,
                             int imageIndex,
                             int channelIndex)

setChannelAnnotationRef

public void setChannelAnnotationRef(String annotation,
                           int imageIndex,
                           int channelIndex,
                           int annotationRefIndex)

setChannelColor

public void setChannelColor(Color color,
                   int imageIndex,
                   int channelIndex)

setChannelContrastMethod

public void setChannelContrastMethod(ContrastMethod contrastMethod,
                            int imageIndex,
                            int channelIndex)

setChannelEmissionWavelength

public void setChannelEmissionWavelength(PositiveInteger emissionWavelength,
                                int imageIndex,
                                int channelIndex)

setChannelExcitationWavelength

public void setChannelExcitationWavelength(PositiveInteger excitationWavelength,
                                  int imageIndex,
                                  int channelIndex)

setChannelFilterSetRef

public void setChannelFilterSetRef(String filterSet,
                          int imageIndex,
                          int channelIndex)

setChannelFluor

public void setChannelFluor(String fluor,
                   int imageIndex,
                   int channelIndex)

setChannelID

public void setChannelID(String id,
                int imageIndex,
                int channelIndex)

setChannelIlluminationType

public void setChannelIlluminationType(IlluminationType illuminationType,
                              int imageIndex,
                              int channelIndex)

setChannelNDFilter

public void setChannelNDFilter(Double ndFilter,
                      int imageIndex,
                      int channelIndex)

setChannelName

public void setChannelName(String name,
                  int imageIndex,
                  int channelIndex)

setChannelPinholeSize

public void setChannelPinholeSize(Double pinholeSize,
                         int imageIndex,
                         int channelIndex)

setChannelPockelCellSetting

public void setChannelPockelCellSetting(Integer pockelCellSetting,
                               int imageIndex,
                               int channelIndex)

setChannelSamplesPerPixel

public void setChannelSamplesPerPixel(PositiveInteger samplesPerPixel,
                             int imageIndex,
                             int channelIndex)

setCommentAnnotationAnnotationRef

public void setCommentAnnotationAnnotationRef(String annotation,
                                     int commentAnnotationIndex,
                                     int annotationRefIndex)

setCommentAnnotationDescription

public void setCommentAnnotationDescription(String description,
                                   int commentAnnotationIndex)

setCommentAnnotationID

public void setCommentAnnotationID(String id,
                          int commentAnnotationIndex)

setCommentAnnotationNamespace

public void setCommentAnnotationNamespace(String namespace,
                                 int commentAnnotationIndex)

setCommentAnnotationValue

public void setCommentAnnotationValue(String value,
                             int commentAnnotationIndex)

setDatasetAnnotationRef

public void setDatasetAnnotationRef(String annotation,
                           int datasetIndex,
                           int annotationRefIndex)

setDatasetDescription

public void setDatasetDescription(String description,
                         int datasetIndex)

setDatasetExperimenterGroupRef

public void setDatasetExperimenterGroupRef(String experimenterGroup,
                                  int datasetIndex)

setDatasetExperimenterRef

public void setDatasetExperimenterRef(String experimenter,
                             int datasetIndex)

setDatasetID

public void setDatasetID(String id,
                int datasetIndex)

setDatasetImageRef

public void setDatasetImageRef(String image,
                      int datasetIndex,
                      int imageRefIndex)

setDatasetName

public void setDatasetName(String name,
                  int datasetIndex)

setDetectorAmplificationGain

public void setDetectorAmplificationGain(Double amplificationGain,
                                int instrumentIndex,
                                int detectorIndex)

setDetectorGain

public void setDetectorGain(Double gain,
                   int instrumentIndex,
                   int detectorIndex)

setDetectorID

public void setDetectorID(String id,
                 int instrumentIndex,
                 int detectorIndex)

setDetectorLotNumber

public void setDetectorLotNumber(String lotNumber,
                        int instrumentIndex,
                        int detectorIndex)

setDetectorManufacturer

public void setDetectorManufacturer(String manufacturer,
                           int instrumentIndex,
                           int detectorIndex)

setDetectorModel

public void setDetectorModel(String model,
                    int instrumentIndex,
                    int detectorIndex)

setDetectorOffset

public void setDetectorOffset(Double offset,
                     int instrumentIndex,
                     int detectorIndex)

setDetectorSerialNumber

public void setDetectorSerialNumber(String serialNumber,
                           int instrumentIndex,
                           int detectorIndex)

setDetectorType

public void setDetectorType(DetectorType type,
                   int instrumentIndex,
                   int detectorIndex)

setDetectorVoltage

public void setDetectorVoltage(Double voltage,
                      int instrumentIndex,
                      int detectorIndex)

setDetectorZoom

public void setDetectorZoom(Double zoom,
                   int instrumentIndex,
                   int detectorIndex)

setDetectorSettingsBinning

public void setDetectorSettingsBinning(Binning binning,
                              int imageIndex,
                              int channelIndex)

setDetectorSettingsGain

public void setDetectorSettingsGain(Double gain,
                           int imageIndex,
                           int channelIndex)

setDetectorSettingsID

public void setDetectorSettingsID(String id,
                         int imageIndex,
                         int channelIndex)

setDetectorSettingsOffset

public void setDetectorSettingsOffset(Double offset,
                             int imageIndex,
                             int channelIndex)

setDetectorSettingsReadOutRate

public void setDetectorSettingsReadOutRate(Double readOutRate,
                                  int imageIndex,
                                  int channelIndex)

setDetectorSettingsVoltage

public void setDetectorSettingsVoltage(Double voltage,
                              int imageIndex,
                              int channelIndex)

setDichroicID

public void setDichroicID(String id,
                 int instrumentIndex,
                 int dichroicIndex)

setDichroicLotNumber

public void setDichroicLotNumber(String lotNumber,
                        int instrumentIndex,
                        int dichroicIndex)

setDichroicManufacturer

public void setDichroicManufacturer(String manufacturer,
                           int instrumentIndex,
                           int dichroicIndex)

setDichroicModel

public void setDichroicModel(String model,
                    int instrumentIndex,
                    int dichroicIndex)

setDichroicSerialNumber

public void setDichroicSerialNumber(String serialNumber,
                           int instrumentIndex,
                           int dichroicIndex)

setDoubleAnnotationAnnotationRef

public void setDoubleAnnotationAnnotationRef(String annotation,
                                    int doubleAnnotationIndex,
                                    int annotationRefIndex)

setDoubleAnnotationDescription

public void setDoubleAnnotationDescription(String description,
                                  int doubleAnnotationIndex)

setDoubleAnnotationID

public void setDoubleAnnotationID(String id,
                         int doubleAnnotationIndex)

setDoubleAnnotationNamespace

public void setDoubleAnnotationNamespace(String namespace,
                                int doubleAnnotationIndex)

setDoubleAnnotationValue

public void setDoubleAnnotationValue(Double value,
                            int doubleAnnotationIndex)

setEllipseFillColor

public void setEllipseFillColor(Color fillColor,
                       int ROIIndex,
                       int shapeIndex)

setEllipseFillRule

public void setEllipseFillRule(FillRule fillRule,
                      int ROIIndex,
                      int shapeIndex)

setEllipseFontFamily

public void setEllipseFontFamily(FontFamily fontFamily,
                        int ROIIndex,
                        int shapeIndex)

setEllipseFontSize

public void setEllipseFontSize(NonNegativeInteger fontSize,
                      int ROIIndex,
                      int shapeIndex)

setEllipseFontStyle

public void setEllipseFontStyle(FontStyle fontStyle,
                       int ROIIndex,
                       int shapeIndex)

setEllipseID

public void setEllipseID(String id,
                int ROIIndex,
                int shapeIndex)

setEllipseLineCap

public void setEllipseLineCap(LineCap lineCap,
                     int ROIIndex,
                     int shapeIndex)

setEllipseLocked

public void setEllipseLocked(Boolean locked,
                    int ROIIndex,
                    int shapeIndex)

setEllipseStrokeColor

public void setEllipseStrokeColor(Color strokeColor,
                         int ROIIndex,
                         int shapeIndex)

setEllipseStrokeDashArray

public void setEllipseStrokeDashArray(String strokeDashArray,
                             int ROIIndex,
                             int shapeIndex)

setEllipseStrokeWidth

public void setEllipseStrokeWidth(Double strokeWidth,
                         int ROIIndex,
                         int shapeIndex)

setEllipseText

public void setEllipseText(String text,
                  int ROIIndex,
                  int shapeIndex)

setEllipseTheC

public void setEllipseTheC(NonNegativeInteger theC,
                  int ROIIndex,
                  int shapeIndex)

setEllipseTheT

public void setEllipseTheT(NonNegativeInteger theT,
                  int ROIIndex,
                  int shapeIndex)

setEllipseTheZ

public void setEllipseTheZ(NonNegativeInteger theZ,
                  int ROIIndex,
                  int shapeIndex)

setEllipseTransform

public void setEllipseTransform(AffineTransform transform,
                       int ROIIndex,
                       int shapeIndex)

setEllipseVisible

public void setEllipseVisible(Boolean visible,
                     int ROIIndex,
                     int shapeIndex)

setEllipseRadiusX

public void setEllipseRadiusX(Double radiusX,
                     int ROIIndex,
                     int shapeIndex)

setEllipseRadiusY

public void setEllipseRadiusY(Double radiusY,
                     int ROIIndex,
                     int shapeIndex)

setEllipseX

public void setEllipseX(Double x,
               int ROIIndex,
               int shapeIndex)

setEllipseY

public void setEllipseY(Double y,
               int ROIIndex,
               int shapeIndex)

setExperimentDescription

public void setExperimentDescription(String description,
                            int experimentIndex)

setExperimentExperimenterRef

public void setExperimentExperimenterRef(String experimenter,
                                int experimentIndex)

setExperimentID

public void setExperimentID(String id,
                   int experimentIndex)

setExperimentType

public void setExperimentType(ExperimentType type,
                     int experimentIndex)

setExperimenterAnnotationRef

public void setExperimenterAnnotationRef(String annotation,
                                int experimenterIndex,
                                int annotationRefIndex)

setExperimenterEmail

public void setExperimenterEmail(String email,
                        int experimenterIndex)

setExperimenterFirstName

public void setExperimenterFirstName(String firstName,
                            int experimenterIndex)

setExperimenterID

public void setExperimenterID(String id,
                     int experimenterIndex)

setExperimenterInstitution

public void setExperimenterInstitution(String institution,
                              int experimenterIndex)

setExperimenterLastName

public void setExperimenterLastName(String lastName,
                           int experimenterIndex)

setExperimenterMiddleName

public void setExperimenterMiddleName(String middleName,
                             int experimenterIndex)

setExperimenterUserName

public void setExperimenterUserName(String userName,
                           int experimenterIndex)

setExperimenterGroupAnnotationRef

public void setExperimenterGroupAnnotationRef(String annotation,
                                     int experimenterGroupIndex,
                                     int annotationRefIndex)

setExperimenterGroupDescription

public void setExperimenterGroupDescription(String description,
                                   int experimenterGroupIndex)

setExperimenterGroupExperimenterRef

public void setExperimenterGroupExperimenterRef(String experimenter,
                                       int experimenterGroupIndex,
                                       int experimenterRefIndex)

setExperimenterGroupID

public void setExperimenterGroupID(String id,
                          int experimenterGroupIndex)

setExperimenterGroupLeader

public void setExperimenterGroupLeader(String leader,
                              int experimenterGroupIndex,
                              int leaderIndex)

setExperimenterGroupName

public void setExperimenterGroupName(String name,
                            int experimenterGroupIndex)

setFilamentID

public void setFilamentID(String id,
                 int instrumentIndex,
                 int lightSourceIndex)

setFilamentLotNumber

public void setFilamentLotNumber(String lotNumber,
                        int instrumentIndex,
                        int lightSourceIndex)

setFilamentManufacturer

public void setFilamentManufacturer(String manufacturer,
                           int instrumentIndex,
                           int lightSourceIndex)

setFilamentModel

public void setFilamentModel(String model,
                    int instrumentIndex,
                    int lightSourceIndex)

setFilamentPower

public void setFilamentPower(Double power,
                    int instrumentIndex,
                    int lightSourceIndex)

setFilamentSerialNumber

public void setFilamentSerialNumber(String serialNumber,
                           int instrumentIndex,
                           int lightSourceIndex)

setFilamentType

public void setFilamentType(FilamentType type,
                   int instrumentIndex,
                   int lightSourceIndex)

setFileAnnotationAnnotationRef

public void setFileAnnotationAnnotationRef(String annotation,
                                  int fileAnnotationIndex,
                                  int annotationRefIndex)

setFileAnnotationDescription

public void setFileAnnotationDescription(String description,
                                int fileAnnotationIndex)

setFileAnnotationID

public void setFileAnnotationID(String id,
                       int fileAnnotationIndex)

setFileAnnotationNamespace

public void setFileAnnotationNamespace(String namespace,
                              int fileAnnotationIndex)

setFilterFilterWheel

public void setFilterFilterWheel(String filterWheel,
                        int instrumentIndex,
                        int filterIndex)

setFilterID

public void setFilterID(String id,
               int instrumentIndex,
               int filterIndex)

setFilterLotNumber

public void setFilterLotNumber(String lotNumber,
                      int instrumentIndex,
                      int filterIndex)

setFilterManufacturer

public void setFilterManufacturer(String manufacturer,
                         int instrumentIndex,
                         int filterIndex)

setFilterModel

public void setFilterModel(String model,
                  int instrumentIndex,
                  int filterIndex)

setFilterSerialNumber

public void setFilterSerialNumber(String serialNumber,
                         int instrumentIndex,
                         int filterIndex)

setFilterType

public void setFilterType(FilterType type,
                 int instrumentIndex,
                 int filterIndex)

setFilterSetDichroicRef

public void setFilterSetDichroicRef(String dichroic,
                           int instrumentIndex,
                           int filterSetIndex)

setFilterSetEmissionFilterRef

public void setFilterSetEmissionFilterRef(String emissionFilter,
                                 int instrumentIndex,
                                 int filterSetIndex,
                                 int emissionFilterRefIndex)

setFilterSetExcitationFilterRef

public void setFilterSetExcitationFilterRef(String excitationFilter,
                                   int instrumentIndex,
                                   int filterSetIndex,
                                   int excitationFilterRefIndex)

setFilterSetID

public void setFilterSetID(String id,
                  int instrumentIndex,
                  int filterSetIndex)

setFilterSetLotNumber

public void setFilterSetLotNumber(String lotNumber,
                         int instrumentIndex,
                         int filterSetIndex)

setFilterSetManufacturer

public void setFilterSetManufacturer(String manufacturer,
                            int instrumentIndex,
                            int filterSetIndex)

setFilterSetModel

public void setFilterSetModel(String model,
                     int instrumentIndex,
                     int filterSetIndex)

setFilterSetSerialNumber

public void setFilterSetSerialNumber(String serialNumber,
                            int instrumentIndex,
                            int filterSetIndex)

setImageAcquisitionDate

public void setImageAcquisitionDate(Timestamp acquisitionDate,
                           int imageIndex)

setImageAnnotationRef

public void setImageAnnotationRef(String annotation,
                         int imageIndex,
                         int annotationRefIndex)

setImageDescription

public void setImageDescription(String description,
                       int imageIndex)

setImageExperimentRef

public void setImageExperimentRef(String experiment,
                         int imageIndex)

setImageExperimenterGroupRef

public void setImageExperimenterGroupRef(String experimenterGroup,
                                int imageIndex)

setImageExperimenterRef

public void setImageExperimenterRef(String experimenter,
                           int imageIndex)

setImageID

public void setImageID(String id,
              int imageIndex)

setImageInstrumentRef

public void setImageInstrumentRef(String instrument,
                         int imageIndex)

setImageMicrobeamManipulationRef

public void setImageMicrobeamManipulationRef(String microbeamManipulation,
                                    int imageIndex,
                                    int microbeamManipulationRefIndex)

setImageName

public void setImageName(String name,
                int imageIndex)

setImageROIRef

public void setImageROIRef(String roi,
                  int imageIndex,
                  int ROIRefIndex)

setImagingEnvironmentAirPressure

public void setImagingEnvironmentAirPressure(Double airPressure,
                                    int imageIndex)

setImagingEnvironmentCO2Percent

public void setImagingEnvironmentCO2Percent(PercentFraction co2Percent,
                                   int imageIndex)

setImagingEnvironmentHumidity

public void setImagingEnvironmentHumidity(PercentFraction humidity,
                                 int imageIndex)

setImagingEnvironmentTemperature

public void setImagingEnvironmentTemperature(Double temperature,
                                    int imageIndex)

setInstrumentID

public void setInstrumentID(String id,
                   int instrumentIndex)

setLabelFillColor

public void setLabelFillColor(Color fillColor,
                     int ROIIndex,
                     int shapeIndex)

setLabelFillRule

public void setLabelFillRule(FillRule fillRule,
                    int ROIIndex,
                    int shapeIndex)

setLabelFontFamily

public void setLabelFontFamily(FontFamily fontFamily,
                      int ROIIndex,
                      int shapeIndex)

setLabelFontSize

public void setLabelFontSize(NonNegativeInteger fontSize,
                    int ROIIndex,
                    int shapeIndex)

setLabelFontStyle

public void setLabelFontStyle(FontStyle fontStyle,
                     int ROIIndex,
                     int shapeIndex)

setLabelID

public void setLabelID(String id,
              int ROIIndex,
              int shapeIndex)

setLabelLineCap

public void setLabelLineCap(LineCap lineCap,
                   int ROIIndex,
                   int shapeIndex)

setLabelLocked

public void setLabelLocked(Boolean locked,
                  int ROIIndex,
                  int shapeIndex)

setLabelStrokeColor

public void setLabelStrokeColor(Color strokeColor,
                       int ROIIndex,
                       int shapeIndex)

setLabelStrokeDashArray

public void setLabelStrokeDashArray(String strokeDashArray,
                           int ROIIndex,
                           int shapeIndex)

setLabelStrokeWidth

public void setLabelStrokeWidth(Double strokeWidth,
                       int ROIIndex,
                       int shapeIndex)

setLabelText

public void setLabelText(String text,
                int ROIIndex,
                int shapeIndex)

setLabelTheC

public void setLabelTheC(NonNegativeInteger theC,
                int ROIIndex,
                int shapeIndex)

setLabelTheT

public void setLabelTheT(NonNegativeInteger theT,
                int ROIIndex,
                int shapeIndex)

setLabelTheZ

public void setLabelTheZ(NonNegativeInteger theZ,
                int ROIIndex,
                int shapeIndex)

setLabelTransform

public void setLabelTransform(AffineTransform transform,
                     int ROIIndex,
                     int shapeIndex)

setLabelVisible

public void setLabelVisible(Boolean visible,
                   int ROIIndex,
                   int shapeIndex)

setLabelX

public void setLabelX(Double x,
             int ROIIndex,
             int shapeIndex)

setLabelY

public void setLabelY(Double y,
             int ROIIndex,
             int shapeIndex)

setLaserID

public void setLaserID(String id,
              int instrumentIndex,
              int lightSourceIndex)

setLaserLotNumber

public void setLaserLotNumber(String lotNumber,
                     int instrumentIndex,
                     int lightSourceIndex)

setLaserManufacturer

public void setLaserManufacturer(String manufacturer,
                        int instrumentIndex,
                        int lightSourceIndex)

setLaserModel

public void setLaserModel(String model,
                 int instrumentIndex,
                 int lightSourceIndex)

setLaserPower

public void setLaserPower(Double power,
                 int instrumentIndex,
                 int lightSourceIndex)

setLaserSerialNumber

public void setLaserSerialNumber(String serialNumber,
                        int instrumentIndex,
                        int lightSourceIndex)

setLaserFrequencyMultiplication

public void setLaserFrequencyMultiplication(PositiveInteger frequencyMultiplication,
                                   int instrumentIndex,
                                   int lightSourceIndex)

setLaserLaserMedium

public void setLaserLaserMedium(LaserMedium laserMedium,
                       int instrumentIndex,
                       int lightSourceIndex)

setLaserPockelCell

public void setLaserPockelCell(Boolean pockelCell,
                      int instrumentIndex,
                      int lightSourceIndex)

setLaserPulse

public void setLaserPulse(Pulse pulse,
                 int instrumentIndex,
                 int lightSourceIndex)

setLaserPump

public void setLaserPump(String pump,
                int instrumentIndex,
                int lightSourceIndex)

setLaserRepetitionRate

public void setLaserRepetitionRate(Double repetitionRate,
                          int instrumentIndex,
                          int lightSourceIndex)

setLaserTuneable

public void setLaserTuneable(Boolean tuneable,
                    int instrumentIndex,
                    int lightSourceIndex)

setLaserType

public void setLaserType(LaserType type,
                int instrumentIndex,
                int lightSourceIndex)

setLaserWavelength

public void setLaserWavelength(PositiveInteger wavelength,
                      int instrumentIndex,
                      int lightSourceIndex)

setLightEmittingDiodeID

public void setLightEmittingDiodeID(String id,
                           int instrumentIndex,
                           int lightSourceIndex)

setLightEmittingDiodeLotNumber

public void setLightEmittingDiodeLotNumber(String lotNumber,
                                  int instrumentIndex,
                                  int lightSourceIndex)

setLightEmittingDiodeManufacturer

public void setLightEmittingDiodeManufacturer(String manufacturer,
                                     int instrumentIndex,
                                     int lightSourceIndex)

setLightEmittingDiodeModel

public void setLightEmittingDiodeModel(String model,
                              int instrumentIndex,
                              int lightSourceIndex)

setLightEmittingDiodePower

public void setLightEmittingDiodePower(Double power,
                              int instrumentIndex,
                              int lightSourceIndex)

setLightEmittingDiodeSerialNumber

public void setLightEmittingDiodeSerialNumber(String serialNumber,
                                     int instrumentIndex,
                                     int lightSourceIndex)

setLightPathDichroicRef

public void setLightPathDichroicRef(String dichroic,
                           int imageIndex,
                           int channelIndex)

setLightPathEmissionFilterRef

public void setLightPathEmissionFilterRef(String emissionFilter,
                                 int imageIndex,
                                 int channelIndex,
                                 int emissionFilterRefIndex)

setLightPathExcitationFilterRef

public void setLightPathExcitationFilterRef(String excitationFilter,
                                   int imageIndex,
                                   int channelIndex,
                                   int excitationFilterRefIndex)

setChannelLightSourceSettingsAttenuation

public void setChannelLightSourceSettingsAttenuation(PercentFraction attenuation,
                                            int imageIndex,
                                            int channelIndex)

setMicrobeamManipulationLightSourceSettingsAttenuation

public void setMicrobeamManipulationLightSourceSettingsAttenuation(PercentFraction attenuation,
                                                          int experimentIndex,
                                                          int microbeamManipulationIndex,
                                                          int lightSourceSettingsIndex)

setChannelLightSourceSettingsID

public void setChannelLightSourceSettingsID(String id,
                                   int imageIndex,
                                   int channelIndex)

setMicrobeamManipulationLightSourceSettingsID

public void setMicrobeamManipulationLightSourceSettingsID(String id,
                                                 int experimentIndex,
                                                 int microbeamManipulationIndex,
                                                 int lightSourceSettingsIndex)

setChannelLightSourceSettingsWavelength

public void setChannelLightSourceSettingsWavelength(PositiveInteger wavelength,
                                           int imageIndex,
                                           int channelIndex)

setMicrobeamManipulationLightSourceSettingsWavelength

public void setMicrobeamManipulationLightSourceSettingsWavelength(PositiveInteger wavelength,
                                                         int experimentIndex,
                                                         int microbeamManipulationIndex,
                                                         int lightSourceSettingsIndex)

setLineFillColor

public void setLineFillColor(Color fillColor,
                    int ROIIndex,
                    int shapeIndex)

setLineFillRule

public void setLineFillRule(FillRule fillRule,
                   int ROIIndex,
                   int shapeIndex)

setLineFontFamily

public void setLineFontFamily(FontFamily fontFamily,
                     int ROIIndex,
                     int shapeIndex)

setLineFontSize

public void setLineFontSize(NonNegativeInteger fontSize,
                   int ROIIndex,
                   int shapeIndex)

setLineFontStyle

public void setLineFontStyle(FontStyle fontStyle,
                    int ROIIndex,
                    int shapeIndex)

setLineID

public void setLineID(String id,
             int ROIIndex,
             int shapeIndex)

setLineLineCap

public void setLineLineCap(LineCap lineCap,
                  int ROIIndex,
                  int shapeIndex)

setLineLocked

public void setLineLocked(Boolean locked,
                 int ROIIndex,
                 int shapeIndex)

setLineStrokeColor

public void setLineStrokeColor(Color strokeColor,
                      int ROIIndex,
                      int shapeIndex)

setLineStrokeDashArray

public void setLineStrokeDashArray(String strokeDashArray,
                          int ROIIndex,
                          int shapeIndex)

setLineStrokeWidth

public void setLineStrokeWidth(Double strokeWidth,
                      int ROIIndex,
                      int shapeIndex)

setLineText

public void setLineText(String text,
               int ROIIndex,
               int shapeIndex)

setLineTheC

public void setLineTheC(NonNegativeInteger theC,
               int ROIIndex,
               int shapeIndex)

setLineTheT

public void setLineTheT(NonNegativeInteger theT,
               int ROIIndex,
               int shapeIndex)

setLineTheZ

public void setLineTheZ(NonNegativeInteger theZ,
               int ROIIndex,
               int shapeIndex)

setLineTransform

public void setLineTransform(AffineTransform transform,
                    int ROIIndex,
                    int shapeIndex)

setLineVisible

public void setLineVisible(Boolean visible,
                  int ROIIndex,
                  int shapeIndex)

setLineMarkerEnd

public void setLineMarkerEnd(Marker markerEnd,
                    int ROIIndex,
                    int shapeIndex)

setLineMarkerStart

public void setLineMarkerStart(Marker markerStart,
                      int ROIIndex,
                      int shapeIndex)

setLineX1

public void setLineX1(Double x1,
             int ROIIndex,
             int shapeIndex)

setLineX2

public void setLineX2(Double x2,
             int ROIIndex,
             int shapeIndex)

setLineY1

public void setLineY1(Double y1,
             int ROIIndex,
             int shapeIndex)

setLineY2

public void setLineY2(Double y2,
             int ROIIndex,
             int shapeIndex)

setListAnnotationAnnotationRef

public void setListAnnotationAnnotationRef(String annotation,
                                  int listAnnotationIndex,
                                  int annotationRefIndex)

setListAnnotationDescription

public void setListAnnotationDescription(String description,
                                int listAnnotationIndex)

setListAnnotationID

public void setListAnnotationID(String id,
                       int listAnnotationIndex)

setListAnnotationNamespace

public void setListAnnotationNamespace(String namespace,
                              int listAnnotationIndex)

setLongAnnotationAnnotationRef

public void setLongAnnotationAnnotationRef(String annotation,
                                  int longAnnotationIndex,
                                  int annotationRefIndex)

setLongAnnotationDescription

public void setLongAnnotationDescription(String description,
                                int longAnnotationIndex)

setLongAnnotationID

public void setLongAnnotationID(String id,
                       int longAnnotationIndex)

setLongAnnotationNamespace

public void setLongAnnotationNamespace(String namespace,
                              int longAnnotationIndex)

setLongAnnotationValue

public void setLongAnnotationValue(Long value,
                          int longAnnotationIndex)

setMaskFillColor

public void setMaskFillColor(Color fillColor,
                    int ROIIndex,
                    int shapeIndex)

setMaskFillRule

public void setMaskFillRule(FillRule fillRule,
                   int ROIIndex,
                   int shapeIndex)

setMaskFontFamily

public void setMaskFontFamily(FontFamily fontFamily,
                     int ROIIndex,
                     int shapeIndex)

setMaskFontSize

public void setMaskFontSize(NonNegativeInteger fontSize,
                   int ROIIndex,
                   int shapeIndex)

setMaskFontStyle

public void setMaskFontStyle(FontStyle fontStyle,
                    int ROIIndex,
                    int shapeIndex)

setMaskID

public void setMaskID(String id,
             int ROIIndex,
             int shapeIndex)

setMaskLineCap

public void setMaskLineCap(LineCap lineCap,
                  int ROIIndex,
                  int shapeIndex)

setMaskLocked

public void setMaskLocked(Boolean locked,
                 int ROIIndex,
                 int shapeIndex)

setMaskStrokeColor

public void setMaskStrokeColor(Color strokeColor,
                      int ROIIndex,
                      int shapeIndex)

setMaskStrokeDashArray

public void setMaskStrokeDashArray(String strokeDashArray,
                          int ROIIndex,
                          int shapeIndex)

setMaskStrokeWidth

public void setMaskStrokeWidth(Double strokeWidth,
                      int ROIIndex,
                      int shapeIndex)

setMaskText

public void setMaskText(String text,
               int ROIIndex,
               int shapeIndex)

setMaskTheC

public void setMaskTheC(NonNegativeInteger theC,
               int ROIIndex,
               int shapeIndex)

setMaskTheT

public void setMaskTheT(NonNegativeInteger theT,
               int ROIIndex,
               int shapeIndex)

setMaskTheZ

public void setMaskTheZ(NonNegativeInteger theZ,
               int ROIIndex,
               int shapeIndex)

setMaskTransform

public void setMaskTransform(AffineTransform transform,
                    int ROIIndex,
                    int shapeIndex)

setMaskVisible

public void setMaskVisible(Boolean visible,
                  int ROIIndex,
                  int shapeIndex)

setMaskHeight

public void setMaskHeight(Double height,
                 int ROIIndex,
                 int shapeIndex)

setMaskWidth

public void setMaskWidth(Double width,
                int ROIIndex,
                int shapeIndex)

setMaskX

public void setMaskX(Double x,
            int ROIIndex,
            int shapeIndex)

setMaskY

public void setMaskY(Double y,
            int ROIIndex,
            int shapeIndex)

setMicrobeamManipulationDescription

public void setMicrobeamManipulationDescription(String description,
                                       int experimentIndex,
                                       int microbeamManipulationIndex)

setMicrobeamManipulationExperimenterRef

public void setMicrobeamManipulationExperimenterRef(String experimenter,
                                           int experimentIndex,
                                           int microbeamManipulationIndex)

setMicrobeamManipulationID

public void setMicrobeamManipulationID(String id,
                              int experimentIndex,
                              int microbeamManipulationIndex)

setMicrobeamManipulationROIRef

public void setMicrobeamManipulationROIRef(String roi,
                                  int experimentIndex,
                                  int microbeamManipulationIndex,
                                  int ROIRefIndex)

setMicrobeamManipulationType

public void setMicrobeamManipulationType(MicrobeamManipulationType type,
                                int experimentIndex,
                                int microbeamManipulationIndex)

setMicroscopeLotNumber

public void setMicroscopeLotNumber(String lotNumber,
                          int instrumentIndex)

setMicroscopeManufacturer

public void setMicroscopeManufacturer(String manufacturer,
                             int instrumentIndex)

setMicroscopeModel

public void setMicroscopeModel(String model,
                      int instrumentIndex)

setMicroscopeSerialNumber

public void setMicroscopeSerialNumber(String serialNumber,
                             int instrumentIndex)

setMicroscopeType

public void setMicroscopeType(MicroscopeType type,
                     int instrumentIndex)

setObjectiveCalibratedMagnification

public void setObjectiveCalibratedMagnification(Double calibratedMagnification,
                                       int instrumentIndex,
                                       int objectiveIndex)

setObjectiveCorrection

public void setObjectiveCorrection(Correction correction,
                          int instrumentIndex,
                          int objectiveIndex)

setObjectiveID

public void setObjectiveID(String id,
                  int instrumentIndex,
                  int objectiveIndex)

setObjectiveImmersion

public void setObjectiveImmersion(Immersion immersion,
                         int instrumentIndex,
                         int objectiveIndex)

setObjectiveIris

public void setObjectiveIris(Boolean iris,
                    int instrumentIndex,
                    int objectiveIndex)

setObjectiveLensNA

public void setObjectiveLensNA(Double lensNA,
                      int instrumentIndex,
                      int objectiveIndex)

setObjectiveLotNumber

public void setObjectiveLotNumber(String lotNumber,
                         int instrumentIndex,
                         int objectiveIndex)

setObjectiveManufacturer

public void setObjectiveManufacturer(String manufacturer,
                            int instrumentIndex,
                            int objectiveIndex)

setObjectiveModel

public void setObjectiveModel(String model,
                     int instrumentIndex,
                     int objectiveIndex)

setObjectiveNominalMagnification

public void setObjectiveNominalMagnification(PositiveInteger nominalMagnification,
                                    int instrumentIndex,
                                    int objectiveIndex)

setObjectiveSerialNumber

public void setObjectiveSerialNumber(String serialNumber,
                            int instrumentIndex,
                            int objectiveIndex)

setObjectiveWorkingDistance

public void setObjectiveWorkingDistance(Double workingDistance,
                               int instrumentIndex,
                               int objectiveIndex)

setObjectiveSettingsCorrectionCollar

public void setObjectiveSettingsCorrectionCollar(Double correctionCollar,
                                        int imageIndex)

setObjectiveSettingsID

public void setObjectiveSettingsID(String id,
                          int imageIndex)

setObjectiveSettingsMedium

public void setObjectiveSettingsMedium(Medium medium,
                              int imageIndex)

setObjectiveSettingsRefractiveIndex

public void setObjectiveSettingsRefractiveIndex(Double refractiveIndex,
                                       int imageIndex)

setPixelsAnnotationRef

public void setPixelsAnnotationRef(String annotation,
                          int imageIndex,
                          int annotationRefIndex)

setPixelsDimensionOrder

public void setPixelsDimensionOrder(DimensionOrder dimensionOrder,
                           int imageIndex)

setPixelsID

public void setPixelsID(String id,
               int imageIndex)

setPixelsPhysicalSizeX

public void setPixelsPhysicalSizeX(PositiveFloat physicalSizeX,
                          int imageIndex)

setPixelsPhysicalSizeY

public void setPixelsPhysicalSizeY(PositiveFloat physicalSizeY,
                          int imageIndex)

setPixelsPhysicalSizeZ

public void setPixelsPhysicalSizeZ(PositiveFloat physicalSizeZ,
                          int imageIndex)

setPixelsSizeC

public void setPixelsSizeC(PositiveInteger sizeC,
                  int imageIndex)

setPixelsSizeT

public void setPixelsSizeT(PositiveInteger sizeT,
                  int imageIndex)

setPixelsSizeX

public void setPixelsSizeX(PositiveInteger sizeX,
                  int imageIndex)

setPixelsSizeY

public void setPixelsSizeY(PositiveInteger sizeY,
                  int imageIndex)

setPixelsSizeZ

public void setPixelsSizeZ(PositiveInteger sizeZ,
                  int imageIndex)

setPixelsTimeIncrement

public void setPixelsTimeIncrement(Double timeIncrement,
                          int imageIndex)

setPixelsType

public void setPixelsType(PixelType type,
                 int imageIndex)

setPlaneAnnotationRef

public void setPlaneAnnotationRef(String annotation,
                         int imageIndex,
                         int planeIndex,
                         int annotationRefIndex)

setPlaneDeltaT

public void setPlaneDeltaT(Double deltaT,
                  int imageIndex,
                  int planeIndex)

setPlaneExposureTime

public void setPlaneExposureTime(Double exposureTime,
                        int imageIndex,
                        int planeIndex)

setPlaneHashSHA1

public void setPlaneHashSHA1(String hashSHA1,
                    int imageIndex,
                    int planeIndex)

setPlanePositionX

public void setPlanePositionX(Double positionX,
                     int imageIndex,
                     int planeIndex)

setPlanePositionY

public void setPlanePositionY(Double positionY,
                     int imageIndex,
                     int planeIndex)

setPlanePositionZ

public void setPlanePositionZ(Double positionZ,
                     int imageIndex,
                     int planeIndex)

setPlaneTheC

public void setPlaneTheC(NonNegativeInteger theC,
                int imageIndex,
                int planeIndex)

setPlaneTheT

public void setPlaneTheT(NonNegativeInteger theT,
                int imageIndex,
                int planeIndex)

setPlaneTheZ

public void setPlaneTheZ(NonNegativeInteger theZ,
                int imageIndex,
                int planeIndex)

setPlateAnnotationRef

public void setPlateAnnotationRef(String annotation,
                         int plateIndex,
                         int annotationRefIndex)

setPlateColumnNamingConvention

public void setPlateColumnNamingConvention(NamingConvention columnNamingConvention,
                                  int plateIndex)

setPlateColumns

public void setPlateColumns(PositiveInteger columns,
                   int plateIndex)

setPlateDescription

public void setPlateDescription(String description,
                       int plateIndex)

setPlateExternalIdentifier

public void setPlateExternalIdentifier(String externalIdentifier,
                              int plateIndex)

setPlateFieldIndex

public void setPlateFieldIndex(NonNegativeInteger fieldIndex,
                      int plateIndex)

setPlateID

public void setPlateID(String id,
              int plateIndex)

setPlateName

public void setPlateName(String name,
                int plateIndex)

setPlateRowNamingConvention

public void setPlateRowNamingConvention(NamingConvention rowNamingConvention,
                               int plateIndex)

setPlateRows

public void setPlateRows(PositiveInteger rows,
                int plateIndex)

setPlateStatus

public void setPlateStatus(String status,
                  int plateIndex)

setPlateWellOriginX

public void setPlateWellOriginX(Double wellOriginX,
                       int plateIndex)

setPlateWellOriginY

public void setPlateWellOriginY(Double wellOriginY,
                       int plateIndex)

setPlateAcquisitionAnnotationRef

public void setPlateAcquisitionAnnotationRef(String annotation,
                                    int plateIndex,
                                    int plateAcquisitionIndex,
                                    int annotationRefIndex)

setPlateAcquisitionDescription

public void setPlateAcquisitionDescription(String description,
                                  int plateIndex,
                                  int plateAcquisitionIndex)

setPlateAcquisitionEndTime

public void setPlateAcquisitionEndTime(Timestamp endTime,
                              int plateIndex,
                              int plateAcquisitionIndex)

setPlateAcquisitionID

public void setPlateAcquisitionID(String id,
                         int plateIndex,
                         int plateAcquisitionIndex)

setPlateAcquisitionMaximumFieldCount

public void setPlateAcquisitionMaximumFieldCount(PositiveInteger maximumFieldCount,
                                        int plateIndex,
                                        int plateAcquisitionIndex)

setPlateAcquisitionName

public void setPlateAcquisitionName(String name,
                           int plateIndex,
                           int plateAcquisitionIndex)

setPlateAcquisitionStartTime

public void setPlateAcquisitionStartTime(Timestamp startTime,
                                int plateIndex,
                                int plateAcquisitionIndex)

setPlateAcquisitionWellSampleRef

public void setPlateAcquisitionWellSampleRef(String wellSample,
                                    int plateIndex,
                                    int plateAcquisitionIndex,
                                    int wellSampleRefIndex)

setPointFillColor

public void setPointFillColor(Color fillColor,
                     int ROIIndex,
                     int shapeIndex)

setPointFillRule

public void setPointFillRule(FillRule fillRule,
                    int ROIIndex,
                    int shapeIndex)

setPointFontFamily

public void setPointFontFamily(FontFamily fontFamily,
                      int ROIIndex,
                      int shapeIndex)

setPointFontSize

public void setPointFontSize(NonNegativeInteger fontSize,
                    int ROIIndex,
                    int shapeIndex)

setPointFontStyle

public void setPointFontStyle(FontStyle fontStyle,
                     int ROIIndex,
                     int shapeIndex)

setPointID

public void setPointID(String id,
              int ROIIndex,
              int shapeIndex)

setPointLineCap

public void setPointLineCap(LineCap lineCap,
                   int ROIIndex,
                   int shapeIndex)

setPointLocked

public void setPointLocked(Boolean locked,
                  int ROIIndex,
                  int shapeIndex)

setPointStrokeColor

public void setPointStrokeColor(Color strokeColor,
                       int ROIIndex,
                       int shapeIndex)

setPointStrokeDashArray

public void setPointStrokeDashArray(String strokeDashArray,
                           int ROIIndex,
                           int shapeIndex)

setPointStrokeWidth

public void setPointStrokeWidth(Double strokeWidth,
                       int ROIIndex,
                       int shapeIndex)

setPointText

public void setPointText(String text,
                int ROIIndex,
                int shapeIndex)

setPointTheC

public void setPointTheC(NonNegativeInteger theC,
                int ROIIndex,
                int shapeIndex)

setPointTheT

public void setPointTheT(NonNegativeInteger theT,
                int ROIIndex,
                int shapeIndex)

setPointTheZ

public void setPointTheZ(NonNegativeInteger theZ,
                int ROIIndex,
                int shapeIndex)

setPointTransform

public void setPointTransform(AffineTransform transform,
                     int ROIIndex,
                     int shapeIndex)

setPointVisible

public void setPointVisible(Boolean visible,
                   int ROIIndex,
                   int shapeIndex)

setPointX

public void setPointX(Double x,
             int ROIIndex,
             int shapeIndex)

setPointY

public void setPointY(Double y,
             int ROIIndex,
             int shapeIndex)

setPolygonFillColor

public void setPolygonFillColor(Color fillColor,
                       int ROIIndex,
                       int shapeIndex)

setPolygonFillRule

public void setPolygonFillRule(FillRule fillRule,
                      int ROIIndex,
                      int shapeIndex)

setPolygonFontFamily

public void setPolygonFontFamily(FontFamily fontFamily,
                        int ROIIndex,
                        int shapeIndex)

setPolygonFontSize

public void setPolygonFontSize(NonNegativeInteger fontSize,
                      int ROIIndex,
                      int shapeIndex)

setPolygonFontStyle

public void setPolygonFontStyle(FontStyle fontStyle,
                       int ROIIndex,
                       int shapeIndex)

setPolygonID

public void setPolygonID(String id,
                int ROIIndex,
                int shapeIndex)

setPolygonLineCap

public void setPolygonLineCap(LineCap lineCap,
                     int ROIIndex,
                     int shapeIndex)

setPolygonLocked

public void setPolygonLocked(Boolean locked,
                    int ROIIndex,
                    int shapeIndex)

setPolygonStrokeColor

public void setPolygonStrokeColor(Color strokeColor,
                         int ROIIndex,
                         int shapeIndex)

setPolygonStrokeDashArray

public void setPolygonStrokeDashArray(String strokeDashArray,
                             int ROIIndex,
                             int shapeIndex)

setPolygonStrokeWidth

public void setPolygonStrokeWidth(Double strokeWidth,
                         int ROIIndex,
                         int shapeIndex)

setPolygonText

public void setPolygonText(String text,
                  int ROIIndex,
                  int shapeIndex)

setPolygonTheC

public void setPolygonTheC(NonNegativeInteger theC,
                  int ROIIndex,
                  int shapeIndex)

setPolygonTheT

public void setPolygonTheT(NonNegativeInteger theT,
                  int ROIIndex,
                  int shapeIndex)

setPolygonTheZ

public void setPolygonTheZ(NonNegativeInteger theZ,
                  int ROIIndex,
                  int shapeIndex)

setPolygonTransform

public void setPolygonTransform(AffineTransform transform,
                       int ROIIndex,
                       int shapeIndex)

setPolygonVisible

public void setPolygonVisible(Boolean visible,
                     int ROIIndex,
                     int shapeIndex)

setPolygonPoints

public void setPolygonPoints(String points,
                    int ROIIndex,
                    int shapeIndex)

setPolylineFillColor

public void setPolylineFillColor(Color fillColor,
                        int ROIIndex,
                        int shapeIndex)

setPolylineFillRule

public void setPolylineFillRule(FillRule fillRule,
                       int ROIIndex,
                       int shapeIndex)

setPolylineFontFamily

public void setPolylineFontFamily(FontFamily fontFamily,
                         int ROIIndex,
                         int shapeIndex)

setPolylineFontSize

public void setPolylineFontSize(NonNegativeInteger fontSize,
                       int ROIIndex,
                       int shapeIndex)

setPolylineFontStyle

public void setPolylineFontStyle(FontStyle fontStyle,
                        int ROIIndex,
                        int shapeIndex)

setPolylineID

public void setPolylineID(String id,
                 int ROIIndex,
                 int shapeIndex)

setPolylineLineCap

public void setPolylineLineCap(LineCap lineCap,
                      int ROIIndex,
                      int shapeIndex)

setPolylineLocked

public void setPolylineLocked(Boolean locked,
                     int ROIIndex,
                     int shapeIndex)

setPolylineStrokeColor

public void setPolylineStrokeColor(Color strokeColor,
                          int ROIIndex,
                          int shapeIndex)

setPolylineStrokeDashArray

public void setPolylineStrokeDashArray(String strokeDashArray,
                              int ROIIndex,
                              int shapeIndex)

setPolylineStrokeWidth

public void setPolylineStrokeWidth(Double strokeWidth,
                          int ROIIndex,
                          int shapeIndex)

setPolylineText

public void setPolylineText(String text,
                   int ROIIndex,
                   int shapeIndex)

setPolylineTheC

public void setPolylineTheC(NonNegativeInteger theC,
                   int ROIIndex,
                   int shapeIndex)

setPolylineTheT

public void setPolylineTheT(NonNegativeInteger theT,
                   int ROIIndex,
                   int shapeIndex)

setPolylineTheZ

public void setPolylineTheZ(NonNegativeInteger theZ,
                   int ROIIndex,
                   int shapeIndex)

setPolylineTransform

public void setPolylineTransform(AffineTransform transform,
                        int ROIIndex,
                        int shapeIndex)

setPolylineVisible

public void setPolylineVisible(Boolean visible,
                      int ROIIndex,
                      int shapeIndex)

setPolylineMarkerEnd

public void setPolylineMarkerEnd(Marker markerEnd,
                        int ROIIndex,
                        int shapeIndex)

setPolylineMarkerStart

public void setPolylineMarkerStart(Marker markerStart,
                          int ROIIndex,
                          int shapeIndex)

setPolylinePoints

public void setPolylinePoints(String points,
                     int ROIIndex,
                     int shapeIndex)

setProjectAnnotationRef

public void setProjectAnnotationRef(String annotation,
                           int projectIndex,
                           int annotationRefIndex)

setProjectDatasetRef

public void setProjectDatasetRef(String dataset,
                        int projectIndex,
                        int datasetRefIndex)

setProjectDescription

public void setProjectDescription(String description,
                         int projectIndex)

setProjectExperimenterGroupRef

public void setProjectExperimenterGroupRef(String experimenterGroup,
                                  int projectIndex)

setProjectExperimenterRef

public void setProjectExperimenterRef(String experimenter,
                             int projectIndex)

setProjectID

public void setProjectID(String id,
                int projectIndex)

setProjectName

public void setProjectName(String name,
                  int projectIndex)

setROIAnnotationRef

public void setROIAnnotationRef(String annotation,
                       int ROIIndex,
                       int annotationRefIndex)

setROIDescription

public void setROIDescription(String description,
                     int ROIIndex)

setROIID

public void setROIID(String id,
            int ROIIndex)

setROIName

public void setROIName(String name,
              int ROIIndex)

setROINamespace

public void setROINamespace(String namespace,
                   int ROIIndex)

setReagentAnnotationRef

public void setReagentAnnotationRef(String annotation,
                           int screenIndex,
                           int reagentIndex,
                           int annotationRefIndex)

setReagentDescription

public void setReagentDescription(String description,
                         int screenIndex,
                         int reagentIndex)

setReagentID

public void setReagentID(String id,
                int screenIndex,
                int reagentIndex)

setReagentName

public void setReagentName(String name,
                  int screenIndex,
                  int reagentIndex)

setReagentReagentIdentifier

public void setReagentReagentIdentifier(String reagentIdentifier,
                               int screenIndex,
                               int reagentIndex)

setRectangleFillColor

public void setRectangleFillColor(Color fillColor,
                         int ROIIndex,
                         int shapeIndex)

setRectangleFillRule

public void setRectangleFillRule(FillRule fillRule,
                        int ROIIndex,
                        int shapeIndex)

setRectangleFontFamily

public void setRectangleFontFamily(FontFamily fontFamily,
                          int ROIIndex,
                          int shapeIndex)

setRectangleFontSize

public void setRectangleFontSize(NonNegativeInteger fontSize,
                        int ROIIndex,
                        int shapeIndex)

setRectangleFontStyle

public void setRectangleFontStyle(FontStyle fontStyle,
                         int ROIIndex,
                         int shapeIndex)

setRectangleID

public void setRectangleID(String id,
                  int ROIIndex,
                  int shapeIndex)

setRectangleLineCap

public void setRectangleLineCap(LineCap lineCap,
                       int ROIIndex,
                       int shapeIndex)

setRectangleLocked

public void setRectangleLocked(Boolean locked,
                      int ROIIndex,
                      int shapeIndex)

setRectangleStrokeColor

public void setRectangleStrokeColor(Color strokeColor,
                           int ROIIndex,
                           int shapeIndex)

setRectangleStrokeDashArray

public void setRectangleStrokeDashArray(String strokeDashArray,
                               int ROIIndex,
                               int shapeIndex)

setRectangleStrokeWidth

public void setRectangleStrokeWidth(Double strokeWidth,
                           int ROIIndex,
                           int shapeIndex)

setRectangleText

public void setRectangleText(String text,
                    int ROIIndex,
                    int shapeIndex)

setRectangleTheC

public void setRectangleTheC(NonNegativeInteger theC,
                    int ROIIndex,
                    int shapeIndex)

setRectangleTheT

public void setRectangleTheT(NonNegativeInteger theT,
                    int ROIIndex,
                    int shapeIndex)

setRectangleTheZ

public void setRectangleTheZ(NonNegativeInteger theZ,
                    int ROIIndex,
                    int shapeIndex)

setRectangleTransform

public void setRectangleTransform(AffineTransform transform,
                         int ROIIndex,
                         int shapeIndex)

setRectangleVisible

public void setRectangleVisible(Boolean visible,
                       int ROIIndex,
                       int shapeIndex)

setRectangleHeight

public void setRectangleHeight(Double height,
                      int ROIIndex,
                      int shapeIndex)

setRectangleWidth

public void setRectangleWidth(Double width,
                     int ROIIndex,
                     int shapeIndex)

setRectangleX

public void setRectangleX(Double x,
                 int ROIIndex,
                 int shapeIndex)

setRectangleY

public void setRectangleY(Double y,
                 int ROIIndex,
                 int shapeIndex)

setScreenAnnotationRef

public void setScreenAnnotationRef(String annotation,
                          int screenIndex,
                          int annotationRefIndex)

setScreenDescription

public void setScreenDescription(String description,
                        int screenIndex)

setScreenID

public void setScreenID(String id,
               int screenIndex)

setScreenName

public void setScreenName(String name,
                 int screenIndex)

setScreenPlateRef

public void setScreenPlateRef(String plate,
                     int screenIndex,
                     int plateRefIndex)

setScreenProtocolDescription

public void setScreenProtocolDescription(String protocolDescription,
                                int screenIndex)

setScreenProtocolIdentifier

public void setScreenProtocolIdentifier(String protocolIdentifier,
                               int screenIndex)

setScreenReagentSetDescription

public void setScreenReagentSetDescription(String reagentSetDescription,
                                  int screenIndex)

setScreenReagentSetIdentifier

public void setScreenReagentSetIdentifier(String reagentSetIdentifier,
                                 int screenIndex)

setScreenType

public void setScreenType(String type,
                 int screenIndex)

setStageLabelName

public void setStageLabelName(String name,
                     int imageIndex)

setStageLabelX

public void setStageLabelX(Double x,
                  int imageIndex)

setStageLabelY

public void setStageLabelY(Double y,
                  int imageIndex)

setStageLabelZ

public void setStageLabelZ(Double z,
                  int imageIndex)

setTagAnnotationAnnotationRef

public void setTagAnnotationAnnotationRef(String annotation,
                                 int tagAnnotationIndex,
                                 int annotationRefIndex)

setTagAnnotationDescription

public void setTagAnnotationDescription(String description,
                               int tagAnnotationIndex)

setTagAnnotationID

public void setTagAnnotationID(String id,
                      int tagAnnotationIndex)

setTagAnnotationNamespace

public void setTagAnnotationNamespace(String namespace,
                             int tagAnnotationIndex)

setTagAnnotationValue

public void setTagAnnotationValue(String value,
                         int tagAnnotationIndex)

setTermAnnotationAnnotationRef

public void setTermAnnotationAnnotationRef(String annotation,
                                  int termAnnotationIndex,
                                  int annotationRefIndex)

setTermAnnotationDescription

public void setTermAnnotationDescription(String description,
                                int termAnnotationIndex)

setTermAnnotationID

public void setTermAnnotationID(String id,
                       int termAnnotationIndex)

setTermAnnotationNamespace

public void setTermAnnotationNamespace(String namespace,
                              int termAnnotationIndex)

setTermAnnotationValue

public void setTermAnnotationValue(String value,
                          int termAnnotationIndex)

setTiffDataFirstC

public void setTiffDataFirstC(NonNegativeInteger firstC,
                     int imageIndex,
                     int tiffDataIndex)

setTiffDataFirstT

public void setTiffDataFirstT(NonNegativeInteger firstT,
                     int imageIndex,
                     int tiffDataIndex)

setTiffDataFirstZ

public void setTiffDataFirstZ(NonNegativeInteger firstZ,
                     int imageIndex,
                     int tiffDataIndex)

setTiffDataIFD

public void setTiffDataIFD(NonNegativeInteger ifd,
                  int imageIndex,
                  int tiffDataIndex)

setTiffDataPlaneCount

public void setTiffDataPlaneCount(NonNegativeInteger planeCount,
                         int imageIndex,
                         int tiffDataIndex)

setTimestampAnnotationAnnotationRef

public void setTimestampAnnotationAnnotationRef(String annotation,
                                       int timestampAnnotationIndex,
                                       int annotationRefIndex)

setTimestampAnnotationDescription

public void setTimestampAnnotationDescription(String description,
                                     int timestampAnnotationIndex)

setTimestampAnnotationID

public void setTimestampAnnotationID(String id,
                            int timestampAnnotationIndex)

setTimestampAnnotationNamespace

public void setTimestampAnnotationNamespace(String namespace,
                                   int timestampAnnotationIndex)

setTimestampAnnotationValue

public void setTimestampAnnotationValue(Timestamp value,
                               int timestampAnnotationIndex)

setTransmittanceRangeCutIn

public void setTransmittanceRangeCutIn(PositiveInteger cutIn,
                              int instrumentIndex,
                              int filterIndex)

setTransmittanceRangeCutInTolerance

public void setTransmittanceRangeCutInTolerance(NonNegativeInteger cutInTolerance,
                                       int instrumentIndex,
                                       int filterIndex)

setTransmittanceRangeCutOut

public void setTransmittanceRangeCutOut(PositiveInteger cutOut,
                               int instrumentIndex,
                               int filterIndex)

setTransmittanceRangeCutOutTolerance

public void setTransmittanceRangeCutOutTolerance(NonNegativeInteger cutOutTolerance,
                                        int instrumentIndex,
                                        int filterIndex)

setTransmittanceRangeTransmittance

public void setTransmittanceRangeTransmittance(PercentFraction transmittance,
                                      int instrumentIndex,
                                      int filterIndex)

setUUIDFileName

public void setUUIDFileName(String fileName,
                   int imageIndex,
                   int tiffDataIndex)

setWellAnnotationRef

public void setWellAnnotationRef(String annotation,
                        int plateIndex,
                        int wellIndex,
                        int annotationRefIndex)

setWellColor

public void setWellColor(Color color,
                int plateIndex,
                int wellIndex)

setWellColumn

public void setWellColumn(NonNegativeInteger column,
                 int plateIndex,
                 int wellIndex)

setWellExternalDescription

public void setWellExternalDescription(String externalDescription,
                              int plateIndex,
                              int wellIndex)

setWellExternalIdentifier

public void setWellExternalIdentifier(String externalIdentifier,
                             int plateIndex,
                             int wellIndex)

setWellID

public void setWellID(String id,
             int plateIndex,
             int wellIndex)

setWellReagentRef

public void setWellReagentRef(String reagent,
                     int plateIndex,
                     int wellIndex)

setWellRow

public void setWellRow(NonNegativeInteger row,
              int plateIndex,
              int wellIndex)

setWellType

public void setWellType(String type,
               int plateIndex,
               int wellIndex)

setWellSampleAnnotationRef

public void setWellSampleAnnotationRef(String annotation,
                              int plateIndex,
                              int wellIndex,
                              int wellSampleIndex,
                              int annotationRefIndex)

setWellSampleID

public void setWellSampleID(String id,
                   int plateIndex,
                   int wellIndex,
                   int wellSampleIndex)

setWellSampleImageRef

public void setWellSampleImageRef(String image,
                         int plateIndex,
                         int wellIndex,
                         int wellSampleIndex)

setWellSampleIndex

public void setWellSampleIndex(NonNegativeInteger index,
                      int plateIndex,
                      int wellIndex,
                      int wellSampleIndex)

setWellSamplePositionX

public void setWellSamplePositionX(Double positionX,
                          int plateIndex,
                          int wellIndex,
                          int wellSampleIndex)

setWellSamplePositionY

public void setWellSamplePositionY(Double positionY,
                          int plateIndex,
                          int wellIndex,
                          int wellSampleIndex)

setWellSampleTimepoint

public void setWellSampleTimepoint(Timestamp timepoint,
                          int plateIndex,
                          int wellIndex,
                          int wellSampleIndex)

setXMLAnnotationAnnotationRef

public void setXMLAnnotationAnnotationRef(String annotation,
                                 int XMLAnnotationIndex,
                                 int annotationRefIndex)

setXMLAnnotationDescription

public void setXMLAnnotationDescription(String description,
                               int XMLAnnotationIndex)

setXMLAnnotationID

public void setXMLAnnotationID(String id,
                      int XMLAnnotationIndex)

setXMLAnnotationNamespace

public void setXMLAnnotationNamespace(String namespace,
                             int XMLAnnotationIndex)

setXMLAnnotationValue

public void setXMLAnnotationValue(String value,
                         int XMLAnnotationIndex)

Class OMEXMLMetadataImpl

Field Summary

Fields inherited from class loci.formats.ome.AbstractOMEXMLMetadata

Constructor Summary

Method Summary

Methods inherited from class loci.formats.ome.AbstractOMEXMLMetadata

Methods inherited from class java.lang.Object

Constructor Detail

OMEXMLMetadataImpl

Method Detail

createRoot

getRoot

setRoot

dumpXML

resolveReferences

getPixelsBinDataCount

getBooleanAnnotationAnnotationCount

getCommentAnnotationAnnotationCount

getDoubleAnnotationAnnotationCount

getFileAnnotationAnnotationCount

getListAnnotationAnnotationCount

getLongAnnotationAnnotationCount

getTagAnnotationAnnotationCount

getTermAnnotationAnnotationCount

getTimestampAnnotationAnnotationCount

getXMLAnnotationAnnotationCount

getLightSourceType

getShapeType

getROIAnnotationRefCount

getPlateAcquisitionAnnotationRefCount

getPlateAnnotationRefCount

getExperimenterGroupAnnotationRefCount

getImageAnnotationRefCount

getScreenAnnotationRefCount

getWellAnnotationRefCount

getDatasetAnnotationRefCount

getProjectAnnotationRefCount

getReagentAnnotationRefCount

getPlaneAnnotationRefCount

getExperimenterAnnotationRefCount

getWellSampleAnnotationRefCount

getPixelsAnnotationRefCount

getChannelAnnotationRefCount

getBooleanAnnotationCount

getChannelCount

getCommentAnnotationCount

getDatasetCount

getDatasetRefCount

getDetectorCount

getDichroicCount

getDoubleAnnotationCount

getLightPathEmissionFilterRefCount

getFilterSetEmissionFilterRefCount

getLightPathExcitationFilterRefCount

getFilterSetExcitationFilterRefCount

getExperimentCount

getExperimenterCount

getExperimenterGroupCount

getExperimenterGroupExperimenterRefCount

getFileAnnotationCount

getFilterCount

getFilterSetCount

getImageCount

getDatasetImageRefCount

getInstrumentCount

getLeaderCount

getLightSourceCount

getMicrobeamManipulationLightSourceSettingsCount

getListAnnotationCount

getLongAnnotationCount

getMicrobeamManipulationCount

getMicrobeamManipulationRefCount

getObjectiveCount

getPlaneCount

getPlateCount

getPlateAcquisitionCount

getPlateRefCount

getProjectCount

getROICount

getImageROIRefCount