## Uses of Interface
loci.formats.meta.MetadataStore

- Packages that use MetadataStore
  Package | Description
  --- | ---
  loci.formats | Bio-Formats: a library for reading and writing popular microscopy file formats.
  loci.formats.gui | Package containing Bio-Formats graphical user interface code.
  loci.formats.in | Package containing Bio-Formats file format readers.
  loci.formats.in.LeicaMicrosystemsMetadata |
  loci.formats.internal | Package containing common classes for internal use by Bio-Formats readers/writers.
  loci.formats.meta | Package containing core Bio-Formats metadata interfaces for the OME data model.
  loci.formats.ome | Package containing Bio-Formats OME-related logic for OME-XML metadata, and database import, upload and download.
  loci.formats.services |
  loci.plugins.util | Utility classes and methods for the Bio-Formats plugins for ImageJ.

- - ### Uses of MetadataStore in loci.formats

    Fields in loci.formats declared as MetadataStore
    Modifier and Type | Field and Description
    --- | ---
    `protected MetadataStore` | FormatReader.`metadataStore` Current metadata store.
    `private MetadataStore` | Memoizer.`replacementMetadataStore` `MetadataStore` created internally.
    `private MetadataStore` | FileStitcher.`store`
    `private MetadataStore` | Memoizer.`userMetadataStore` `MetadataStore` set by the caller.

    Methods in loci.formats that return MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `MetadataStore` | Memoizer.`getMetadataStore()`
    `MetadataStore` | FileStitcher.`getMetadataStore()`
    `MetadataStore` | ReaderWrapper.`getMetadataStore()`
    `MetadataStore` | ImageReader.`getMetadataStore()`
    `MetadataStore` | IFormatReader.`getMetadataStore()` Retrieves the current metadata store for this reader.
    `MetadataStore` | FormatReader.`getMetadataStore()`
    `protected MetadataStore` | FormatReader.`makeFilterMetadata()` Return a properly configured loci.formats.meta.FilterMetadata.

    Methods in loci.formats with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `static void` | MetadataTools.`populateMetadata(MetadataStore store, int series, java.lang.String imageName, boolean littleEndian, java.lang.String dimensionOrder, java.lang.String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)` Populates the given `MetadataStore`, for the specified series, using the provided values.
    `static void` | MetadataTools.`populateMetadata(MetadataStore store, int series, java.lang.String imageName, CoreMetadata coreMeta)` Populates the given `MetadataStore`, for the specified series, using the values from the provided `CoreMetadata`.
    `static void` | MetadataTools.`populateMetadata(MetadataStore store, java.lang.String file, int series, java.lang.String imageName, boolean littleEndian, java.lang.String dimensionOrder, java.lang.String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)` Populates the given `MetadataStore`, for the specified series, using the provided values.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r, boolean doPlane)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixels(MetadataStore store, IFormatReader r, boolean doPlane, boolean doImageName)` Populates the Pixels element of the given metadata store, using core metadata from the given reader.
    `static void` | MetadataTools.`populatePixelsOnly(MetadataStore store, IFormatReader r)`
    `static void` | MetadataTools.`populatePixelsOnly(MetadataStore store, int series, boolean littleEndian, java.lang.String dimensionOrder, java.lang.String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)`
    `static void` | MetadataTools.`setDefaultCreationDate(MetadataStore store, java.lang.String id, int series)` Sets a default creation date.
    `void` | Memoizer.`setMetadataStore(MetadataStore store)`
    `void` | FileStitcher.`setMetadataStore(MetadataStore store)`
    `void` | ReaderWrapper.`setMetadataStore(MetadataStore store)`
    `void` | ImageReader.`setMetadataStore(MetadataStore store)`
    `void` | IFormatReader.`setMetadataStore(MetadataStore store)` Sets the default metadata store for this reader.
    `void` | FormatReader.`setMetadataStore(MetadataStore store)`
    `void` | DelegateReader.`setMetadataStore(MetadataStore store)`

  - ### Uses of MetadataStore in loci.formats.gui

    Fields in loci.formats.gui declared as MetadataStore
    Modifier and Type | Field and Description
    --- | ---
    `protected MetadataStore` | ImageViewer.`omeMeta` Attached OME metadata store, if available.

  - ### Uses of MetadataStore in loci.formats.in

    Fields in loci.formats.in declared as MetadataStore
    Modifier and Type | Field and Description
    --- | ---
    `private MetadataStore` | ZeissCZIReader.`store`
    `private MetadataStore` | LeicaHandler.`store`
    `private MetadataStore` | InCellReader.InCellHandler.`store`
    `private MetadataStore` | FlexReader.FlexHandler.`store`
    `private MetadataStore` | KLBReader.`store`
    `private MetadataStore` | CellH5Reader.`store`
    `private MetadataStore` | BDVReader.`store`

    Methods in loci.formats.in that return MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `MetadataStore` | FilePatternReader.`getMetadataStore()`
    `MetadataStore` | OMETiffReader.`getMetadataStoreForConversion()` Deprecated. Use the general `FormatReader.getMetadataStore()` method.
    `MetadataStore` | OMETiffReader.`getMetadataStoreForDisplay()` Deprecated. Use the general `FormatReader.getMetadataStore()` method.

    Methods in loci.formats.in with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `protected int` | SlideBook7Reader.`addAnnotation(MetadataStore store, SlideBook7Reader.CAnnotation70 inAnn, int inCapture, int inRegionIndex, int inRoiManagerRoiIndex)`
    `private java.lang.String` | GatanReader.`createROI(MetadataStore store, int index)` Create an empty ROI and link it to the Image.
    `private void` | FakeReader.`fillAcquisitionDate(MetadataStore store, java.lang.String date, int imageIndex)`
    `private void` | FakeReader.`fillAnnotations(MetadataStore store, int imageIndex)`
    `private void` | FakeReader.`fillChannelWavelengths(MetadataStore store)`
    `private void` | FakeReader.`fillExposureTime(MetadataStore store)`
    `private void` | FakeReader.`fillInstrumentRefs(MetadataStore store)`
    `protected void` | ZeissZVIReader.`fillMetadataPass1(MetadataStore store)`
    `protected void` | ZeissTIFFReader.`fillMetadataPass1(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass1(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissTIFFReader.`fillMetadataPass2(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass2(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissZVIReader.`fillMetadataPass3(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass3(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass4(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | ZeissZVIReader.`fillMetadataPass5(MetadataStore store)`
    `protected void` | ZeissTIFFReader.`fillMetadataPass5(MetadataStore store)`
    `protected void` | BaseZeissReader.`fillMetadataPass5(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass6(MetadataStore store)` Read and store basic dimensions in model
    `protected void` | BaseZeissReader.`fillMetadataPass7(MetadataStore store)` Store basic dimensions in model
    `private void` | FakeReader.`fillPhysicalSizes(MetadataStore store)`
    `private void` | FakeReader.`fillRegions(MetadataStore store, int imageIndex)`
    `private void` | FlexReader.`groupFiles(java.lang.String[] fileList, MetadataStore store)`
    `private void` | DeltavisionReader.`parseDeconvolutionLog(loci.common.RandomAccessInputStream s, MetadataStore store)` Parse deconvolution output, if it exists.
    `private void` | FlexReader.`parseFlexFile(int currentWell, int wellRow, int wellCol, int field, boolean firstFile, MetadataStore store)` Parses XML metadata from the Flex file corresponding to the given well.
    `private void` | LeicaReader.`parseInstrumentData(MetadataStore store, int blockNum)`
    `private boolean` | DeltavisionReader.`parseLogFile(MetadataStore store)` Extract metadata from associated log file, if it exists.
    `(package private) void` | BaseZeissReader.`parseMainTags(int image, MetadataStore store, java.util.ArrayList<BaseZeissReader.Tag> tags)`
    `void` | MIASReader.`parseMasks(MetadataStore overlayStore)` Parse masks into a separate overlay-specific MetadataStore.
    `private int` | MIASReader.`parseMasks(MetadataStore store, int series, int roi, java.lang.String overlayTiff)` Parse Mask ROIs from the given TIFF and place them in the given MetadataStore.
    `private boolean` | BioRadReader.`parseNotes(MetadataStore store)`
    `protected void` | ZeissLSMReader.`parseOverlays(int series, long data, java.lang.String suffix, MetadataStore store)` Parses overlay-related fields.
    `private int` | FV1000Reader.`parseROIFile(java.lang.String filename, MetadataStore store, int nextROI, int plane)`
    `private void` | TrestleReader.`parseROIs(MetadataStore store)`
    `private void` | BDReader.`parseROIs(MetadataStore store)`
    `private void` | ZeissZVIReader.`parseROIs(loci.common.RandomAccessInputStream s, int imageNum, java.lang.String name, MetadataStore store)` Parse ROI data from the given RandomAccessInputStream and store it in the given MetadataStore.
    `private void` | FakeReader.`parseSeriesTable(loci.common.IniTable table, MetadataStore store, int newSeries)` Translate key/value pairs from the INI table for the specified series.
    `private void` | ZeissZVIReader.`parseTags(int image, java.lang.String file, MetadataStore store)` Parse all of the tags in a stream.
    `private void` | IPLabReader.`parseTags(MetadataStore store)`
    `private void` | MIASReader.`parseTemplateFile(MetadataStore store)` Parse metadata from the Nugenesistemplate.txt file.
    `protected void` | MetaxpressTiffReader.`parseWellLogFile(int wellIndex, MetadataStore store)`
    `protected void` | CellWorxReader.`parseWellLogFile(int wellIndex, MetadataStore store)` Parse metadata from a well log file.
    `private void` | FakeReader.`populateInstrument(MetadataStore store)`
    `boolean` | MIASReader.`populateMaskPixels(int imageIndex, int roiIndex, int shapeIndex, MetadataStore store)` Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.
    `private void` | FlexReader.`populateMetadataStore(MetadataStore store)`
    `private void` | FV1000Reader.`populateMetadataStore(MetadataStore store, java.lang.String path)`
    `protected void` | ZeissLSMReader.`populateMetadataStore(ZeissLSMReader.SubBlock block, MetadataStore store, int series)`
    `private void` | TiffReader.`populateMetadataStoreImageJ(MetadataStore store)` Checks the original metadata table for ImageJ-specific information to propagate into the metadata store.
    `protected void` | RCPNLReader.`populateObjective(MetadataStore store, int lensID)`
    `protected void` | DeltavisionReader.`populateObjective(MetadataStore store, int lensID)` Populate an Objective based upon the lens ID.
    `private void` | HitachiReader.`populateOMEMetadata(loci.common.IniTable image, MetadataStore store)`
    `private void` | MIASReader.`populateROI(java.util.List<java.lang.String> columns, java.lang.String[] data, int series, int roi, int time, int z, MetadataStore store)`
    `private void` | SPEReader.`populateRoiMetaData(MetadataStore store)` Reads and populates ROI Meta Data values.
    `void` | ND2Handler.`populateROIs(MetadataStore store)`
    `private int` | FakeReader.`populateSPW(MetadataStore store, int screens, int plates, int rows, int cols, int fields, int acqs, boolean withMicrobeam)`
    `private void` | KodakReader.`readExtraMetadata(MetadataStore store)`
    `private void` | KodakReader.`readFileInfoMetadata(MetadataStore store)`
    `private void` | DeltavisionReader.`readWavelength(int channel, MetadataStore store)`
    `void` | FilePatternReader.`setMetadataStore(MetadataStore store)`
    `void` | LeicaHandler.ROI.`storeROI(MetadataStore store, int series, int roi)`
    `void` | LIFReader.ROI.`storeROI(MetadataStore store, int series, int roi, int roiIndex)`
    `protected void` | BaseZeissReader.`storeROIs(MetadataStore store)` Store basic dimensions in model

    Constructors in loci.formats.in with parameters of type MetadataStore
    Constructor and Description
    `FlexHandler(java.util.List<java.lang.String> names, java.util.List<java.lang.String> factors, MetadataStore store, boolean populateCore, int well, int thisField)`
    `InCellHandler(MetadataStore store)`
    `LeicaHandler(MetadataStore store, MetadataLevel level)`
    `LeicaHandler(MetadataStore store, MetadataLevel level, boolean planesInStore)`

  - ### Uses of MetadataStore in loci.formats.in.LeicaMicrosystemsMetadata

    Fields in loci.formats.in.LeicaMicrosystemsMetadata declared as MetadataStore
    Modifier and Type | Field and Description
    --- | ---
    `(package private) MetadataStore` | MetadataStoreInitializer.`store`

    Methods in loci.formats.in.LeicaMicrosystemsMetadata that return MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `MetadataStore` | LMSFileReader.`makeFilterMetadata()`

    Methods in loci.formats.in.LeicaMicrosystemsMetadata with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `void` | ROI.`storeROI(MetadataStore store, int series, int roi, int roiIndex, int sizeX, int sizeY, boolean alternateCenter, MetadataLevel level)`

  - ### Uses of MetadataStore in loci.formats.internal

    Methods in loci.formats.internal with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `void` | WellContainer.`fillMetadataStore(MetadataStore store, int plate, int plateAcq, int wellSampleStart, int nextImage)`
    `void` | WellContainer.`fillMetadataStore(MetadataStore store, int plate, int plateAcq, int well, int wellSampleStart, int nextImage)`

  - ### Uses of MetadataStore in loci.formats.meta

    Subinterfaces of MetadataStore in loci.formats.meta
    Modifier and Type | Interface and Description
    --- | ---
    `interface` | `IMetadata`

    Constructors in loci.formats.meta with parameters of type MetadataStore
    Constructor and Description
    `FilterMetadata(MetadataStore store, boolean filter)`

  - ### Uses of MetadataStore in loci.formats.ome

    Subinterfaces of MetadataStore in loci.formats.ome
    Modifier and Type | Interface and Description
    --- | ---
    `interface` | `OMEXMLMetadata`

  - ### Uses of MetadataStore in loci.formats.services

    Methods in loci.formats.services that return MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `MetadataStore` | OMEXMLServiceImpl.`asStore(MetadataRetrieve meta)`
    `MetadataStore` | OMEXMLService.`asStore(MetadataRetrieve meta)` Gets the given `MetadataRetrieve` object as a `MetadataStore`.

    Methods in loci.formats.services with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `MetadataRetrieve` | OMEXMLServiceImpl.`asRetrieve(MetadataStore meta)`
    `MetadataRetrieve` | OMEXMLService.`asRetrieve(MetadataStore meta)` Gets the given `MetadataStore` object as a `MetadataRetrieve`.
    `void` | OMEXMLServiceImpl.`convertMetadata(MetadataRetrieve src, MetadataStore dest)`
    `void` | OMEXMLService.`convertMetadata(MetadataRetrieve src, MetadataStore dest)` Copies information from a metadata retrieval object (source) into a metadata store (destination).
    `void` | OMEXMLServiceImpl.`convertMetadata(java.lang.String xml, MetadataStore dest)`
    `void` | OMEXMLService.`convertMetadata(java.lang.String xml, MetadataStore dest)` Converts information from an OME-XML string (source) into a metadata store (destination).

  - ### Uses of MetadataStore in loci.plugins.util

    Methods in loci.plugins.util with parameters of type MetadataStore
    Modifier and Type | Method and Description
    --- | ---
    `static void` | ROIHandler.`saveROIs(MetadataStore store)` Save ROIs in the ROI manager to the given MetadataStore.
    `private static void` | ROIHandler.`storeLine(ij.gui.Line roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the Line ROI into the specified metadata store.
    `private static void` | ROIHandler.`storeOval(ij.gui.OvalRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the Oval ROI into the specified metadata store.
    `private static void` | ROIHandler.`storePoint(ij.gui.PointRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the Point ROI into the specified metadata store.
    `private static void` | ROIHandler.`storePolygon(ij.gui.PolygonRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the Polygon ROI into the specified metadata store.
    `private static void` | ROIHandler.`storeRectangle(ij.gui.Roi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the Rectangle ROI into the specified metadata store.
    `private static void` | ROIHandler.`storeText(ij.gui.TextRoi roi, MetadataStore store, int roiNum, int shape, int c, int z, int t)` Stores the text ROI into the metadata stored.

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