# Package loci.formats.in

Package containing Bio-Formats file format readers.

See: Description

- Interface Summary
  Interface | Description
  --- | ---
  AmiraReader.PlaneReader | This is the common interface for all formats, compressed or not.
  MetadataOptions | Holds metadata-related options.
  PrairieMetadata.Value | A value in a Prairie metadata dictionary.

- Class Summary
  Class | Description
  --- | ---
  AFIReader | AFIReader is the file format reader for Aperio AFI files.
  AIMReader | AIMReader is the file format reader for .aim files.
  AliconaReader | AliconaReader is the file format reader for Alicona AL3D files.
  AmiraReader | This is a file format reader for AmiraMesh data.
  AnalyzeReader | AnalyzeReader is the file format reader for Analyze 7.5 files.
  APLReader | APLReader is the file format reader for Olympus APL files.
  APNGReader | APNGReader is the file format reader for Animated Portable Network Graphics (APNG) images.
  ARFReader | ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.
  AVIReader | AVIReader is the file format reader for AVI files.
  BaseTiffReader | BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
  BaseZeissReader | BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.
  BDReader | BDReader is the file format reader for BD Pathway datasets.
  BDVReader | Reader for BDV files.
  BIFormatReader | BIFormatReader is the superclass for file format readers that use java.awt.image.BufferedImage as the native data type.
  BioRadGelReader | BioRadGelReader is the file format reader for Bio-Rad gel files.
  BioRadReader | BioRadReader is the file format reader for Bio-Rad PIC files.
  BioRadSCNReader | BioRadSCNReader is the reader for Bio-Rad .scn files
  BMPReader | BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
  BrukerReader | BrukerReader is the file format reader for Bruker MRI files.
  BurleighReader | BurleighReader is the file format reader for Burleigh .img files.
  CanonRawReader | CanonRawReader is the file format reader for Canon RAW files.
  CellH5Reader | Reader for CellH5 (HDF) files.
  CellomicsReader | Reader for Cellomics C01 files.
  CellSensReader | CellSensReader is the file format reader for cellSens .vsi files.
  CellVoyagerReader | A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).
  CellVoyagerReader.AreaInfo |
  CellVoyagerReader.ChannelInfo |
  CellVoyagerReader.FieldInfo |
  CellVoyagerReader.WellInfo |
  CellWorxReader | CellWorxReader is the file format reader for CellWorx .pnl files.
  ColumbusReader | ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
  CV7000Reader |
  DCIMGReader | DCIMGReader reads Hamamatsu DCIMG files.
  DefaultMetadataOptions | Default implementation of `MetadataOptions`.
  DeltavisionReader | DeltavisionReader is the file format reader for Deltavision files.
  DeltavisionReader.DVExtHdrFields | This private class structure holds the details for the extended header.
  DicomReader | DicomReader is the file format reader for DICOM files.
  DNGReader | DNGReader is the file format reader for Canon DNG (TIFF) files.
  DynamicMetadataOptions | Configuration object for readers and writers.
  Ecat7Reader | Ecat7Reader is the file format reader for ECAT 7 files.
  EPSReader | Reader is the file format reader for Encapsulated PostScript (EPS) files.
  FakeReader | FakeReader is the file format reader for faking input data.
  FakeReader.TextLine |
  FEIReader | FEIReader is the file format reader for FEI and Philips .img files.
  FEITiffReader | FEITiffReader is the file format reader for TIFF files produced by various FEI software.
  FilePatternReader |
  FitsReader | FitsReader is the file format reader for Flexible Image Transport System (FITS) images.
  FlexReader | FlexReader is a file format reader for Evotec Flex files.
  FlowSightReader |
  FluoviewReader | FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
  FujiReader | FujiReader is the file format reader for Fuji LAS 3000 datasets.
  FV1000Reader | FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.
  GatanDM2Reader | GatanDM2Reader is the file format reader for Gatan .dm2 files.
  GatanReader | GatanReader is the file format reader for Gatan files.
  GelReader | GelReader is the file format reader for Molecular Dynamics GEL TIFF files.
  GIFReader | GIFReader is the file format reader for Graphics Interchange Format (GIF) files.
  HamamatsuVMSReader | HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
  HISReader | HISReader is the file format reader for Hamamatsu .his files.
  HitachiReader | HitachiReader is the file format reader for S-4800 files.
  HRDGDFReader | HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.
  I2IReader | I2IReader is the file format reader for I2I files.
  ICSReader | ICSReader is the file format reader for ICS (Image Cytometry Standard) files.
  IM3Reader |
  IM3Reader.BooleanIM3Record | A record containing boolean values
  IM3Reader.ContainerRecord |
  IM3Reader.FloatIM3Record |
  IM3Reader.IM3Record |
  IM3Reader.IntIM3Record |
  IM3Reader.Spectrum |
  IM3Reader.StringIM3Record |
  ImaconReader | ImaconReader is the file format reader for Imacon .fff (TIFF) files.
  ImageIOReader | ImageIOReader is the superclass for file format readers that use the javax.imageio package.
  ImagicReader | ImagicReader is the file format reader for IMAGIC files.
  ImarisHDFReader | Reader for Bitplane Imaris 5.5 (HDF) files.
  ImarisReader | ImarisReader is the file format reader for Bitplane Imaris files.
  ImarisTiffReader | ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).
  IMODReader | Reader for IMOD binary files.
  ImprovisionTiffReader | ImprovisionTiffReader is the file format reader for Improvision TIFF files.
  ImspectorReader | ImspectorReader is the file format reader for Imspector .msr files.
  InCell3000Reader | InCell3000Reader is the file format reader for InCell 3000.
  InCellReader | InCellReader is the file format reader for InCell 1000/2000 datasets.
  INRReader | INRReader is the file format reader for INR files.
  InveonReader | InveonReader is the file format reader for Inveon files.
  IonpathMIBITiffReader | IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
  IPLabReader | IPLabReader is the file format reader for IPLab (.IPL) files.
  IPWReader | IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
  IvisionReader | IvisionReader is the file format reader for IVision (.IPM) files.
  JDCEReader | JDCEReader is the file format reader for Molecular Devices JDCE plates.
  JEOLReader | JEOLReader is the file format reader for JEOL files.
  JPEG2000MetadataParser | A parser for JPEG 2000 metadata.
  JPEG2000Reader | JPEG2000Reader is the file format reader for JPEG-2000 images.
  JPEGReader | JPEGReader is the file format reader for JPEG images.
  JPEGReader.DefaultJPEGReader |
  JPKReader | JPKReader is the file format reader for JPK Instruments files.
  JPXReader | JPXReader is the file format reader for JPX (3D JPEG-2000) images.
  KhorosReader | Reader for Khoros XV files.
  KLBReader | Reader for Keller Lab Block (KLB) files.
  KodakReader | KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
  L2DReader | L2DReader is the file format reader for Li-Cor L2D datasets.
  LeicaHandler | SAX handler for parsing XML in Leica LIF and Leica TCS files.
  LeicaReader | LeicaReader is the file format reader for Leica files.
  LeicaSCNReader | LeicaSCNReader is the file format reader for Leica SCN TIFF files.
  LEOReader | LEOReader is the file format reader for LEO EM files.
  LiFlimReader | LiFlimReader is the file format reader for LI-FLIM files.
  LIFReader | LIFReader is the file format reader for Leica LIF files.
  LIMReader | LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
  LIPixelFormat |
  LOFReader | LOFReader is the file format reader for Leica Microsystems' LOF files.
  MetamorphHandler | MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
  MetamorphReader | Reader is the file format reader for Metamorph STK files.
  MetamorphTiffReader | MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.
  MetaxpressTiffReader | MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.
  MIASReader | MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
  MicroCTReader | MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
  MicromanagerReader | MicromanagerReader is the file format reader for Micro-Manager files.
  MikroscanTiffReader | MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
  MINCReader | MINCReader is the file format reader for MINC MRI files.
  MinimalTiffReader | MinimalTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.
  MNGReader | MNGReader is the file format reader for Multiple-image Network Graphics (MNG) files.
  MolecularImagingReader | MolecularImagingReader is the file format reader for Molecular Imaging files.
  MRCReader | MRCReader is the file format reader for MRC files.
  MRWReader | MRWReader is the file format reader for Minolta MRW files.
  NAFReader | NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
  ND2Handler | DefaultHandler implementation for handling XML produced by Nikon Elements.
  ND2Reader | ND2Reader is the file format reader for Nikon ND2 files.
  ND2Reader.ChunkMapEntry |
  NDPIReader | NDPIReader is the file format reader for Hamamatsu .ndpi files.
  NDPISReader | NDPISReader is the file format reader for Hamamatsu .ndpis files.
  NiftiReader | NiftiReader is the file format reader for NIfTI files.
  NikonElementsTiffReader | NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.
  NikonReader | NikonReader is the file format reader for Nikon NEF (TIFF) files.
  NikonTiffReader | NikonTiffReader is the file format reader for Nikon TIFF files.
  NRRDReader | File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
  OBFReader | OBFReader is the file format reader for Imspector OBF files.
  OIRReader | OIRReader is the file format reader for Olympus .oir files.
  OIRReader.CZTKey | This is a class that wraps three numbers c,z,t and an object can be used as a key in a hashmap.
  OlympusTileReader | OlympusTileReader is the file format reader for Olympus .omp2info files.
  OMETiffReader | OMETiffReader is the file format reader for OME-TIFF files.
  OMEXMLReader | OMEXMLReader is the file format reader for OME-XML files.
  OpenlabRawReader | OpenlabRawReader is the file format reader for Openlab RAW files.
  OpenlabReader | OpenlabReader is the file format reader for Openlab LIFF files.
  OperettaReader | OperettaReader is the file format reader for PerkinElmer Operetta data.
  OxfordInstrumentsReader | OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.
  PCIReader | PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
  PCORAWReader | PCORAWReader is the file format reader for PCORAW files.
  PCXReader | PCXReader is the file format reader for PCX files (originally used by PC Paintbrush; now used in Zeiss' LSM Image Browser).
  PDSReader | PDSReader is the file format reader for Perkin Elmer densitometer files.
  PerkinElmerReader | PerkinElmerReader is the file format reader for PerkinElmer files.
  PGMReader | PGMReader is the file format reader for Portable Gray Map (PGM) images.
  PhotoshopTiffReader | PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.
  PictReader | PictReader is the file format reader for Apple PICT files.
  PovrayReader | PovrayReader is the file format reader for POV-Ray .df3 files.
  PQBinReader | PQBinReader is the file format reader for PicoQuant .bin files.
  PrairieMetadata | Metadata structure for Prairie Technologies' TIFF-based format.
  PrairieMetadata.ValueItem | A leaf value with an actual `PrairieMetadata.ValueItem.value()` as well as an optional `PrairieMetadata.ValueItem.description()`.
  PrairieMetadata.ValueTable | A table of values.
  PrairieReader | PrairieReader is the file format reader for Prairie Technologies' TIFF variant.
  PSDReader | PSDReader is the file format reader for Photoshop PSD files.
  PyramidTiffReader | PyramidTiffReader is the file format reader for pyramid TIFFs.
  QTReader | QTReader is the file format reader for QuickTime movie files.
  QuesantReader | QuesantReader is the file format reader for Quesant .afm files.
  RCPNLReader |
  RHKReader | RHKReader is the file format reader for RHK Technologies files.
  SBIGReader | SBIGReader is the file format reader for SBIG files.
  ScanrReader | ScanrReader is the file format reader for Olympus ScanR datasets.
  SDTInfo | SDTInfo encapsulates the header information for Becker & Hickl SPC-Image SDT files.
  SDTReader | SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.
  SeikoReader | SeikoReader is the file format reader for Seiko .xqd/.xqf files.
  SEQReader | SEQReader is the file format reader for Image-Pro Sequence files.
  SIFReader | SIFReader is the file format reader for Andor SIF files.
  SimplePCITiffReader | SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.
  SISReader | SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.
  SlideBook7Reader |
  SlideBook7Reader.IntIntPair |
  SlideBook7Reader.StrIntPair |
  SlidebookReader | SlidebookReader is the file format reader for 3I Slidebook files.
  SlidebookTiffReader |
  SMCameraReader | SMCameraReader is the file format reader for SM camera files.
  SPCReader | SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.
  SPEReader | SPEReader is the file format reader for Princeton Instruments SPE .spe files.
  SpiderReader | SpiderReader is the file format reader for SPIDER files.
  SVSCoreMetadata |
  SVSReader | SVSReader is the file format reader for Aperio SVS TIFF files.
  TargaReader | File format reader for Truevision Targa files.
  TCSReader | TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.
  TecanReader |
  TextReader | Reader for text files containing tables of data.
  TiffDelegateReader | TiffDelegateReader is a file format reader for TIFF files.
  TiffJAIReader | TiffJAIReader is a file format reader for TIFF images.
  TiffReader | TiffReader is the file format reader for regular TIFF files, not of any specific TIFF variant.
  TileJPEGReader | Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
  TillVisionReader | TillVisionReader is the file format reader for TillVision files.
  TissueFAXSReader | Reader for TissueFAXS format from TissueGnostics.
  TopometrixReader | TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.
  TrestleReader | TrestleReader is the file format reader for Trestle slide datasets.
  UBMReader | UBMReader is the file format reader for UBM .pr3 files.
  UnisokuReader | UnisokuReader is the file format reader for Unisoku STM files.
  VarianFDFReader | VarianFDFReader is the file format reader for Varian FDF files.
  VectraReader | VectraReader is the reader for PerkinElmer Vectra QPTIFF data
  VeecoReader | VeecoReader is the file format reader for Veeco HDF files.
  VentanaReader | VentanaReader is the file format reader for Ventana .bif files.
  VGSAMReader | VGSAMReader is the file format reader for VG SAM .dti files.
  VisitechReader | VisitechReader is the file format reader for Visitech XYS files.
  VolocityClippingReader | VolocityClippingReader is the file format reader for Volocity library clipping files.
  VolocityReader | VolocityReader is the file format reader for Volocity library files.
  WATOPReader | WATOPReader is the file format reader for WA Technology .wat files.
  XLEFReader | XLEFReader is the file format reader for Leica Microsystems' XLEF files.
  XLEFReader.PathComparator | Helper class to sort file paths by name and depth
  ZeissCZIReader | ZeissCZIReader is the file format reader for Zeiss .czi files.
  ZeissCZIReader.AttachmentEntry |
  ZeissCZIReader.Channel |
  ZeissCZIReader.Coordinate |
  ZeissCZIReader.DimensionEntry |
  ZeissLMSReader | Zeiss LMS reader for data from Zeiss CSM 700 systems.
  ZeissLSMReader | ZeissLSMReader is the file format reader for Zeiss LSM files.
  ZeissTIFFHandler | SAX handler for parsing XML in Zeiss TIFF files.
  ZeissTIFFReader | ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.
  ZeissXRMReader | ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.
  ZeissZVIReader | ZeissZVIReader is the file format reader for Zeiss ZVI files.
  ZipReader | Reader for Zip files.

- Enum Summary
  Enum | Description
  --- | ---
  BaseZeissReader.Charset |
  BaseZeissReader.Context |
  BaseZeissReader.DrawStyle | Line drawing styles.
  BaseZeissReader.FeatureType | Feature types.
  BaseZeissReader.FillStyle | Fill styles.
  BaseZeissReader.LineEndPositions |
  BaseZeissReader.LineEndStyle | Line ending styles.
  BaseZeissReader.PointStyle | Point styles.
  BaseZeissReader.TextAlignment |
  LOFReader.MetadataSource |
  MetadataLevel |
  SlideBook7Reader.EGraphicType |
  SPEReader.SpeHeaderEntry | SpeHeaderEntry is an Enum which provides a list of all available SPE header entries along with the offset value from the top of the header in bytes and their associated data type
  SPEReader.SpeHeaderType | SpeHeaderType is an Enum representing the available data types stored in the SPE header

## Package loci.formats.in Description

Package containing Bio-Formats file format readers.

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