Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

accumulate - Variable in class loci.formats.in.SDTInfo

acquiredDate - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

acquisitionDate - Variable in class loci.formats.in.BaseZeissReader

activeDetector - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

adcDE - Variable in class loci.formats.in.SDTInfo

ADC sample delay (SPC-930).

adcRE - Variable in class loci.formats.in.SDTInfo

adcZoom - Variable in class loci.formats.in.SDTInfo

addChannelDimension(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Adds channel dimension

addDimension(int, Dimension) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Inserts dimension to buffer and optionally adapts other dimension-dependent values

addMissingDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Adds Z, T and S dimension if they haven't been added already

addSeriesMeta(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

addSeriesMetaList(String, Object) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

AFIReader - Class in loci.formats.in

AFIReader is the file format reader for Aperio AFI files.

AFIReader() - Constructor for class loci.formats.in.AFIReader

Constructs a new AFI reader.

AIMReader - Class in loci.formats.in

AIMReader is the file format reader for .aim files.

AIMReader() - Constructor for class loci.formats.in.AIMReader

Constructs a new AIM reader.

AL3D_MAGIC_STRING - Static variable in class loci.formats.in.AliconaReader

AliconaReader - Class in loci.formats.in

AliconaReader is the file format reader for Alicona AL3D files.

AliconaReader() - Constructor for class loci.formats.in.AliconaReader

Constructs a new Alicona reader.

allBlockLengths - Variable in class loci.formats.in.SDTInfo

allBlockOffsets - Variable in class loci.formats.in.SDTInfo

ALLOW_AUTOSTITCHING_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader

ALLOW_AUTOSTITCHING_KEY - Static variable in class loci.formats.in.ZeissCZIReader

allowAutostitching() - Method in class loci.formats.in.ZeissCZIReader

alternateCenter - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

AmiraReader - Class in loci.formats.in

This is a file format reader for AmiraMesh data.

AmiraReader() - Constructor for class loci.formats.in.AmiraReader

AnalyzeReader - Class in loci.formats.in

AnalyzeReader is the file format reader for Analyze 7.5 files.

AnalyzeReader() - Constructor for class loci.formats.in.AnalyzeReader

Constructs a new Analyze reader.

ANO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

APLReader - Class in loci.formats.in

APLReader is the file format reader for Olympus APL files.

APLReader() - Constructor for class loci.formats.in.APLReader

Constructs a new APL reader.

appendServerMap(String, String) - Static method in class loci.formats.in.FlexReader

Add the path 'realName' to the mapping for the server named 'alias'.

applyTransformation(byte[], int, int, int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader

Extension point for doing something to an FOV immediately after decompression, before any stitching or cropping.

ARCHIVE - Static variable in class loci.formats.in.FlexReader

ARFReader - Class in loci.formats.in

ARFReader is the file format reader for Axon Raw Format (ARF) files, produced by INDEC BioSystems's Imaging Workbench software.

ARFReader() - Constructor for class loci.formats.in.ARFReader

Constructs a new ARF reader.

associatedXmlDoc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

B

BACKGROUND_TABLE - Static variable in class loci.formats.in.LiFlimReader

basename - Variable in class loci.formats.in.ZeissTIFFHandler.Plane

BaseZeissReader - Class in loci.formats.in

BaseZeissReader contains common functionality required by readers for Zeiss AxioVision formats.

BaseZeissReader(String, String) - Constructor for class loci.formats.in.BaseZeissReader

Constructs a new ZeissZVI reader.

BaseZeissReader(String, String[]) - Constructor for class loci.formats.in.BaseZeissReader

Constructs a new ZeissZVI reader.

BaseZeissReader.Context - Enum in loci.formats.in

BaseZeissReader.Tag - Class in loci.formats.in

Content of a single tag from a Tags block.

BDReader - Class in loci.formats.in

BDReader is the file format reader for BD Pathway datasets.

BDReader() - Constructor for class loci.formats.in.BDReader

Constructs a new ScanR reader.

BH_HEADER_CHKSUM - Static variable in class loci.formats.in.SDTInfo

BH_HEADER_NOT_VALID - Static variable in class loci.formats.in.SDTInfo

BH_HEADER_VALID - Static variable in class loci.formats.in.SDTInfo

BINARY_SETUP - Static variable in class loci.formats.in.SDTInfo

BioRadGelReader - Class in loci.formats.in

BioRadGelReader is the file format reader for Bio-Rad gel files.

BioRadGelReader() - Constructor for class loci.formats.in.BioRadGelReader

Constructs a new Bio-Rad gel reader.

BioRadReader - Class in loci.formats.in

BioRadReader is the file format reader for Bio-Rad PIC files.

BioRadReader() - Constructor for class loci.formats.in.BioRadReader

Constructs a new BioRadReader.

BioRadSCNReader - Class in loci.formats.in

BioRadSCNReader is the reader for Bio-Rad .scn files

BioRadSCNReader() - Constructor for class loci.formats.in.BioRadSCNReader

Constructs a new Bio-Rad .scn reader.

bitInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

blockLength - Variable in class loci.formats.in.PQBinReader

No of timeBins pre-loaded as a block

blockLength - Variable in class loci.formats.in.SDTInfo

reserved2 now contains block (set) length.

blockLength - Variable in class loci.formats.in.SDTReader

No of timeBins pre-loaded as a block

blockNo - Variable in class loci.formats.in.SDTInfo

Number of the block in the file.

blockType - Variable in class loci.formats.in.SDTInfo

See blockType defines below.

BLUE - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

BMP - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

bordL - Variable in class loci.formats.in.SDTInfo

bordU - Variable in class loci.formats.in.SDTInfo

bpp - Variable in class loci.formats.in.BaseZeissReader

Number of bytes per pixel.

BrukerReader - Class in loci.formats.in

BrukerReader is the file format reader for Bruker MRI files.

BrukerReader() - Constructor for class loci.formats.in.BrukerReader

Constructs a new Bruker reader.

bufLength - Variable in class loci.formats.in.SPCReader

BurleighReader - Class in loci.formats.in

BurleighReader is the file format reader for Burleigh .img files.

BurleighReader() - Constructor for class loci.formats.in.BurleighReader

Constructs a new Burleigh reader.

bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

bytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

C

C - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

C_KEY - Static variable in class loci.formats.in.LiFlimReader

C_STRING - Static variable in class loci.formats.in.SDTInfo

C01_MAGIC_BYTES - Static variable in class loci.formats.in.CellomicsReader

calcPhotons - Variable in class loci.formats.in.SDTInfo

No of photons.

CanonRawReader - Class in loci.formats.in

CanonRawReader is the file format reader for Canon RAW files.

CanonRawReader() - Constructor for class loci.formats.in.CanonRawReader

Constructs a new Canon RAW reader.

canReadAttachments() - Method in class loci.formats.in.ZeissCZIReader

CellomicsReader - Class in loci.formats.in

Reader for Cellomics C01 files.

CellomicsReader() - Constructor for class loci.formats.in.CellomicsReader

Constructs a new Cellomics reader.

CellSensReader - Class in loci.formats.in

CellSensReader is the file format reader for cellSens .vsi files.

CellSensReader() - Constructor for class loci.formats.in.CellSensReader

Constructs a new cellSens reader.

CellVoyagerReader - Class in loci.formats.in

A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope ( http://www.yokogawa.com/scanner/products/cv1000e.htm).

CellVoyagerReader() - Constructor for class loci.formats.in.CellVoyagerReader

CellWorxReader - Class in loci.formats.in

CellWorxReader is the file format reader for CellWorx .pnl files.

CellWorxReader() - Constructor for class loci.formats.in.CellWorxReader

Constructs a new CellWorx reader.

CellWorxReader(String, String[]) - Constructor for class loci.formats.in.CellWorxReader

cfdHF - Variable in class loci.formats.in.SDTInfo

cfdLH - Variable in class loci.formats.in.SDTInfo

cfdLL - Variable in class loci.formats.in.SDTInfo

cfdZC - Variable in class loci.formats.in.SDTInfo

CFG_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

CFG_SUFFIX - Static variable in class loci.formats.in.PrairieReader

chan - Variable in class loci.formats.in.SDTInfo

Routing channel number.

Channel - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class represents image channels extracted from LMS image xmls.

Channel(int, int, double, double, String, String, long) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Channel

Channel.ChannelType - Enum in loci.formats.in.LeicaMicrosystemsMetadata

channelColors - Variable in class loci.formats.in.BaseZeissReader

channelColors - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

channelIndices - Variable in class loci.formats.in.BaseZeissReader

channelName - Variable in class loci.formats.in.BaseZeissReader

channelName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

channelNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

channelPrios - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

channels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

channels - Variable in class loci.formats.in.SDTInfo

channels - Variable in class loci.formats.in.SDTReader

Number of spectral channels.

channelTag - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

channelType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

characters(char[], int, int) - Method in class loci.formats.in.FlexReader.FlexHandler

characters(char[], int, int) - Method in class loci.formats.in.ZeissTIFFHandler

checkFlip(boolean, Length) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

chksum - Variable in class loci.formats.in.SDTInfo

cIndex - Variable in class loci.formats.in.BaseZeissReader

close() - Method in interface loci.formats.services.MDBService

Close the currently initialized file.

close() - Method in class loci.formats.services.MDBServiceImpl

close() - Method in interface loci.formats.services.MetakitService

close() - Method in class loci.formats.services.MetakitServiceImpl

close() - Method in interface loci.formats.services.NetCDFService

Closes and resets the service.

close() - Method in class loci.formats.services.NetCDFServiceImpl

close() - Method in interface loci.formats.services.POIService

Close the current POI file system.

close() - Method in class loci.formats.services.POIServiceImpl

close(boolean) - Method in class loci.formats.in.AFIReader

close(boolean) - Method in class loci.formats.in.AIMReader

close(boolean) - Method in class loci.formats.in.AliconaReader

close(boolean) - Method in class loci.formats.in.AmiraReader

close(boolean) - Method in class loci.formats.in.AnalyzeReader

close(boolean) - Method in class loci.formats.in.APLReader

close(boolean) - Method in class loci.formats.in.BaseZeissReader

close(boolean) - Method in class loci.formats.in.BDReader

close(boolean) - Method in class loci.formats.in.BioRadReader

close(boolean) - Method in class loci.formats.in.BioRadSCNReader

close(boolean) - Method in class loci.formats.in.BrukerReader

close(boolean) - Method in class loci.formats.in.BurleighReader

close(boolean) - Method in class loci.formats.in.CanonRawReader

close(boolean) - Method in class loci.formats.in.CellomicsReader

close(boolean) - Method in class loci.formats.in.CellSensReader

close(boolean) - Method in class loci.formats.in.CellWorxReader

close(boolean) - Method in class loci.formats.in.ColumbusReader

close(boolean) - Method in class loci.formats.in.CV7000Reader

close(boolean) - Method in class loci.formats.in.DCIMGReader

close(boolean) - Method in class loci.formats.in.DeltavisionReader

close(boolean) - Method in class loci.formats.in.DNGReader

close(boolean) - Method in class loci.formats.in.FEIReader

close(boolean) - Method in class loci.formats.in.FEITiffReader

close(boolean) - Method in class loci.formats.in.FlexReader

close(boolean) - Method in class loci.formats.in.FluoviewReader

close(boolean) - Method in class loci.formats.in.FujiReader

close(boolean) - Method in class loci.formats.in.FV1000Reader

close(boolean) - Method in class loci.formats.in.GatanDM2Reader

close(boolean) - Method in class loci.formats.in.GatanReader

close(boolean) - Method in class loci.formats.in.HamamatsuVMSReader

close(boolean) - Method in class loci.formats.in.HitachiReader

close(boolean) - Method in class loci.formats.in.HRDGDFReader

close(boolean) - Method in class loci.formats.in.ImaconReader

close(boolean) - Method in class loci.formats.in.ImagicReader

close(boolean) - Method in class loci.formats.in.ImarisHDFReader

close(boolean) - Method in class loci.formats.in.ImarisReader

close(boolean) - Method in class loci.formats.in.IMODReader

close(boolean) - Method in class loci.formats.in.ImprovisionTiffReader

close(boolean) - Method in class loci.formats.in.ImspectorReader

close(boolean) - Method in class loci.formats.in.InCell3000Reader

close(boolean) - Method in class loci.formats.in.InCellReader

close(boolean) - Method in class loci.formats.in.InveonReader

close(boolean) - Method in class loci.formats.in.IonpathMIBITiffReader

close(boolean) - Method in class loci.formats.in.IPLabReader

close(boolean) - Method in class loci.formats.in.IPWReader

close(boolean) - Method in class loci.formats.in.IvisionReader

close(boolean) - Method in class loci.formats.in.JDCEReader

close(boolean) - Method in class loci.formats.in.JEOLReader

close(boolean) - Method in class loci.formats.in.JPXReader

close(boolean) - Method in class loci.formats.in.KhorosReader

close(boolean) - Method in class loci.formats.in.KodakReader

close(boolean) - Method in class loci.formats.in.L2DReader

close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

close(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

close(boolean) - Method in class loci.formats.in.LeicaReader

close(boolean) - Method in class loci.formats.in.LeicaSCNReader

close(boolean) - Method in class loci.formats.in.LiFlimReader

close(boolean) - Method in class loci.formats.in.LIFReader

close(boolean) - Method in class loci.formats.in.LIMReader

close(boolean) - Method in class loci.formats.in.LOFReader

close(boolean) - Method in class loci.formats.in.MetamorphReader

close(boolean) - Method in class loci.formats.in.MetamorphTiffReader

close(boolean) - Method in class loci.formats.in.MIASReader

close(boolean) - Method in class loci.formats.in.MicroCTReader

close(boolean) - Method in class loci.formats.in.MINCReader

close(boolean) - Method in class loci.formats.in.MolecularImagingReader

close(boolean) - Method in class loci.formats.in.MRCReader

close(boolean) - Method in class loci.formats.in.MRWReader

close(boolean) - Method in class loci.formats.in.NAFReader

close(boolean) - Method in class loci.formats.in.ND2Reader

close(boolean) - Method in class loci.formats.in.NDPIReader

close(boolean) - Method in class loci.formats.in.NDPISReader

close(boolean) - Method in class loci.formats.in.NiftiReader

close(boolean) - Method in class loci.formats.in.NikonElementsTiffReader

close(boolean) - Method in class loci.formats.in.NikonReader

close(boolean) - Method in class loci.formats.in.NikonTiffReader

close(boolean) - Method in class loci.formats.in.OIRReader

close(boolean) - Method in class loci.formats.in.OlympusTileReader

close(boolean) - Method in class loci.formats.in.OpenlabRawReader

close(boolean) - Method in class loci.formats.in.OpenlabReader

close(boolean) - Method in class loci.formats.in.OperettaReader

close(boolean) - Method in class loci.formats.in.PCIReader

close(boolean) - Method in class loci.formats.in.PCORAWReader

close(boolean) - Method in class loci.formats.in.PDSReader

close(boolean) - Method in class loci.formats.in.PerkinElmerReader

close(boolean) - Method in class loci.formats.in.PhotoshopTiffReader

close(boolean) - Method in class loci.formats.in.PQBinReader

close(boolean) - Method in class loci.formats.in.PrairieReader

close(boolean) - Method in class loci.formats.in.PSDReader

close(boolean) - Method in class loci.formats.in.QuesantReader

close(boolean) - Method in class loci.formats.in.RHKReader

close(boolean) - Method in class loci.formats.in.SBIGReader

close(boolean) - Method in class loci.formats.in.ScanrReader

close(boolean) - Method in class loci.formats.in.SDTReader

close(boolean) - Method in class loci.formats.in.SEQReader

close(boolean) - Method in class loci.formats.in.SIFReader

close(boolean) - Method in class loci.formats.in.SimplePCITiffReader

close(boolean) - Method in class loci.formats.in.SISReader

close(boolean) - Method in class loci.formats.in.SlidebookReader

close(boolean) - Method in class loci.formats.in.SlidebookTiffReader

close(boolean) - Method in class loci.formats.in.SPCReader

close(boolean) - Method in class loci.formats.in.SPEReader

close(boolean) - Method in class loci.formats.in.SpiderReader

close(boolean) - Method in class loci.formats.in.SVSReader

close(boolean) - Method in class loci.formats.in.TargaReader

close(boolean) - Method in class loci.formats.in.TCSReader

close(boolean) - Method in class loci.formats.in.TecanReader

close(boolean) - Method in class loci.formats.in.TillVisionReader

close(boolean) - Method in class loci.formats.in.TissueFAXSReader

close(boolean) - Method in class loci.formats.in.TopometrixReader

close(boolean) - Method in class loci.formats.in.TrestleReader

close(boolean) - Method in class loci.formats.in.UBMReader

close(boolean) - Method in class loci.formats.in.UnisokuReader

close(boolean) - Method in class loci.formats.in.VarianFDFReader

close(boolean) - Method in class loci.formats.in.VectraReader

close(boolean) - Method in class loci.formats.in.VeecoReader

close(boolean) - Method in class loci.formats.in.VentanaReader

close(boolean) - Method in class loci.formats.in.VisitechReader

close(boolean) - Method in class loci.formats.in.VolocityClippingReader

close(boolean) - Method in class loci.formats.in.VolocityReader

close(boolean) - Method in class loci.formats.in.XLEFReader

close(boolean) - Method in class loci.formats.in.ZeissCZIReader

close(boolean) - Method in class loci.formats.in.ZeissLMSReader

close(boolean) - Method in class loci.formats.in.ZeissLSMReader

close(boolean) - Method in class loci.formats.in.ZeissTIFFReader

close(boolean) - Method in class loci.formats.in.ZeissXRMReader

close(boolean) - Method in class loci.formats.in.ZeissZVIReader

colCount - Variable in class loci.formats.in.BaseZeissReader

colT - Variable in class loci.formats.in.SDTInfo

ColumbusReader - Class in loci.formats.in

ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.

ColumbusReader() - Constructor for class loci.formats.in.ColumbusReader

Constructs a new Columbus reader.

compressed - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

COMPRESSION_GZIP - Static variable in class loci.formats.in.LiFlimReader

COMPRESSION_KEY - Static variable in class loci.formats.in.LiFlimReader

COMPRESSION_NONE - Static variable in class loci.formats.in.LiFlimReader

coordinates - Variable in class loci.formats.in.BaseZeissReader

coreMetaData - Static variable in class loci.formats.in.SPEReader

corrections - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

cortime - Variable in class loci.formats.in.SDTInfo

Correlation time [ms].

countImages() - Method in class loci.formats.in.BaseZeissReader

countImages() - Method in class loci.formats.in.ZeissTIFFReader

countImages() - Method in class loci.formats.in.ZeissZVIReader

create(Map<String, Object>) - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider

createChannelDimension(int, long) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

crossChan - Variable in class loci.formats.in.SDTInfo

Cross FCS routing channel number when chan = crossChan and mod == crossMod - Auto FCS otherwise - Cross FCS.

crossMod - Variable in class loci.formats.in.SDTInfo

Cross FCS module number.

crossMtResol - Variable in class loci.formats.in.SDTInfo

Macro time clock of cross FCS module in 0.1 ns units.

CSV_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

curCycle - Variable in class loci.formats.in.SDTInfo

Current cycle (accumulation cycle in FLOW mode) - (if multi-cycle measurement).

curPage - Variable in class loci.formats.in.SDTInfo

Current measured page.

currentBlock - Variable in class loci.formats.in.PQBinReader

Block of time bins currently stored for faster loading.

currentBlock - Variable in class loci.formats.in.SDTReader

Block of time bins currently stored for faster loading.

currentPlane - Variable in class loci.formats.in.ZeissZVIReader

currentPlaneIndex - Variable in class loci.formats.in.ZeissZVIReader

curStep - Variable in class loci.formats.in.SDTInfo

Current step (if multi-step measurement).

cutIns - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

cutOuts - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

CV7000Reader - Class in loci.formats.in

CV7000Reader() - Constructor for class loci.formats.in.CV7000Reader

Constructs a new Yokogawa CV7000 reader.

cycles - Variable in class loci.formats.in.SDTInfo

Cycles (accumulation cycles in FLOW mode).

CYTELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader

D

DarkImage_KEY - Static variable in class loci.formats.in.LiFlimReader

DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For normal .sdt files (setup + data).

dataBlockLength - Variable in class loci.formats.in.SDTInfo

dataBlockOffs - Variable in class loci.formats.in.SDTInfo

Offset of the first data block.

dataOffs - Variable in class loci.formats.in.SDTInfo

Offset of the data block from the beginning of the file.

dataStore - Variable in class loci.formats.in.PQBinReader

dataStore - Variable in class loci.formats.in.SDTReader

dataType - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

DATATYPE_INT16 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_INT32 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_INT8 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_KEY - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_REAL32 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_REAL64 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_UINT12 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_UINT16 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_UINT32 - Static variable in class loci.formats.in.LiFlimReader

DATATYPE_UINT8 - Static variable in class loci.formats.in.LiFlimReader

date - Variable in class loci.formats.in.SDTInfo

Date of creation.

DATE_FORMAT - Static variable in class loci.formats.in.CellWorxReader

DATE_FORMAT - Static variable in class loci.formats.in.DeltavisionReader

Deprecated.

Use DeltavisionReader.DATE_FORMATS instead

DATE_FORMAT - Static variable in class loci.formats.in.FV1000Reader

DATE_FORMAT - Static variable in class loci.formats.in.GelReader

DATE_FORMAT - Static variable in class loci.formats.in.IvisionReader

DATE_FORMAT - Static variable in class loci.formats.in.L2DReader

DATE_FORMAT - Static variable in class loci.formats.in.PerkinElmerReader

DATE_FORMAT - Static variable in class loci.formats.in.TCSReader

DATE_FORMATS - Static variable in class loci.formats.in.DeltavisionReader

DATE_TIME_FORMAT - Static variable in class loci.formats.in.GelReader

DCIMGReader - Class in loci.formats.in

DCIMGReader reads Hamamatsu DCIMG files.

DCIMGReader() - Constructor for class loci.formats.in.DCIMGReader

deadTimeComp - Variable in class loci.formats.in.SDTInfo

decode(byte[]) - Method in class loci.formats.filter.LZ4Filter

decodeDate(int) - Static method in class loci.formats.in.MetamorphReader

Converts a Julian date value into a human-readable string.

decodeTime(int) - Static method in class loci.formats.in.MetamorphReader

Converts a time value in milliseconds into a human-readable string.

DeltavisionReader - Class in loci.formats.in

DeltavisionReader is the file format reader for Deltavision files.

DeltavisionReader() - Constructor for class loci.formats.in.DeltavisionReader

Constructs a new Deltavision reader.

description() - Method in interface loci.formats.in.PrairieMetadata.Value

description() - Method in class loci.formats.in.PrairieMetadata.ValueItem

description() - Method in class loci.formats.in.PrairieMetadata.ValueTable

descriptions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

detectorGain - Variable in class loci.formats.in.BaseZeissReader

detectorIndexes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

detectorModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

detectorOffset - Variable in class loci.formats.in.BaseZeissReader

detectorOffsets - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

detType - Variable in class loci.formats.in.SDTInfo

Detector type (SPC-930 in camera mode).

Dimension - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class represents image dimensions extracted from LMS image xmls.

Dimension(Dimension.DimensionKey, int, long, String, Double, boolean) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

Dimension.DimensionKey - Enum in loci.formats.in.LeicaMicrosystemsMetadata

dir - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

directoryList - Variable in class loci.formats.in.CellWorxReader

dither - Variable in class loci.formats.in.SDTInfo

DLL_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created using DLL function SPC_save_data_to_sdtfile (no setup, only data).

DM3_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader

DM4_MAGIC_BYTES - Static variable in class loci.formats.in.GatanReader

DNGReader - Class in loci.formats.in

DNGReader is the file format reader for Canon DNG (TIFF) files.

DNGReader() - Constructor for class loci.formats.in.DNGReader

Constructs a new DNG reader.

doc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

doChannels - Variable in class loci.formats.in.CellWorxReader

DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.CV7000Reader

DUPLICATE_PLANES_DEFAULT - Static variable in class loci.formats.in.InCellReader

DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.CV7000Reader

DUPLICATE_PLANES_KEY - Static variable in class loci.formats.in.InCellReader

duplicatePlanes() - Method in class loci.formats.in.CV7000Reader

duplicatePlanes() - Method in class loci.formats.in.InCellReader

DV_MAGIC_BYTES_1 - Static variable in class loci.formats.in.DeltavisionReader

DV_MAGIC_BYTES_2 - Static variable in class loci.formats.in.DeltavisionReader

E

ealDE - Variable in class loci.formats.in.SDTInfo

ECAT7_MAGIC - Static variable in class loci.formats.in.Ecat7Reader

ECAT7_MAGIC_REGEX - Static variable in class loci.formats.in.Ecat7Reader

Ecat7Reader - Class in loci.formats.in

Ecat7Reader is the file format reader for ECAT 7 files.

Ecat7Reader() - Constructor for class loci.formats.in.Ecat7Reader

Constructs a new ECAT7 reader.

emWavelength - Variable in class loci.formats.in.BaseZeissReader

encode(byte[]) - Method in class loci.formats.filter.LZ4Filter

endDocument() - Method in class loci.formats.in.ND2Handler

endElement(String, String, String) - Method in class loci.formats.in.FlexReader.FlexHandler

endElement(String, String, String) - Method in class loci.formats.in.LeicaHandler

endElement(String, String, String) - Method in class loci.formats.in.ZeissTIFFHandler

endElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler

endTime - Variable in class loci.formats.in.SDTInfo

Macro time of the last photon.

ENV_SUFFIX - Static variable in class loci.formats.in.PrairieReader

epxDiv - Variable in class loci.formats.in.SDTInfo

evalFile(String) - Method in class loci.formats.in.ZeissTIFFReader

Evaluate the metadata of a TIFF/XML file collection, and return this to the user.

exposureTime - Variable in class loci.formats.in.BaseZeissReader

expTimes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

extHdrFields - Variable in class loci.formats.in.DeltavisionReader

Initialize an array of Extended Header Field structures.

exWavelength - Variable in class loci.formats.in.BaseZeissReader

exWaves - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

F

F_KEY - Static variable in class loci.formats.in.LiFlimReader

FAIL_ON_MISSING_DEFAULT - Static variable in class loci.formats.in.CellSensReader

FAIL_ON_MISSING_KEY - Static variable in class loci.formats.in.CellSensReader

failOnMissingETS() - Method in class loci.formats.in.CellSensReader

FCS_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created in FIFO mode (setup, data blocks = Decay, FCS, FIDA, FILDA & MCS curves for each used routing channel).

fcsDecayCalc - Variable in class loci.formats.in.SDTInfo

Bit 0 = 1 - decay curve calculated.

fcsPoints - Variable in class loci.formats.in.SDTInfo

No of FCS values.

fcsType - Variable in class loci.formats.in.SDTInfo

0 - linear FCS with log binning (100 bins/log) when bit 15 = 1 (0x8000) - Multi-Tau FCS where bits 14-0 = ktau parameter.

FEI_MAGIC_STRING - Static variable in class loci.formats.in.FEIReader

FEIReader - Class in loci.formats.in

FEIReader is the file format reader for FEI and Philips .img files.

FEIReader() - Constructor for class loci.formats.in.FEIReader

Constructs a new FEI reader.

FEITiffReader - Class in loci.formats.in

FEITiffReader is the file format reader for TIFF files produced by various FEI software.

FEITiffReader() - Constructor for class loci.formats.in.FEITiffReader

fidaPoints - Variable in class loci.formats.in.SDTInfo

No of FIDA values.

fidaTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for FIDA histogram.

fieldCount - Variable in class loci.formats.in.CellWorxReader

fieldPosX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

fieldPosY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

fifoTyp - Variable in class loci.formats.in.SDTInfo

fildaPoints - Variable in class loci.formats.in.SDTInfo

No of FILDA values.

fildaTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for FILDA histogram.

fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

Checks if file at path exists

fileExists(String) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Checks if file at path exists and corrects paths to be case sensitive

fileGroupOption(String) - Method in class loci.formats.in.AFIReader

fileGroupOption(String) - Method in class loci.formats.in.AnalyzeReader

fileGroupOption(String) - Method in class loci.formats.in.APLReader

fileGroupOption(String) - Method in class loci.formats.in.BDReader

fileGroupOption(String) - Method in class loci.formats.in.BioRadReader

fileGroupOption(String) - Method in class loci.formats.in.BrukerReader

fileGroupOption(String) - Method in class loci.formats.in.CellomicsReader

fileGroupOption(String) - Method in class loci.formats.in.CellSensReader

fileGroupOption(String) - Method in class loci.formats.in.CellVoyagerReader

fileGroupOption(String) - Method in class loci.formats.in.CellWorxReader

fileGroupOption(String) - Method in class loci.formats.in.ColumbusReader

fileGroupOption(String) - Method in class loci.formats.in.CV7000Reader

fileGroupOption(String) - Method in class loci.formats.in.DCIMGReader

fileGroupOption(String) - Method in class loci.formats.in.FlexReader

fileGroupOption(String) - Method in class loci.formats.in.FujiReader

fileGroupOption(String) - Method in class loci.formats.in.FV1000Reader

fileGroupOption(String) - Method in class loci.formats.in.HitachiReader

fileGroupOption(String) - Method in class loci.formats.in.ImagicReader

fileGroupOption(String) - Method in class loci.formats.in.InCellReader

fileGroupOption(String) - Method in class loci.formats.in.JDCEReader

fileGroupOption(String) - Method in class loci.formats.in.L2DReader

fileGroupOption(String) - Method in class loci.formats.in.LeicaReader

fileGroupOption(String) - Method in class loci.formats.in.MetamorphReader

fileGroupOption(String) - Method in class loci.formats.in.MIASReader

fileGroupOption(String) - Method in class loci.formats.in.MicroCTReader

fileGroupOption(String) - Method in class loci.formats.in.NDPIReader

fileGroupOption(String) - Method in class loci.formats.in.NDPISReader

fileGroupOption(String) - Method in class loci.formats.in.NiftiReader

fileGroupOption(String) - Method in class loci.formats.in.OIRReader

fileGroupOption(String) - Method in class loci.formats.in.OlympusTileReader

fileGroupOption(String) - Method in class loci.formats.in.OperettaReader

fileGroupOption(String) - Method in class loci.formats.in.PerkinElmerReader

fileGroupOption(String) - Method in class loci.formats.in.PrairieReader

fileGroupOption(String) - Method in class loci.formats.in.ScanrReader

fileGroupOption(String) - Method in class loci.formats.in.SPCReader

fileGroupOption(String) - Method in class loci.formats.in.SVSReader

fileGroupOption(String) - Method in class loci.formats.in.TCSReader

fileGroupOption(String) - Method in class loci.formats.in.TecanReader

fileGroupOption(String) - Method in class loci.formats.in.TillVisionReader

fileGroupOption(String) - Method in class loci.formats.in.TrestleReader

fileGroupOption(String) - Method in class loci.formats.in.VentanaReader

fileGroupOption(String) - Method in class loci.formats.in.VisitechReader

fileGroupOption(String) - Method in class loci.formats.in.XLEFReader

fileGroupOption(String) - Method in class loci.formats.in.ZeissLSMReader

fileGroupOption(String) - Method in class loci.formats.in.ZeissTIFFReader

filepath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

FILEPATH - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom

files - Variable in class loci.formats.in.LeicaReader

Array of image file names.

files - Variable in class loci.formats.in.PerkinElmerReader

List of files to open.

files - Variable in class loci.formats.in.ZeissZVIReader

fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader

fillMetadataPass1(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader

fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass2(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader

fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass3(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader

fillMetadataPass4(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissTIFFReader

fillMetadataPass5(MetadataStore) - Method in class loci.formats.in.ZeissZVIReader

fillMetadataPass6(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Read and store basic dimensions in model

fillMetadataPass7(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Store basic dimensions in model

filterModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

findPixelsFiles() - Method in class loci.formats.in.CellWorxReader

findPixelsFiles() - Method in class loci.formats.in.MetaxpressTiffReader

flags - Variable in class loci.formats.in.SDTInfo

Scan clocks bits 2-0 (frame, line, pixel), rates_read - bit 15.

flbckX - Variable in class loci.formats.in.SDTInfo

flbckY - Variable in class loci.formats.in.SDTInfo

FLEX - Static variable in class loci.formats.in.FlexReader

Custom IFD entry for Flex XML.

FLEX_SUFFIX - Static variable in class loci.formats.in.FlexReader

FlexHandler(List<String>, List<String>, MetadataStore, boolean, int, int) - Constructor for class loci.formats.in.FlexReader.FlexHandler

FlexReader - Class in loci.formats.in

FlexReader is a file format reader for Evotec Flex files.

FlexReader() - Constructor for class loci.formats.in.FlexReader

Constructs a new Flex reader.

FlexReader.FlexHandler - Class in loci.formats.in

SAX handler for parsing XML.

FlexReader.MeaHandler - Class in loci.formats.in

SAX handler for parsing XML from .mea files.

FlexReader.ResHandler - Class in loci.formats.in

SAX handler for parsing XML from .res files.

flipX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

flipY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

FLOAT - Static variable in class loci.formats.in.SPEReader

FLOW_DATA_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .sdt files created automatically in Continuous Flow mode measurement (no setup, only data).

FluoviewReader - Class in loci.formats.in

FluoviewReader is the file format reader for Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.

FluoviewReader() - Constructor for class loci.formats.in.FluoviewReader

Constructs a new Fluoview TIFF reader.

FORMATS - Static variable in class loci.formats.in.GelReader

foundHTDFile(String) - Method in class loci.formats.in.CellWorxReader

Frame(PrairieMetadata.Sequence, Element) - Constructor for class loci.formats.in.PrairieMetadata.Frame

Creates a new frame by parsing the given <Frame> element.

frameIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

FujiReader - Class in loci.formats.in

FujiReader is the file format reader for Fuji LAS 3000 datasets.

FujiReader() - Constructor for class loci.formats.in.FujiReader

Constructs a new Fuji reader.

FV1000_MAGIC_STRING_1 - Static variable in class loci.formats.in.FV1000Reader

FV1000_MAGIC_STRING_2 - Static variable in class loci.formats.in.FV1000Reader

FV1000_SUFFIXES - Static variable in class loci.formats.in.FV1000Reader

FV1000Reader - Class in loci.formats.in

FV1000Reader is the file format reader for Fluoview FV 1000 OIB and Fluoview FV 1000 OIF files.

FV1000Reader() - Constructor for class loci.formats.in.FV1000Reader

Constructs a new FV1000 reader.

G

gains - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

GatanDM2Reader - Class in loci.formats.in

GatanDM2Reader is the file format reader for Gatan .dm2 files.

GatanDM2Reader() - Constructor for class loci.formats.in.GatanDM2Reader

Constructs a new Gatan .dm2 reader.

GatanReader - Class in loci.formats.in

GatanReader is the file format reader for Gatan files.

GatanReader() - Constructor for class loci.formats.in.GatanReader

Constructs a new Gatan reader.

GelReader - Class in loci.formats.in

GelReader is the file format reader for Molecular Dynamics GEL TIFF files.

GelReader() - Constructor for class loci.formats.in.GelReader

Constructs a new GEL reader.

get(int) - Method in interface loci.formats.in.PrairieMetadata.Value

get(int) - Method in class loci.formats.in.PrairieMetadata.ValueItem

get(int) - Method in class loci.formats.in.PrairieMetadata.ValueTable

get(Object) - Method in interface loci.formats.in.PrairieMetadata.Value

get(Object) - Method in class loci.formats.in.PrairieMetadata.ValueItem

get16BitLookupTable() - Method in class loci.formats.in.BaseZeissReader

get16BitLookupTable() - Method in class loci.formats.in.FV1000Reader

get16BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader

get16BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader

get16BitLookupTable() - Method in class loci.formats.in.InCellReader

get16BitLookupTable() - Method in class loci.formats.in.JPXReader

get16BitLookupTable() - Method in class loci.formats.in.LeicaReader

get16BitLookupTable() - Method in class loci.formats.in.LIFReader

get16BitLookupTable() - Method in class loci.formats.in.LOFReader

get16BitLookupTable() - Method in class loci.formats.in.MIASReader

get16BitLookupTable() - Method in class loci.formats.in.ND2Reader

get16BitLookupTable() - Method in class loci.formats.in.OIRReader

get16BitLookupTable() - Method in class loci.formats.in.PDSReader

get16BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader

get16BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader

get16BitLookupTable() - Method in class loci.formats.in.TCSReader

get16BitLookupTable() - Method in class loci.formats.in.VentanaReader

get16BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader

get16BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader

get8BitLookupTable() - Method in class loci.formats.in.AmiraReader

get8BitLookupTable() - Method in class loci.formats.in.BaseZeissReader

get8BitLookupTable() - Method in class loci.formats.in.BioRadReader

get8BitLookupTable() - Method in class loci.formats.in.ImarisHDFReader

get8BitLookupTable() - Method in class loci.formats.in.ImprovisionTiffReader

get8BitLookupTable() - Method in class loci.formats.in.InCellReader

get8BitLookupTable() - Method in class loci.formats.in.IPWReader

get8BitLookupTable() - Method in class loci.formats.in.JPXReader

get8BitLookupTable() - Method in class loci.formats.in.KhorosReader

get8BitLookupTable() - Method in class loci.formats.in.LeicaReader

get8BitLookupTable() - Method in class loci.formats.in.LIFReader

get8BitLookupTable() - Method in class loci.formats.in.LOFReader

get8BitLookupTable() - Method in class loci.formats.in.MIASReader

get8BitLookupTable() - Method in class loci.formats.in.ND2Reader

get8BitLookupTable() - Method in class loci.formats.in.OIRReader

get8BitLookupTable() - Method in class loci.formats.in.OpenlabReader

get8BitLookupTable() - Method in class loci.formats.in.PerkinElmerReader

get8BitLookupTable() - Method in class loci.formats.in.PSDReader

get8BitLookupTable() - Method in class loci.formats.in.SlidebookTiffReader

get8BitLookupTable() - Method in class loci.formats.in.TargaReader

get8BitLookupTable() - Method in class loci.formats.in.TCSReader

get8BitLookupTable() - Method in class loci.formats.in.VentanaReader

get8BitLookupTable() - Method in class loci.formats.in.ZeissCZIReader

get8BitLookupTable() - Method in class loci.formats.in.ZeissLMSReader

get8BitLookupTable() - Method in class loci.formats.in.ZeissLSMReader

getAbsoluteTime() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the absoluteTime associated with this Frame.

getAcquisitionMode(String) - Method in class loci.formats.in.OperettaReader

Deprecated.

getActiveChannels() - Method in class loci.formats.in.PrairieMetadata

Gets the list of active channel indices, in sorted order.

getArray(String, int[], int[]) - Method in interface loci.formats.services.NetCDFService

Retrieves an HDF path's values.

getArray(String, int[], int[]) - Method in class loci.formats.services.NetCDFServiceImpl

getAttr(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Returns the value of an attribute of a node, if existing

getAttributeList() - Method in interface loci.formats.services.NetCDFService

Retrieves an exhaustive list of the HDF paths for all attributes in the HDF document.

getAttributeList() - Method in class loci.formats.services.NetCDFServiceImpl

getAttributeValue(String) - Method in interface loci.formats.services.NetCDFService

Retrieves an attribute's value.

getAttributeValue(String) - Method in class loci.formats.services.NetCDFServiceImpl

getAvailableOptions() - Method in class loci.formats.in.CellSensReader

getAvailableOptions() - Method in class loci.formats.in.CV7000Reader

getAvailableOptions() - Method in class loci.formats.in.GatanReader

getAvailableOptions() - Method in class loci.formats.in.InCellReader

getAvailableOptions() - Method in class loci.formats.in.LIFReader

getAvailableOptions() - Method in class loci.formats.in.ND2Reader

getAvailableOptions() - Method in class loci.formats.in.ScanrReader

getAvailableOptions() - Method in class loci.formats.in.SVSReader

getAvailableOptions() - Method in class loci.formats.in.VentanaReader

getAvailableOptions() - Method in class loci.formats.in.ZeissCZIReader

getBinning() - Method in class loci.formats.in.MetamorphHandler

getBinnings() - Method in class loci.formats.in.ND2Handler

getBitDepth() - Method in class loci.formats.in.PrairieMetadata

Gets the bitDepth recorded in the configuration.

getBitsPerPixel() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

getCameraModel() - Method in class loci.formats.in.ND2Handler

getCategory() - Method in class loci.formats.in.BaseZeissReader.Tag

getChannel() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the channel associated with this File.

getChannelColors() - Method in class loci.formats.in.ND2Handler

getChannelCount() - Method in class loci.formats.in.SDTReader

Gets the number of spectral channels.

getChannelIndex(Element) - Static method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

getChannelName() - Method in class loci.formats.in.MetamorphHandler

getChannelName() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the channelName associated with this File.

getChannelNames() - Method in class loci.formats.in.MetamorphHandler

getChannelNames() - Method in class loci.formats.in.ND2Handler

getChildrenFiles(boolean) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument

Returns filepaths of all files which are referenced by this document.

GetChildWithName(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

getColumNames(int) - Method in interface loci.formats.services.MetakitService

getColumNames(int) - Method in class loci.formats.services.MetakitServiceImpl

getColumnNames(String) - Method in interface loci.formats.services.MetakitService

getColumnNames(String) - Method in class loci.formats.services.MetakitServiceImpl

getColumnTypes(int) - Method in interface loci.formats.services.MetakitService

getColumnTypes(int) - Method in class loci.formats.services.MetakitServiceImpl

getColumnTypes(String) - Method in interface loci.formats.services.MetakitService

getColumnTypes(String) - Method in class loci.formats.services.MetakitServiceImpl

getConfig() - Method in class loci.formats.in.PrairieMetadata

Gets the map of configuration key/value pairs.

getConfig(String) - Method in class loci.formats.in.PrairieMetadata

Gets the value of the given configuration key.

getCore() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

getCoreMetadataList() - Method in class loci.formats.in.LeicaHandler

getCoreMetadataList() - Method in class loci.formats.in.ND2Handler

getCorrection() - Method in class loci.formats.in.ND2Handler

getCycle() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the cycle associated with this Sequence.

getCycleCount() - Method in class loci.formats.in.PrairieMetadata

Gets the number of recorded cycles.

getCycleMax() - Method in class loci.formats.in.PrairieMetadata

Gets the maximum cycle value.

getCycleMin() - Method in class loci.formats.in.PrairieMetadata

Gets the minimum cycle value.

getDate() - Method in class loci.formats.in.MetamorphHandler

getDate() - Method in class loci.formats.in.ND2Handler

getDate() - Method in class loci.formats.in.PrairieMetadata

Gets the date of the acquisition.

getDatestamp() - Method in class loci.formats.in.SVSReader

getDeltaT() - Method in class loci.formats.in.LeicaHandler

getDimension(int, Dimension.DimensionKey) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

getDimension(String) - Method in interface loci.formats.services.NetCDFService

Retrieves the length of a dimension.

getDimension(String) - Method in class loci.formats.services.NetCDFServiceImpl

getDimensionOrder(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Returns the dimension order as a string

getDimensions(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

getDisplayColor() - Method in class loci.formats.in.SVSReader

getDoc() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

getDocumentBytes(String) - Method in interface loci.formats.services.POIService

Retrieve all of the raw bytes that correspond to the given file name.

getDocumentBytes(String) - Method in class loci.formats.services.POIServiceImpl

getDocumentBytes(String, int) - Method in interface loci.formats.services.POIService

Retrieve at most 'length' bytes that correspond to the given file name.

getDocumentBytes(String, int) - Method in class loci.formats.services.POIServiceImpl

getDocumentList() - Method in interface loci.formats.services.POIService

Retrieve a list of all files in the current POI file system.

getDocumentList() - Method in class loci.formats.services.POIServiceImpl

getDocumentStream(String) - Method in interface loci.formats.services.POIService

Retrieve a RandomAccessInputStream corresponding to the given file name.

getDocumentStream(String) - Method in class loci.formats.services.POIServiceImpl

getDomains() - Method in class loci.formats.in.CellomicsReader

getDomains() - Method in class loci.formats.in.MetamorphReader

getDomains() - Method in class loci.formats.in.MetamorphTiffReader

getDomains() - Method in class loci.formats.in.NiftiReader

getDyeNames() - Method in class loci.formats.in.SVSReader

getElementNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getEmission() - Method in class loci.formats.in.SVSReader

getEmissionWavelengths() - Method in class loci.formats.in.ND2Handler

getExcitation() - Method in class loci.formats.in.SVSReader

getExcitationWavelengths() - Method in class loci.formats.in.ND2Handler

getExposures() - Method in class loci.formats.in.MetamorphHandler

getExposureTime() - Method in class loci.formats.in.SVSReader

getExposureTimes() - Method in class loci.formats.in.LeicaHandler

getExposureTimes() - Method in class loci.formats.in.ND2Handler

getFieldIndex() - Method in class loci.formats.in.ND2Handler

getFile() - Method in interface loci.formats.services.NetCDFService

Retrieves the current initialized file path.

getFile() - Method in class loci.formats.services.NetCDFServiceImpl

getFile(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the File with the given channel.

getFile(int, int) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the Frame at the given (cycle, index, channel).

getFile(int, int, int) - Method in class loci.formats.in.PrairieMetadata

Gets the Frame at the given (cycle, index, channel).

getFilename() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the filename associated with this File.

getFilepath() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

getFileSize(String) - Method in interface loci.formats.services.POIService

Retrieve the total number of bytes in the given file.

getFileSize(String) - Method in class loci.formats.services.POIServiceImpl

getFillColor() - Method in class loci.formats.in.ZeissCZIReader

getFirstFile() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the first File of the Sequence.

getFirstFrame() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the first Frame of the Sequence.

getFirstSequence() - Method in class loci.formats.in.PrairieMetadata

Gets the first Sequence.

getFlexFiles() - Method in class loci.formats.in.FlexReader.MeaHandler

getFrame() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the <Frame> containing this <File>.

getFrame(int) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the Frame with the given index.

getFrame(int, int) - Method in class loci.formats.in.PrairieMetadata

Gets the Frame at the given (cycle and index).

getGain() - Method in class loci.formats.in.MetamorphHandler

getGain(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the cth gain for this Frame.

getGains() - Method in class loci.formats.in.ND2Handler

getGlobalMetadata() - Method in class loci.formats.in.LeicaHandler

getId() - Method in class loci.formats.filter.LZ4Filter

getId() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider

getIFD(int) - Method in class loci.formats.in.SVSReader

Get the IFD corresponding to the given plane in the current series.

getImageCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument

Returns number of images which are referenced by xlifs

getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

Returns the file format in which actual image bytes are stored

getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

getImageFormat() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getImageFormat() - Method in class loci.formats.in.LOFReader

getImageFormat() - Method in class loci.formats.in.XLEFReader

getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument

Returns the name of the image (it might be contained in the XML or otherwise e.g.

getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument

getImageName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getImageName() - Method in class loci.formats.in.MetamorphHandler

getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument

Returns the image node of the xml document which contains image metadata

getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument

getImageNode() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getImagePaths() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getImagingDevice() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the imaging device associated with this Frame.

getImmersion() - Method in class loci.formats.in.ND2Handler

getImmersion() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the immersion from the objective lens string.

getIndex() - Method in class loci.formats.in.BaseZeissReader.Tag

getIndex() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the index associated with this Frame.

getIndexCount() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the number of recorded indices at this Sequence.

getIndexMax() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the maximum index value.

getIndexMin() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the minimum index value.

getInfo() - Method in class loci.formats.in.SDTReader

Gets object containing SDT header information.

getInputStream(String) - Method in interface loci.formats.services.POIService

Retrieve an InputStream corresponding to the given file name.

getInputStream(String) - Method in class loci.formats.services.POIServiceImpl

getKey() - Method in class loci.formats.in.BaseZeissReader.Tag

getKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag

Return the string corresponding to the given ID.

getKeyID() - Method in class loci.formats.in.BaseZeissReader.Tag

getLaserPower() - Method in class loci.formats.in.PrairieMetadata

Gets the first laserPower recorded in the configuration.

getLength() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

getLensNA() - Method in class loci.formats.in.MetamorphHandler

getLensRI() - Method in class loci.formats.in.MetamorphHandler

getLinesPerFrame() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the lines per frame for this Frame.

getLutNames() - Method in class loci.formats.in.LeicaHandler

getMagnification() - Method in class loci.formats.in.ND2Handler

getMagnification() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the magnification from the objective lens string.

getMagnification() - Method in class loci.formats.in.SVSReader

getMetadata() - Method in class loci.formats.in.ND2Handler

getMicronsPerPixelX() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the microns per pixel along X for this Frame.

getMicronsPerPixelY() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the microns per pixel along Y for this Frame.

getModalities() - Method in class loci.formats.in.ND2Handler

getName() - Method in class loci.formats.filter.LZ4Filter

getName() - Method in class loci.formats.filter.LZ4Filter.LZ4FilterProvider

getName() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

getNativeDataType() - Method in class loci.formats.TileStitcher

getNumericalAperture() - Method in class loci.formats.in.ND2Handler

getObjectiveLens() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the objective lens string for this Frame.

getObjectiveLensNA() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the numerical aperture of the lens for this Frame.

getObjectiveManufacturer() - Method in class loci.formats.in.PrairieMetadata.Frame

Extracts the objective manufacturer from the objective lens string.

getObjectiveModel() - Method in class loci.formats.in.ND2Handler

getOffset(int) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the cth offset for this Frame.

getOffsets() - Method in class loci.formats.in.ND2Reader

getOpticalZoom() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the optical zoom associated with this Frame.

getOptimalTileHeight() - Method in class loci.formats.in.AFIReader

getOptimalTileHeight() - Method in class loci.formats.in.AmiraReader

getOptimalTileHeight() - Method in class loci.formats.in.APLReader

getOptimalTileHeight() - Method in class loci.formats.in.BaseZeissReader

getOptimalTileHeight() - Method in class loci.formats.in.BDReader

getOptimalTileHeight() - Method in class loci.formats.in.BioRadReader

getOptimalTileHeight() - Method in class loci.formats.in.CellSensReader

getOptimalTileHeight() - Method in class loci.formats.in.FlexReader

getOptimalTileHeight() - Method in class loci.formats.in.FV1000Reader

getOptimalTileHeight() - Method in class loci.formats.in.HamamatsuVMSReader

getOptimalTileHeight() - Method in class loci.formats.in.ImarisHDFReader

getOptimalTileHeight() - Method in class loci.formats.in.InCellReader

getOptimalTileHeight() - Method in class loci.formats.in.IPWReader

getOptimalTileHeight() - Method in class loci.formats.in.JDCEReader

getOptimalTileHeight() - Method in class loci.formats.in.L2DReader

getOptimalTileHeight() - Method in class loci.formats.in.LeicaReader

getOptimalTileHeight() - Method in class loci.formats.in.LeicaSCNReader

getOptimalTileHeight() - Method in class loci.formats.in.LIFReader

getOptimalTileHeight() - Method in class loci.formats.in.LOFReader

getOptimalTileHeight() - Method in class loci.formats.in.MIASReader

getOptimalTileHeight() - Method in class loci.formats.in.NDPIReader

getOptimalTileHeight() - Method in class loci.formats.in.NDPISReader

getOptimalTileHeight() - Method in class loci.formats.in.OIRReader

getOptimalTileHeight() - Method in class loci.formats.in.OlympusTileReader

getOptimalTileHeight() - Method in class loci.formats.in.OpenlabReader

getOptimalTileHeight() - Method in class loci.formats.in.PCIReader

getOptimalTileHeight() - Method in class loci.formats.in.PerkinElmerReader

getOptimalTileHeight() - Method in class loci.formats.in.PrairieReader

getOptimalTileHeight() - Method in class loci.formats.in.PyramidTiffReader

getOptimalTileHeight() - Method in class loci.formats.in.ScanrReader

getOptimalTileHeight() - Method in class loci.formats.in.SVSReader

getOptimalTileHeight() - Method in class loci.formats.in.TissueFAXSReader

getOptimalTileHeight() - Method in class loci.formats.in.TrestleReader

getOptimalTileHeight() - Method in class loci.formats.in.VectraReader

getOptimalTileHeight() - Method in class loci.formats.in.VentanaReader

getOptimalTileHeight() - Method in class loci.formats.in.VisitechReader

getOptimalTileHeight() - Method in class loci.formats.in.ZeissCZIReader

getOptimalTileHeight() - Method in class loci.formats.in.ZeissLSMReader

getOptimalTileWidth() - Method in class loci.formats.in.AFIReader

getOptimalTileWidth() - Method in class loci.formats.in.APLReader

getOptimalTileWidth() - Method in class loci.formats.in.BDReader

getOptimalTileWidth() - Method in class loci.formats.in.CellSensReader

getOptimalTileWidth() - Method in class loci.formats.in.FlexReader

getOptimalTileWidth() - Method in class loci.formats.in.FV1000Reader

getOptimalTileWidth() - Method in class loci.formats.in.HamamatsuVMSReader

getOptimalTileWidth() - Method in class loci.formats.in.ImarisHDFReader

getOptimalTileWidth() - Method in class loci.formats.in.InCellReader

getOptimalTileWidth() - Method in class loci.formats.in.IPWReader

getOptimalTileWidth() - Method in class loci.formats.in.JDCEReader

getOptimalTileWidth() - Method in class loci.formats.in.L2DReader

getOptimalTileWidth() - Method in class loci.formats.in.LeicaReader

getOptimalTileWidth() - Method in class loci.formats.in.LeicaSCNReader

getOptimalTileWidth() - Method in class loci.formats.in.MIASReader

getOptimalTileWidth() - Method in class loci.formats.in.NDPIReader

getOptimalTileWidth() - Method in class loci.formats.in.NDPISReader

getOptimalTileWidth() - Method in class loci.formats.in.OIRReader

getOptimalTileWidth() - Method in class loci.formats.in.OlympusTileReader

getOptimalTileWidth() - Method in class loci.formats.in.PCIReader

getOptimalTileWidth() - Method in class loci.formats.in.PerkinElmerReader

getOptimalTileWidth() - Method in class loci.formats.in.PrairieReader

getOptimalTileWidth() - Method in class loci.formats.in.PyramidTiffReader

getOptimalTileWidth() - Method in class loci.formats.in.ScanrReader

getOptimalTileWidth() - Method in class loci.formats.in.SVSReader

getOptimalTileWidth() - Method in class loci.formats.in.TissueFAXSReader

getOptimalTileWidth() - Method in class loci.formats.in.TrestleReader

getOptimalTileWidth() - Method in class loci.formats.in.VectraReader

getOptimalTileWidth() - Method in class loci.formats.in.VentanaReader

getOptimalTileWidth() - Method in class loci.formats.in.ZeissCZIReader

getOptimalWidth() - Method in class loci.formats.in.ZeissLSMReader

getPacking(String) - Static method in class loci.formats.in.LIPixelFormat

getPage() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the page associated with this File.

getParentFiles() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Returns all files which directly or indirectly reference this LMS xml file.

getPhysicalSizes() - Method in class loci.formats.in.SVSReader

getPinholeSize() - Method in class loci.formats.in.ND2Handler

getPixelSizeX() - Method in class loci.formats.in.MetamorphHandler

getPixelSizeX() - Method in class loci.formats.in.ND2Handler

getPixelSizeY() - Method in class loci.formats.in.MetamorphHandler

getPixelSizeY() - Method in class loci.formats.in.ND2Handler

getPixelSizeZ() - Method in class loci.formats.in.ND2Handler

getPixelsPerLine() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the pixels per line for this Frame.

getPixelType() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

getPlaneByteOffset(int, int, int) - Method in class loci.formats.in.DeltavisionReader

Given any specific Z, W, and T of a plane, determine the absolute byte offset of the plane in the file.

getPlateName(String) - Method in class loci.formats.in.CellWorxReader

getPositionNames() - Method in class loci.formats.in.ND2Handler

getPositionX() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the X stage position associated with this Frame.

getPositionY() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the Y stage position associated with this Frame.

getPositionZ() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the Z stage position associated with this Frame.

getPowers() - Method in class loci.formats.in.ND2Handler

getPrefix(String) - Method in class loci.formats.in.ZeissTIFFReader

getPyramidHeight() - Method in class loci.formats.in.NDPIReader

getReader(String, boolean) - Method in class loci.formats.in.CellWorxReader

getReader(String, boolean) - Method in class loci.formats.in.MetaxpressTiffReader

getReadOutRate() - Method in class loci.formats.in.MetamorphHandler

getRefractiveIndex() - Method in class loci.formats.in.ND2Handler

getRelativeTime() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the relativeTime associated with this Frame.

getRequiredDirectories(String[]) - Method in class loci.formats.in.BrukerReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.CellVoyagerReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.ColumbusReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.CV7000Reader

getRequiredDirectories(String[]) - Method in class loci.formats.in.MIASReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.MicroCTReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.OperettaReader

getRequiredDirectories(String[]) - Method in class loci.formats.in.TecanReader

getRGBChannelCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

getROIs() - Method in class loci.formats.in.ND2Handler

getRowCount(int) - Method in interface loci.formats.services.MetakitService

getRowCount(int) - Method in class loci.formats.services.MetakitServiceImpl

getRowCount(String) - Method in interface loci.formats.services.MetakitService

getRowCount(String) - Method in class loci.formats.services.MetakitServiceImpl

getRowData(int, int) - Method in interface loci.formats.services.MetakitService

getRowData(int, int) - Method in class loci.formats.services.MetakitServiceImpl

getRowData(int, String) - Method in interface loci.formats.services.MetakitService

getRowData(int, String) - Method in class loci.formats.services.MetakitServiceImpl

getScanProfileXML() - Method in class loci.formats.in.VectraReader

Returns an XML string corresponding to the ScanProfile node.

getSequence() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the <Sequence> containing this <Frame>.

getSequence(int) - Method in class loci.formats.in.PrairieMetadata

Gets the Sequence at the given cycle.

getSequences() - Method in class loci.formats.in.PrairieMetadata

Gets all Sequences, ordered by cycle.

getSeriesCount() - Method in class loci.formats.in.ND2Handler

getSeriesCount() - Method in class loci.formats.TileStitcher

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AFIReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.AnalyzeReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.APLReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BDReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BioRadReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.BrukerReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellSensReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellVoyagerReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CellWorxReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ColumbusReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DCIMGReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.DeltavisionReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FlexReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FujiReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.FV1000Reader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HamamatsuVMSReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.HitachiReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImagicReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ImprovisionTiffReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.InCellReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JDCEReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.JEOLReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.L2DReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LeicaReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LIFReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.LOFReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetamorphReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MIASReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.MicroCTReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NDPISReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.NiftiReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OIRReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OlympusTileReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PCORAWReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PDSReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PerkinElmerReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.PrairieReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ScanrReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SEQReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SlidebookTiffReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.SPCReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TCSReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TecanReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TillVisionReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TissueFAXSReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.TrestleReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VarianFDFReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VectraReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VisitechReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.VolocityReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissCZIReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissLSMReader

getSeriesUsedFiles(boolean) - Method in class loci.formats.in.ZeissTIFFReader

getSizeC() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

getSizeX() - Method in class loci.formats.TileStitcher

getSizeY() - Method in class loci.formats.TileStitcher

getSpeeds() - Method in class loci.formats.in.ND2Handler

getStageLabel() - Method in class loci.formats.in.MetamorphHandler

getStagePositionX() - Method in class loci.formats.in.MetamorphHandler

getStagePositionY() - Method in class loci.formats.in.MetamorphHandler

getStageX() - Method in class loci.formats.in.MetamorphReader

getStageY() - Method in class loci.formats.in.MetamorphReader

getTableCount() - Method in interface loci.formats.services.MetakitService

getTableCount() - Method in class loci.formats.services.MetakitServiceImpl

getTableData(int) - Method in interface loci.formats.services.MetakitService

getTableData(int) - Method in class loci.formats.services.MetakitServiceImpl

getTableData(String) - Method in interface loci.formats.services.MetakitService

getTableData(String) - Method in class loci.formats.services.MetakitServiceImpl

getTableNames() - Method in interface loci.formats.services.MetakitService

getTableNames() - Method in class loci.formats.services.MetakitServiceImpl

getTemperature() - Method in class loci.formats.in.MetamorphHandler

getTemperatures() - Method in class loci.formats.in.ND2Handler

getThumbSizeX() - Method in class loci.formats.in.LeicaSCNReader

getThumbSizeX() - Method in class loci.formats.in.VentanaReader

getThumbSizeY() - Method in class loci.formats.in.LeicaSCNReader

getThumbSizeY() - Method in class loci.formats.in.VentanaReader

getTileCodec(int) - Method in class loci.formats.in.NDPIReader

getTileCodec(int) - Method in class loci.formats.in.SVSReader

getTileCodec(int) - Method in class loci.formats.TileStitcher

getTileCodecOptions(int, int, int) - Method in class loci.formats.in.NDPIReader

getTileCodecOptions(int, int, int) - Method in class loci.formats.in.SVSReader

getTileCodecOptions(int, int, int) - Method in class loci.formats.TileStitcher

getTileColumns(int) - Method in class loci.formats.in.NDPIReader

getTileColumns(int) - Method in class loci.formats.in.SVSReader

getTileColumns(int) - Method in class loci.formats.TileStitcher

getTileCount() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

Returns the number of tiles referenced by this xlif

getTileIndex(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

getTileRows(int) - Method in class loci.formats.in.NDPIReader

getTileRows(int) - Method in class loci.formats.in.SVSReader

getTileRows(int) - Method in class loci.formats.TileStitcher

getTimeBinCount() - Method in class loci.formats.in.SDTReader

Gets the number of bins in the lifetime histogram.

getTimepoints() - Method in class loci.formats.in.ND2Handler

getTimestamps() - Method in class loci.formats.in.MetamorphHandler

getType() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the type associated with this Sequence.

getUsedFiles(boolean) - Method in class loci.formats.in.CellomicsReader

getUsedFiles(boolean) - Method in class loci.formats.in.CV7000Reader

getUsedFiles(boolean) - Method in class loci.formats.in.InveonReader

getUsedFiles(boolean) - Method in class loci.formats.in.MetamorphTiffReader

getUsedFiles(boolean) - Method in class loci.formats.in.MetaxpressTiffReader

getUsedFiles(boolean) - Method in class loci.formats.in.OperettaReader

getUsedFiles(boolean) - Method in class loci.formats.in.TecanReader

getUsedFiles(boolean) - Method in class loci.formats.in.UnisokuReader

getUsedFiles(boolean) - Method in class loci.formats.in.XLEFReader

getValue() - Method in class loci.formats.in.BaseZeissReader.Tag

getValue(String) - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the value of the given key, beneath this Frame, inferring the value from the parent <Sequence> or grandparent <PVScan> section as needed.

getValue(String) - Method in class loci.formats.in.PrairieMetadata

Gets the value of the given key, at the top-level <PVScan> element.

getValue(String) - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the value of the given key, beneath this Sequence, inferring the value from the parent <PVScan> section as needed.

getValues() - Method in class loci.formats.in.PrairieMetadata.Frame

Gets the table of Frame key/value pairs.

getValues() - Method in class loci.formats.in.PrairieMetadata

Gets the table of PVScan key/value pairs.

getValues() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets the table of Frame key/value pairs.

getVariableAttributes(String) - Method in interface loci.formats.services.NetCDFService

Retrieves all of a variable's attributes.

getVariableAttributes(String) - Method in class loci.formats.services.NetCDFServiceImpl

getVariableList() - Method in interface loci.formats.services.NetCDFService

Retrieves an exhaustive list of the HDF paths for all variables in the HDF document.

getVariableList() - Method in class loci.formats.services.NetCDFServiceImpl

getVariableValue(String) - Method in interface loci.formats.services.NetCDFService

Retrieves a variable's value.

getVariableValue(String) - Method in class loci.formats.services.NetCDFServiceImpl

getVoltage() - Method in class loci.formats.in.ND2Handler

getWaitTime() - Method in class loci.formats.in.PrairieMetadata

Gets the waitTime recorded in the configuration.

getWavelengthMax() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the wavelengthMax associated with this File.

getWavelengthMin() - Method in class loci.formats.in.PrairieMetadata.PFile

Gets the wavelengthMin associated with this File.

getWavelengths() - Method in class loci.formats.in.MetamorphHandler

getWellColumn(int) - Method in class loci.formats.in.CellWorxReader

Retrieve the well column corresponding to the given series.

getWellRow(int) - Method in class loci.formats.in.CellWorxReader

Retrieve the well row corresponding to the given series.

getXFields() - Method in class loci.formats.in.ND2Handler

getXlifs() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument

Returns all XlifDocuments referenced by this and by all referenced XlcfDocuments

getXPositions() - Method in class loci.formats.in.ND2Handler

getYPositions() - Method in class loci.formats.in.ND2Handler

getZoom() - Method in class loci.formats.in.MetamorphHandler

getZPositions() - Method in class loci.formats.in.MetamorphHandler

getZPositions() - Method in class loci.formats.in.ND2Handler

getZSections() - Method in class loci.formats.in.ND2Handler

GREEN - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

H

HamamatsuVMSReader - Class in loci.formats.in

HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.

HamamatsuVMSReader() - Constructor for class loci.formats.in.HamamatsuVMSReader

Constructs a new Hamamatsu VMS reader.

hasDualCamera() - Method in class loci.formats.in.MetamorphHandler

hasExtendedMeasureInfo - Variable in class loci.formats.in.SDTInfo

hasMeasFCSInfo - Variable in class loci.formats.in.SDTInfo

hasMeasHISTInfo - Variable in class loci.formats.in.SDTInfo

hasMeasStopInfo - Variable in class loci.formats.in.SDTInfo

hasMeasureInfo - Variable in class loci.formats.in.SDTInfo

HDF_MAGIC_STRING - Static variable in class loci.formats.in.ImarisHDFReader

HEADER_MARKER - Static variable in class loci.formats.in.VisitechReader

HEADER_SIZE - Static variable in class loci.formats.in.PQBinReader

HEADER_SIZE - Static variable in class loci.formats.in.UBMReader

headerIFDs - Variable in class loci.formats.in.LeicaReader

Array of IFD-like structures containing metadata.

headerValid - Variable in class loci.formats.in.SDTInfo

height - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

height - Variable in class loci.formats.in.SDTInfo

HELIOS_TAG - Static variable in class loci.formats.in.FEITiffReader

HIS_MAGIC_STRING - Static variable in class loci.formats.in.HISReader

HISReader - Class in loci.formats.in

HISReader is the file format reader for Hamamatsu .his files.

HISReader() - Constructor for class loci.formats.in.HISReader

Constructs a new Hamamatsu .his reader.

HitachiReader - Class in loci.formats.in

HitachiReader is the file format reader for S-4800 files.

HitachiReader() - Constructor for class loci.formats.in.HitachiReader

Constructs a new Hitachi reader.

HRDGDFReader - Class in loci.formats.in

HRDGDFReader is the file format reader for the Gridded Data Format used by NOAA's Hurricane Research Division.

HRDGDFReader() - Constructor for class loci.formats.in.HRDGDFReader

Constructs a new Gridded Data Format reader.

HTM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

HTML_REGEX - Static variable in class loci.formats.in.PerkinElmerReader

HTML_SUFFIX - Static variable in class loci.formats.in.VisitechReader

I

I2IReader - Class in loci.formats.in

I2IReader is the file format reader for I2I files.

I2IReader() - Constructor for class loci.formats.in.I2IReader

Constructs a new I2I reader.

id - Variable in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

ifds - Variable in class loci.formats.in.LeicaReader

ImaconReader - Class in loci.formats.in

ImaconReader is the file format reader for Imacon .fff (TIFF) files.

ImaconReader() - Constructor for class loci.formats.in.ImaconReader

Constructs a new Imacon reader.

IMAGE_SOURCE_DATA - Static variable in class loci.formats.in.PhotoshopTiffReader

imageDescription - Variable in class loci.formats.in.BaseZeissReader

imageFiles - Variable in class loci.formats.in.BaseZeissReader

imageMetadataLVExists - Variable in class loci.formats.in.ND2Handler

imageNames - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

imageROIs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

imageRX - Variable in class loci.formats.in.SDTInfo

imageRY - Variable in class loci.formats.in.SDTInfo

imageX - Variable in class loci.formats.in.SDTInfo

4 subsequent fields valid only for Camera mode or FIFO_IMAGE mode.

imageY - Variable in class loci.formats.in.SDTInfo

ImagicReader - Class in loci.formats.in

ImagicReader is the file format reader for IMAGIC files.

ImagicReader() - Constructor for class loci.formats.in.ImagicReader

Constructs a new IMAGIC reader.

ImarisHDFReader - Class in loci.formats.in

Reader for Bitplane Imaris 5.5 (HDF) files.

ImarisHDFReader() - Constructor for class loci.formats.in.ImarisHDFReader

Constructs a new Imaris HDF reader.

ImarisReader - Class in loci.formats.in

ImarisReader is the file format reader for Bitplane Imaris files.

ImarisReader() - Constructor for class loci.formats.in.ImarisReader

Constructs a new Imaris reader.

ImarisTiffReader - Class in loci.formats.in

ImarisTiffReader is the file format reader for Bitplane Imaris 3 files (TIFF variant).

ImarisTiffReader() - Constructor for class loci.formats.in.ImarisTiffReader

Constructs a new Imaris TIFF reader.

immersions - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

IMODReader - Class in loci.formats.in

Reader for IMOD binary files.

IMODReader() - Constructor for class loci.formats.in.IMODReader

Constructs a new IMOD reader.

IMPROVISION_MAGIC_STRING - Static variable in class loci.formats.in.ImprovisionTiffReader

ImprovisionTiffReader - Class in loci.formats.in

ImprovisionTiffReader is the file format reader for Improvision TIFF files.

ImprovisionTiffReader() - Constructor for class loci.formats.in.ImprovisionTiffReader

ImspectorReader - Class in loci.formats.in

ImspectorReader is the file format reader for Imspector .msr files.

ImspectorReader() - Constructor for class loci.formats.in.ImspectorReader

Constructs a new Imspector reader.

INCELL_MAGIC_STRING - Static variable in class loci.formats.in.InCellReader

InCell3000Reader - Class in loci.formats.in

InCell3000Reader is the file format reader for InCell 3000.

InCell3000Reader() - Constructor for class loci.formats.in.InCell3000Reader

Constructs a new InCell 3000 reader.

InCellReader - Class in loci.formats.in

InCellReader is the file format reader for InCell 1000/2000 datasets.

InCellReader() - Constructor for class loci.formats.in.InCellReader

Constructs a new InCell 1000/2000 reader.

INCLUDE_ATTACHMENTS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader

INCLUDE_ATTACHMENTS_KEY - Static variable in class loci.formats.in.ZeissCZIReader

incr - Variable in class loci.formats.in.SDTInfo

info - Variable in class loci.formats.in.SDTInfo

info - Variable in class loci.formats.in.SDTReader

Object containing SDT header information.

INFO_TABLE - Static variable in class loci.formats.in.LiFlimReader

infoLength - Variable in class loci.formats.in.SDTInfo

Length of the info part.

infoOffs - Variable in class loci.formats.in.SDTInfo

Offset of the info part which contains general text information (Title, date, time, contents etc.).

initChildren() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument

Adds all referenced xlcfs and valid xlifs as children

initCoreMetadata(int, int) - Method in class loci.formats.in.LeicaSCNReader

initDetectorModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Adds detector and channel color details from the reader's MetadataTempBuffer to its MetadataStore

initExtraMetadata() - Method in class loci.formats.in.DeltavisionReader

initFile(String) - Method in class loci.formats.in.AFIReader

initFile(String) - Method in class loci.formats.in.AIMReader

initFile(String) - Method in class loci.formats.in.AliconaReader

initFile(String) - Method in class loci.formats.in.AmiraReader

initFile(String) - Method in class loci.formats.in.AnalyzeReader

initFile(String) - Method in class loci.formats.in.APLReader

initFile(String) - Method in class loci.formats.in.ARFReader

initFile(String) - Method in class loci.formats.in.BDReader

initFile(String) - Method in class loci.formats.in.BioRadGelReader

initFile(String) - Method in class loci.formats.in.BioRadReader

initFile(String) - Method in class loci.formats.in.BioRadSCNReader

initFile(String) - Method in class loci.formats.in.BrukerReader

initFile(String) - Method in class loci.formats.in.BurleighReader

initFile(String) - Method in class loci.formats.in.CanonRawReader

initFile(String) - Method in class loci.formats.in.CellomicsReader

initFile(String) - Method in class loci.formats.in.CellSensReader

initFile(String) - Method in class loci.formats.in.CellVoyagerReader

initFile(String) - Method in class loci.formats.in.CellWorxReader

initFile(String) - Method in class loci.formats.in.ColumbusReader

initFile(String) - Method in class loci.formats.in.CV7000Reader

initFile(String) - Method in class loci.formats.in.DCIMGReader

initFile(String) - Method in class loci.formats.in.DeltavisionReader

initFile(String) - Method in class loci.formats.in.DNGReader

initFile(String) - Method in class loci.formats.in.Ecat7Reader

initFile(String) - Method in class loci.formats.in.FEIReader

initFile(String) - Method in class loci.formats.in.FlexReader

initFile(String) - Method in class loci.formats.in.FujiReader

initFile(String) - Method in class loci.formats.in.FV1000Reader

initFile(String) - Method in class loci.formats.in.GatanDM2Reader

initFile(String) - Method in class loci.formats.in.GatanReader

initFile(String) - Method in class loci.formats.in.HamamatsuVMSReader

initFile(String) - Method in class loci.formats.in.HISReader

initFile(String) - Method in class loci.formats.in.HitachiReader

initFile(String) - Method in class loci.formats.in.HRDGDFReader

initFile(String) - Method in class loci.formats.in.I2IReader

initFile(String) - Method in class loci.formats.in.ImagicReader

initFile(String) - Method in class loci.formats.in.ImarisHDFReader

initFile(String) - Method in class loci.formats.in.ImarisReader

initFile(String) - Method in class loci.formats.in.ImarisTiffReader

initFile(String) - Method in class loci.formats.in.IMODReader

initFile(String) - Method in class loci.formats.in.ImspectorReader

initFile(String) - Method in class loci.formats.in.InCell3000Reader

initFile(String) - Method in class loci.formats.in.InCellReader

initFile(String) - Method in class loci.formats.in.INRReader

initFile(String) - Method in class loci.formats.in.InveonReader

initFile(String) - Method in class loci.formats.in.IPLabReader

initFile(String) - Method in class loci.formats.in.IPWReader

initFile(String) - Method in class loci.formats.in.IvisionReader

initFile(String) - Method in class loci.formats.in.JDCEReader

initFile(String) - Method in class loci.formats.in.JEOLReader

initFile(String) - Method in class loci.formats.in.JPXReader

initFile(String) - Method in class loci.formats.in.KhorosReader

initFile(String) - Method in class loci.formats.in.KodakReader

initFile(String) - Method in class loci.formats.in.L2DReader

initFile(String) - Method in class loci.formats.in.LeicaReader

initFile(String) - Method in class loci.formats.in.LiFlimReader

initFile(String) - Method in class loci.formats.in.LIFReader

initFile(String) - Method in class loci.formats.in.LIMReader

initFile(String) - Method in class loci.formats.in.LOFReader

initFile(String) - Method in class loci.formats.in.MetamorphReader

initFile(String) - Method in class loci.formats.in.MetamorphTiffReader

initFile(String) - Method in class loci.formats.in.MIASReader

initFile(String) - Method in class loci.formats.in.MicroCTReader

initFile(String) - Method in class loci.formats.in.MINCReader

initFile(String) - Method in class loci.formats.in.MolecularImagingReader

initFile(String) - Method in class loci.formats.in.MRCReader

initFile(String) - Method in class loci.formats.in.MRWReader

initFile(String) - Method in class loci.formats.in.NAFReader

initFile(String) - Method in class loci.formats.in.ND2Reader

initFile(String) - Method in class loci.formats.in.NDPIReader

initFile(String) - Method in class loci.formats.in.NDPISReader

initFile(String) - Method in class loci.formats.in.NiftiReader

initFile(String) - Method in class loci.formats.in.NikonReader

initFile(String) - Method in class loci.formats.in.OIRReader

initFile(String) - Method in class loci.formats.in.OlympusTileReader

initFile(String) - Method in class loci.formats.in.OpenlabRawReader

initFile(String) - Method in class loci.formats.in.OpenlabReader

initFile(String) - Method in class loci.formats.in.OperettaReader

initFile(String) - Method in class loci.formats.in.OxfordInstrumentsReader

initFile(String) - Method in class loci.formats.in.PCIReader

initFile(String) - Method in class loci.formats.in.PCORAWReader

initFile(String) - Method in class loci.formats.in.PDSReader

initFile(String) - Method in class loci.formats.in.PerkinElmerReader

initFile(String) - Method in class loci.formats.in.PhotoshopTiffReader

initFile(String) - Method in class loci.formats.in.PovrayReader

initFile(String) - Method in class loci.formats.in.PQBinReader

initFile(String) - Method in class loci.formats.in.PrairieReader

initFile(String) - Method in class loci.formats.in.PSDReader

initFile(String) - Method in class loci.formats.in.QuesantReader

initFile(String) - Method in class loci.formats.in.RHKReader

initFile(String) - Method in class loci.formats.in.SBIGReader

initFile(String) - Method in class loci.formats.in.ScanrReader

initFile(String) - Method in class loci.formats.in.SDTReader

initFile(String) - Method in class loci.formats.in.SeikoReader

initFile(String) - Method in class loci.formats.in.SEQReader

initFile(String) - Method in class loci.formats.in.SIFReader

initFile(String) - Method in class loci.formats.in.SlidebookReader

initFile(String) - Method in class loci.formats.in.SMCameraReader

initFile(String) - Method in class loci.formats.in.SPCReader

initFile(String) - Method in class loci.formats.in.SPEReader

initFile(String) - Method in class loci.formats.in.SpiderReader

initFile(String) - Method in class loci.formats.in.TargaReader

initFile(String) - Method in class loci.formats.in.TCSReader

initFile(String) - Method in class loci.formats.in.TecanReader

initFile(String) - Method in class loci.formats.in.TillVisionReader

initFile(String) - Method in class loci.formats.in.TissueFAXSReader

initFile(String) - Method in class loci.formats.in.TopometrixReader

initFile(String) - Method in class loci.formats.in.TrestleReader

initFile(String) - Method in class loci.formats.in.UBMReader

initFile(String) - Method in class loci.formats.in.UnisokuReader

initFile(String) - Method in class loci.formats.in.VarianFDFReader

initFile(String) - Method in class loci.formats.in.VeecoReader

initFile(String) - Method in class loci.formats.in.VGSAMReader

initFile(String) - Method in class loci.formats.in.VisitechReader

initFile(String) - Method in class loci.formats.in.VolocityClippingReader

initFile(String) - Method in class loci.formats.in.VolocityReader

initFile(String) - Method in class loci.formats.in.WATOPReader

initFile(String) - Method in class loci.formats.in.XLEFReader

initFile(String) - Method in class loci.formats.in.ZeissCZIReader

initFile(String) - Method in class loci.formats.in.ZeissLMSReader

initFile(String) - Method in class loci.formats.in.ZeissLSMReader

initFile(String) - Method in class loci.formats.in.ZeissTIFFReader

initFile(String) - Method in class loci.formats.in.ZeissXRMReader

initFile(String) - Method in class loci.formats.in.ZeissZVIReader

initFileMain(String) - Method in class loci.formats.in.BaseZeissReader

initFilterModels(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Adds filter details from the reader's MetadataTempBuffer to its MetadataStore

initialize(String) - Method in interface loci.formats.services.MDBService

Prepare the given .mdb file for reading.

initialize(String) - Method in class loci.formats.services.MDBServiceImpl

initialize(String) - Method in interface loci.formats.services.MetakitService

initialize(String) - Method in class loci.formats.services.MetakitServiceImpl

initialize(String) - Method in interface loci.formats.services.POIService

Construct a new POI filesystem around the given file.

initialize(String) - Method in class loci.formats.services.POIServiceImpl

initialize(RandomAccessInputStream) - Method in interface loci.formats.services.MetakitService

initialize(RandomAccessInputStream) - Method in class loci.formats.services.MetakitServiceImpl

initialize(RandomAccessInputStream) - Method in interface loci.formats.services.POIService

Construct a new POI filesystem around the given stream.

initialize(RandomAccessInputStream) - Method in class loci.formats.services.POIServiceImpl

initImageDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Adds image and ROI details from the reader's MetadataTempBuffer to its MetadataStore

initLasers(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Adds laser and light source details from the reader's MetadataTempBuffer to its MetadataStore

initMetadata() - Method in class loci.formats.in.GelReader

initMetadata(int) - Method in class loci.formats.in.ZeissLSMReader

initMetadataStore() - Method in class loci.formats.in.FEITiffReader

initMetadataStore() - Method in class loci.formats.in.FluoviewReader

initMetadataStore() - Method in class loci.formats.in.ImaconReader

initMetadataStore() - Method in class loci.formats.in.ImprovisionTiffReader

initMetadataStore() - Method in class loci.formats.in.IonpathMIBITiffReader

initMetadataStore() - Method in class loci.formats.in.JPKReader

initMetadataStore() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Translates metadata information from the reader's MetadataTempBuffer and adds it to its MetadataStore

initMetadataStore() - Method in class loci.formats.in.LeicaSCNReader

initMetadataStore() - Method in class loci.formats.in.LEOReader

initMetadataStore() - Method in class loci.formats.in.NDPIReader

initMetadataStore() - Method in class loci.formats.in.NikonElementsTiffReader

initMetadataStore() - Method in class loci.formats.in.NikonTiffReader

initMetadataStore() - Method in class loci.formats.in.PyramidTiffReader

initMetadataStore() - Method in class loci.formats.in.SimplePCITiffReader

initMetadataStore() - Method in class loci.formats.in.SISReader

initMetadataStore() - Method in class loci.formats.in.SlidebookTiffReader

initMetadataStore() - Method in class loci.formats.in.SVSReader

initMetadataStore() - Method in class loci.formats.in.TrestleReader

initMetadataStore() - Method in class loci.formats.in.VectraReader

initMetadataStore() - Method in class loci.formats.in.VentanaReader

initPixels() - Method in class loci.formats.in.DeltavisionReader

initReader(IFormatReader, String, boolean) - Method in class loci.formats.in.CellWorxReader

initStandardMetadata() - Method in class loci.formats.in.DNGReader

initStandardMetadata() - Method in class loci.formats.in.FEITiffReader

initStandardMetadata() - Method in class loci.formats.in.FluoviewReader

initStandardMetadata() - Method in class loci.formats.in.ImaconReader

initStandardMetadata() - Method in class loci.formats.in.ImprovisionTiffReader

initStandardMetadata() - Method in class loci.formats.in.IonpathMIBITiffReader

initStandardMetadata() - Method in class loci.formats.in.JPKReader

initStandardMetadata() - Method in class loci.formats.in.LeicaSCNReader

initStandardMetadata() - Method in class loci.formats.in.LEOReader

initStandardMetadata() - Method in class loci.formats.in.MetamorphReader

initStandardMetadata() - Method in class loci.formats.in.NDPIReader

initStandardMetadata() - Method in class loci.formats.in.NikonElementsTiffReader

initStandardMetadata() - Method in class loci.formats.in.NikonReader

initStandardMetadata() - Method in class loci.formats.in.NikonTiffReader

initStandardMetadata() - Method in class loci.formats.in.PyramidTiffReader

initStandardMetadata() - Method in class loci.formats.in.SEQReader

initStandardMetadata() - Method in class loci.formats.in.SimplePCITiffReader

initStandardMetadata() - Method in class loci.formats.in.SISReader

initStandardMetadata() - Method in class loci.formats.in.SlidebookTiffReader

initStandardMetadata() - Method in class loci.formats.in.SVSReader

initStandardMetadata() - Method in class loci.formats.in.TrestleReader

initStandardMetadata() - Method in class loci.formats.in.VectraReader

initStandardMetadata() - Method in class loci.formats.in.VentanaReader

initStandDetails(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

Adds microscope and objective details from the reader's MetadataTempBuffer to its MetadataStore

initTiffParser() - Method in class loci.formats.in.LeicaSCNReader

initTiffParser() - Method in class loci.formats.in.LEOReader

initVars(String) - Method in class loci.formats.in.BaseZeissReader

initVars(String) - Method in class loci.formats.in.ZeissTIFFReader

initVars(String) - Method in class loci.formats.in.ZeissZVIReader

INRReader - Class in loci.formats.in

INRReader is the file format reader for INR files.

INRReader() - Constructor for class loci.formats.in.INRReader

Constructs a new INR reader.

INT16 - Static variable in class loci.formats.in.SPEReader

INT32 - Static variable in class loci.formats.in.SPEReader

intensity - Variable in class loci.formats.in.SDTReader

Whether to combine lifetime bins into single intensity image planes.

intFormat(int, int) - Static method in class loci.formats.in.MetamorphReader

Formats an integer value with leading 0s if needed.

intFormatMax(int, int) - Static method in class loci.formats.in.MetamorphReader

Formats an integer with leading 0 using maximum sequence number.

InveonReader - Class in loci.formats.in

InveonReader is the file format reader for Inveon files.

InveonReader() - Constructor for class loci.formats.in.InveonReader

Constructs a new Inveon reader.

inverseRgb - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

IONPATH_MIBI_SOFTWARE_PREFIX - Static variable in class loci.formats.in.IonpathMIBITiffReader

TIFF software tag prefix for Ionpath MIBI files.

IonpathMIBITiffReader - Class in loci.formats.in

IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.

IonpathMIBITiffReader() - Constructor for class loci.formats.in.IonpathMIBITiffReader

Constructs a new Ionpath MIBI reader.

IPLabReader - Class in loci.formats.in

IPLabReader is the file format reader for IPLab (.IPL) files.

IPLabReader() - Constructor for class loci.formats.in.IPLabReader

Constructs a new IPLab reader.

IPW_MAGIC_BYTES - Static variable in class loci.formats.in.IPWReader

IPWReader - Class in loci.formats.in

IPWReader is the file format reader for Image-Pro Workspace (IPW) files.

IPWReader() - Constructor for class loci.formats.in.IPWReader

Constructs a new IPW reader.

isDimensions(String) - Method in class loci.formats.in.ND2Handler

Returns whether or not the specified key is denotes dimensions.

isIntensity() - Method in class loci.formats.in.SDTReader

Gets whether the reader is combining each lifetime histogram into a summed intensity image plane.

isInterleaved(int) - Method in class loci.formats.in.SDTReader

isInvertX() - Method in class loci.formats.in.PrairieMetadata

Gets whether the stage position X coordinates are inverted (i.e., left-to-right).

isInvertY() - Method in class loci.formats.in.PrairieMetadata

Gets whether the stage position Y coordinates are inverted (i.e., bottom-to-top).

isJPEG - Variable in class loci.formats.in.BaseZeissReader

isLossless() - Method in class loci.formats.in.ND2Handler

isLutInverted - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

isRGB() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

isSingleFile(String) - Method in class loci.formats.in.AFIReader

isSingleFile(String) - Method in class loci.formats.in.AnalyzeReader

isSingleFile(String) - Method in class loci.formats.in.APLReader

isSingleFile(String) - Method in class loci.formats.in.BDReader

isSingleFile(String) - Method in class loci.formats.in.BioRadReader

isSingleFile(String) - Method in class loci.formats.in.BrukerReader

isSingleFile(String) - Method in class loci.formats.in.CellSensReader

isSingleFile(String) - Method in class loci.formats.in.CellVoyagerReader

isSingleFile(String) - Method in class loci.formats.in.ColumbusReader

isSingleFile(String) - Method in class loci.formats.in.CV7000Reader

isSingleFile(String) - Method in class loci.formats.in.DCIMGReader

isSingleFile(String) - Method in class loci.formats.in.DeltavisionReader

isSingleFile(String) - Method in class loci.formats.in.FlexReader

isSingleFile(String) - Method in class loci.formats.in.FujiReader

isSingleFile(String) - Method in class loci.formats.in.FV1000Reader

isSingleFile(String) - Method in class loci.formats.in.HitachiReader

isSingleFile(String) - Method in class loci.formats.in.ImagicReader

isSingleFile(String) - Method in class loci.formats.in.InCellReader

isSingleFile(String) - Method in class loci.formats.in.JDCEReader

isSingleFile(String) - Method in class loci.formats.in.L2DReader

isSingleFile(String) - Method in class loci.formats.in.LeicaReader

isSingleFile(String) - Method in class loci.formats.in.MetamorphReader

isSingleFile(String) - Method in class loci.formats.in.MIASReader

isSingleFile(String) - Method in class loci.formats.in.MicroCTReader

isSingleFile(String) - Method in class loci.formats.in.NDPISReader

isSingleFile(String) - Method in class loci.formats.in.NiftiReader

isSingleFile(String) - Method in class loci.formats.in.OIRReader

isSingleFile(String) - Method in class loci.formats.in.OlympusTileReader

isSingleFile(String) - Method in class loci.formats.in.OperettaReader

isSingleFile(String) - Method in class loci.formats.in.PerkinElmerReader

isSingleFile(String) - Method in class loci.formats.in.PrairieReader

isSingleFile(String) - Method in class loci.formats.in.ScanrReader

isSingleFile(String) - Method in class loci.formats.in.SPCReader

isSingleFile(String) - Method in class loci.formats.in.TCSReader

isSingleFile(String) - Method in class loci.formats.in.TecanReader

isSingleFile(String) - Method in class loci.formats.in.TillVisionReader

isSingleFile(String) - Method in class loci.formats.in.VisitechReader

isSingleFile(String) - Method in class loci.formats.in.XLEFReader

isSingleFile(String) - Method in class loci.formats.in.ZeissLSMReader

isSingleFile(String) - Method in class loci.formats.in.ZeissTIFFReader

isSpectralMode() - Method in class loci.formats.in.PrairieMetadata.Sequence

isTable() - Method in interface loci.formats.in.PrairieMetadata.Value

isTable() - Method in class loci.formats.in.PrairieMetadata.ValueItem

isTable() - Method in class loci.formats.in.PrairieMetadata.ValueTable

isThisType(String, boolean) - Method in class loci.formats.in.AnalyzeReader

isThisType(String, boolean) - Method in class loci.formats.in.APLReader

isThisType(String, boolean) - Method in class loci.formats.in.BDReader

isThisType(String, boolean) - Method in class loci.formats.in.BioRadReader

isThisType(String, boolean) - Method in class loci.formats.in.BrukerReader

isThisType(String, boolean) - Method in class loci.formats.in.CellVoyagerReader

isThisType(String, boolean) - Method in class loci.formats.in.CellWorxReader

isThisType(String, boolean) - Method in class loci.formats.in.ColumbusReader

isThisType(String, boolean) - Method in class loci.formats.in.DeltavisionReader

isThisType(String, boolean) - Method in class loci.formats.in.FujiReader

isThisType(String, boolean) - Method in class loci.formats.in.FV1000Reader

isThisType(String, boolean) - Method in class loci.formats.in.HitachiReader

isThisType(String, boolean) - Method in class loci.formats.in.ImagicReader

isThisType(String, boolean) - Method in class loci.formats.in.InCellReader

isThisType(String, boolean) - Method in class loci.formats.in.InveonReader

isThisType(String, boolean) - Method in class loci.formats.in.JEOLReader

isThisType(String, boolean) - Method in class loci.formats.in.JPKReader

isThisType(String, boolean) - Method in class loci.formats.in.L2DReader

isThisType(String, boolean) - Method in class loci.formats.in.LeicaReader

isThisType(String, boolean) - Method in class loci.formats.in.LeicaSCNReader

isThisType(String, boolean) - Method in class loci.formats.in.MetamorphReader

isThisType(String, boolean) - Method in class loci.formats.in.MetaxpressTiffReader

isThisType(String, boolean) - Method in class loci.formats.in.MIASReader

isThisType(String, boolean) - Method in class loci.formats.in.MikroscanTiffReader

isThisType(String, boolean) - Method in class loci.formats.in.NDPIReader

isThisType(String, boolean) - Method in class loci.formats.in.NiftiReader

isThisType(String, boolean) - Method in class loci.formats.in.NikonReader

isThisType(String, boolean) - Method in class loci.formats.in.OperettaReader

isThisType(String, boolean) - Method in class loci.formats.in.PCORAWReader

isThisType(String, boolean) - Method in class loci.formats.in.PDSReader

isThisType(String, boolean) - Method in class loci.formats.in.PerkinElmerReader

isThisType(String, boolean) - Method in class loci.formats.in.PrairieReader

isThisType(String, boolean) - Method in class loci.formats.in.RCPNLReader

isThisType(String, boolean) - Method in class loci.formats.in.ScanrReader

isThisType(String, boolean) - Method in class loci.formats.in.SEQReader

isThisType(String, boolean) - Method in class loci.formats.in.SPCReader

isThisType(String, boolean) - Method in class loci.formats.in.SVSReader

isThisType(String, boolean) - Method in class loci.formats.in.TCSReader

isThisType(String, boolean) - Method in class loci.formats.in.TecanReader

isThisType(String, boolean) - Method in class loci.formats.in.TillVisionReader

isThisType(String, boolean) - Method in class loci.formats.in.TrestleReader

isThisType(String, boolean) - Method in class loci.formats.in.UnisokuReader

isThisType(String, boolean) - Method in class loci.formats.in.VectraReader

isThisType(String, boolean) - Method in class loci.formats.in.VentanaReader

isThisType(String, boolean) - Method in class loci.formats.in.VisitechReader

isThisType(String, boolean) - Method in class loci.formats.in.VolocityReader

isThisType(String, boolean) - Method in class loci.formats.in.ZeissTIFFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AFIReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AliconaReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AmiraReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.AnalyzeReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ARFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BDReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadGelReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BioRadSCNReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BrukerReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.BurleighReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CanonRawReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.CellomicsReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ColumbusReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DCIMGReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DeltavisionReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.DNGReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.Ecat7Reader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEIReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FEITiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FluoviewReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FujiReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.FV1000Reader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanDM2Reader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GatanReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.GelReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HISReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HitachiReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.HRDGDFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.I2IReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImaconReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisHDFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImarisReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IMODReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImprovisionTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ImspectorReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCell3000Reader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InCellReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.INRReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.InveonReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IonpathMIBITiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPLabReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IPWReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.IvisionReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JEOLReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.JPXReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KhorosReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.KodakReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.L2DReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LeicaReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LEOReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LIFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.LOFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MetamorphTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MIASReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MicroCTReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MolecularImagingReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRCReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.MRWReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ND2Reader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NDPISReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NiftiReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonElementsTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.NikonTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OIRReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabRawReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OpenlabReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OperettaReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.OxfordInstrumentsReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCIReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PCORAWReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PDSReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PhotoshopTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PQBinReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PrairieReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PSDReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.PyramidTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SBIGReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ScanrReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SEQReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SIFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SimplePCITiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SISReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SlidebookTiffReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SMCameraReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SPEReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.SpiderReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TCSReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TopometrixReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.TrestleReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.UnisokuReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VarianFDFReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VGSAMReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityClippingReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.VolocityReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.WATOPReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissCZIReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLMSReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissLSMReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissXRMReader

isThisType(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader

isTimeSeries() - Method in class loci.formats.in.PrairieMetadata.Sequence

Gets whether this Sequence should be considered a time series.

isValid() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

isZlib - Variable in class loci.formats.in.BaseZeissReader

IvisionReader - Class in loci.formats.in

IvisionReader is the file format reader for IVision (.IPM) files.

IvisionReader() - Constructor for class loci.formats.in.IvisionReader

Constructs a new Ivision reader.

J

JDCEReader - Class in loci.formats.in

JDCEReader is the file format reader for Molecular Devices JDCE plates.

JDCEReader() - Constructor for class loci.formats.in.JDCEReader

Constructs a new JDCE reader.

JEOLReader - Class in loci.formats.in

JEOLReader is the file format reader for JEOL files.

JEOLReader() - Constructor for class loci.formats.in.JEOLReader

Constructs a new JEOL reader.

JPEG - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

JPKReader - Class in loci.formats.in

JPKReader is the file format reader for JPK Instruments files.

JPKReader() - Constructor for class loci.formats.in.JPKReader

Constructs a new JPK reader.

JPXReader - Class in loci.formats.in

JPXReader is the file format reader for JPX (3D JPEG-2000) images.

JPXReader() - Constructor for class loci.formats.in.JPXReader

Constructs a new JPX Reader.

K

key - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

KHOROS_MAGIC_BYTES - Static variable in class loci.formats.in.KhorosReader

KhorosReader - Class in loci.formats.in

Reader for Khoros XV files.

KhorosReader() - Constructor for class loci.formats.in.KhorosReader

Constructs a new Khoros reader.

KNOWN_VERSIONS - Static variable in class loci.formats.in.LiFlimReader

KodakReader - Class in loci.formats.in

KodakReader is the file format reader for Kodak Molecular Imaging .bip files.

KodakReader() - Constructor for class loci.formats.in.KodakReader

Constructs a new Kodak reader.

L

L2DReader - Class in loci.formats.in

L2DReader is the file format reader for Li-Cor L2D datasets.

L2DReader() - Constructor for class loci.formats.in.L2DReader

Construct a new L2D reader.

laserActive - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

laserFrap - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

laserIntensity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

laserWavelength - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

lastPlane - Variable in class loci.formats.in.BaseZeissReader

layers - Variable in class loci.formats.in.BaseZeissReader

layers - Variable in class loci.formats.in.ZeissTIFFHandler

LAYOUT_TABLE - Static variable in class loci.formats.in.LiFlimReader

lblockNo - Variable in class loci.formats.in.SDTInfo

Long blockNo - see remarks below.

LEI_SUFFIX - Static variable in class loci.formats.in.LeicaReader

LeicaHandler - Class in loci.formats.in

SAX handler for parsing XML in Leica LIF and Leica TCS files.

LeicaHandler(MetadataStore, MetadataLevel) - Constructor for class loci.formats.in.LeicaHandler

LeicaHandler(MetadataStore, MetadataLevel, boolean) - Constructor for class loci.formats.in.LeicaHandler

LeicaReader - Class in loci.formats.in

LeicaReader is the file format reader for Leica files.

LeicaReader() - Constructor for class loci.formats.in.LeicaReader

Constructs a new Leica reader.

LeicaSCNReader - Class in loci.formats.in

LeicaSCNReader is the file format reader for Leica SCN TIFF files.

LeicaSCNReader() - Constructor for class loci.formats.in.LeicaSCNReader

Constructs a new LeicaSCN reader.

lensNA - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

LEO_TAG - Static variable in class loci.formats.in.LEOReader

LEOReader - Class in loci.formats.in

LEOReader is the file format reader for LEO EM files.

LEOReader() - Constructor for class loci.formats.in.LEOReader

Constructs a new LEO reader.

LIF_MAGIC_BYTE - Static variable in class loci.formats.in.LIFReader

LIF_MEMORY_BYTE - Static variable in class loci.formats.in.LIFReader

LIFF_MAGIC_BYTES - Static variable in class loci.formats.in.OpenlabReader

LiFlimReader - Class in loci.formats.in

LiFlimReader is the file format reader for LI-FLIM files.

LiFlimReader() - Constructor for class loci.formats.in.LiFlimReader

Constructs a new LI-FLIM reader.

LIFReader - Class in loci.formats.in

LIFReader is the file format reader for Leica LIF files.

LIFReader() - Constructor for class loci.formats.in.LIFReader

Constructs a new Leica LIF reader.

LIMReader - Class in loci.formats.in

LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.

LIMReader() - Constructor for class loci.formats.in.LIMReader

Constructs a new LIM reader.

linediv - Variable in class loci.formats.in.SDTInfo

Line predivider = 2 ** (linediv).

LIPixelFormat - Class in loci.formats.in

LIPixelFormat() - Constructor for class loci.formats.in.LIPixelFormat

LMSCollectionXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class represents an LMS xml file that references other LMS xml files such as xlcfs and xlifs.

LMSCollectionXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSCollectionXmlDocument

LMSFileReader - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class can be extended by readers of Leica Microsystems file formats that include LASX generated XML (e.g.

LMSFileReader(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

LMSFileReader.ImageFormat - Enum in loci.formats.in.LeicaMicrosystemsMetadata

file format in which actual image bytes are stored

LMSImageXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class loads and represents a Leica Microsystems image XML document that contains image metadata

LMSImageXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument

LMSImageXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSImageXmlDocument

LMSMetadataExtractor - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class extracts metadata information from Leica Microsystems image XML and stores it in the reader's CoreMetadata and MetadataTempBuffer

LMSMetadataExtractor(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

LMSXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class loads and represents a Leica Microsystems XML document (from file or xml string)

LMSXmlDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

LMSXmlDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

LMSXmlDocument.InitFrom - Enum in loci.formats.in.LeicaMicrosystemsMetadata

loci.formats - package loci.formats

Bio-Formats: a library for reading and writing popular microscopy file formats.

loci.formats.filter - package loci.formats.filter

loci.formats.in - package loci.formats.in

Package containing Bio-Formats file format readers.

loci.formats.in.LeicaMicrosystemsMetadata - package loci.formats.in.LeicaMicrosystemsMetadata

loci.formats.services - package loci.formats.services

LOF - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

LOF - Enum constant in enum loci.formats.in.LOFReader.MetadataSource

LOF_MAGIC_BYTE - Static variable in class loci.formats.in.LOFReader

LOF_MEMORY_BYTE - Static variable in class loci.formats.in.LOFReader

LOFReader - Class in loci.formats.in

LOFReader is the file format reader for Leica Microsystems' LOF files.

LOFReader() - Constructor for class loci.formats.in.LOFReader

Constructs a new Leica LOF reader.

LOFReader(XlifDocument) - Constructor for class loci.formats.in.LOFReader

LOFReader.MetadataSource - Enum in loci.formats.in

LofXmlDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class loads and represents a Leica Microsystems XML document that has been extracted from a LOF file

LofXmlDocument(String, String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.LofXmlDocument

log - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

LOGGER - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

LONG_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader

LUT_LENGTH - Static variable in class loci.formats.in.BioRadReader

lutName - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

LZ4Filter - Class in loci.formats.filter

LZ4Filter(Map<String, Object>) - Constructor for class loci.formats.filter.LZ4Filter

LZ4Filter.LZ4FilterProvider - Class in loci.formats.filter

LZ4FilterProvider() - Constructor for class loci.formats.filter.LZ4Filter.LZ4FilterProvider

M

magnification - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

MAIN - Enum constant in enum loci.formats.in.BaseZeissReader.Context

main_tagset - Variable in class loci.formats.in.ZeissTIFFHandler

makeFilterMetadata() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

makerNoteOffset - Variable in class loci.formats.in.NikonReader

Offset to the Nikon Maker Note.

makeTileStitcher(IFormatReader) - Static method in class loci.formats.TileStitcher

Converts the given reader into a TileStitcher, wrapping if needed.

mapServer(String, String) - Static method in class loci.formats.in.FlexReader

Map the server named 'alias' to the path 'realName'.

mapServer(String, String[]) - Static method in class loci.formats.in.FlexReader

Map the server named 'alias' to the paths in 'realNames'.

mapServersFromConfigurationFile(String) - Static method in class loci.formats.in.FlexReader

Read a configuration file with lines of the form: <server alias>=<real server name> and call mapServer(String, String) accordingly.

masterClock - Variable in class loci.formats.in.SDTInfo

Use or not Master Clock (SPC140 multi-module).

max - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

MAX_HEADER_SIZE - Static variable in class loci.formats.in.QuesantReader

maxAdcRate - Variable in class loci.formats.in.SDTInfo

maxCfdRate - Variable in class loci.formats.in.SDTInfo

(-1.0 - not set).

maxSyncRate - Variable in class loci.formats.in.SDTInfo

Maximum rates during the measurement.

maxTacRate - Variable in class loci.formats.in.SDTInfo

mcsPoints - Variable in class loci.formats.in.SDTInfo

No of MCS values.

mcstaPoints - Variable in class loci.formats.in.SDTInfo

Number of MCS_TA points.

mcsTime - Variable in class loci.formats.in.SDTInfo

Interval time [ms] for MCS histogram.

MDB_SUFFIX - Static variable in class loci.formats.in.ZeissLSMReader

MDBService - Interface in loci.formats.services

Interface defining methods for parsing MDB database files.

MDBServiceImpl - Class in loci.formats.services

Implementation of MDBService for parsing MDB database files.

MDBServiceImpl() - Constructor for class loci.formats.services.MDBServiceImpl

Default constructor.

MEA_SUFFIX - Static variable in class loci.formats.in.FlexReader

MeaHandler() - Constructor for class loci.formats.in.FlexReader.MeaHandler

measDescBlockLength - Variable in class loci.formats.in.SDTInfo

measDescBlockNo - Variable in class loci.formats.in.SDTInfo

Number of the measurement description block corresponding to this data block.

measDescBlockOffs - Variable in class loci.formats.in.SDTInfo

measMode - Variable in class loci.formats.in.SDTInfo

MEASUREMENT_SUFFIXES - Static variable in class loci.formats.in.FlexReader

memBank - Variable in class loci.formats.in.SDTInfo

MetadataStoreInitializer - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class initializes the MetadataStore of a given LMSFileReader, using its MetadataTempBuffer

MetadataStoreInitializer(LMSFileReader) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataStoreInitializer

MetadataTempBuffer - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class is used to temporarily store metadata information extracted from Leica XML before it is written to the reader's MetadataStore

MetadataTempBuffer(int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Constructs a MetadataTempBuffer for a given number of images.

MetakitService - Interface in loci.formats.services

Interface defining methods for interacting with the OME Metakit library.

MetakitServiceImpl - Class in loci.formats.services

Implementation of MetakitService for interacting with the OME Metakit library.

MetakitServiceImpl() - Constructor for class loci.formats.services.MetakitServiceImpl

MetamorphHandler - Class in loci.formats.in

MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.

MetamorphHandler() - Constructor for class loci.formats.in.MetamorphHandler

MetamorphHandler(Hashtable) - Constructor for class loci.formats.in.MetamorphHandler

MetamorphReader - Class in loci.formats.in

Reader is the file format reader for Metamorph STK files.

MetamorphReader() - Constructor for class loci.formats.in.MetamorphReader

Constructs a new Metamorph reader.

MetamorphTiffReader - Class in loci.formats.in

MetamorphTiffReader is the file format reader for TIFF files produced by Metamorph software version 7.5 and above.

MetamorphTiffReader() - Constructor for class loci.formats.in.MetamorphTiffReader

Constructs a new Metamorph TIFF reader.

metaTemp - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

MetaxpressTiffReader - Class in loci.formats.in

MetaxpressTiffReader is the file format reader for MetaXpress .htd + TIFF files.

MetaxpressTiffReader() - Constructor for class loci.formats.in.MetaxpressTiffReader

Constructs a new MetaXpress TIFF reader.

MIASReader - Class in loci.formats.in

MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.

MIASReader() - Constructor for class loci.formats.in.MIASReader

Constructs a new MIAS reader.

MicroCTReader - Class in loci.formats.in

MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.

MicroCTReader() - Constructor for class loci.formats.in.MicroCTReader

Constructs a new MicroCT reader.

microscopeModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

MikroscanTiffReader - Class in loci.formats.in

MikroscanTiffReader is the file format reader for Mikroscan TIFF files.

MikroscanTiffReader() - Constructor for class loci.formats.in.MikroscanTiffReader

Constructs a new Mikroscan TIF reader.

min - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

minAdcRate - Variable in class loci.formats.in.SDTInfo

minCfdRate - Variable in class loci.formats.in.SDTInfo

(-1.0 - not set).

MINCReader - Class in loci.formats.in

MINCReader is the file format reader for MINC MRI files.

MINCReader() - Constructor for class loci.formats.in.MINCReader

Constructs a new MINC reader.

minSyncRate - Variable in class loci.formats.in.SDTInfo

Minimum rates during the measurement.

minTacRate - Variable in class loci.formats.in.SDTInfo

mod - Variable in class loci.formats.in.SDTInfo

Module number.

modFpgaVer - Variable in class loci.formats.in.SDTInfo

New in v.8.4.

modSerNo - Variable in class loci.formats.in.SDTInfo

Serial number of the module.

modType - Variable in class loci.formats.in.SDTInfo

Module type.

modTypeCode - Variable in class loci.formats.in.SDTInfo

MolecularImagingReader - Class in loci.formats.in

MolecularImagingReader is the file format reader for Molecular Imaging files.

MolecularImagingReader() - Constructor for class loci.formats.in.MolecularImagingReader

Constructs a new Molecular Imaging reader.

MONO - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

MRCReader - Class in loci.formats.in

MRCReader is the file format reader for MRC files.

MRCReader() - Constructor for class loci.formats.in.MRCReader

Constructs a new MRC reader.

mReserved1 - Variable in class loci.formats.in.SDTInfo

mReserved2 - Variable in class loci.formats.in.SDTInfo

MRW_MAGIC_STRING - Static variable in class loci.formats.in.MRWReader

MRWReader - Class in loci.formats.in

MRWReader is the file format reader for Minolta MRW files.

MRWReader() - Constructor for class loci.formats.in.MRWReader

Constructs a new MRW reader.

mtResol - Variable in class loci.formats.in.SDTInfo

Macro time clock in 0.1 ns units.

MultipleImagesReader - Class in loci.formats.in.LeicaMicrosystemsMetadata

MultipleImagesReader presents a number of image files as one image reference

MultipleImagesReader(XlifDocument, int) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

N

NAFReader - Class in loci.formats.in

NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.

NAFReader() - Constructor for class loci.formats.in.NAFReader

Constructs a new NAF reader.

nameOfMeasuredQuantity - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

nChannels - Variable in class loci.formats.in.SPCReader

Number of spectral nChannels.

ncx - Variable in class loci.formats.in.SDTInfo

ncy - Variable in class loci.formats.in.SDTInfo

ND_SUFFIX - Static variable in class loci.formats.in.MetamorphReader

ND2_MAGIC_BYTES_1 - Static variable in class loci.formats.in.ND2Reader

ND2_MAGIC_BYTES_2 - Static variable in class loci.formats.in.ND2Reader

ND2Handler - Class in loci.formats.in

DefaultHandler implementation for handling XML produced by Nikon Elements.

ND2Handler(CoreMetadataList, boolean, int) - Constructor for class loci.formats.in.ND2Handler

ND2Handler(CoreMetadataList, int) - Constructor for class loci.formats.in.ND2Handler

ND2Reader - Class in loci.formats.in

ND2Reader is the file format reader for Nikon ND2 files.

ND2Reader() - Constructor for class loci.formats.in.ND2Reader

Constructs a new ND2 reader.

NDPIReader - Class in loci.formats.in

NDPIReader is the file format reader for Hamamatsu .ndpi files.

NDPIReader() - Constructor for class loci.formats.in.NDPIReader

Constructs a new NDPI reader.

NDPISReader - Class in loci.formats.in

NDPISReader is the file format reader for Hamamatsu .ndpis files.

NDPISReader() - Constructor for class loci.formats.in.NDPISReader

Constructs a new NDPIS reader.

NEF_SUFFIX - Static variable in class loci.formats.in.NikonReader

NetCDFService - Interface in loci.formats.services

Utility class for working with NetCDF/HDF files.

NetCDFServiceImpl - Class in loci.formats.services

Utility class for working with NetCDF/HDF files.

NetCDFServiceImpl() - Constructor for class loci.formats.services.NetCDFServiceImpl

Default constructor.

nextBlockOffs - Variable in class loci.formats.in.SDTInfo

Offset to the data block header of the next data block.

nextChName - Variable in class loci.formats.in.BaseZeissReader

nextEmWave - Variable in class loci.formats.in.BaseZeissReader

nextExWave - Variable in class loci.formats.in.BaseZeissReader

NiftiReader - Class in loci.formats.in

NiftiReader is the file format reader for NIfTI files.

NiftiReader() - Constructor for class loci.formats.in.NiftiReader

Constructs a new NIfTI reader.

NikonElementsTiffReader - Class in loci.formats.in

NikonElementsTiffReader is the file format reader for TIFF files produced by Nikon Elements.

NikonElementsTiffReader() - Constructor for class loci.formats.in.NikonElementsTiffReader

NikonReader - Class in loci.formats.in

NikonReader is the file format reader for Nikon NEF (TIFF) files.

NikonReader() - Constructor for class loci.formats.in.NikonReader

Constructs a new Nikon reader.

NikonTiffReader - Class in loci.formats.in

NikonTiffReader is the file format reader for Nikon TIFF files.

NikonTiffReader() - Constructor for class loci.formats.in.NikonTiffReader

NO_NETCDF_MSG - Static variable in class loci.formats.services.NetCDFServiceImpl

nodeToString(Node) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

noOfDataBlocks - Variable in class loci.formats.in.SDTInfo

no_of_data_blocks valid only when in 0 ..

noOfMeasDescBlocks - Variable in class loci.formats.in.SDTInfo

NOTE_NAMES - Static variable in class loci.formats.in.BioRadReader

List of note types.

NOTE_TYPE_4D_SERIES - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_ARROW - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_COLLECT - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_FILE1 - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_FILE2 - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_LINE - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_LIVE - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_MERGE - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_NUMBER - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_SCALEBAR - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_STRUCTURE - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_THRUVIEW - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_USER - Static variable in class loci.formats.in.BioRadReader

NOTE_TYPE_VARIABLE - Static variable in class loci.formats.in.BioRadReader

nTimebins - Variable in class loci.formats.in.SPCReader

Number of time bins in lifetime histogram.

nTimepoints - Variable in class loci.formats.in.CellWorxReader

NUMBEROFDARKIMAGES_KEY - Static variable in class loci.formats.in.LiFlimReader

NUMBEROFFRAMES_KEY - Static variable in class loci.formats.in.LiFlimReader

numFloatsPerSection - Variable in class loci.formats.in.DeltavisionReader

numIntsPerSection - Variable in class loci.formats.in.DeltavisionReader

The number of ints in each extended header section.

O

objectiveModels - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

offset - Variable in class loci.formats.in.SDTInfo

offsets - Variable in class loci.formats.in.BaseZeissReader

offsets - Variable in class loci.formats.in.OpenlabRawReader

Offset to each image's pixel data.

OIB_SUFFIX - Static variable in class loci.formats.in.FV1000Reader

OIF_SUFFIX - Static variable in class loci.formats.in.FV1000Reader

OIRReader - Class in loci.formats.in

OIRReader is the file format reader for Olympus .oir files.

OIRReader() - Constructor for class loci.formats.in.OIRReader

Constructs a new OIR reader.

OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

OLD_PHYSICAL_SIZE_DEFAULT - Static variable in class loci.formats.in.LIFReader

OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

OLD_PHYSICAL_SIZE_KEY - Static variable in class loci.formats.in.LIFReader

oldPhysicalSize - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

OlympusTileReader - Class in loci.formats.in

OlympusTileReader is the file format reader for Olympus .omp2info files.

OlympusTileReader() - Constructor for class loci.formats.in.OlympusTileReader

Constructs a new Olympus .omp2info reader.

openBytes(int) - Method in class loci.formats.TileStitcher

openBytes(int, byte[]) - Method in class loci.formats.TileStitcher

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AFIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AIMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AliconaReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AmiraReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.AnalyzeReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.APLReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ARFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BDReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadGelReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BioRadSCNReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BrukerReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.BurleighReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CanonRawReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellomicsReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellSensReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellVoyagerReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CellWorxReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ColumbusReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.CV7000Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DCIMGReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DeltavisionReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.DNGReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.Ecat7Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FEIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FlexReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FluoviewReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FujiReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.FV1000Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanDM2Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GatanReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.GelReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HamamatsuVMSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HISReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HitachiReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.HRDGDFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.I2IReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImaconReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImagicReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisHDFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImarisReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IMODReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImprovisionTiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ImspectorReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCell3000Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InCellReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.INRReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.InveonReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IonpathMIBITiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPLabReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IPWReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.IvisionReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JDCEReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JEOLReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPKReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.JPXReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KhorosReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.KodakReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.L2DReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LeicaSCNReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LiFlimReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LIMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.LOFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MetamorphTiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MIASReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MicroCTReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MINCReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MolecularImagingReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRCReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.MRWReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NAFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ND2Reader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NDPISReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NiftiReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.NikonReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OIRReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OlympusTileReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabRawReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OpenlabReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OperettaReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.OxfordInstrumentsReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PCORAWReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PDSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PerkinElmerReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PhotoshopTiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PovrayReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PQBinReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PrairieReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PSDReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.PyramidTiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.QuesantReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.RHKReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SBIGReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ScanrReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SDTReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SeikoReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SEQReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SIFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SimplePCITiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SlidebookTiffReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SMCameraReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPCReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SPEReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SpiderReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.SVSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TargaReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TCSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TecanReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TillVisionReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TissueFAXSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TopometrixReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.TrestleReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UBMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.UnisokuReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VarianFDFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VectraReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VeecoReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VentanaReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VGSAMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VisitechReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityClippingReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.VolocityReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.WATOPReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.XLEFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissCZIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLMSReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissLSMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissTIFFReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissXRMReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.in.ZeissZVIReader

openBytes(int, byte[], int, int, int, int) - Method in class loci.formats.TileStitcher

openBytes(int, int, int, int, int) - Method in class loci.formats.in.XLEFReader

openBytes(int, int, int, int, int) - Method in class loci.formats.TileStitcher

openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.NDPIReader

openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.in.SVSReader

openCompressedBytes(int, byte[], int, int) - Method in class loci.formats.TileStitcher

openCompressedBytes(int, int, int) - Method in class loci.formats.in.NDPIReader

openCompressedBytes(int, int, int) - Method in class loci.formats.in.SVSReader

openCompressedBytes(int, int, int) - Method in class loci.formats.TileStitcher

OPENLAB_RAW_MAGIC_STRING - Static variable in class loci.formats.in.OpenlabRawReader

OpenlabRawReader - Class in loci.formats.in

OpenlabRawReader is the file format reader for Openlab RAW files.

OpenlabRawReader() - Constructor for class loci.formats.in.OpenlabRawReader

Constructs a new RAW reader.

OpenlabReader - Class in loci.formats.in

OpenlabReader is the file format reader for Openlab LIFF files.

OpenlabReader() - Constructor for class loci.formats.in.OpenlabReader

Constructs a new OpenlabReader.

OpenlabReader.PlaneInfo - Class in loci.formats.in

Helper class for storing plane info.

openThumbBytes(int) - Method in class loci.formats.in.AFIReader

openThumbBytes(int) - Method in class loci.formats.in.CellSensReader

openThumbBytes(int) - Method in class loci.formats.in.LeicaSCNReader

openThumbBytes(int) - Method in class loci.formats.in.NDPIReader

openThumbBytes(int) - Method in class loci.formats.in.SVSReader

openThumbBytes(int) - Method in class loci.formats.in.VectraReader

openThumbBytes(int) - Method in class loci.formats.in.VentanaReader

OperettaReader - Class in loci.formats.in

OperettaReader is the file format reader for PerkinElmer Operetta data.

OperettaReader() - Constructor for class loci.formats.in.OperettaReader

Constructs a new Operetta reader.

original - Variable in class loci.formats.in.DNGReader

The original IFD.

original - Variable in class loci.formats.in.NikonReader

The original IFD.

overfl - Variable in class loci.formats.in.SDTInfo

overflowCorrFactor - Variable in class loci.formats.in.SDTInfo

overruns - Variable in class loci.formats.in.SDTInfo

No of Fifo overruns when > 0 fcs curve & endTime are not valid.

OXFORD_MAGIC_STRING - Static variable in class loci.formats.in.OxfordInstrumentsReader

OxfordInstrumentsReader - Class in loci.formats.in

OxfordInstrumentsReader is the file format reader for Oxford Instruments .top files.

OxfordInstrumentsReader() - Constructor for class loci.formats.in.OxfordInstrumentsReader

Constructs a new Oxford Instruments reader.

P

P_KEY - Static variable in class loci.formats.in.LiFlimReader

PACKBITS - Static variable in class loci.formats.in.PhotoshopTiffReader

PACKING_KEY - Static variable in class loci.formats.in.LiFlimReader

page - Variable in class loci.formats.in.SDTInfo

panelSize - Variable in class loci.formats.in.DeltavisionReader

parse(Element) - Method in class loci.formats.in.PrairieMetadata.Frame

Parses metadata from the given Frame element.

parse(Element) - Method in class loci.formats.in.PrairieMetadata.PFile

Parses metadata from the given File element.

parse(Element) - Method in class loci.formats.in.PrairieMetadata.Sequence

Parses metadata from the given Sequence element.

parseColor(byte, byte, byte) - Static method in class loci.formats.in.BaseZeissReader

parseColor(byte, byte, byte) - Static method in class loci.formats.in.ZeissTIFFHandler

parseDatabase() - Method in interface loci.formats.services.MDBService

Read all tables from a pre-initialized .mdb files.

parseDatabase() - Method in class loci.formats.services.MDBServiceImpl

parseDouble(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

parseFilePath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Translates Leica XML file paths to absolute url decoded paths

parseHTD() - Method in class loci.formats.in.CellWorxReader

parseInt(String) - Static method in class loci.formats.in.BaseZeissReader

Parse an Integer from a String.

parseInt(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

parseInt(String, int) - Static method in class loci.formats.in.BaseZeissReader

Parse an Integer from a String.

parseKeyAndValue(String, String, String) - Method in class loci.formats.in.ND2Handler

parseLong(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

parseMasks(MetadataStore) - Method in class loci.formats.in.MIASReader

Parse masks into a separate overlay-specific MetadataStore.

parseOverlays(int, long, String, MetadataStore) - Method in class loci.formats.in.ZeissLSMReader

Parses overlay-related fields.

parseROIString(RandomAccessInputStream) - Method in class loci.formats.in.ZeissZVIReader

parseTable(String) - Method in interface loci.formats.services.MDBService

Read named table from a pre-initialized .mdb files.

parseTable(String) - Method in class loci.formats.services.MDBServiceImpl

parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.CellWorxReader

Parse metadata from a well log file.

parseWellLogFile(int, MetadataStore) - Method in class loci.formats.in.MetaxpressTiffReader

PCI_MAGIC_BYTES - Static variable in class loci.formats.in.PCIReader

PCIReader - Class in loci.formats.in

PCIReader is the file format reader for SimplePCI (Compix) .cxd files.

PCIReader() - Constructor for class loci.formats.in.PCIReader

Constructs a new SimplePCI reader.

PCORAWReader - Class in loci.formats.in

PCORAWReader is the file format reader for PCORAW files.

PCORAWReader() - Constructor for class loci.formats.in.PCORAWReader

Constructs a new PCORAW reader.

PDSReader - Class in loci.formats.in

PDSReader is the file format reader for Perkin Elmer densitometer files.

PDSReader() - Constructor for class loci.formats.in.PDSReader

Constructs a new PDS reader.

PerkinElmerReader - Class in loci.formats.in

PerkinElmerReader is the file format reader for PerkinElmer files.

PerkinElmerReader() - Constructor for class loci.formats.in.PerkinElmerReader

Constructs a new PerkinElmer reader.

PFile(PrairieMetadata.Frame, Element) - Constructor for class loci.formats.in.PrairieMetadata.PFile

Creates a new file by parsing the given <File> element.

PhotoshopTiffReader - Class in loci.formats.in

PhotoshopTiffReader is the file format reader for Adobe Photoshop TIFF files.

PhotoshopTiffReader() - Constructor for class loci.formats.in.PhotoshopTiffReader

Constructs a new Photoshop TIFF reader.

physicalSizeX - Variable in class loci.formats.in.BaseZeissReader

physicalSizeXs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

physicalSizeY - Variable in class loci.formats.in.BaseZeissReader

physicalSizeYs - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

physicalSizeZ - Variable in class loci.formats.in.BaseZeissReader

PIC_SUFFIX - Static variable in class loci.formats.in.BioRadReader

pict - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

pinholes - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

pixClk - Variable in class loci.formats.in.SDTInfo

PIXEL_OFFSET - Static variable in class loci.formats.in.VGSAMReader

PIXELFORMAT_BAYERBG12 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERBG12P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERBG12PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERBG16 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERBG8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGB12 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGB12P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGB12PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGB16 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGB8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR10 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR12 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR12P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR12PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR16 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERGR8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG10 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG12 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG12P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG12PACKED - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG12PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG16 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BAYERRG8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BGR8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_BGR8PACKED - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_KEY - Static variable in class loci.formats.in.LiFlimReader

PIXELFORMAT_MONO10 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO10P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO10PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO12 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO12P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO12PACKED - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO12PMSB - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO14 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO14P - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO16 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_MONO8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_RGB8 - Static variable in class loci.formats.in.LIPixelFormat

PIXELFORMAT_RGB8PACKED - Static variable in class loci.formats.in.LIPixelFormat

pixelFormatEqualsBitSize(Integer, String) - Static method in class loci.formats.in.LIPixelFormat

PIXELS_MARKER - Static variable in class loci.formats.in.VisitechReader

pixTime - Variable in class loci.formats.in.SDTInfo

PLANE - Enum constant in enum loci.formats.in.BaseZeissReader.Context

PlaneInfo() - Constructor for class loci.formats.in.OpenlabReader.PlaneInfo

planeName - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

planeOffset - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

planes - Variable in class loci.formats.in.ZeissTIFFHandler

PNG - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

poi - Variable in class loci.formats.in.ZeissZVIReader

POI_MAGIC_BYTES - Static variable in class loci.formats.services.POIServiceImpl

POIService - Interface in loci.formats.services

Interface defining methods for reading Microsoft OLE2 documents using OME's fork of Apache POI.

POIServiceImpl - Class in loci.formats.services

POIServiceImpl() - Constructor for class loci.formats.services.POIServiceImpl

Default constructor.

polarityF - Variable in class loci.formats.in.SDTInfo

polarityL - Variable in class loci.formats.in.SDTInfo

2 = disabled line markers.

polarityP - Variable in class loci.formats.in.SDTInfo

populateMaskPixels(int, int, int, MetadataStore) - Method in class loci.formats.in.MIASReader

Populate the MaskPixels.BinData attribute for the Mask identified by the given Image index, ROI index, and Shape index.

populateMetadata() - Method in class loci.formats.in.CellWorxReader

populateMetadataStore(ZeissLSMReader.SubBlock, MetadataStore, int) - Method in class loci.formats.in.ZeissLSMReader

populateObjective(MetadataStore, int) - Method in class loci.formats.in.DeltavisionReader

Populate an Objective based upon the lens ID.

populateObjective(MetadataStore, int) - Method in class loci.formats.in.RCPNLReader

populateROIs(MetadataStore) - Method in class loci.formats.in.ND2Handler

positionInT - Variable in class loci.formats.in.DeltavisionReader

posX - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

posY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

posZ - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

PovrayReader - Class in loci.formats.in

PovrayReader is the file format reader for POV-Ray .df3 files.

PovrayReader() - Constructor for class loci.formats.in.PovrayReader

Constructs a new POV-Ray reader.

PQBinReader - Class in loci.formats.in

PQBinReader is the file format reader for PicoQuant .bin files.

PQBinReader() - Constructor for class loci.formats.in.PQBinReader

Constructs a new PQBin reader.

PRAIRIE_SUFFIXES - Static variable in class loci.formats.in.PrairieReader

PrairieMetadata - Class in loci.formats.in

Metadata structure for Prairie Technologies' TIFF-based format.

PrairieMetadata(Document, Document, Document) - Constructor for class loci.formats.in.PrairieMetadata

Creates a new Prairie metadata by parsing the given XML, CFG and/or ENV documents.

PrairieMetadata.Frame - Class in loci.formats.in

A Prairie <Frame>, beneath a <Sequence>.

PrairieMetadata.PFile - Class in loci.formats.in

A Prairie <File> beneath a <Frame>.

PrairieMetadata.Sequence - Class in loci.formats.in

A Prairie <Sequence>.

PrairieMetadata.Value - Interface in loci.formats.in

A value in a Prairie metadata dictionary.

PrairieMetadata.ValueItem - Class in loci.formats.in

A leaf value with an actual PrairieMetadata.ValueItem.value() as well as an optional PrairieMetadata.ValueItem.description().

PrairieMetadata.ValueTable - Class in loci.formats.in

A table of values.

PrairieReader - Class in loci.formats.in

PrairieReader is the file format reader for Prairie Technologies' TIFF variant.

PrairieReader() - Constructor for class loci.formats.in.PrairieReader

Constructs a new Prairie TIFF reader.

PREFIX - Static variable in class loci.formats.in.TCSReader

preLoad - Variable in class loci.formats.in.SDTReader

Whether to pre-load all lifetime bins for faster loading.

PREVIEWNAME_PREFIXES - Static variable in class loci.formats.in.FV1000Reader

printReferences() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument

printXlifInfo() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

PSD_MAGIC_STRING - Static variable in class loci.formats.in.PSDReader

PSDReader - Class in loci.formats.in

PSDReader is the file format reader for Photoshop PSD files.

PSDReader() - Constructor for class loci.formats.in.PSDReader

Constructs a new PSD reader.

PyramidTiffReader - Class in loci.formats.in

PyramidTiffReader is the file format reader for pyramid TIFFs.

PyramidTiffReader() - Constructor for class loci.formats.in.PyramidTiffReader

Constructs a new pyramid TIFF reader.

Q

QuesantReader - Class in loci.formats.in

QuesantReader is the file format reader for Quesant .afm files.

QuesantReader() - Constructor for class loci.formats.in.QuesantReader

Constructs a new Quesant reader.

R

rawBuf - Variable in class loci.formats.in.SPCReader

rawCount - Variable in class loci.formats.in.BaseZeissReader

RCPNLReader - Class in loci.formats.in

RCPNLReader() - Constructor for class loci.formats.in.RCPNLReader

read(Kryo, Input) - Method in class loci.formats.services.NetCDFServiceImpl

realHeight - Variable in class loci.formats.in.BaseZeissReader

realWidth - Variable in class loci.formats.in.BaseZeissReader

REC_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

RED - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

refractiveIndex - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

RELATIVE_POSITIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader

RELATIVE_POSITIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader

REMOVE_THUMBNAIL_DEFAULT - Static variable in class loci.formats.in.SVSReader

REMOVE_THUMBNAIL_KEY - Static variable in class loci.formats.in.SVSReader

removeThumbnail() - Method in class loci.formats.in.SVSReader

reopenFile() - Method in class loci.formats.in.AnalyzeReader

reopenFile() - Method in class loci.formats.in.CellSensReader

reopenFile() - Method in class loci.formats.in.HitachiReader

reopenFile() - Method in class loci.formats.in.ImagicReader

reopenFile() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

reopenFile() - Method in class loci.formats.in.NiftiReader

reopenFile() - Method in class loci.formats.in.SPCReader

reopenFile() - Method in class loci.formats.in.XLEFReader

repT - Variable in class loci.formats.in.SDTInfo

RES_SUFFIX - Static variable in class loci.formats.in.FlexReader

reserved1 - Variable in class loci.formats.in.SDTInfo

reserved2 - Variable in class loci.formats.in.SDTInfo

ResHandler() - Constructor for class loci.formats.in.FlexReader.ResHandler

resolution - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

revision - Variable in class loci.formats.in.SDTInfo

Software revision number (lower 4 bits >= 10(decimal)).

RHKReader - Class in loci.formats.in

RHKReader is the file format reader for RHK Technologies files.

RHKReader() - Constructor for class loci.formats.in.RHKReader

Constructs a new RHK reader.

roiIDs - Variable in class loci.formats.in.BaseZeissReader

rowCount - Variable in class loci.formats.in.BaseZeissReader

S

S - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

sanitizeControl(String) - Static method in class loci.formats.in.ND2Reader

Remove control and invalid characters from the given string.

SBIGReader - Class in loci.formats.in

SBIGReader is the file format reader for SBIG files.

SBIGReader() - Constructor for class loci.formats.in.SBIGReader

Constructs a new SBIG reader.

SCALING - Enum constant in enum loci.formats.in.BaseZeissReader.Context

scalings - Variable in class loci.formats.in.ZeissTIFFHandler

ScanrReader - Class in loci.formats.in

ScanrReader is the file format reader for Olympus ScanR datasets.

ScanrReader() - Constructor for class loci.formats.in.ScanrReader

Constructs a new ScanR reader.

scanRX - Variable in class loci.formats.in.SDTInfo

scanRY - Variable in class loci.formats.in.SDTInfo

scanX - Variable in class loci.formats.in.SDTInfo

scanY - Variable in class loci.formats.in.SDTInfo

SCREENING - Static variable in class loci.formats.in.FlexReader

SDTInfo - Class in loci.formats.in

SDTInfo encapsulates the header information for Becker & Hickl SPC-Image SDT files.

SDTInfo(RandomAccessInputStream, Hashtable) - Constructor for class loci.formats.in.SDTInfo

Constructs a new SDT header by reading values from the given input source, populating the given metadata table.

SDTReader - Class in loci.formats.in

SDTReader is the file format reader for Becker & Hickl SPC-Image SDT files.

SDTReader() - Constructor for class loci.formats.in.SDTReader

Constructs a new SDT reader.

SeikoReader - Class in loci.formats.in

SeikoReader is the file format reader for Seiko .xqd/.xqf files.

SeikoReader() - Constructor for class loci.formats.in.SeikoReader

Constructs a new Seiko reader.

SEQReader - Class in loci.formats.in

SEQReader is the file format reader for Image-Pro Sequence files.

SEQReader() - Constructor for class loci.formats.in.SEQReader

Constructs a new Image-Pro SEQ reader.

Sequence(Element) - Constructor for class loci.formats.in.PrairieMetadata.Sequence

Creates a new sequence by parsing the given <Sequence> element.

serialNumber - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

series - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

setAutomaticallyParseMasks(boolean) - Method in class loci.formats.in.MIASReader

Toggle whether or not Mask pixel data should be parsed in setId.

setCategory(int) - Method in class loci.formats.in.BaseZeissReader.Tag

setCore(ArrayList<CoreMetadata>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

setCoreIndex(int) - Method in class loci.formats.in.ZeissLSMReader

setCoreMetadata(CoreMetadata) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

setFile(String) - Method in interface loci.formats.services.NetCDFService

Initializes the service on a given file path.

setFile(String) - Method in class loci.formats.services.NetCDFServiceImpl

setId(String) - Method in class loci.formats.TileStitcher

setIdWithMetadata(String, XlifDocument) - Method in class loci.formats.in.LOFReader

Inits the LOFReader using passed xml (from XLIF) for metadata initiation, instead of reading the LOF's included xml

setIndex(int) - Method in class loci.formats.in.BaseZeissReader.Tag

setIntensity(boolean) - Method in class loci.formats.in.SDTReader

Toggles whether the reader should return intensity data only (the sum of each lifetime histogram).

setKey(int) - Method in class loci.formats.in.BaseZeissReader.Tag

setLength(Double) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

setMetadataTempBuffer(MetadataTempBuffer) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

setOffsets(String, long[][]) - Method in class loci.formats.in.ND2Reader

Change the underlying file path and pixel data offsets, keeping all other metadata the same.

setPreLoad(boolean) - Method in class loci.formats.in.SDTReader

Toggles whether the reader should pre-load data for increased performance.

setSeries(int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

Sets the field MultipleImagesReader.series.

setSeries(int) - Method in class loci.formats.in.ZeissLSMReader

setTruncatedFileFlag(boolean) - Method in class loci.formats.in.DeltavisionReader

This flag indicates if the file is known to be truncated.

setup - Variable in class loci.formats.in.SDTInfo

SETUP_IDENTIFIER - Static variable in class loci.formats.in.SDTInfo

For .set files (setup only).

setupLength - Variable in class loci.formats.in.SDTInfo

Length of the setup data.

setupOffs - Variable in class loci.formats.in.SDTInfo

Offset of the setup text data (system parameters, display parameters, trace parameters etc.).

setValue(String) - Method in class loci.formats.in.BaseZeissReader.Tag

SFEG_TAG - Static variable in class loci.formats.in.FEITiffReader

SHORT_DATE_FORMAT - Static variable in class loci.formats.in.MetamorphReader

SIFReader - Class in loci.formats.in

SIFReader is the file format reader for Andor SIF files.

SIFReader() - Constructor for class loci.formats.in.SIFReader

Constructs a new SIF reader.

SimplePCITiffReader - Class in loci.formats.in

SimplePCITiffReader is the file format reader for TIFF files produced by SimplePCI software.

SimplePCITiffReader() - Constructor for class loci.formats.in.SimplePCITiffReader

SISReader - Class in loci.formats.in

SISReader is the file format reader for Olympus Soft Imaging Solutions TIFF files.

SISReader() - Constructor for class loci.formats.in.SISReader

size - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

SKIP_MISSING_WELLS - Static variable in class loci.formats.in.ScanrReader

SKIP_MISSING_WELLS_DEFAULT - Static variable in class loci.formats.in.ScanrReader

skipMissingWells() - Method in class loci.formats.in.ScanrReader

SLD_MAGIC_BYTES_1_0 - Static variable in class loci.formats.in.SlidebookReader

SLD_MAGIC_BYTES_1_1 - Static variable in class loci.formats.in.SlidebookReader

SLD_MAGIC_BYTES_1_2 - Static variable in class loci.formats.in.SlidebookReader

SLD_MAGIC_BYTES_2_0 - Static variable in class loci.formats.in.SlidebookReader

SLD_MAGIC_BYTES_2_1 - Static variable in class loci.formats.in.SlidebookReader

SLD_MAGIC_BYTES_3 - Static variable in class loci.formats.in.SlidebookReader

SLIDEBOOK_MAGIC_STRING - Static variable in class loci.formats.in.SlidebookTiffReader

SlidebookReader - Class in loci.formats.in

SlidebookReader is the file format reader for 3I Slidebook files.

SlidebookReader() - Constructor for class loci.formats.in.SlidebookReader

Constructs a new Slidebook reader.

SlidebookTiffReader - Class in loci.formats.in

SlidebookTiffReader() - Constructor for class loci.formats.in.SlidebookTiffReader

SMCameraReader - Class in loci.formats.in

SMCameraReader is the file format reader for SM camera files.

SMCameraReader() - Constructor for class loci.formats.in.SMCameraReader

Constructs a new SM camera reader.

SPCReader - Class in loci.formats.in

SPCReader is the file format reader for Becker & Hickl SPC-Image SPC FIFO files.

SPCReader() - Constructor for class loci.formats.in.SPCReader

Constructs a new SPC reader.

SPEReader - Class in loci.formats.in

SPEReader is the file format reader for Princeton Instruments SPE .spe files.

SPEReader() - Constructor for class loci.formats.in.SPEReader

Constructs a new SPE reader.

SpiderReader - Class in loci.formats.in

SpiderReader is the file format reader for SPIDER files.

SpiderReader() - Constructor for class loci.formats.in.SpiderReader

Constructs a new SPIDER reader.

SPLIT_MONTAGE - Static variable in class loci.formats.in.GatanReader

SPLIT_MONTAGE_DEFAULT - Static variable in class loci.formats.in.GatanReader

SPLIT_TILES_DEFAULT - Static variable in class loci.formats.in.VentanaReader

Default value of VentanaReader.SPLIT_TILES_KEY

SPLIT_TILES_KEY - Static variable in class loci.formats.in.VentanaReader

MetadataOptions key for determining whether to report each tile as a separate series.

splitMontage() - Method in class loci.formats.in.GatanReader

splitTiles() - Method in class loci.formats.in.VentanaReader

stageX - Variable in class loci.formats.in.BaseZeissReader

stageY - Variable in class loci.formats.in.BaseZeissReader

startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.FlexHandler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.MeaHandler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.FlexReader.ResHandler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.LeicaHandler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.MetamorphHandler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.ND2Handler

startElement(String, String, String, Attributes) - Method in class loci.formats.in.ZeissTIFFHandler

status - Variable in class loci.formats.in.SDTInfo

Last SPC_test_state return value (status).

steps - Variable in class loci.formats.in.SDTInfo

STK_SUFFIX - Static variable in class loci.formats.in.MetamorphReader

stopt - Variable in class loci.formats.in.SDTInfo

stopTime - Variable in class loci.formats.in.SDTInfo

Time from start to - disarm (simple measurement) - or to the end of the cycle (for complex measurement).

storedChannel - Variable in class loci.formats.in.SDTReader

storedChannel - Variable in class loci.formats.in.SPCReader

storedSeries - Variable in class loci.formats.in.SDTReader

storedT - Variable in class loci.formats.in.SPCReader

storeRelativePositions() - Method in class loci.formats.in.ZeissCZIReader

storeROIs(MetadataStore) - Method in class loci.formats.in.BaseZeissReader

Store basic dimensions in model

STRUCTURE_LABELS_1 - Static variable in class loci.formats.in.BioRadReader

Structure labels.

STRUCTURE_LABELS_2 - Static variable in class loci.formats.in.BioRadReader

STRUCTURE_LABELS_3 - Static variable in class loci.formats.in.BioRadReader

STRUCTURE_LABELS_4 - Static variable in class loci.formats.in.BioRadReader

STRUCTURE_LABELS_5 - Static variable in class loci.formats.in.BioRadReader

STRUCTURE_LABELS_6 - Static variable in class loci.formats.in.BioRadReader

subdirectories - Variable in class loci.formats.in.CellWorxReader

SUFFIX - Static variable in class loci.formats.in.TCSReader

SUFFIXES - Static variable in class loci.formats.in.FlexReader

SVSReader - Class in loci.formats.in

SVSReader is the file format reader for Aperio SVS TIFF files.

SVSReader() - Constructor for class loci.formats.in.SVSReader

Constructs a new SVS reader.

SVSReader(String, String[]) - Constructor for class loci.formats.in.SVSReader

swapDimensions() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.MultipleImagesReader

Rearranges frame order from ZSTC order (used in XLIFs) to desired CoreMetadata.dimensionOrder

swapXY - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

synFD - Variable in class loci.formats.in.SDTInfo

synHF - Variable in class loci.formats.in.SDTInfo

synTH - Variable in class loci.formats.in.SDTInfo

synZC - Variable in class loci.formats.in.SDTInfo

T

T - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

T_KEY - Static variable in class loci.formats.in.LiFlimReader

T_STRING - Static variable in class loci.formats.in.SDTInfo

TAC_GAIN - Static variable in class loci.formats.in.SPCReader

TAC_RANGE - Static variable in class loci.formats.in.SPCReader

tacG - Variable in class loci.formats.in.SDTInfo

tacLH - Variable in class loci.formats.in.SDTInfo

tacLL - Variable in class loci.formats.in.SDTInfo

tacOF - Variable in class loci.formats.in.SDTInfo

tacR - Variable in class loci.formats.in.SDTInfo

Tag(int, String, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag

Constructor.

Tag(int, BaseZeissReader.Context) - Constructor for class loci.formats.in.BaseZeissReader.Tag

Constructor.

tagset - Variable in class loci.formats.in.ZeissTIFFHandler.Plane

tagsToParse - Variable in class loci.formats.in.BaseZeissReader

TargaReader - Class in loci.formats.in

File format reader for Truevision Targa files.

TargaReader() - Constructor for class loci.formats.in.TargaReader

Constructs a new Targa reader.

TCSReader - Class in loci.formats.in

TCSReader is the file format reader for Leica TCS TIFF files and their companion XML file.

TCSReader() - Constructor for class loci.formats.in.TCSReader

TecanReader - Class in loci.formats.in

TecanReader() - Constructor for class loci.formats.in.TecanReader

Constructs a new Tecan Spark Cyto reader.

TIF - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

tiff - Variable in class loci.formats.in.LeicaReader

Helper readers.

tiff - Variable in class loci.formats.in.PerkinElmerReader

Helper reader.

TIFF_SUFFIXES - Static variable in class loci.formats.in.ZeissTIFFReader

tileBytesInc - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

tileCount - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

tileIndices - Variable in class loci.formats.in.BaseZeissReader

tiles - Variable in class loci.formats.in.BaseZeissReader

TileStitcher - Class in loci.formats

TileStitcher() - Constructor for class loci.formats.TileStitcher

Constructs a TileStitcher around a new image reader.

TileStitcher(IFormatReader) - Constructor for class loci.formats.TileStitcher

Constructs a TileStitcher with the given reader.

TillVisionReader - Class in loci.formats.in

TillVisionReader is the file format reader for TillVision files.

TillVisionReader() - Constructor for class loci.formats.in.TillVisionReader

Constructs a new TillVision reader.

TIM_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

time - Variable in class loci.formats.in.SDTInfo

Time of creation.

TIME_FORMAT - Static variable in class loci.formats.in.GelReader

timeBins - Variable in class loci.formats.in.PQBinReader

timeBins - Variable in class loci.formats.in.SDTInfo

timeBins - Variable in class loci.formats.in.SDTReader

Number of time bins in lifetime histogram.

timepoint - Variable in class loci.formats.in.BaseZeissReader

timepoint - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

timepointIndices - Variable in class loci.formats.in.BaseZeissReader

timepoints - Variable in class loci.formats.in.SDTInfo

timestamp - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

TIMESTAMP_KEY - Static variable in class loci.formats.in.LiFlimReader

timestamps - Variable in class loci.formats.in.BaseZeissReader

timestamps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

TissueFAXSReader - Class in loci.formats.in

Reader for TissueFAXS format from TissueGnostics.

TissueFAXSReader() - Constructor for class loci.formats.in.TissueFAXSReader

Constructs a new TissueGnostics TissueFAXS reader.

TITAN_TAG - Static variable in class loci.formats.in.FEITiffReader

token - Variable in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

TopometrixReader - Class in loci.formats.in

TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr, .zfr, .zfp, and .2fl files.

TopometrixReader() - Constructor for class loci.formats.in.TopometrixReader

Constructs a new TopoMetrix reader.

toString() - Method in class loci.formats.in.BaseZeissReader.Tag

toString() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

toString() - Method in class loci.formats.in.PrairieMetadata.ValueItem

toString() - Method in class loci.formats.in.ZeissTIFFHandler.Plane

toString() - Method in class loci.formats.in.ZeissTIFFHandler

translateAttachmentNodes(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts information from dimension descriptions and writes it to reader's MetadataTempBuffer

translateChannelDescriptions(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts i.a.

translateDetectors(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts detector information and writes it to reader's MetadataTempBuffer

translateFilterSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts filter information and writes it to reader's MetadataTempBuffer

translateImage(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts information from element node and writes it to reader's CoreMetadata and MetadataTempBuffer

translateLaserLines(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts laser information and writes it to reader's MetadataTempBuffer

translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

Extracts metadata from a list of Leica image XML Documents and writes them to the reader's CoreMetadata, MetadataTempBuffer and MetadataStore

translateMetadata(List<LMSImageXmlDocument>) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts all information from Leica image xml Documents and writes it to reader's CoreMetadata and MetadataTempBuffer

translateMetadata(LMSImageXmlDocument) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

translateROIs(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts ROIs and writes them to reader's MetadataTempBuffer

translateScannerSettings(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts scanner information and writes it to reader's CoreMetadata and MetadataTempBuffer

translateSingleROIs(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts single ROIs and writes them to reader's MetadataTempBuffer

translateTimestamps(Element, int) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSMetadataExtractor

Extracts timestamps and writes them to reader's MetadataTempBuffer

TrestleReader - Class in loci.formats.in

TrestleReader is the file format reader for Trestle slide datasets.

TrestleReader() - Constructor for class loci.formats.in.TrestleReader

Constructs a new Trestle reader.

trigger - Variable in class loci.formats.in.SDTInfo

TRIM_DIMENSIONS_DEFAULT - Static variable in class loci.formats.in.ZeissCZIReader

TRIM_DIMENSIONS_KEY - Static variable in class loci.formats.in.ZeissCZIReader

trimDimensions() - Method in class loci.formats.in.ZeissCZIReader

tSize - Variable in class loci.formats.in.DeltavisionReader

Size of one time element in the extended header.

tSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

Tstore - Variable in class loci.formats.in.SPCReader

U

UBMReader - Class in loci.formats.in

UBMReader is the file format reader for UBM .pr3 files.

UBMReader() - Constructor for class loci.formats.in.UBMReader

Constructs a new UBM reader.

UNINT16 - Static variable in class loci.formats.in.SPEReader

UNINT32 - Static variable in class loci.formats.in.SPEReader

UNISOKU_MAGIC_STRING - Static variable in class loci.formats.in.UnisokuReader

UnisokuReader - Class in loci.formats.in

UnisokuReader is the file format reader for Unisoku STM files.

UnisokuReader() - Constructor for class loci.formats.in.UnisokuReader

Constructs a new Unisoku reader.

unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Channel

unit - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.Dimension

UNKNOWN - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

USE_CHUNKMAP_DEFAULT - Static variable in class loci.formats.in.ND2Reader

USE_CHUNKMAP_KEY - Static variable in class loci.formats.in.ND2Reader

USE_CHUNKMAP_LEGACY_KEY - Static variable in class loci.formats.in.ND2Reader

Deprecated.

useChunkMap() - Method in class loci.formats.in.ND2Reader

useMotor - Variable in class loci.formats.in.SDTInfo

useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader

useOldPhysicalSizeCalculation() - Method in class loci.formats.in.LIFReader

V

valid() - Method in class loci.formats.in.BaseZeissReader.Tag

Check if the tag is valid (key, value and category have been set).

value() - Method in interface loci.formats.in.PrairieMetadata.Value

value() - Method in class loci.formats.in.PrairieMetadata.ValueItem

value() - Method in class loci.formats.in.PrairieMetadata.ValueTable

ValueItem(String, String) - Constructor for class loci.formats.in.PrairieMetadata.ValueItem

valueOf(String) - Static method in enum loci.formats.in.BaseZeissReader.Context

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum loci.formats.in.LOFReader.MetadataSource

Returns the enum constant of this type with the specified name.

values() - Static method in enum loci.formats.in.BaseZeissReader.Context

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Channel.ChannelType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSFileReader.ImageFormat

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum loci.formats.in.LOFReader.MetadataSource

Returns an array containing the constants of this enum type, in the order they are declared.

ValueTable() - Constructor for class loci.formats.in.PrairieMetadata.ValueTable

VarianFDFReader - Class in loci.formats.in

VarianFDFReader is the file format reader for Varian FDF files.

VarianFDFReader() - Constructor for class loci.formats.in.VarianFDFReader

Constructs a new Varian FDF reader.

VectraReader - Class in loci.formats.in

VectraReader is the reader for PerkinElmer Vectra QPTIFF data

VectraReader() - Constructor for class loci.formats.in.VectraReader

Constructs a new Vectra reader.

VeecoReader - Class in loci.formats.in

VeecoReader is the file format reader for Veeco HDF files.

VeecoReader() - Constructor for class loci.formats.in.VeecoReader

Constructs a new Veeco reader.

VentanaReader - Class in loci.formats.in

VentanaReader is the file format reader for Ventana .bif files.

VentanaReader() - Constructor for class loci.formats.in.VentanaReader

Constructs a new Ventana reader.

VERSION_KEY - Static variable in class loci.formats.in.LiFlimReader

VG_MAGIC_STRING - Static variable in class loci.formats.in.VGSAMReader

VGSAMReader - Class in loci.formats.in

VGSAMReader is the file format reader for VG SAM .dti files.

VGSAMReader() - Constructor for class loci.formats.in.VGSAMReader

Constructs a new VG SAM reader.

VisitechReader - Class in loci.formats.in

VisitechReader is the file format reader for Visitech XYS files.

VisitechReader() - Constructor for class loci.formats.in.VisitechReader

VolocityClippingReader - Class in loci.formats.in

VolocityClippingReader is the file format reader for Volocity library clipping files.

VolocityClippingReader() - Constructor for class loci.formats.in.VolocityClippingReader

Constructs a new Volocity clipping reader.

VolocityReader - Class in loci.formats.in

VolocityReader is the file format reader for Volocity library files.

VolocityReader() - Constructor for class loci.formats.in.VolocityReader

Constructs a new Volocity reader.

volumeType - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

W

WATOPReader - Class in loci.formats.in

WATOPReader is the file format reader for WA Technology .wat files.

WATOPReader() - Constructor for class loci.formats.in.WATOPReader

Constructs a new WA Technology reader.

wavelength - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

wavelengths - Variable in class loci.formats.in.CellWorxReader

WELL_COORDS - Static variable in class loci.formats.in.MetamorphReader

wellCount - Variable in class loci.formats.in.CellWorxReader

wellFiles - Variable in class loci.formats.in.CellWorxReader

width - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

width - Variable in class loci.formats.in.SDTInfo

with(int) - Static method in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

write(Kryo, Output) - Method in class loci.formats.services.NetCDFServiceImpl

wSize - Variable in class loci.formats.in.DeltavisionReader

Size of one wave in the extended header.

X

X - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

X_IMG_STRING - Static variable in class loci.formats.in.SDTInfo

X_KEY - Static variable in class loci.formats.in.LiFlimReader

X_STRING - Static variable in class loci.formats.in.SDTInfo

xAxis - Variable in class loci.formats.in.SDTInfo

X axis representation (SPC-930).

XlcfDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class loads and represents a Leica Microsystems XLCF xml document

XlcfDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlcfDocument

XlefDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class represents a Leica Microsystems XLEF xml document, a project file which references xlifs and optionally xlcfs

XlefDocument(String) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlefDocument

XLEFReader - Class in loci.formats.in

XLEFReader is the file format reader for Leica Microsystems' XLEF files.

XLEFReader() - Constructor for class loci.formats.in.XLEFReader

Constructs a new Leica XLEF reader.

XLIF - Enum constant in enum loci.formats.in.LOFReader.MetadataSource

XlifDocument - Class in loci.formats.in.LeicaMicrosystemsMetadata

This class loads and represents a Leica Microsystems XLIF xml document

XlifDocument(String, LMSCollectionXmlDocument) - Constructor for class loci.formats.in.LeicaMicrosystemsMetadata.XlifDocument

XML - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument.InitFrom

XML_NAME - Static variable in class loci.formats.in.ZeissTIFFReader

XML_SUFFIX - Static variable in class loci.formats.in.PrairieReader

XML_SUFFIX - Static variable in class loci.formats.in.TCSReader

xPath - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

xPath(String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Searches the XML document for expressions using xPath.

xPath(Node, String) - Method in class loci.formats.in.LeicaMicrosystemsMetadata.LMSXmlDocument

Searches a node for expressions using xPath.

xyGain - Variable in class loci.formats.in.SDTInfo

Gain for XY ADCs (SPC930).

Y

Y - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

Y_IMG_STRING - Static variable in class loci.formats.in.SDTInfo

Y_KEY - Static variable in class loci.formats.in.LiFlimReader

Y_STRING - Static variable in class loci.formats.in.SDTInfo

Z

Z - Enum constant in enum loci.formats.in.LeicaMicrosystemsMetadata.Dimension.DimensionKey

Z_KEY - Static variable in class loci.formats.in.LiFlimReader

ZeissCZIReader - Class in loci.formats.in

ZeissCZIReader is the file format reader for Zeiss .czi files.

ZeissCZIReader() - Constructor for class loci.formats.in.ZeissCZIReader

Constructs a new Zeiss .czi reader.

ZeissLMSReader - Class in loci.formats.in

Zeiss LMS reader for data from Zeiss CSM 700 systems.

ZeissLMSReader() - Constructor for class loci.formats.in.ZeissLMSReader

Constructs a new LMS reader.

ZeissLSMReader - Class in loci.formats.in

ZeissLSMReader is the file format reader for Zeiss LSM files.

ZeissLSMReader() - Constructor for class loci.formats.in.ZeissLSMReader

Constructs a new Zeiss LSM reader.

ZeissTIFFHandler - Class in loci.formats.in

SAX handler for parsing XML in Zeiss TIFF files.

ZeissTIFFHandler.Plane - Class in loci.formats.in

Metadata for a single image plane.

ZeissTIFFReader - Class in loci.formats.in

ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF files and their companion XML file.

ZeissTIFFReader() - Constructor for class loci.formats.in.ZeissTIFFReader

ZeissXRMReader - Class in loci.formats.in

ZeissXRMReader is the file format reader for Zeiss X-Ray Microscopy .txm and .txrm files.

ZeissXRMReader() - Constructor for class loci.formats.in.ZeissXRMReader

Constructs a new Zeiss XRM reader.

ZeissZVIReader - Class in loci.formats.in

ZeissZVIReader is the file format reader for Zeiss ZVI files.

ZeissZVIReader() - Constructor for class loci.formats.in.ZeissZVIReader

Constructs a new ZeissZVI reader.

zIndices - Variable in class loci.formats.in.BaseZeissReader

ZIP - Static variable in class loci.formats.in.PhotoshopTiffReader

zooms - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

ZPO_SUFFIX - Static variable in class loci.formats.in.PerkinElmerReader

zPosition - Variable in class loci.formats.in.OpenlabReader.PlaneInfo

zSize - Variable in class loci.formats.in.DeltavisionReader

Size of one z section in the extended header.

zSteps - Variable in class loci.formats.in.CellWorxReader

zSteps - Variable in class loci.formats.in.LeicaMicrosystemsMetadata.MetadataTempBuffer

ZVI_MAGIC_BYTES - Static variable in class loci.formats.in.ZeissZVIReader

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