Package | Description |
---|---|
loci.formats |
Bio-Formats: a library for reading and writing popular microscopy file
formats.
|
loci.formats.cache |
Package containing Bio-Formats caching logic, for managing
subsets of large collections of image planes in memory.
|
loci.formats.gui |
Package containing Bio-Formats graphical user interface code.
|
loci.formats.in |
Package containing Bio-Formats file format readers.
|
loci.formats.tools |
Package containing utility methods corresponding
to the Bio-Formats command line tools.
|
loci.plugins.in |
Bio-Formats Importer plugin for ImageJ.
|
loci.plugins.macro |
Bio-Formats Macro Extensions plugin for ImageJ.
|
loci.plugins.util |
Utility classes and methods for the Bio-Formats plugins for ImageJ.
|
Modifier and Type | Class and Description |
---|---|
class |
ChannelFiller
For indexed color data representing true color, factors out
the indices, replacing them with the color table values directly.
|
class |
ChannelMerger
Logic to automatically merge channels in a file.
|
class |
ChannelSeparator
Logic to automatically separate the channels in a file.
|
class |
DelegateReader
DelegateReader is a file format reader that selects which reader to use
for a format if there are two readers which handle the same format.
|
class |
DimensionSwapper
Handles swapping the dimension order of an image series.
|
class |
FileStitcher
Logic to stitch together files with similar names.
|
class |
FormatReader
Abstract superclass of all biological file format readers.
|
class |
ImageReader
ImageReader is the master file format reader for all supported formats.
|
class |
Memoizer
ReaderWrapper implementation which caches the state of the
delegate (including and other ReaderWrapper instances)
after Memoizer.setId(String) has been called. |
class |
MinMaxCalculator
Logic to compute minimum and maximum values for each channel.
|
class |
ReaderWrapper
Abstract superclass of reader logic that wraps other readers.
|
class |
SubResolutionFormatReader
Abstract superclass of all biological file format readers
that can handle image pyramids.
|
class |
TileStitcher |
class |
WrappedReader
Helper class for readers which wrap other readers.
|
Modifier and Type | Field and Description |
---|---|
protected IFormatReader |
DelegateReader.legacyReader
Legacy reader.
|
protected IFormatReader |
DelegateReader.nativeReader
Native reader.
|
protected IFormatReader |
ReaderWrapper.reader
FormatReader used to read the file.
|
private IFormatReader[] |
ImageReader.readers
List of supported file format readers.
|
Modifier and Type | Field and Description |
---|---|
private ClassList<IFormatReader> |
FileStitcher.classList |
private static ClassList<IFormatReader> |
ImageReader.defaultClasses
Default list of reader classes, for use with noargs constructor.
|
Modifier and Type | Method and Description |
---|---|
IFormatReader |
FileStitcher.getReader()
Gets the wrapped reader prototype.
|
IFormatReader |
ReaderWrapper.getReader()
Gets the wrapped reader.
|
IFormatReader |
ImageReader.getReader()
Gets the reader used to open the current file.
|
IFormatReader |
ImageReader.getReader(java.lang.Class<? extends IFormatReader> c)
Gets the file format reader instance matching the given class.
|
static IFormatReader |
FormatTools.getReader(IFormatReader r,
java.lang.Class<? extends IFormatReader> c)
Recursively look for the first underlying reader that is an
instance of the given class.
|
IFormatReader |
FileStitcher.getReader(int no)
Gets the reader appropriate for use with the given image plane.
|
IFormatReader |
ImageReader.getReader(java.lang.String id)
Gets the reader used to open the given file.
|
IFormatReader[] |
ImageReader.getReaders()
Gets all constituent file format readers.
|
IFormatReader[] |
FileStitcher.getUnderlyingReaders() |
IFormatReader[] |
WrappedReader.getUnderlyingReaders() |
IFormatReader[] |
ReaderWrapper.getUnderlyingReaders() |
IFormatReader[] |
ImageReader.getUnderlyingReaders() |
IFormatReader[] |
IFormatReader.getUnderlyingReaders()
Retrieves all underlying readers.
|
IFormatReader[] |
FormatReader.getUnderlyingReaders() |
protected IFormatReader |
Memoizer.handleMetadataStore(IFormatReader memo)
Return the
IFormatReader instance that is passed in or null if
it has been invalidated, which will include the instance being closed. |
IFormatReader |
Memoizer.loadMemo()
Load a memo file if possible, returning a null if not.
|
IFormatReader |
Memoizer.Deser.loadReader() |
IFormatReader |
Memoizer.KryoDeser.loadReader() |
IFormatReader |
Memoizer.RandomAccessDeser.loadReader() |
protected abstract IFormatReader |
Memoizer.RandomAccessDeser.readerFromBytes(java.lang.Class<IFormatReader> c,
byte[] rArr) |
IFormatReader |
ReaderWrapper.unwrap()
Unwraps nested wrapped readers until the core reader (i.e., not
a
ReaderWrapper or ImageReader ) is found. |
IFormatReader |
ReaderWrapper.unwrap(java.lang.Class<? extends IFormatReader> readerClass,
java.lang.String id)
Unwraps nested wrapped readers until the given reader class is found.
|
IFormatReader |
ReaderWrapper.unwrap(java.lang.String id)
Unwraps nested wrapped readers until the core reader (i.e., not
a
ReaderWrapper or ImageReader ) is found. |
Modifier and Type | Method and Description |
---|---|
static ClassList<IFormatReader> |
ImageReader.getDefaultReaderClasses() |
Modifier and Type | Method and Description |
---|---|
protected abstract byte[] |
Memoizer.RandomAccessDeser.bytesFromReader(IFormatReader reader) |
static void |
FormatTools.checkBufferSize(IFormatReader r,
int len) |
static void |
FormatTools.checkBufferSize(IFormatReader r,
int len,
int w,
int h)
Checks that the given buffer size is large enough to hold a w * h
image as returned by the given reader.
|
static void |
FormatTools.checkPlaneNumber(IFormatReader r,
int no)
Checks that the given plane number is valid for the given reader.
|
static void |
FormatTools.checkPlaneParameters(IFormatReader r,
int no,
int bufLength,
int x,
int y,
int w,
int h)
Convenience method for checking that the plane number, tile size and
buffer sizes are all valid for the given reader.
|
static void |
FormatTools.checkTileSize(IFormatReader r,
int x,
int y,
int w,
int h)
Checks that the given tile size is valid for the given reader.
|
CoreMetadata |
SwappableMetadata.clone(IFormatReader r,
int coreIndex) |
CoreMetadata |
CoreMetadata.clone(IFormatReader r,
int coreIndex) |
static void |
FormatTools.convert(IFormatReader input,
IFormatWriter output,
java.lang.String outputFile)
Convenience method for writing all of the images and metadata obtained
from the specified IFormatReader into the specified IFormatWriter.
|
static boolean |
FormatTools.equalReaders(IFormatReader a,
IFormatReader b)
Check if the two given readers are equal.
|
static java.lang.String |
FormatTools.getFilename(int series,
int image,
IFormatReader r,
java.lang.String pattern) |
static java.lang.String |
FormatTools.getFilename(int series,
int image,
IFormatReader r,
java.lang.String pattern,
boolean padded) |
static java.lang.String[] |
FormatTools.getFilenames(java.lang.String pattern,
IFormatReader r) |
static int |
FormatTools.getImagesPerFile(java.lang.String pattern,
IFormatReader r) |
static int |
FormatTools.getIndex(IFormatReader reader,
int z,
int c,
int t)
Gets the rasterized index corresponding
to the given Z, C and T coordinates (real sizes).
|
static int |
FormatTools.getIndex(IFormatReader reader,
int z,
int c,
int t,
int moduloZ,
int moduloC,
int moduloT)
Gets the rasterized index corresponding to the given Z, C, T,
ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
|
static int |
FormatTools.getPlaneSize(IFormatReader r)
Returns the size in bytes of a single plane.
|
static int |
FormatTools.getPlaneSize(IFormatReader r,
int w,
int h)
Returns the size in bytes of a w * h tile.
|
static IFormatReader |
FormatTools.getReader(IFormatReader r,
java.lang.Class<? extends IFormatReader> c)
Recursively look for the first underlying reader that is an
instance of the given class.
|
static int |
FormatTools.getReorderedIndex(IFormatReader reader,
java.lang.String newOrder,
int newIndex)
Converts index from the given dimension order to the reader's native one.
|
static int[] |
FormatTools.getZCTCoords(IFormatReader reader,
int index)
Gets the Z, C and T coordinates corresponding
to the given rasterized index value (real sizes).
|
static int[] |
FormatTools.getZCTModuloCoords(IFormatReader reader,
int index)
Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates
corresponding to the given rasterized index value (effective
sizes).
|
protected IFormatReader |
Memoizer.handleMetadataStore(IFormatReader memo)
Return the
IFormatReader instance that is passed in or null if
it has been invalidated, which will include the instance being closed. |
static boolean |
FormatTools.isFloatingPoint(IFormatReader reader)
Determines whether the given reader represents any floating point data.
|
private boolean |
ImageReader.isThisType(IFormatReader reader,
byte[] block) |
private boolean |
ImageReader.isThisType(IFormatReader reader,
loci.common.RandomAccessInputStream rais) |
private boolean |
ImageReader.isThisType(IFormatReader reader,
java.lang.String name,
boolean allowOpen) |
private void |
ImageReader.logIsThisTypeError(IFormatReader reader,
java.lang.Exception e) |
static ChannelFiller |
ChannelFiller.makeChannelFiller(IFormatReader r)
Converts the given reader into a ChannelFiller, wrapping if needed.
|
static ChannelMerger |
ChannelMerger.makeChannelMerger(IFormatReader r)
Converts the given reader into a ChannelMerger, wrapping if needed.
|
static ChannelSeparator |
ChannelSeparator.makeChannelSeparator(IFormatReader r)
Converts the given reader into a ChannelSeparator, wrapping if needed.
|
static DimensionSwapper |
DimensionSwapper.makeDimensionSwapper(IFormatReader r)
Converts the given reader into a DimensionSwapper, wrapping if needed.
|
static MinMaxCalculator |
MinMaxCalculator.makeMinMaxCalculator(IFormatReader r)
Converts the given reader into a MinMaxCalculator, wrapping if needed.
|
static TileStitcher |
TileStitcher.makeTileStitcher(IFormatReader r)
Converts the given reader into a TileStitcher, wrapping if needed.
|
static byte[] |
FormatTools.openThumbBytes(IFormatReader reader,
int no)
Default implementation for
openThumbBytes(int) . |
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r,
boolean doPlane)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixels(MetadataStore store,
IFormatReader r,
boolean doPlane,
boolean doImageName)
Populates the Pixels element of the given metadata store, using core
metadata from the given reader.
|
static void |
MetadataTools.populatePixelsOnly(MetadataStore store,
IFormatReader r) |
void |
Memoizer.Deser.saveReader(IFormatReader reader) |
void |
Memoizer.KryoDeser.saveReader(IFormatReader reader) |
void |
Memoizer.RandomAccessDeser.saveReader(IFormatReader reader) |
Modifier and Type | Method and Description |
---|---|
ReaderWrapper |
ReaderWrapper.duplicate(java.lang.Class<? extends IFormatReader> imageReaderClass)
Performs a deep copy of the reader, including nested wrapped readers.
|
private ReaderWrapper |
ReaderWrapper.duplicateRecurse(java.lang.Class<? extends IFormatReader> imageReaderClass) |
IFormatReader |
ImageReader.getReader(java.lang.Class<? extends IFormatReader> c)
Gets the file format reader instance matching the given class.
|
static IFormatReader |
FormatTools.getReader(IFormatReader r,
java.lang.Class<? extends IFormatReader> c)
Recursively look for the first underlying reader that is an
instance of the given class.
|
protected abstract IFormatReader |
Memoizer.RandomAccessDeser.readerFromBytes(java.lang.Class<IFormatReader> c,
byte[] rArr) |
void |
FileStitcher.setReaderClassList(ClassList<IFormatReader> classList)
Set the ClassList object to use when constructing any helper readers.
|
IFormatReader |
ReaderWrapper.unwrap(java.lang.Class<? extends IFormatReader> readerClass,
java.lang.String id)
Unwraps nested wrapped readers until the given reader class is found.
|
Constructor and Description |
---|
ChannelFiller(IFormatReader r)
Constructs a ChannelFiller with a given reader.
|
ChannelMerger(IFormatReader r)
Constructs a ChannelMerger with the given reader.
|
ChannelSeparator(IFormatReader r)
Constructs a ChannelSeparator with the given reader.
|
CoreMetadata(IFormatReader r,
int coreIndex) |
DimensionSwapper(IFormatReader r)
Constructs a DimensionSwapper with the given reader.
|
FileStitcher(IFormatReader r)
Constructs a FileStitcher with the given reader.
|
FileStitcher(IFormatReader r,
boolean patternIds)
Constructs a FileStitcher with the given reader.
|
Memoizer(IFormatReader r)
Constructs a memoizer around the given
IFormatReader creating
memo files under the same directory as the original file only if the
call to Memoizer.setId(java.lang.String) takes longer than
100L in milliseconds. |
Memoizer(IFormatReader r,
long minimumElapsed)
Constructs a memoizer around the given
IFormatReader creating
memo files under the same directory as the original file only if the
call to Memoizer.setId(java.lang.String) takes longer than minimumElapsed in
milliseconds. |
Memoizer(IFormatReader r,
long minimumElapsed,
java.io.File directory)
Constructs a memoizer around the given
IFormatReader creating
memo files under the directory argument including the full path
of the original file only if the call to Memoizer.setId(java.lang.String) takes longer than
minimumElapsed in milliseconds. |
MinMaxCalculator(IFormatReader r)
Constructs a MinMaxCalculator with the given reader.
|
ReaderWrapper(IFormatReader r)
Constructs a reader wrapper around the given reader.
|
SwappableMetadata(IFormatReader r,
int seriesNo) |
TileStitcher(IFormatReader r)
Constructs a TileStitcher with the given reader.
|
Constructor and Description |
---|
ImageReader(ClassList<IFormatReader> classList)
Constructs a new ImageReader from the given list of reader classes.
|
Modifier and Type | Field and Description |
---|---|
protected IFormatReader |
CacheSource.reader
Reader from which to draw image planes.
|
Constructor and Description |
---|
ByteArraySource(IFormatReader r)
Constructs a byte array source from the given Bio-Formats reader.
|
CacheSource(IFormatReader r)
Constructs a cache source from the given Bio-Formats reader.
|
Modifier and Type | Class and Description |
---|---|
class |
BufferedImageReader
A reader wrapper for reading image planes as BufferedImage objects.
|
Modifier and Type | Field and Description |
---|---|
protected IFormatReader |
ImageViewer.fileReader
Reader for files on disk.
|
protected IFormatReader |
ImageViewer.in |
private IFormatReader |
FormatFileFilter.reader
Associated file format reader.
|
Modifier and Type | Method and Description |
---|---|
IFormatReader |
FormatFileFilter.getReader()
Returns the filter's reader.
|
Modifier and Type | Method and Description |
---|---|
static BufferedImageReader |
BufferedImageReader.makeBufferedImageReader(IFormatReader r)
Converts the given reader into a BufferedImageReader, wrapping if needed.
|
protected void |
ImageViewer.open(java.lang.String id,
IFormatReader r)
Opens from the given data source using the specified reader
in a separate thread.
|
static java.awt.image.BufferedImage |
AWTImageTools.openImage(byte[] buf,
IFormatReader r,
int w,
int h)
Creates an image from the given byte array, using the given
IFormatReader to retrieve additional information.
|
static java.awt.image.BufferedImage |
AWTImageTools.openImage(byte[] buf,
IFormatReader r,
int w,
int h,
boolean normal)
Creates an image from the given byte array, using the given
IFormatReader to retrieve additional information.
|
void |
ImageViewer.setImages(IFormatReader reader,
java.awt.image.BufferedImage[] img)
Sets the viewer to display the given images, obtaining
corresponding core metadata from the specified format reader.
|
Constructor and Description |
---|
BufferedImageReader(IFormatReader r)
Constructs a BufferedImageReader with the given reader.
|
BufferedImageSource(IFormatReader reader) |
FormatFileFilter(IFormatReader reader)
Constructs a new filter that accepts files of the given reader's type.
|
FormatFileFilter(IFormatReader reader,
boolean allowOpen)
Constructs a new filter that accepts files of the given reader's type,
allowing the reader to open files only if the allowOpen flag is set.
|
Modifier and Type | Class and Description |
---|---|
class |
AFIReader
AFIReader is the file format reader for Aperio AFI files.
|
class |
AIMReader
AIMReader is the file format reader for .aim files.
|
class |
AliconaReader
AliconaReader is the file format reader for Alicona AL3D files.
|
class |
AmiraReader
This is a file format reader for AmiraMesh data.
|
class |
AnalyzeReader
AnalyzeReader is the file format reader for Analyze 7.5 files.
|
class |
APLReader
APLReader is the file format reader for Olympus APL files.
|
class |
APNGReader
APNGReader is the file format reader for
Animated Portable Network Graphics (APNG) images.
|
class |
ARFReader
ARFReader is the file format reader for Axon Raw Format (ARF) files,
produced by INDEC BioSystems's
Imaging Workbench
software.
|
class |
AVIReader
AVIReader is the file format reader for AVI files.
|
class |
BaseTiffReader
BaseTiffReader is the superclass for file format readers compatible with
or derived from the TIFF 6.0 file format.
|
class |
BaseZeissReader
BaseZeissReader contains common functionality required by
readers for Zeiss AxioVision formats.
|
class |
BDReader
BDReader is the file format reader for BD Pathway datasets.
|
class |
BDVReader
Reader for BDV files.
|
class |
BIFormatReader
BIFormatReader is the superclass for file format readers
that use java.awt.image.BufferedImage as the native data type.
|
class |
BioRadGelReader
BioRadGelReader is the file format reader for Bio-Rad gel files.
|
class |
BioRadReader
BioRadReader is the file format reader for Bio-Rad PIC files.
|
class |
BioRadSCNReader
BioRadSCNReader is the reader for Bio-Rad .scn files
|
class |
BMPReader
BMPReader is the file format reader for Microsoft Bitmap (BMP) files.
|
class |
BrukerReader
BrukerReader is the file format reader for Bruker MRI files.
|
class |
BurleighReader
BurleighReader is the file format reader for Burleigh .img files.
|
class |
CanonRawReader
CanonRawReader is the file format reader for Canon RAW files.
|
class |
CellH5Reader
Reader for CellH5 (HDF) files.
|
class |
CellomicsReader
Reader for Cellomics C01 files.
|
class |
CellSensReader
CellSensReader is the file format reader for cellSens .vsi files.
|
class |
CellVoyagerReader
A bioformat reader for the Yokagawa Cellvoyager CV1000 automated microscope (
http://www.yokogawa.com/scanner/products/cv1000e.htm).
|
class |
CellWorxReader
CellWorxReader is the file format reader for CellWorx .pnl files.
|
class |
ColumbusReader
ColumbusReader is the file format reader for screens exported from PerkinElmer Columbus.
|
class |
CV7000Reader |
class |
DeltavisionReader
DeltavisionReader is the file format reader for Deltavision files.
|
class |
DicomReader
DicomReader is the file format reader for DICOM files.
|
class |
DNGReader
DNGReader is the file format reader for Canon DNG (TIFF) files.
|
class |
Ecat7Reader
Ecat7Reader is the file format reader for ECAT 7 files.
|
class |
EPSReader
Reader is the file format reader for Encapsulated PostScript (EPS) files.
|
class |
FakeReader
FakeReader is the file format reader for faking input data.
|
class |
FEIReader
FEIReader is the file format reader for FEI and Philips .img files.
|
class |
FEITiffReader
FEITiffReader is the file format reader for TIFF files produced by various
FEI software.
|
class |
FilePatternReader |
class |
FitsReader
FitsReader is the file format reader for
Flexible Image Transport System (FITS) images.
|
class |
FlexReader
FlexReader is a file format reader for Evotec Flex files.
|
class |
FlowSightReader |
class |
FluoviewReader
FluoviewReader is the file format reader for
Olympus Fluoview TIFF files AND Andor Bio-imaging Division (ABD) TIFF files.
|
class |
FujiReader
FujiReader is the file format reader for Fuji LAS 3000 datasets.
|
class |
FV1000Reader
FV1000Reader is the file format reader for Fluoview FV 1000 OIB and
Fluoview FV 1000 OIF files.
|
class |
GatanDM2Reader
GatanDM2Reader is the file format reader for Gatan .dm2 files.
|
class |
GatanReader
GatanReader is the file format reader for Gatan files.
|
class |
GelReader
GelReader is the file format reader for
Molecular Dynamics GEL TIFF files.
|
class |
GIFReader
GIFReader is the file format reader for Graphics Interchange Format
(GIF) files.
|
class |
HamamatsuVMSReader
HamamatsuVMSReader is the file format reader for Hamamatsu VMS datasets.
|
class |
HISReader
HISReader is the file format reader for Hamamatsu .his files.
|
class |
HitachiReader
HitachiReader is the file format reader for S-4800 files.
|
class |
HRDGDFReader
HRDGDFReader is the file format reader for the Gridded Data Format used
by NOAA's Hurricane Research Division.
|
class |
I2IReader
I2IReader is the file format reader for I2I files.
|
class |
ICSReader
ICSReader is the file format reader for ICS (Image Cytometry Standard)
files.
|
class |
IM3Reader |
class |
ImaconReader
ImaconReader is the file format reader for Imacon .fff (TIFF) files.
|
class |
ImageIOReader
ImageIOReader is the superclass for file format readers
that use the javax.imageio package.
|
class |
ImagicReader
ImagicReader is the file format reader for IMAGIC files.
|
class |
ImarisHDFReader
Reader for Bitplane Imaris 5.5 (HDF) files.
|
class |
ImarisReader
ImarisReader is the file format reader for Bitplane Imaris files.
|
class |
ImarisTiffReader
ImarisTiffReader is the file format reader for
Bitplane Imaris 3 files (TIFF variant).
|
class |
IMODReader
Reader for IMOD binary files.
|
class |
ImprovisionTiffReader
ImprovisionTiffReader is the file format reader for
Improvision TIFF files.
|
class |
ImspectorReader
ImspectorReader is the file format reader for Imspector .msr files.
|
class |
InCell3000Reader
InCell3000Reader is the file format reader for InCell 3000.
|
class |
InCellReader
InCellReader is the file format reader for InCell 1000/2000 datasets.
|
class |
INRReader
INRReader is the file format reader for INR files.
|
class |
InveonReader
InveonReader is the file format reader for Inveon files.
|
class |
IonpathMIBITiffReader
IonpathMIBITiffReader is the file format reader for Ionpath MIBI TIFF files.
|
class |
IPLabReader
IPLabReader is the file format reader for IPLab (.IPL) files.
|
class |
IPWReader
IPWReader is the file format reader for Image-Pro Workspace (IPW) files.
|
class |
IvisionReader
IvisionReader is the file format reader for IVision (.IPM) files.
|
class |
JEOLReader
JEOLReader is the file format reader for JEOL files.
|
class |
JPEG2000Reader
JPEG2000Reader is the file format reader for JPEG-2000 images.
|
class |
JPEGReader
JPEGReader is the file format reader for JPEG images.
|
(package private) static class |
JPEGReader.DefaultJPEGReader |
class |
JPKReader
JPKReader is the file format reader for JPK Instruments files.
|
class |
JPXReader
JPXReader is the file format reader for JPX (3D JPEG-2000) images.
|
class |
KhorosReader
Reader for Khoros XV files.
|
class |
KLBReader
Reader for Keller Lab Block (KLB) files.
|
class |
KodakReader
KodakReader is the file format reader for Kodak Molecular Imaging .bip files.
|
class |
L2DReader
L2DReader is the file format reader for Li-Cor L2D datasets.
|
class |
LegacyND2Reader
LegacyND2Reader is a file format reader for Nikon ND2 files that uses
the Nikon ND2 SDK - it is only usable on Windows machines.
|
class |
LegacyQTReader
LegacyQTReader is a file format reader for QuickTime movie files.
|
class |
LeicaReader
LeicaReader is the file format reader for Leica files.
|
class |
LeicaSCNReader
LeicaSCNReader is the file format reader for Leica SCN TIFF files.
|
class |
LEOReader
LEOReader is the file format reader for LEO EM files.
|
class |
LiFlimReader
LiFlimReader is the file format reader for LI-FLIM files.
|
class |
LIFReader
LIFReader is the file format reader for Leica LIF files.
|
class |
LIMReader
LIMReader is the file format reader for Laboratory Imaging/Nikon LIM files.
|
class |
MetamorphReader
Reader is the file format reader for Metamorph STK files.
|
class |
MetamorphTiffReader
MetamorphTiffReader is the file format reader for TIFF files produced by
Metamorph software version 7.5 and above.
|
class |
MIASReader
MIASReader is the file format reader for Maia Scientific MIAS-2 datasets.
|
class |
MicroCTReader
MicroCTReader is the file format reader for VFF files from a GE MicroCT scanner.
|
class |
MicromanagerReader
MicromanagerReader is the file format reader for Micro-Manager files.
|
class |
MikroscanTiffReader
MikroscanTiffReader is the file format reader for Mikroscan TIFF files.
|
class |
MINCReader
MINCReader is the file format reader for MINC MRI files.
|
class |
MinimalTiffReader
MinimalTiffReader is the superclass for file format readers compatible with
or derived from the TIFF 6.0 file format.
|
class |
MNGReader
MNGReader is the file format reader for Multiple-image Network Graphics
(MNG) files.
|
class |
MolecularImagingReader
MolecularImagingReader is the file format reader for Molecular Imaging files.
|
class |
MRCReader
MRCReader is the file format reader for MRC files.
|
class |
MRWReader
MRWReader is the file format reader for Minolta MRW files.
|
class |
NAFReader
NAFReader is the file format reader for Hamamatsu Aquacosmos NAF files.
|
class |
NativeND2Reader
NativeND2Reader is the file format reader for Nikon ND2 files.
|
class |
NativeQTReader
NativeQTReader is the file format reader for QuickTime movie files.
|
class |
ND2Reader
ND2Reader is the file format reader for Nikon ND2 files.
|
class |
NDPIReader
NDPIReader is the file format reader for Hamamatsu .ndpi files.
|
class |
NDPISReader
NDPISReader is the file format reader for Hamamatsu .ndpis files.
|
class |
NiftiReader
NiftiReader is the file format reader for NIfTI files.
|
class |
NikonElementsTiffReader
NikonElementsTiffReader is the file format reader for TIFF files produced
by Nikon Elements.
|
class |
NikonReader
NikonReader is the file format reader for Nikon NEF (TIFF) files.
|
class |
NikonTiffReader
NikonTiffReader is the file format reader for Nikon TIFF files.
|
class |
NRRDReader
File format reader for NRRD files; see http://teem.sourceforge.net/nrrd.
|
class |
OBFReader
OBFReader is the file format reader for Imspector OBF files.
|
class |
OIRReader
OIRReader is the file format reader for Olympus .oir files.
|
class |
OMETiffReader
OMETiffReader is the file format reader for
OME-TIFF
files.
|
class |
OMEXMLReader
OMEXMLReader is the file format reader for OME-XML files.
|
class |
OpenlabRawReader
OpenlabRawReader is the file format reader for Openlab RAW files.
|
class |
OpenlabReader
OpenlabReader is the file format reader for Openlab LIFF files.
|
class |
OperettaReader
OperettaReader is the file format reader for PerkinElmer Operetta data.
|
class |
OxfordInstrumentsReader
OxfordInstrumentsReader is the file format reader for
Oxford Instruments .top files.
|
class |
PCIReader
PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
|
class |
PCORAWReader
PCORAWReader is the file format reader for PCORAW files.
|
class |
PCXReader
PCXReader is the file format reader for PCX files (originally used by
PC Paintbrush; now used in Zeiss' LSM Image Browser).
|
class |
PDSReader
PDSReader is the file format reader for Perkin Elmer densitometer files.
|
class |
PerkinElmerReader
PerkinElmerReader is the file format reader for PerkinElmer files.
|
class |
PGMReader
PGMReader is the file format reader for Portable Gray Map (PGM) images.
|
class |
PhotoshopTiffReader
PhotoshopTiffReader is the file format reader for
Adobe Photoshop TIFF files.
|
class |
PictReader
PictReader is the file format reader for Apple PICT files.
|
class |
PovrayReader
PovrayReader is the file format reader for POV-Ray .df3 files.
|
class |
PQBinReader
PQBinReader is the file format reader for PicoQuant .bin files.
|
class |
PrairieReader
PrairieReader is the file format reader for
Prairie Technologies' TIFF variant.
|
class |
PSDReader
PSDReader is the file format reader for Photoshop PSD files.
|
class |
PyramidTiffReader
PyramidTiffReader is the file format reader for pyramid TIFFs.
|
class |
QTReader
QTReader is the file format reader for QuickTime movie files.
|
class |
QuesantReader
QuesantReader is the file format reader for Quesant .afm files.
|
class |
RCPNLReader |
class |
RHKReader
RHKReader is the file format reader for RHK Technologies files.
|
class |
SBIGReader
SBIGReader is the file format reader for SBIG files.
|
class |
ScanrReader
ScanrReader is the file format reader for Olympus ScanR datasets.
|
class |
SDTReader
SDTReader is the file format reader for
Becker & Hickl SPC-Image SDT files.
|
class |
SeikoReader
SeikoReader is the file format reader for Seiko .xqd/.xqf files.
|
class |
SEQReader
SEQReader is the file format reader for Image-Pro Sequence files.
|
class |
SIFReader
SIFReader is the file format reader for Andor SIF files.
|
class |
SimplePCITiffReader
SimplePCITiffReader is the file format reader for TIFF files produced by
SimplePCI software.
|
class |
SISReader
SISReader is the file format reader for Olympus Soft Imaging Solutions
TIFF files.
|
class |
SlidebookReader
SlidebookReader is the file format reader for 3I Slidebook files.
|
class |
SlidebookTiffReader |
class |
SMCameraReader
SMCameraReader is the file format reader for SM camera files.
|
class |
SPCReader
SPCReader is the file format reader for
Becker & Hickl SPC-Image SPC FIFO files.
|
class |
SPEReader
SPEReader is the file format reader for Princeton Instruments SPE .spe files.
|
class |
SpiderReader
SpiderReader is the file format reader for SPIDER files.
|
class |
SVSReader
SVSReader is the file format reader for Aperio SVS TIFF files.
|
class |
TargaReader
File format reader for Truevision Targa files.
|
class |
TCSReader
TCSReader is the file format reader for Leica TCS TIFF files and their
companion XML file.
|
class |
TextReader
Reader for text files containing tables of data.
|
class |
TiffDelegateReader
TiffDelegateReader is a file format reader for TIFF files.
|
class |
TiffJAIReader
TiffJAIReader is a file format reader for TIFF images.
|
class |
TiffReader
TiffReader is the file format reader for regular TIFF files,
not of any specific TIFF variant.
|
class |
TileJPEGReader
Reader for decoding JPEG images using java.awt.Toolkit and TurboJPEG.
|
class |
TillVisionReader
TillVisionReader is the file format reader for TillVision files.
|
class |
TopometrixReader
TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr,
.zfr, .zfp, and .2fl files.
|
class |
TrestleReader
TrestleReader is the file format reader for Trestle slide datasets.
|
class |
UBMReader
UBMReader is the file format reader for UBM .pr3 files.
|
class |
UnisokuReader
UnisokuReader is the file format reader for Unisoku STM files.
|
class |
VarianFDFReader
VarianFDFReader is the file format reader for Varian FDF files.
|
class |
VectraReader
VectraReader is the reader for PerkinElmer Vectra QPTIFF data
|
class |
VeecoReader
VeecoReader is the file format reader for Veeco HDF files.
|
class |
VentanaReader
VentanaReader is the file format reader for Ventana .bif files.
|
class |
VGSAMReader
VGSAMReader is the file format reader for VG SAM .dti files.
|
class |
VisitechReader
VisitechReader is the file format reader for Visitech XYS files.
|
class |
VolocityClippingReader
VolocityClippingReader is the file format reader for Volocity library
clipping files.
|
class |
VolocityReader
VolocityReader is the file format reader for Volocity library files.
|
class |
WATOPReader
WATOPReader is the file format reader for WA Technology .wat files.
|
class |
WlzReader
WlzReader is a file format reader for Woolz files.
|
class |
ZeissCZIReader
ZeissCZIReader is the file format reader for Zeiss .czi files.
|
class |
ZeissLMSReader
Zeiss LMS reader for data from Zeiss CSM 700 systems.
|
class |
ZeissLSMReader
ZeissLSMReader is the file format reader for Zeiss LSM files.
|
class |
ZeissTIFFReader
ZeissTIFFReader is the file format reader for Zeiss AxioVision TIFF
files and their companion XML file.
|
class |
ZeissZVIReader
ZeissZVIReader is the file format reader for Zeiss ZVI files.
|
class |
ZipReader
Reader for Zip files.
|
Modifier and Type | Field and Description |
---|---|
private IFormatReader |
CellWorxReader.lastReader |
IFormatReader |
OMETiffReader.OMETiffPlane.reader
Reader to use for accessing this plane.
|
Modifier and Type | Method and Description |
---|---|
private IFormatReader |
CellWorxReader.getReader(java.lang.String file,
boolean omexml) |
Modifier and Type | Method and Description |
---|---|
private void |
OMETiffReader.initializeReader(IFormatReader r,
java.lang.String file) |
private void |
OMETiffReader.removeIFDComments(IFormatReader r) |
Modifier and Type | Method and Description |
---|---|
private static int[] |
CacheConsole.getLengths(IFormatReader r)
Helper utility for constructing lengths array, used by main.
|
Modifier and Type | Field and Description |
---|---|
private IFormatReader |
ImportProcess.baseReader |
Modifier and Type | Method and Description |
---|---|
IFormatReader |
ImportProcess.getBaseReader()
Valid only after
ImportStep.READER . |
Modifier and Type | Method and Description |
---|---|
private void |
ImportProcess.computeSeriesLabels(IFormatReader r) |
private java.lang.String |
ImagePlusReader.constructImageTitle(IFormatReader r,
java.lang.String file,
java.lang.String seriesName,
boolean groupFiles) |
private java.lang.String |
ImagePlusReader.constructSliceLabel(int ndx,
IFormatReader r,
IMetadata meta,
int series,
int zCount,
int cCount,
int tCount) |
Constructor and Description |
---|
ImporterMetadata(IFormatReader r,
ImportProcess process,
boolean usePrefix) |
ThumbLoader(IFormatReader ir,
java.awt.Panel[] p,
java.awt.Dialog dialog)
Constructs a new thumbnail loader.
|
Modifier and Type | Method and Description |
---|---|
private static int |
LociFunctions.getPlaneIndex(IFormatReader r,
int no)
Finds the Plane index corresponding to the given image plane number.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageProcessorReader
A low-level reader for
ImageProcessor objects. |
class |
VirtualReader
TODO
|
Modifier and Type | Field and Description |
---|---|
private IFormatReader |
VirtualImagePlus.r |
Modifier and Type | Method and Description |
---|---|
protected static int |
BFVirtualStack.getHeight(IFormatReader r,
java.lang.String path,
int series) |
protected static int |
BFVirtualStack.getWidth(IFormatReader r,
java.lang.String path,
int series) |
static boolean |
LociPrefs.isWindowless(IFormatReader r)
Gets whether windowless mode should be used when
opening this reader's currently initialized dataset.
|
static ImageProcessorReader |
ImageProcessorReader.makeImageProcessorReader(IFormatReader r)
Converts the given reader into a ImageProcessorReader, wrapping if needed.
|
void |
VirtualImagePlus.setReader(IFormatReader r) |
Modifier and Type | Method and Description |
---|---|
private static boolean |
LociPrefs.getPref(java.lang.String pref,
java.lang.Class<? extends IFormatReader> c,
boolean defaultValue) |
static boolean |
LociPrefs.isReaderEnabled(java.lang.Class<? extends IFormatReader> c) |
Constructor and Description |
---|
BFVirtualStack(java.lang.String path,
IFormatReader r,
boolean colorize,
boolean merge,
boolean record) |
ImageProcessorReader(IFormatReader r)
Constructs an ImageProcessorReader with the given reader.
|
ImageProcessorSource(IFormatReader reader) |
VirtualReader(IFormatReader r) |
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