Index

A B C D E F G I J L M N O P Q R S T U V W Z 
All Classes and Interfaces|All Packages

A

actionWriter - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.OmeTiffWriterAction
 
actionWriter - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.OmeZarrWriterAction
 
ALLOW_MEMOIZATION_PROPERTY - Static variable in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
System property controlling whether memoization is allowed or not.
allowMemoization() - Static method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Check whether memoization should be allowed or not.
allTimePoints() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that all timepoints of a time series will be written.
allZSlices() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that all z-slices are exported.

B

bigTiff() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that the image is written in BigTIFF format.
bigTiff(boolean) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify whether the image should be written in BigTIFF format.
bioformatsEnabled() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Returns true if Bio-Formats is enabled and may be used to read images.
BioFormatsImageServer - Class in qupath.lib.images.servers.bioformats
QuPath ImageServer that uses the Bio-Formats library to read image data.
BioFormatsImageServer(URI, String...) - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Create an ImageServer using the Bio-Formats library.
BioFormatsOptionsExtension - Class in qupath.lib.images.servers.bioformats
A QuPath extension that adds options relating to the BioFormatsImageServer to the main QuPath preference pane.
BioFormatsOptionsExtension() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
 
BioFormatsOptionsExtension.BioFormatsPreferences - Class in qupath.lib.images.servers.bioformats
 
BioFormatsOptionsExtension.OmeTiffWriterAction - Class in qupath.lib.images.servers.bioformats
 
BioFormatsOptionsExtension.OmeZarrWriterAction - Class in qupath.lib.images.servers.bioformats
 
BioFormatsServerBuilder - Class in qupath.lib.images.servers.bioformats
Builder for ImageServers that make use of the Bio-Formats library.
BioFormatsServerBuilder() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
BioFormatsServerOptions - Class in qupath.lib.images.servers.bioformats
Container for various options that can customize the behavior of the BioFormatsImageServer.
build() - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
Creates a new OMEPixelParser instance.
build() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Create an OMEPyramidWriter.OMEPyramidSeries to write the OME-TIFF.
build(String) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Create a new instance of OMEZarrWriter.
Builder() - Constructor for class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 
Builder(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Constructor.
Builder(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Create the builder.
buildServer(URI, String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
byteOrder(ByteOrder) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 

C

channels(int...) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Override default of writing all channels in their original order to be able to specify which channels are output, and in which order.
channelsImages() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that channels are written as separate images.
channelsInterleaved() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that channels are written interleaved within a single image plane.
channelsPlanar() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request that channels are written as separate image planes.
checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
clearReaderOptions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Clear all reader options, returning these to their defaults.
close() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
close() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter
Close this writer.
codecOptions(CodecOptions) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Set options for compressing data.
compression(Compressor) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Set the compressor to use when writing tiles.
compression(OMEPyramidWriter.CompressionType) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request the output compression type.
ConvertCommand - Class in qupath.lib.images.writers.ome
Allows command line option to convert an input image to OME-TIFF or OME-Zarr.
ConvertCommand() - Constructor for class qupath.lib.images.writers.ome.ConvertCommand
 
createID() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
createServerBuilder() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Returns a builder capable of creating a server like this one.
createWriter(Collection<OMEPyramidWriter.OMEPyramidSeries>) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Create a writer capable of writing an image with a collection of series.
createWriter(OMEPyramidWriter.OMEPyramidSeries...) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Create a writer capable of writing an image with one or more series.

D

DEFAULT - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Leave it up to the writer to choose the appropriate method.
DEFAULT - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Default (QuPath will select compression option based on image size and type, may be lossless or lossy).
downsamples(double...) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify downsample factors to use in the final pyramid.
downsamples(double...) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Enable the creation of a pyramidal image with the provided downsamples.
dumpMetadata() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Retrieve a string representation of the metadata OME-XML.
dyadicDownsampling() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Downsample by factors of 2.

E

effectiveNChannels(int) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 
enableBioformats - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 

F

filesOnly - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 
fromFriendlyString(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Get the CompressionType corresponding to the given input

G

getAssociatedImage(String) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
getAssociatedImageList() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
getDefaultPyramidCompression() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
Query the default compression type when writing OME-TIFF images.
getDefaultTileSize() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
Query the default tile size when writing OME-TIFF images.
getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
 
getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
getDetails() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
getDetails() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
getExtensions() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
getExtensions() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
getFile() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Get the underlying file.
getFilesOnly() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Returns true if Bio-Formats is restricted to support only local files, not other URLs.
getFormat() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Get the format String, as returned by Bio-Formats IFormatReader.getFormat().
getImageClass() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
getImageClass() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
getImageType() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
getInstance() - Static method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Get the static instance of BioFormatsServerOptions, available to servers being constructed.
getMemoizationTimeMillis() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Returns the number of milliseconds that must elapse when opening an image before a memoization file is generated.
getMetadataStore() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Get the MetadataStore, as used by Bio-Formats.
getMinSizeForTiling() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
Query the default minimum image size when writing OME-TIFF images.
getName() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
 
getName() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
getName() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
getName() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
getOMEString(ImageServer<?>) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Get the String representation understood by OMETiffWriter.
getOriginalMetadata() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
getPathMemoization() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Get the path to the directory where memoization files should be written, or null if no path is set.
getQuPathVersion() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
Returns the version stored within this jar, because it is matched to the QuPath version.
getReaderOptions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Get a map representing additional arguments that should be passed to readers.
getReaderServer() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter
Get the image server used internally by this writer to read the tiles.
getSeries() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
Get the series index, as used by Bio-Formats.
getServerType() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
getSkipAlwaysExtensions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Query the set of file extensions for which Bio-Formats should not be used.
getURIs() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
getUseAlwaysExtensions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Query the set of file extensions for which Bio-Formats should always be used.

I

IMAGES - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Channels are stored as separate images (this is not yet supported!).
installExtension(QuPathGUI) - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
 
INTERLEAVED - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Channels are interleaved ('PLANARCONFIG_CONTIG').
isInterleaved(boolean) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 

J

J2K - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Lossless JPEG-2000 compression.
J2K_LOSSY - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Lossy JPEG-2000 compression.
JPEG - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
JPEG compression (only for single channel or RGB 8-bit images).

L

losslessCompression() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request the default lossless compression method.
lossyCompression() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request the default lossy compression method.
LZW - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
LZW compression.

M

matchClassName(String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
 
memoizationTimeMillis - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 

N

name(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify a series name
normalizeFloats(boolean) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 

O

OMEPixelParser - Class in qupath.lib.images.servers.bioformats
This class can parse raw bytes into a BufferedImage.
OMEPixelParser.Builder - Class in qupath.lib.images.servers.bioformats
Builder for instances of OMEPixelParser.
OMEPyramidWriter - Class in qupath.lib.images.writers.ome
Write OME-TIFF files based on QuPath ImageServers.
OMEPyramidWriter.Builder - Class in qupath.lib.images.writers.ome
Builder class to define parameters when exporting an image region as OME-TIFF, possibly as an image pyramid.
OMEPyramidWriter.ChannelExportType - Enum Class in qupath.lib.images.writers.ome
Enum representing different ways in which channels may be written to a file.
OMEPyramidWriter.CompressionType - Enum Class in qupath.lib.images.writers.ome
Preferred compression type when using Bio-Formats.
OMEPyramidWriter.OMEPyramidSeries - Class in qupath.lib.images.writers.ome
Class representing a single series to write to an OME-TIFF.
OMEPyramidWriterCommand - Class in qupath.lib.images.writers.ome
OME TIFF writer command capable of exporting image pyramids based on QuPath ImageServers.
OMEPyramidWriterCommand(QuPathGUI) - Constructor for class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
Constructor.
OMETiffWriter - Class in qupath.lib.images.writers.ome
ImageWriter for writing OME-TIFF images.
OMETiffWriter() - Constructor for class qupath.lib.images.writers.ome.OMETiffWriter
 
OMEZarrImageWriter - Class in qupath.lib.images.writers.ome.zarr
An ImageWriter for writing OME-zarr files.
OMEZarrImageWriter() - Constructor for class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
OMEZarrWriter - Class in qupath.lib.images.writers.ome.zarr
Create an OME-Zarr file writer as described by version 0.4 of the specifications of the Next-generation file formats (NGFF).
OMEZarrWriter.Builder - Class in qupath.lib.images.writers.ome.zarr
Builder to create an instance of a OMEZarrWriter.
OmeZarrWriterAction(QuPathGUI) - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.OmeZarrWriterAction
 
OMEZarrWriterCommand - Class in qupath.lib.images.writers.ome.zarr
A GUI command to export the current ImageServer to an OME Zarr directory.
OMEZarrWriterCommand(QuPathGUI) - Constructor for class qupath.lib.images.writers.ome.zarr.OMEZarrWriterCommand
Create the command
onTileWritten(Consumer<TileRequest>) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Set a function that will be called each time a TileRequest is successfully or unsuccessfully written.

P

parallelize() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Parallelize tile export, if possible.
parallelize(boolean) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify if tile export should be parallelized if possible, with the default number of threads (current 4).
parallelize(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify if tile export should be parallelized if possible, with the requested number of threads.
parallelize(int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Tiles will be written from a pool of thread.
parse(byte[][], int, int, int, ColorModel) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser
Creates a BufferedImage from a 2-dimensional byte array.
pathMemoization - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 
pixelType(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify the output PixelType as a String, e.g.
pixelType(PixelType) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 
pixelType(PixelType) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify the output PixelType.
PLANAR - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Channels are stored as separate image planes ('PLANARCONFIG_SEPARATE').

Q

qupath.lib.images.servers.bioformats - package qupath.lib.images.servers.bioformats
Read images using Bio-Formats (https://www.openmicroscopy.org/bio-formats/).
qupath.lib.images.writers.ome - package qupath.lib.images.writers.ome
Write OME-TIFF images.
qupath.lib.images.writers.ome.zarr - package qupath.lib.images.writers.ome.zarr
 

R

readPathObjects() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
readTile(TileRequest) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
region(int, int, int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Define the region to export based on a bounding box.
region(ImageRegion) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Define the region to export, including the z-slice and time point.
region(ImageRegion) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Define a region (on the x-axis and y-axis) of the input image to consider.
requestParallelization() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Returns true if multiple readers may be created for different threads, to enable parallel image reading.
run() - Method in class qupath.lib.images.writers.ome.ConvertCommand
 
run() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
 
run() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriterCommand
 

S

samplesPerPixel(int[]) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
 
scaledDownsampling(double) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Downsample by specific increasing factor each time (e.g.
scaledDownsampling(double, double) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Downsample by specific increasing factor each time, with a specified initial downsample value (e.g.
setBioformatsEnabled(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Set whether Bio-Formats should be enabled or disabled (in favor of other readers).
setFilesOnly(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Set whether Bio-Formats should support only local files (rather than any URL).
setMaxNumberOfChunksOnEachSpatialDimension(int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
In Zarr files, data is stored in chunks.
setMemoizationTimeMillis(int) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Set the number of milliseconds that must elapse when opening an image before a memoization file is generated.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
 
setPathMemoization(String) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Set the directory where memoization files should be written.
setReaderOptions(Map<String, String>) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Set additional arguments that should be passed to readers.
setRequestParallelization(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
Optionally enable or disable parallelization when reading images.
skipExtensions - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 
supportsImage(ImageServer<?>) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Returns true if the compression type supports a specific image server, or false if it is incompatible.
supportsImage(PixelType, int, boolean) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Returns true if the compression type supports a specific PixelType output with the given number of channels - and (optionally) RGB status.
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
supportsPixelSize() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsPixelSize() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
supportsPyramidal() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsPyramidal() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
supportsRGB() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsRGB() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
supportsT() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsT() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
supportsZ() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
supportsZ() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 

T

tileSize(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Define the requested tile size (width == height).
tileSize(int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
In Zarr files, data is stored in chunks.
tileSize(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Define the requested tile width and height.
tileSize(int, int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
In Zarr files, data is stored in chunks.
timePoint(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify a single timepoint to be written from a time series.
timePoints(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify a range of timepoints to be written from a time series.
timePoints(int, int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Define the timepoints of the input image to consider.
toFriendlyString() - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Get a friendlier string representation

U

uncompressed() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Request no compression.
UNCOMPRESSED - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
No compression (faster to write, no loss of information, but large file sizes).
useExtensions - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 
useParallelization - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
 

V

valueOf(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
Returns an array containing the constants of this enum class, in the order they are declared.

W

writeImage() - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter
Write the entire image in a background thread.
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writeImage(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Write an image consisting of one or more series to the specified path.
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
Write OME-TIFF image to an output stream.
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Static helper method to write an image using Bio-Formats.
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Static helper method to write an image using Bio-Formats with the specified compression.
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType, ImageRegion) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Static helper method to write an image region using Bio-Formats with the specified compression.
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType, ImageRegion, boolean, boolean) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter
Static helper method to write an image using Bio-Formats for a defined region with the specified compression, optionally including all z-slices or timepoints.
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
Write OME-TIFF image to an output stream.
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
 
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrImageWriter
 
writePyramid(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
writePyramid(PyramidOMETiffWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
writeSeries(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
Write an image to the given file.
writeSeries(IFormatWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
Append an image as a specific series.
writeTile(TileRequest) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter
Write the provided tile in a background thread.

Z

ZLIB - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
ZLIB compression.
zSlice(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify the z-slice to export.
zSlices(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
Specify the start (inclusive) and end (exclusive) z-slices.
zSlices(int, int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
Define the z-slices of the input image to consider.
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