Index
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
OMEPixelParserinstance. - build() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Create an
OMEPyramidWriter.OMEPyramidSeriesto 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
-
ImageWriterfor writing OME-TIFF images. - OMETiffWriter() - Constructor for class qupath.lib.images.writers.ome.OMETiffWriter
- OMEZarrImageWriter - Class in qupath.lib.images.writers.ome.zarr
-
An
ImageWriterfor 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
TileRequestis 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
BufferedImagefrom 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
PixelTypeas 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
PixelTypeoutput 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
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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
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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
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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
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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
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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
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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
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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
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Deprecated.
- writePyramid(PyramidOMETiffWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
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Deprecated.
- writeSeries(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
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Write an image to the given file.
- writeSeries(IFormatWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries
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Append an image as a specific series.
- writeTile(TileRequest) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter
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Write the provided tile in a background thread.
Z
- ZLIB - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType
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ZLIB compression.
- zSlice(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
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Specify the z-slice to export.
- zSlices(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
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Specify the start (inclusive) and end (exclusive) z-slices.
- zSlices(int, int) - Method in class qupath.lib.images.writers.ome.zarr.OMEZarrWriter.Builder
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Define the z-slices of the input image to consider.
All Classes and Interfaces|All Packages
OMEPyramidWriter.OMEPyramidSeries.writeSeries(String)instead