Package qupath.lib.images.writers.ome

Class OMEPyramidWriter

java.lang.Object

qupath.lib.images.writers.ome.OMEPyramidWriter

public class OMEPyramidWriter
extends Object

Write OME-TIFF files based on QuPath ImageServers.

The files may optionally be pyramidal TIFFs. Some key metadata is set (e.g. channel names/colors, pixel size), and an effort is made to support multidimensional images - but this has not been extensively checked.

Currently the magnification is not written, nor is the full OME XML metadata, and images written using this class should not be assumed to contain all the necessary information, correctly or at all (i.e. always keep your original data files!).

Note this requires Bio-Formats v6.0.0 or later.

Author:

Pete Bankhead

modified by @phaub , 04'2021 (JPEG support for nChannels > 1, sanity check)

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	OMEPyramidWriter.Builder	Builder class to define parameters when exporting an image region as OME-TIFF, possibly as an image pyramid.
static enum	OMEPyramidWriter.ChannelExportType	Enum representing different ways in which channels may be written to a file.
static enum	OMEPyramidWriter.CompressionType	Preferred compression type when using Bio-Formats.
static class	OMEPyramidWriter.OMEPyramidSeries	Class representing a single series to write to an OME-TIFF.

Method Summary

Modifier and Type	Method	Description
static OMEPyramidWriter	createWriter(Collection<OMEPyramidWriter.OMEPyramidSeries> series)	Create a writer capable of writing an image with a collection of series.
static OMEPyramidWriter	createWriter(OMEPyramidWriter.OMEPyramidSeries... series)	Create a writer capable of writing an image with one or more series.
void	writeImage(String path)	Write an image consisting of one or more series to the specified path.
static void	writeImage(ImageServer<BufferedImage> server, String path)	Static helper method to write an image using Bio-Formats.
static void	writeImage(ImageServer<BufferedImage> server, String path, OMEPyramidWriter.CompressionType compression)	Static helper method to write an image using Bio-Formats with the specified compression.
static void	writeImage(ImageServer<BufferedImage> server, String path, OMEPyramidWriter.CompressionType compression, ImageRegion region)	Static helper method to write an image region using Bio-Formats with the specified compression.
static void	writeImage(ImageServer<BufferedImage> server, String path, OMEPyramidWriter.CompressionType compression, ImageRegion region, boolean allZ, boolean allT)	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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

writeImage

public void writeImage(String path)
                throws FormatException,
IOException

Write an image consisting of one or more series to the specified path.

Parameters:

path -

Throws:

FormatException

IOException

See Also:

• createWriter(Collection)
• createWriter(OMEPyramidSeries...)

createWriter

public static OMEPyramidWriter createWriter(OMEPyramidWriter.OMEPyramidSeries... series)

Create a writer capable of writing an image with one or more series.

Parameters:

series -

Returns:

createWriter

public static OMEPyramidWriter createWriter(Collection<OMEPyramidWriter.OMEPyramidSeries> series)

Create a writer capable of writing an image with a collection of series.

Parameters:

series -

Returns:

writeImage

public static void writeImage(ImageServer<BufferedImage> server,
 String path)
                       throws FormatException,
IOException

Static helper method to write an image using Bio-Formats. This is primarily intended for saving whole slide images as pyramidal OME-TIFF, but other formats are supported.

Parameters:

server -

path -

Throws:

FormatException

IOException

writeImage

public static void writeImage(ImageServer<BufferedImage> server,
 String path,
 OMEPyramidWriter.CompressionType compression)
                       throws FormatException,
IOException

Static helper method to write an image using Bio-Formats with the specified compression. This is primarily intended for saving whole slide images as pyramidal OME-TIFF, but other formats are supported.

Parameters:

server -

path -

compression -

Throws:

FormatException

IOException

writeImage

public static void writeImage(ImageServer<BufferedImage> server,
 String path,
 OMEPyramidWriter.CompressionType compression,
 ImageRegion region)
                       throws FormatException,
IOException

Static helper method to write an image region using Bio-Formats with the specified compression. If region is null, the entire image will be written. If region is not null, it defines the bounding box of the exported pixels in addition to the z-slice and timepoint.

Parameters:

server - image to write

path - path to output file

compression - image compression method; may be null to use the default compression

region - the region to export. If this is a RegionRequest that defines a downsample other than the default for the server, this downsample will be used.

Throws:

FormatException

IOException

writeImage

public static void writeImage(ImageServer<BufferedImage> server,
 String path,
 OMEPyramidWriter.CompressionType compression,
 ImageRegion region,
 boolean allZ,
 boolean allT)
                       throws FormatException,
IOException

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. This is intended primarily to write (possibly pyramidal) OME-TIFF images; other formats may support fewer image types and dimensions.

Parameters:

server - image to write

path - path to output file

compression - image compression method; may be null to use the default compression

region - the region to export. If this is a RegionRequest that defines a downsample other than the default for the server, this downsample will be used.

allZ - if true, export all z-slices otherwise export slice defined by region (ignored if image is not a z-stack)

allT - if true, export all timepoints otherwise export timepoint defined by region (ignored if image is not a timeseries)

Throws:

FormatException

IOException