[ome-users] Release of Bio-Formats 5.3.0
Kai Schleicher
kai.schleicher at unibas.ch
Tue Dec 13 13:50:28 GMT 2016
Dear Helen,
first of all I'd like to thank you and everyone involved very much for
bringing jpegXR to Bio-formats! I want to stress that we appreciate your
efforts a lot - we know that getting to this point was hard work.
In our facility at the Biozentrum in Basel, we run an Zeiss Axioscan
Slidescanner that produces lots (!) of data. Using JpegXR and our OMERO
installation, we are one big step further in dealing with this data in
an elegant way. Thanks again!
Of course I could not wait to test the new BF on our datasets, two of
which I have uploaded to your servers (QA Bug | 17472).
Unfortunately for me these two compressed files did not open (both
exceptions can be found in the attached txt file).
I also have another question regarding your update:
> added two options to the CZI reader to disable autostitching and
> exclude pyramid file attachments. Added new checkboxes to the CZI
> configuration interface of the ImageJ plugin to activate these options
How can I access these options?
Again, many thanks and regards,
Kai
On 12/12/2016 04:31 PM, Helen Flynn (Staff) wrote:
> Dear All,
> Today we are releasing Bio-Formats 5.3.0 which includes the following
> changes:
> New features/API:
>
> * added support for JPEG-XR compressed CZI data (funded by a
> partnership between Glencoe Software and ZEISS), adding
> ‘ome:jxrlib’ as a new dependency of Bio-Formats
> * improved tile-based image writing
> o added new methods to the loci.formats.IFormatWriter interface
> allowing to set and retrieve the tile along the X and Y dimensions
> o added default implementations to the loci.formats.FormatWriter
> abstract class defaulting to the entire image width/height
> o added functionality to loci.formats.TiffWriter adding support
> for tiled images writing for TIFF and derived formats like
> OME-TIFF
> o added developer documentation and samples for tiled
> reading/writing
> * added a new MetadataOptions implementation supporting arbitrary
> key/value pairs
> * updated the display command line utility to support passing
> key/value options using showinf -option
> * added two options to the CZI reader to disable autostitching and
> exclude pyramid file attachments. Added new checkboxes to the CZI
> configuration interface of the ImageJ plugin to activate these options
>
> Bug fixes/deprecations:
>
> * deprecated loci.formats.meta.MetadataConverter in favor of
> ome.xml.meta.MetadataConverter
> * updated method deprecated in Octave 4.2.0 (thanks to Carnë Draug)
> * OME-XML
> o fixed handling of Mask BinData elements
>
> Component architecture changes/decoupling:
>
> * removed formats-common component - now decoupled to the new
> ome/ome-common-java GitHub repository and consumed as
> ‘org.openmicroscopy:ome-common’ artifact from Maven Central
> * removed ome-poi component - now decoupled to the new ome/ome-poi
> GitHub repository and consumed as ‘org.openmicroscopy:ome-poi’
> artifact from Maven Central
> * removed specification, xsd-fu and ome-xml components - now
> decoupled to the new ome/ome-model GitHub repository and consumed
> as ‘org.openmicroscopy:{specification,ome-xml}’ artifacts from
> Maven Central
> * removed mdbtools component - now decoupled to the new
> ome/ome-mdbtools GitHub repository and consumed as
> ‘org.openmicroscopy:ome-mdbtools’ artifact from Maven Central
> * removed stubs components - now decoupled to the new ome/ome-stubs
> GitHub repository and consumed as
> ‘org.openmicroscopy:{lwf-stubs,mipav-stubs}’ artifacts from Maven
> Central
> * removed metakit component - now decoupled to the new
> ome/ome-metakit GitHub repository and consumed as
> ‘org.openmicroscopy:metakit’ artifacts from Maven Central
> * updated developer documentation for the decoupled components
>
> Updated build system:
>
> * dropped embedded JARs and now use the Maven Ant Tasks plugin to
> unify the dependencies using the POM
> * improved Ant JAR and bundle target
> * dropped deprecated osgi targets, OME Tools bundle and ome-jxr
> component
> * removed PDF generation from the docs-sphinx target
> * added version number to Javadoc zip bundle name
> * migrated unit tests out of test-suite into formats-bsd
> * fixed test-suite targets, paths and symlink handling
> * fixed test-metadata and migrated it into test-suite
> * fixed mismatch between ND2HandlerTest package and location
> * cleaned up test-build to remove obsolete and decoupled components
> and folders simplified Travis build
> * POM repositories clean-up to reduce complexity and use Maven
> Central as the first location to look for dependencies
> * now storing all versions in the top-level POM
> * updated build versioning from Maven by unified versioning
> strategy, reviewing meta information stored in the manifests of
> each JAR and introspecting this information in the FormatTools API
> to retrieve version and revision numbers
> * updated developer documentation on updated build system
>
> Full details can be found at
> http://www.openmicroscopy.org/site/support/bio-formats5.3/about/whats-new.html
> The software is available at:
> http://downloads.openmicroscopy.org/bio-formats/5.3.0
> and is available from the Java 8 update site for Fiji users (note that
> you will need to disable the 'Bio-Formats 5' update site if you
> currently have it enabled, as well as enabling the 'Java 8' updates -
> this functionality is available under "Manage update sites").
> Any problems or comments, please use the OME Forums or mailing lists:
> http://www.openmicroscopy.org/site/community
> Regards,
> The OME Team
>
> Dr Helen Flynn
> OME Technical Writer
> Centre for Gene Regulation & Expression
> Open Microscopy Environment
> University of Dundee
> http://openmicroscopy.org <http://openmicroscopy.org/>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
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20160211_FL_3ch_10x_1z_2sc_onl_jpegxr.czi
---------------------
2sc-online-jpegXR: sees lable and macro image, pyramide and both scenes, asks to choose which one, does not open, fials with exception:
(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 1850MB of 49073MB (3%)
java.lang.UnsatisfiedLinkError: ome.jxrlib.JXRJNI.new_DecodeContext()J
at ome.jxrlib.JXRJNI.new_DecodeContext(Native Method)
at ome.jxrlib.DecodeContext.<init>(DecodeContext.java:43)
at ome.jxrlib.AbstractDecode.decodeFirstFrame(AbstractDecode.java:101)
at ome.jxrlib.Decode.decodeFirstFrame(Decode.java:51)
at loci.formats.services.JPEGXRServiceImpl.decompress(JPEGXRServiceImpl.java:57)
at loci.formats.codec.JPEGXRCodec.decompress(JPEGXRCodec.java:80)
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3399)
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3368)
at loci.formats.in.ZeissCZIReader.openBytes(ZeissCZIReader.java:391)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:227)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
at loci.plugins.in.Importer.readPixels(Importer.java:149)
at loci.plugins.in.Importer.run(Importer.java:86)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:297)
at ij.IJ.run(IJ.java:272)
at ij.macro.Functions.doRun(Functions.java:603)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:230)
at ij.macro.Interpreter.doStatements(Interpreter.java:218)
at ij.macro.Interpreter.run(Interpreter.java:115)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.macro.MacroRunner.run(MacroRunner.java:139)
at java.lang.Thread.run(Thread.java:745)
---------------------
20160211-FL-3ch-40x-3z-1smallsc-online-uncompressed.czi
1sc-online-uncompressed: sees sees lable and macro image and pyramide asks to choose which one, works!
---------------------
BF-20x-1z-1sc-off.czi
1sc-offline-jpegXR: sees sees lable and macro image and pyramide, asks to choose which one, fails with exception:
(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51h; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 2941MB of 49073MB (5%)
java.lang.UnsatisfiedLinkError: ome.jxrlib.JXRJNI.new_DecodeContext()J
at ome.jxrlib.JXRJNI.new_DecodeContext(Native Method)
at ome.jxrlib.DecodeContext.<init>(DecodeContext.java:43)
at ome.jxrlib.AbstractDecode.decodeFirstFrame(AbstractDecode.java:101)
at ome.jxrlib.Decode.decodeFirstFrame(Decode.java:51)
at loci.formats.services.JPEGXRServiceImpl.decompress(JPEGXRServiceImpl.java:57)
at loci.formats.codec.JPEGXRCodec.decompress(JPEGXRCodec.java:80)
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3399)
at loci.formats.in.ZeissCZIReader$SubBlock.readPixelData(ZeissCZIReader.java:3368)
at loci.formats.in.ZeissCZIReader.openBytes(ZeissCZIReader.java:391)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
at loci.plugins.in.Importer.readPixels(Importer.java:149)
at loci.plugins.in.Importer.run(Importer.java:86)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at ij.IJ.run(IJ.java:297)
at ij.IJ.run(IJ.java:272)
at ij.macro.Functions.doRun(Functions.java:603)
at ij.macro.Functions.doFunction(Functions.java:96)
at ij.macro.Interpreter.doStatement(Interpreter.java:230)
at ij.macro.Interpreter.doStatements(Interpreter.java:218)
at ij.macro.Interpreter.run(Interpreter.java:115)
at ij.macro.Interpreter.run(Interpreter.java:85)
at ij.macro.MacroRunner.run(MacroRunner.java:139)
at java.lang.Thread.run(Thread.java:745)
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