[ome-users] Release of Bio-Formats 5.3.0

Tue Dec 13 16:18:00 GMT 2016

Hi Kai,

On 13 Dec 2016, at 13:50, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:

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!

We are very glad to hear so much positive feedback from the community.

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)

Given the error in the attachment, one immediate thought is that jxrlib requires Visual Studio C++ 2015
Redistributable installed on Windows 64 bit platforms [1]. Could you check your system

[1] https://www.openmicroscopy.org/site/support/bio-formats5.3/formats/zeiss-czi.html

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?

Very good question. These features were introduced in [2] and more technically, here are
the relevant lines of codes to set these options in the ImageJ plugin [3].

Which utility/languages do you have in mind for enabling these options? We can certainly
provide more examples of usage if you have concrete use cases.

[2] https://github.com/openmicroscopy/bioformats/pull/2681
[3] https://github.com/openmicroscopy/bioformats/blob/v5.3.0/components/bio-formats-plugins/src/loci/plugins/util/LociPrefs.java#L90

Again, many thanks and regards,

Kai

Best,
Sebastien

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
     *   added new methods to the loci.formats.IFormatWriter interface allowing to set and retrieve the tile along the X and Y dimensions
     *   added default implementations to the loci.formats.FormatWriter abstract class defaulting to the entire image width/height
     *   added functionality to loci.formats.TiffWriter adding support for tiled images writing for TIFF and derived formats like OME-TIFF
     *   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
     *   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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