Release of Bio-Formats 5.3.0

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 in the Bio-Formats version history.

The software is available at archived downloads 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.