Today we are releasing Bio-Formats 5.6.0 which includes the following changes:
File format fixes and improvements:
- Zeiss CZI
- added support for images from Elyra PALM system
- prevented a potential infinite loop when a scene with a pyramid is missing
- cellSens VSI
- a new option has been added to throw an exception rather than logging a warning if .ets file is missing. The option, 'cellsens.fail_on_missing_ets', can be used via the MetadataOptions API, as a parameter in the command line tools or via the Bio-Formats configuration dialog in ImageJ
- MetaMorph Stack (STK)
- fixed an error with HCS style datasets always returning the first plane regardless of the requested index
- updated to use stage labels starting with 'Scan' to detect when a whole plate is saved in a single .stk file
- fixed a bug for ArrayIndexOutOfBoundsException when an image contains a single Z plane
- Gatan Digital Micrograph
- added support for Z stacks and ROIs
- fixed several bugs in tag parsing
- PerkinElmer Operetta
- ensure TIFF files exist before reading
- JPEG
- support added for images with more than Integer.MAX_VALUE pixels
Bug fixes and improvements:
- JPEGTileDecoder
- class now implements AutoCloseable to prevent resource leaks
- Bio-Formats Plugin
- improved performance when using options to concatenate multiple series together
- TiffSaver
- made performance improvements to prevent the writing of a new IFD for each tile, resulting in significant file size reductions for images with a large quantity of tiles
Documentation improvements:
- updated website and URL links for new http://www.openmicroscopy.org website
- added missing Andor SIF to supported formats page
- added a new page Working with whole slide images outlining the API support for pyramids/resolutions
- fixed broken documentation links for external resources which are no longer available
updated the style of Sphinx documentation
Component architecture changes/decoupling:
- decoupled image encoding and decoding routines to the new ome/ome-codecs GitHub repository and consumed as 'org.openmicroscopy:ome-codecs' artifact from Maven Central
- removed components/forks/jai - decoupled to the new ome/ome-jai GitHub repository and consumed as part of 'org.openmicroscopy:ome-jai' artifact from Maven Central
- replaced components/formats-api/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'
- replaced components/formats-bsd/codecs classes with wrappers around 'org.openmicroscopy:ome-codecs'
Updated build system:
- ant now removes the build files of the bundles during 'clean' to prevent a mix of dependencies
Full details can be found at https://docs.openmicroscopy.org/bio-for ... s-new.html
The software is available at:
http://www.openmicroscopy.org/bio-formats/downloads/
and will shortly be available from the Java-8 update site for Fiji users.
Any problems or comments, please use the OME Forums or mailing lists:
http://www.openmicroscopy.org/support
Regards,
The OME Team
