Release of Bio-Formats 6.0.0

[David Gault (Staff)]

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Dear all,

Today we are releasing Bio-Formats 6.0.0  This is a major update that includes support for the updated OME-TIFF file format<http://docs.openmicroscopy.org/latest/ome-model/ome-tiff/specification.html>, which now supports multi-resolution tiled images (so-called pyramidal file format). For more info, see http://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/.  This new version of Bio-Formats also includes support for the KLB format for light sheet microscopy.

Bio-Formats API changes:

  *   Java 8 is now the minimum supported version
  *   Sub-resolution reading:
     *   added MetadataList and CoreMetadataList classes
     *   added a new SubResolutionFormatReader abstract class for handling pyramidal format readers
     *   updated all pyramid format readers to use SubResolutionFormatReader
     *   deprecated getCoreMetadataList, seriesToCoreIndex, coreIndexToSeries, getCoreIndex and setCoreIndex in IFormatWriter
  *   added a new IPyramidHandler interface with the resolution getter methods
  *   Sub-resolution writing changes:
     *   IFormatWriter now extends IPyramidHandler (breaking)
     *   added setResolutions and getResolutions methods to IFormatWriter (breaking)
     *   added examples of using the sub-resolution writing API
  *   Tiled writing API changes:
     *   updated IFormatWriter to use setTileSizeX(0) and setTileSizeY(0) as a way to disable tiling (breaking)
     *   updated FormatWriter to set 0 as the default values of getTileSizeX() and getTileSizeY (breaking)
  *   IFormatWriter.getCompressionTypes now returns the types for the selected writer only
  *   Metadata handling:
     *   added getter methods to MetadataTools for retrieving OME enumerations by value
     *   deprecated OME enumeration getter methods in FormatReader
  *   Refactor FilePatternReader logic in a new WrappedReader abstract class



New file formats:

  *   KLB
     *   added a new reader for Keller Lab Block (KLB) files
  *   CV7000
     *   added a new reader for Yokogawa CV7000 datasets
  *   GE MicroCT
     *   added a new reader for GE MicroCT datasets

File format fixes and improvements:

  *   Aperio SVS/AFI
     *   removed pyramidal resolutions of mismatching pixel types
     *   fixed exposure times, improved image naming of AFI datasets
     *   displayed original metadata keys for each channel of AFI datasets
     *   added support for multiple Z sections
  *   DICOM
     *   improved file grouping and file-to-series mapping for multi-file datasets
  *   Fake
     *   added support for multi-resolution test images
     *   now populating WellSample positions when present using Plane data
  *   Gatan Digital Micrograph
     *   adjusted endianness and record byte count for long values
     *   allowed ROIs to be stored in DocumentObjectList groups
     *   no longer creating an empty ROI when an unsupported shape type is encountered
  *   Image Pro
     *   added support for Image Pro Plus .ips set
  *   GE InCell
     *   added support for parsing minimum and maximum pixel values
  *   Lambert Instruments FLIM
     *   fixed an integer overflow error with large files (thanks to Rolf Harkes)
  *   Leica LIF
     *   unified metadata parsing to use DataTools.parseDouble
  *   Leica SCN
     *   improved support for Versa datasets
  *   Micro-Manager
     *   improved handling of very large metadata.txt files
     *   prevented NumberFormatException for invalid double values
     *   add support for parsing ChannelColor from metadata.txt files
  *   Metamorph
     *   added support for multi-dimensional .scan dataset created from Scan Slide (thanks to Jeremy Muhlich)
  *   MRC (Medical Research Council)
     *   fixed endian detection for old-style headers
  *   Nikon ND2
     *   prevented integer overflow when reading chunkmaps from files larger than 2GB
     *   fixed handling of duplicate and incomplete exposure time lists
     *   fixed chunk map handling when CustomData blocks are between ImageDataSeqs
  *   OME-TIFF
     *   added support for reading OME-TIFF with pyramidal resolutions stored as SubIFDs
     *   added support for writing OME-TIFF with pyramidal resolutions
     *   added support for companion OME-TIFF filesets where TIFF does not link back to the metadata file
     *   improved handling of missing planes in TiffData
  *   PerkinElmer Operetta
     *   improved support to handle datasets generated by the Harmony software
  *   TIFF
     *   split IFDs into separate series if the dimensions or pixel type mismatch
     *   restricted use case for legacy TIFF JAI reader
     *   fixed a bug with FillOrder which resulted in 0 pixel values
  *   Zeiss CZI
     *   reduced duplicate original metadata when reading a pyramid file
  *   Zeiss TIFF
     *   added support for AVI files acquired with Keyence software
  *   Zeiss ZVI
     *   reuse stream for sequential calls to openBytes on the same plane
  *   updated all pyramidal format readers to consume SubResolutionReader
  *   updated all readers to consume MetadataTools getter to retrieve enumerations
  *   reviewed all readers and plugins to close open instances of RandomAccessInputStream
  *   fixed some deprecation warnings in a number of readers
  *   for RGB images using ChannelSeparator all channel metadata is now copied instead of just names

ImageJ plugin improvements:

  *   updated the updater message in the Fiji plugin (thanks to Jan Eglinger)
  *   disabled LUT writing for any plane that has a default grayscale lookup table
  *   added macro option to always skip LUT writing

MATLAB toolbox improvements:

  *   improved performance of bfGetPlane by removing an unnecessary data copy (thanks to Cris Luengo)

Command-line tools improvements:

  *   bfconvert utility
     *   added `-no-flat` option to the command-line tools to convert files with sub-resolutions
     *   added `-pyramid-scale` and `-pyramid-resolutions` options to generate sub-resolutions during conversion
     *   removed `Plate` elements when `-series` is passed as an option
     *   extended usage to describe available formats, extensions and compressions
  *   xmlvalid utility
     *   added new `validate` methods to `loci.formats.tools.XMLValidate` returning the validation status
     *   added a return code to `xmlvalid`

Component changes:

  *   ome-common was upgraded to 6.0.0
  *   ome-codecs was upgraded to 0.2.3
  *   ome-model was upgraded to 6.0.0

Automated test changes:

  *   added `testng.allow-missing` property allowing to skip unconfigured filesets
  *   added `testUnflattenedSaneOMEXML` to compare series count to OME-XML images count when resolution flattening is disabled
  *   added `test-equivalent` target to compare pixel data between two files
  *   added support for storing resolution index and resolution count in the configuration files used for automated testing
  *   tests now fail when a configured file throws UnknownFormatException

Documentation improvements:

  *   fixed the xmlvalid documentation page (thanks to Kouichi C. Nakamura)
  *   improved the memory section of the MATLAB documentation page (thanks to Kouichi C. Nakamura)
  *   extended IFormatReader Javadocs to reflect the reader guide
  *   added reference to current Adobe TIFF specification
  *   switched to image.sc as the reference location for public feedback

Full details can be found at: https://docs.openmicroscopy.org/bio-formats/6.0.0/about/whats-new.html
The software is available at: https://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 please use the image.sc forum<https://forum.image.sc/tags/bio-formats>.

Regards,
The OME Team


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