Release of Bio-Formats 6.0.0

bio-formats
ome-tiff

#1

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, 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 the #bio-formats tag on this forum: https://forum.image.sc/tags/bio-formats

Regards,

The OME Team


Open CV7000 image with Bio-Formats problem