Release of Bio-Formats 6.0.0

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 https://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 Bio-Formats version history.

The software is available at archived downloads and will shortly be available from the Java-8 update site for Fiji users.

Any problems or comments, please use the image.sc forum.