[ome-devel] Release of Bio-Formats 6.0.0

[David Gault (Staff)]

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


The University of Dundee is a registered Scottish Charity, No: SC015096
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