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Release of Bio-Formats 5.1.3

PostPosted: Mon Jul 20, 2015 10:21 am
by sbesson
Dear All,

Today we are releasing Bio-Formats 5.1.3. This is a point release that contains bug-fixes, but also adds several new features to Bio-Formats.

Bio-Formats 5.1.3 improvements include:
  • Native C++ updates:
    • Added cmake superbuild to build core dependencies (zlib, bzip2, png, icu, xerces, boost)
    • Progress on support for Windows
  • Bug fixes, including:
    • Fixed segfault in the showinf tool used with the C++ bindings
    • Allow reading from https URLs
    • ImageJ - improved performance of displaying ROIs
    • Command line tools - fixed bfconvert to correctly create datasets with multiple files
  • File format fixes, including:
    • Metamorph
      • improved detection of time series
      • fixed .nd datasets with variable Z and T counts in each channel
      • fixed .nd datasets that contain invalid TIFF/STK files
      • fixed dimensions when the number of planes does not match the recorded Z, C, and T sizes
    • SlideBook - improved native library detection (thanks to Richard Myers)
    • JPEG - fixed decompression of lossless files with multiple channels (thanks to Aaron Avery)
    • Imspector OBF - updated to support version 2 files (thanks to Bjoern Thiel)
    • Imspector MSR - improved detection of Z stacks
    • PerkinElmer Opera Flex - improved handling of multiple acquisitions of the same plate
    • Zeiss CZI - fixed error when opening single-file datasets whose names contained "(" and ")"
    • TIFF - improved speed of reading files with many tiles
    • AVI - updated to read frame index (idx1) tables
    • Nikon ND2 - fixed channel counts for files with more than 3 channels
    • PNG - fixed decoding of interlaced images with a width or height that is not a multiple of 8
    • PSD - improved reading of compressed images
  • Documentation improvements, including:
    • updated instructions for writing a new file format reader
    • updated usage information for command line tools
    • new Javadocs for the MetadataStore and MetadataRetrieve interfaces

Full details can be found at ... s-new.html

The software is available at:
and the C++ implementation is available from: ... cpp/5.1.3/

Any problems or comments, please use the OME Forums or mailing lists:


The OME Team