Release of Bio-Formats 5.5.1

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Helen Flynn (Staff) Helen Flynn (Staff)
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Release of Bio-Formats 5.5.1

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Dear All,

Today we are releasing Bio-Formats 5.5.1 which includes the following changes:

File format improvements:

  *   CellH5
     *   fix for HDF5SymbolTableException when recycling an IFormatReader to reopen another CellH5 file
     *   bug fix related to opening of subsets of CellH5 files, namely openBytes(r, no, x, y, w, h) for y>0
  *   Zeiss CZI
     *   fix pyramid resolution indexing for pyramids of different depths
     *   fix for incorrect channel names and colors
  *   Zeiss AxioVision ZVI
     *   correct parsing of epoch for Zeiss TIFF and Zeiss ZVI

Bug fixes:

  *   Command line tools
     *   fix for java.lang. NegativeArraySizeException caused by incorrect dimensions when using showinf via command line with options set to autoscale and crop
  *   Format tools
     *   fix for java.lang. IndexOutOfBoundsException when using getFilename[1] with an image containing multiple samples per pixel channels and a single effective channel

Updated build system:

  *   Autogen jobs
     *   fix for gen-meta-support to locate available org.openmicroscopy:ome-xml sources from the Maven repository following the decoupling of the model components
  *   FileHandleTest
     *   exclude JHDF5 native libraries from FileHandleTest to enable CellH5 files to be included in daily tests

Documentation improvements:

  *   added a new example file[2] for reading and writing of XZ and YZ orthogonal planes

Full details can be found at

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

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


The OME Team


Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee<>

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