Open Microscopy Environment

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 http://www.openmicroscopy.org/site/supp ... s-new.html

The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.1.3
and the C++ implementation is available from:
http://downloads.openmicroscopy.org/bio ... cpp/5.1.3/

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

http://www.openmicroscopy.org/site/community

Regards,

The OME Team