Open Microscopy Environment

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 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 for reading and writing of XZ and YZ orthogonal planes

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/5.5.1
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:

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


Regards,

The OME Team