XuvTools File Readers / Writers

This is a collection of the File reader/writer libraries available in the XuvTools framework.

• libBlitzBioFormats: an Java-based biological file reader library using OME-LOCI Bio-Formats, see http://www.loci.wisc.edu/software/bio-formats for details
• libBlitzBioImage: a C-based based biological file reader library using the Bio-Image library from Dmitry Fedorov, see http://biodev.ece.ucsb.edu/projects/imgcnv/wiki/libioimg for details
• libBlitzLSM: a libtiff-based biological file reader library that supports Zeiss LSM with more than 4GB size
• libBlitzImaris: a libhdf5-based biological file reader library that supports reading and writing to/from Bitplane Imaris 5 files, see http://www.bitplane.com/ for details

To fetch the sources, you need access to the SVN repository. Replace <your-svn-username> with the username you have gotten from us. The following assumes you use “$HOME/BioReader” as a default source directory.

svn co --username <your-svn-username> svn://tim.informatik.uni-freiburg.de/lmbsoft/trunk "$HOME/BioReader"

Compiling is rather easy. For starters, you should take a look at our environment setup for Linux/Mac or Windows. If you have access to the build script “xuvbuild.sh”, you can compile from your shell like this:

xuvbuild.sh --verbose --qmake --thirdparty --tools

If you do not want to use (or don't have access to) the build script “xuvbuild.sh”, you can still compile from your shell. Use Cygwin with Visual Studio 2008 on Windows, or Bash on Linux. The following will compile all four available file readers, including their prerequisites.

export LMBSOFTSRC="$HOME/BioReader"
export LMBSOFTDEST="$HOME/BioReaderBin"
export LMBSOFTTEMP="$HOME/BioReaderBin"

export QTDIR="${LMBSOFTDEST}/thirdparty/Qt"
export JAVA_HOME="/usr/lib/jvm/java-6-openjdk"

export PATH="$QTDIR/bin:$PATH"
export LD_LIBRARY_PATH="$QTDIR/lib:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/amd64/server:${LD_LIBRARY_PATH}"
export LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/i386/server:${LD_LIBRARY_PATH}"

cd "$LMBSOFTSRC/thirdparty/"
make all
cd "$LMBSOFTSRC/project/qt/"
qmake -r CONFIG+="tools" FileIO.pro
make clean
make