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CellProfiler plugins

Installation

  1. When you start CellProfiler set the CellProfiler plugins directory to the cp_plugins directory, and the ImageJ plugin directory to the ij_plugins directory.

  2. Set the CLASSPATH environment variable to include the jars DImageSVN_.jar and jsch.jar in the jarlib directory. There are various ways to set the classpath. For general instructions (Windows and Linux) see here.

    (Linux) Another way to set the classpath is on application basis like I did on the server in the /usr/local/bin/cellprofiler script:

    #!/bin/sh
#
# Wrapper script used to start CellProfiler on Linux.

PREFIX=/opt/cellprofiler
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/amd64/server
export CLASSPATH=/data/shared/cellprofiler_plugins/jarlib/DImageSVN_.jar:/data/shared/cellprofiler_plugins/jarlib/jsch.jar
python2 $PREFIX/CellProfiler/CellProfiler.py "$@"

  3. (Linux) Make sure python-suds is available.