The instructions below apply to CellProfiler 3.1.9 and earlier versions. Instructions for CellProfiler 4.0 installation will be added shortly for all compatible platforms. Please check out the image.sc forum or our Github issues (and submit new issues as needed) if these instructions fail to work for you.

This is one user's log of getting CP running on Ubuntu 9.10 (note that much of step 9 could be handed via pip/virtualenv, instead):

1. Install Ubuntu 9.10 Karmic amd64

2. Change /etc/apt/sources.list to include partner, universe and multiverse - see below for a sample file (must use sudo to change)

3. Now, update the packages from sources and update the system: sudo aptitude update && sudo aptitude dist-upgrade

4. Install C/C++, make and subversion packages: sudo aptitude install build-essential subversion

5. Create CellProfiler target directory: CPTARGET=$HOME/usr/cp2 ; mkdir -pv $CPTARGET

6. Get CellProfiler: svn co https://github.com/CellProfiler/CellProfiler.git/trunk/ $CPTARGET/CellProfiler

7. Install Java: sudo aptitude install java-package sun-java6-bin sun-java6-fonts sun-java6-jdk sun-java6-jre

8. Configure Java environment variables: echo "JAVA_HOME=/usr/lib/jvm/java-6-sun" | sudo tee -a /etc/environment

9. Configure shared library loading: echo 'export LD_LIBRARY_PATH=/usr/lib/jvm/java-6-sun/jre/lib/amd64/server:${LD_LIBRARY_PATH}' | sudo tee -a /etc/bash.bashrc

10. Install Cython, numpy, scipy, setuptools, numeric, matplotlib, wxgtk, decorator, mysql, nose, zmq, h5py and development libraries for Python sudo aptitude install cython python-numpy python-scipy python-setuptools python-numeric python-matplotlib python-wxgtk2.8 python-decorator python-mysqldb python-nose python-dev python-h5py hdf5-helpers libhdf5-dev libjpeg8-dev libpgm-5.1-0 libzmq1 python-zmq

11. Restart system

12. Run CellProfiler: cd $CPTARGET/CellProfiler ; python CellProfiler.py

/etc/apt/sources.list example

deb http://archive.ubuntu.com/ubuntu/ karmic main restricted multiverse universe
deb http://archive.ubuntu.com/ubuntu/ karmic-security main restricted multiverse universe
deb http://archive.ubuntu.com/ubuntu/ karmic-updates main restricted multiverse universe
deb http://archive.canonical.com/ubuntu karmic partner
deb-src http://archive.ubuntu.com/ubuntu/ karmic restricted main multiverse universe
deb-src http://archive.ubuntu.com/ubuntu/ karmic-security restricted main multiverse universe
deb-src http://archive.ubuntu.com/ubuntu/ karmic-updates restricted main multiverse universe
deb-src http://archive.canonical.com/ubuntu karmic partner