CellProfiler OMERO integration¶

In this tutorial we provide information on how to interface CellProfiler with OMERO

Using Ubuntu 16 LTS¶

- Have a updated installation of Ubuntu 16 LTS. Working with the release on January 29th 2018

then:

$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install \
    build-essential    \
    cython             \
    git                \
    libmysqlclient-dev \
    libhdf5-dev        \
    libxml2-dev        \
    libxslt1-dev       \
    openjdk-8-jdk      \
    python-dev         \
    python-pip         \
    python-h5py        \
    python-matplotlib  \
    python-mysqldb     \
    python-scipy       \
    python-numpy       \
    python-vigra       \
    python-wxgtk3.0    \
    python-zmq

- Checkout

git clone https://github.com/CellProfiler/CellProfiler.git
cd CellProfiler

... and

$ git checkout v3.0.0

$ git checkout 2.2.0

- Finally when you have checked out the version you want, you are ready to start the compile / install of python dependencies.

$ sudo pip install --editable .