Install CellProfiler and OMERO Python bindings

In this section, we show how to install CellProfiler in a Conda environment. We will use the CellProfiler API to analyze data stored in an OMERO server.

CellProfiler currently runs on Python 2.7. It does not yet support Python 3.


We recommend to install the dependencies using Conda. Conda manages programming environments in a manner similar to virtualenv. You can install the various dependencies following the steps below (Option 1) or build locally a Docker Image using repo2docker (Option 2). When the installation is done, you should be ready to use the CellProfiler API and OMERO, see Getting started with CellProfiler and OMERO.

The installation below is needed to run the scripts and/or notebooks. If you wish to start your own environment without the scripts/notebooks, copy locally into an environment.yml file the content of binder/environment.yml, remove or add the dependencies you need and run the commands below to create a conda environment.

Option 1

  • Install Miniconda if necessary.

  • If you do not have a local copy of the omero-guide-cellprofiler repository, first clone the repository:

    $ git clone
  • Go into the directory:

    $ cd omero-guide-cellprofiler
  • Create a programming environment using Conda:

    $ conda create -n cellprofiler python=2.7
  • Install CellProfiler, its dependencies and omero-py in order to connect to an OMERO server using an installation file:

    $ conda env update -n cellprofiler --file binder/environment.yml
  • Activate the environment:

    $ conda activate cellprofiler

Option 2

Alternatively you can create a local Docker Image using repo2docker, see

$ repo2docker .

When the Image is ready:

  • Copy the URL displayed in the terminal in your favorite browser
  • Click the New button on the right-hand side of the window
  • Select Terminal
  • A Terminal will open in a new Tab

  • A Conda environment has already been created when the Docker Image was built

  • To list all the Conda environment, run:

    $ conda env list
  • The environment with CellProfiler and the OMERO Python bindings is named kernel, activate it:

    $ conda activate kernel