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Guide on how to integrate CellProfiler and OMERO

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The documentation is deployed at Using CellProfiler

This guide demonstrates how to use the CellProfiler Python API to analyze data stored in IDR or in another OMERO server.

This repository contains documentation and notebooks.

Run the notebooks

Running on cloud resources


The OMERO server used will need to have websockets support enabled.

Running in Docker

Alternatively, if you have Docker installed, you can use the repo2docker tool to run this repository as a local Docker instance:

$ git clone
$ cd omero-guide-cellprofiler
$ repo2docker .

Running locally

Finally, if you would like to install the necessary requirements locally, we suggest using conda.

Then, create the environment:

$ git clone
$ cd omero-guide-cellprofiler
$ conda env create -n omero-guide-cellprofiler -f binder/environment.yml

and activate the newly created environment:

$ conda activate omero-guide-cellprofiler

The following steps are only required if you want to run the notebooks

  • If you have Anaconda installed:
    • Start Jupyter from the Anaconda-navigator
    • In the conda environment, run conda install ipykernel
    • To register the environment, run python -m ipykernel install --user --name omero-guide-cellprofiler
    • Select the notebook you wish to run and select the Kernel>Change kernel>Python [conda env:omero-guide-cellprofiler] or Kernel>Change kernel>omero-guide-cellprofiler
  • If Anaconda is not installed:
    • In the environment, install jupyter e.g. pip install jupyter
    • Add the virtualenv as a jupyter kernel i.e. ipython kernel install --name "omero-guide-cellprofiler" --user
    • Open jupyter notebook i.e. jupyter notebook and select the omero-guide-cellprofiler kernel or [conda env:omero-guide-cellprofiler] according to what is available

An additional benefit of installing the requirements locally is that you can then use the tools without needing to launch Jupyter itself.

See also setup.rst

This is a Sphinx based documentation. If you are unfamiliar with Sphinx, we recommend that you first read Getting Started with Sphinx.