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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.

To run the notebooks, you can either run on or build locally with repo2docker.

To build locally:

  • Install Docker if required
  • Create a virtual environment and install repo2docker from PyPI.
  • Clone this repository
  • Run repo2docker.
  • Depending on the permissions, you might have to run the command as an admin
pip install jupyter-repo2docker
git clone
cd omero-guide-cellprofiler
repo2docker .

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