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Guide on how to integrate ilastik and OMERO

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The documentation is deployed at Use Ilastik.

This guide demonstrates how to use ilastik to analyze data stored in IDR or an 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
  • Open a terminal as administrator
  • Create a virtual environment and install repo2docker from PyPI.
  • Clone this repository
  • Run repo2docker
pip install jupyter-repo2docker
git clone
cd omero-guide-ilastik
repo2docker .

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