User guide for Orbit and OMERO

The documentation is deployed at Using Orbit.

This guide demonstrates how to analyze data stored in OMERO in Orbit. This can be done using the User Interface or via the scripting facility in Orbit.

To run the notebooks, you can either run on mybinder.org 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 https://github.com/ome/omero-guide-orbit.git
cd omero-guide-fiji
repo2docker .

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

When creating a new repository, this template could be used.

The values in docs/conf.py should be replaced by the name of your project.