User guides for the OMERO Python API

The documentation is deployed at Use Python API

This guide demonstrates how to use the OMERO Python API.

Run the notebooks

Running on cloud resources

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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 https://github.com/ome/omero-guide-python
$ cd omero-guide-python
$ repo2docker .

Then follow the instructions that are printed after the Docker image is built.

Running locally

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

Then, create the environment:

$ git clone https://github.com/ome/omero-guide-python
$ cd omero-guide-python
$ conda env create -n omero-guide-python -f binder/environment.yml

and activate the newly created environment:

$ conda activate omero-guide-python

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

• If you have Anaconda installed:
  • Start Jupyter from the Anaconda-navigator
  • Select the notebook you wish to run and select the Kernel>Change kernel>Python [conda env:omero-guide-python]
• 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-python" --user
  • Open jupyter notebook i.e. jupyter notebook and select the omero-guide-python kernel or [conda env:omero-guide-python] 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.