Installing rOMERO-gateway

rOMERO-gateway will use rJava to communicate with an OMERO server.

Install in a Conda environment

In this section, we show how to install rOMERO-gateway and additional packages for image analysis (see environment.yml and postBuild) in a Conda environment.

  • Install Miniconda if necessary.

  • If you do not have a local copy of the omero-guide-r repository, first clone the repository:

    $ git clone
  • Go into the directory:

    $ cd omero-guide-r
  • Create a programming environment using Conda:

    $ conda create -n rgateway
  • Install dependencies and some packages used in the notebooks using an installation file:

    $ conda env update -n rgateway --file binder/environment.yml
  • Run a bash script to install rOMERO-gateway and the Java dependencies:

    $ bash binder/postBuild
  • Activate the environment:

    $ conda activate rgateway