The CLI is currently untested on Windows but may be supported in the future.
Since OMERO 5.6, only Python 3 is supported.
We assume that you have already installed Python 3.6 or higher. You can ensure that your python executable is correct with the
python --version command.
We recommend installing client library
omero-py and the CLI plugins
in a Python virtual environment.
You can create one using either
If you opt for Conda, you will need
to install it first, see miniconda for more details.
On Ubuntu 20.09, you may need to install
libssl-dev before installing the CLI.
omero-py using conda (preferred):
conda create -n myenv -c conda-forge python=3.8 omero-py conda activate myenv
omero-py using venv with Python 3.7 or higher:
python -m venv myenv . myenv/bin/activate pip install omero-py
omero command is now available in the terminal where the environment has been activated:
If you install
omero-py>=5.8.0 the CLI provides all functionalities except the
import functionality requires a supported version of Java, and some JARs which are automatically downloaded the first time you do an import.
To install Java, go to OMERO.server installation and select the walkthrough corresponding to your OS.
omero-py < 5.8.0¶
If you are using an older version of
omero-py you must download the JARs manually and place them under the
download the OMERO.server zip from the Downloads page
unzip the zip file
$OMERODIRto the unzipped directory:
import functionality is now available:
omero import /path/to/image.tiff