Installation - NL-BioImaging Advanced Image Analysis Course 2026

Conda¶

Windows¶

First we create a new conda environment.

conda create -n nlbi26-day2-omero python=3.12 ipykernel numpy tifffile scipy scikit-image imageio pandas matplotlib seaborn

Activate the environment

conda activate nlbi26-day2-omero

A few packages is not available on conda so we need to install with pip.

pip install https://github.com/glencoesoftware/zeroc-ice-py-win-x86_64/releases/download/20240325/zeroc_ice-3.6.5-cp312-cp312-win_amd64.whl

then

pip install omero-py ezomero ngff-zarr

Linux/Mac¶

conda create -n nlbi26-day2-omero python=3.12 ipykernel omero-py numpy tifffile scipy scikit-image imageio pandas matplotlib seaborn omero-py zeroc-ice

conda activate nlbi26-day2-omero

pip install ezomero ngff-zarr

Activate the conda environment with jupyter lab you already installed named jlab during the preparation.

conda activate jlab
jupyter-lab

Open omero.ipynb in Jupyter lab.

Useful documentation¶

ezomero documentation - https://thejacksonlaboratory.github.io/ezomero/index.html

Zeroc binaries required to install omero-py - https://www.glencoesoftware.com/blog/2023/12/08/ice-binaries-for-omero.html

Alternative option: uv virtual environment¶

Windows¶

uv venv --python 3.12
source .venv/bin/activate
uv pip install zeroc-ice@https://github.com/glencoesoftware/zeroc-ice-py-win-x86_64/releases/download/20240325/zeroc_ice-3.6.5-cp312-cp312-win_amd64.whl
uv pip install omero-py jupyterlab

Linux¶

uv venv --python 3.12
source .venv/bin/activate
uv pip install zeroc-ice@https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp312-cp312-manylinux_2_28_x86_64.whl
uv pip install omero-py jupyterlab ezomero matplotlib numpy