Please follow these instructions before participating in the workshop.
- Install miniforge for example by following these instructions: https://biapol.github.io/blog/mara_lampert/getting_started_with_mambaforge_and_python/readme.html (just the first part about Installation of miniforge)
- Start miniforge
- Set up a python environment with some basic libraries
conda create -n omero -c conda-forge omero-py ipykernel matplotlib numpy pip
- Activate the omero environment
conda activate omero
- Install ezomero and juypter labs (more information about installing jupyterLab can be found here https://jupyterlab.readthedocs.io/en/4.2.x/getting_started/installation.html)
pip install ezomero
pip install jupyterlab
python -m ipykernel install --user --name=omero
- Optional (to upload data)
- Prepare sample data to upload to OMERO
- Install OMERO.insight: https://www.openmicroscopy.org/omero/downloads/
Clone to your local computer and open the notebooks in nbs with jupyter lab:
Open Miniforge prompt
conda activate omero
jupyter lab