OMERO for Developers

Materials for the OMERO for Developers workshop at the Jackson Laboratory, which covers:

• Using BlitzGateway and ezomero to view images from OMERO in Python
• Retrieving thumbnails using the JSON API
• Introduction to the Zarr file format

Set up your environment

With any conda-like (I recommend miniforge):

conda env create -f environment.yml

Otherwise:

You'll need to install dependencies yourself. This workshop will use jupyterlab, ezomero, matplotlib, ome-zarr and omero-cli-zarr. Latest versions should be fine.

Running notebooks

Just go to your command-line, conda activate omero_devs and then run jupyter lab. Either you'll get a browser window open with Jupyter Lab, or you'll get an address to paste in your browser.

Next, we'll need to set up config.py - use config_template.py as a starting point and change it accordingly based on instructions during the workshop.

If you're using the JAX dev server (as we will during the workshop), you'll need to be on the VPN.

Workshop notebooks

1-Introduction.ipynb

2-JSON_API.ipynb

3-Blitz_API.ipynb

4-Zarr.ipynb