Our GerBI team Young Microscopists and Image Analysts (YMIA) organises a mini series focusing on data management and subsequent image analysis with OMERO.
This mini-series includes two events with Tom Boissonet:
- 13.11.24 – Seminar: Getting started with Omero: Data management and Metadata annotation (Event page here)
- 21.11.24 – Workshop: How to use Omero for image processing with Jupyter Notebooks
The events both start at 2pm and are scheduled until 5pm (2h of presentation/workshop including a break, 1h for questions and troubleshooting).
For registration and access to the meeting link (will be the same for both events), please register here. All times and dates are in CEST, 2024. All participants can receive a document confirming their participation in the event series, upon request. Additionally, for those who haven’t filled out our poll for the next event series starting in January, please take a short moment to let us know what kind of events you would like to participacte in.
Requirements for the workshop:
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/
About YMIA:
Microscopy and image analysis are so strongly intertwined that it is impossible to talk about one without the other. We aim to form an international network among young scientists in which we can discuss our specific imaging and analysis issues in an informal, peer-based environment. Participation in the YMIA network is supported by GerBI, but does not require a GerBI membership.
For more information about the YMIA, check out our website: https://gerbi-gmb.de/teams/ymia/
