The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data. OME supports more than 150 image data formats across many imaging modalities including medical imaging, high-content screening and whole-slide imaging.

OME supports and visualize multi-channel 3D timelapse images. OMERO, a component of OME, is a software platform for image data management and analysis which will be presented in this workshop. Import, organisation, viewing, searching, annotation and publishing of imaging data with OMERO will be shown.

The first day of the workshop concentrates on basics of OMERO and does not assume any programming skills. During the second day, we will show how to transition from manual data processing to automated processing workflows using applications against the OMERO API, how to integrate a variety of processing tools with OMERO such as CellProfiler, Orbit, ImageJ, R and how to programmatically generate output ready for publication. We will also demonstrate command line tools available to facility managers and system administrators to administrate an OMERO server.

This workshop is dedicated to all researchers and research students dealing microscopic image data  who wish to learn how an image data storage solution could look like. The workshop includes presentations and hands-on session from OME developers and experts in the field as well as open question sessions and multiple hands-on sessions.

Prior knowledge in microscopy, scripting and data analysis is not required.
Any student / researcher dealing with scientific images is more than welcome to join this workshop.

Please note that it is recommended to bring your own laptop to the workshop.

Please let us know during the registration if you wish to attend only single days or the complete workshop!

The registration fee of 25 € per person and day covers lunch (finger food), refreshments and coffee & tea with some snacks and sweets for all days of the workshop.


University of Basel
Biozentrum, Imaging Core Facility
Klingelbergstr. 50/70
4056 Basel



Microscopy and Image Analysis Platform (MIAP)

Tobias Wernet
e-mail: tobias.wernet@zbsa.uni-freiburg.de

Martin Zeeb
e-mail: martin.zeeb@zbsa.uni-freiburg.de

web: https://miap.eu
e-mail: info@miap.eu

Workshop Details