The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable visualization, analysis, sharing and publication of biological image data.


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


September 3rd  - 4th 2018

Booking Period: July 23rd – August 26th

Registration Fee:
25,00 € / day
Total (for both days): 50,00 €



Dr. Petr Walczysko

Position:QA Software Specialist



Dr. Jean-Marie Burel 

Position:Senior Software Architect



Dr. Oliver Biehlmaier

Position:Head IMCF Technology Platform

Dr. Petr Walczysko, QA Software Specialist, University of Dundee.

Petr Walczysko joined the OME project in October 2012 as a software specialist for testing and quality assurance. He studied at Charles University of Prague where he received Master of Science degree in Physics and the University of Freiburg in Germany where he received PhD in Biology. Throughout his PhD studies and his further career as a researcher he was intensively using conventional, confocal and multiphoton fluorescence microscopy applications on biological systems. He was adapting these optical microscopy techniques for particular biological problems, and also worked on the subsequent image analysis of microscopic images in a range of image analysis programmes. He enjoys yoga, reading and chess.


Dr. Jean-Marie Burel, Senior Software Architect, University of Dundee. 

Jean-Marie Burel joined the staff of the Swedlow lab in 2003. Since then, he's been contributing to the development of OME, and spends most of his time working on the OMERO.insight project. He received is PhD in mathematics from the University of Brest in 2000. His research interests lie in the area of harmonic maps, harmonic morphisms and geometric structure. After his PhD, he worked in a private company as developer then moved (September 2001) to Lund University, Sweden, where he held a post-doctoral research position. Jean-Marie now enjoys the muddy rugby pitches of Scotland.


Dr. Oliver Biehlmaier, Head of IMCF Technology Platform, University of Basel. 

Since 2011 Head of the Imaging Core Facility at the Biozentrum of the University Basel, Switzerland
2008 – 2011 Advanced Microscopy Scientist at the Light Microscopy Centre of the ETH Zürich, Switzerland 2003 – 2008 Research Associate in the Laboratory of Professor Stephan Neuhauss at the Institute of Zoology at the University of Zurich, Switzerland
2001 – 2003 Postdoctoral Scientist in the Laboratory of Professor Konrad Kohler at the University Eye Hospital Tübingen, Germany

1997 – 2001 Graduate student in the Laboratory of Professor Konrad Kohler at the University Eye Hospital Tübingen
1996 – 1997 Master student in the Laboratory of Professor Konrad Kohler at the University Eye Hospital Tübingen
1991 – 1996 Studies in Biology at the University of Tübingen Selected Memberships:
Since 2008 European Light Microscopy Initiative
2000 – 2008 Association for Research in Vision & Ophtalmology (ARVO)
Since 1997 German Society of Neurobiologists