EMBL Imaging Centre

Open access to cutting-edge electron and light microscopy

We provide researchers from Europe and beyond with a synergistic portfolio of imaging services including cryo-EM, super-resolution and intravital microscopy to enable new ground-breaking research that crosses the scales of biology.


The EMBL Imaging Centre User Symposium will take place on Thursday 17th and Friday 18th October 2024, at EMBL Heidelberg, Germany, and will bring together the user community of the EMBL Imaging Centre. 

Invited and selected speakers have already used the facility and will present their research during the symposium. We aim to stimulate the exchange of experience among users and strengthen collaborations and interactions within the community. 

Besides the invited speakers, all participants are welcome to present their research during the poster or flash-talk session. The meeting will be rounded out with a discussion and feedback from our users.  



Day 1 – Thursday 17th October 2024
12:30 – 14:00Registration and light refreshmentsEMBL Imaging Centre 
registration desk
13:00 – 13:45Industry workshops (pre-registration required)

Leica: With the user, for the user – Leica Labs at the EMBL Imaging Centre supporting IC users and driving innovation in visualization and analysis (room 15-041)

Zeiss: Dynamics in Life: Analyse large 4D datasets seamlessly with ZEISS arivis Cloud (room 15-104)
14:00 – 14:15Opening remarks
Jan Ellenberg – EMBL
EMBL IC Lecture Hall
14:15 – 15:35Session 1Electron Microscopy
Chair: Simone Mattei – EMBL
EMBL IC Lecture Hall
14:15 – 14:35Molecular basis of mRNA delivery to the bacterial ribosome.
Albert Weixlbaumer – University of Strasbourg Institute for Advanced Study, France
14:35 – 14:55Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes.
Giulia Zanetti – Birkbeck University of London, UK
14:55 – 15:15Cryo-EM, a Breakthrough in Solving the Structure and Understanding the Mechanism of Photosynthetic Membrane Complexes.
Nathan Nelson – Tel Aviv University, Israel
15:15 – 15:35How bacteria float: Structural basis of buoyancy control with gas vesicles.
Arjen Jakobi – Delft University of Technology, Netherlands
15:35 – 15:45Group Photo
15:45 – 16:45Coffee Break (sponsored by Zeiss)EMBL IC kitchenette
16:45 – 17:45Session 2CLEM
Chair: Simone Mattei – EMBL
EMBL IC Lecture Hall
16:45 – 17:05TBC
Johan Decelle – Grenoble Alpes University, France
17:05 – 17:25Linking cell architecture to genomics in the giant bacterium Achromatium.
Danny Ionescu – Leibniz Institute for Freshwater Ecology and Inland Fisheries, Germany
17:25 – 17:45Organization of condensin proteins in the chromosomal environment in situ.
Mikhail Eltsov – IGBMC, France
17:45 – 18:45Conference dinnerEMBL Canteen
18:45 – 20:30Poster session / Sponsor booths
Wine, dessert and cheese
EMBL IC Atrium
Day 2 – Friday 18th October 2024
09:00 – 10:00Session 3Light Microscopy
Chair: Timo Zimmermann – EMBL
EMBL IC Lecture Hall
09:00 – 09:20Organization of crossover sites in C. elegans.
Simone Köhler – EMBL
09:20 – 09:40Neurodevelopmental principles underlying pediatric brain cancer.
Lena Kutscher – DKFZ, Germany
09:40 – 10:00Imaging nanoparticles, one molecule at the time.
Lorenzo Albertazzi – Eindhoven University of Technology, Netherlands
10:00 – 10:45Coffee Break (sponsored by Zeiss)EMBL IC kitchenette
10:45 – 11:00Session 4Flash Talks
Chair: Timo Zimmermann – EMBL
EMBL IC Lecture Hall
10:45 – 10:47Flash talk
10:47 – 10:49Flash talk
10:49 – 10:51Flash talk
10:51 – 10:53Flash talk
10:53 – 10:55Flash talk
10:55 – 10:57Flash talk
11:00 – 12:20Panel discussion
Chair: Jan Ellenberg – EMBL
EMBL IC Lecture Hall
12:20-12:50Closing remarks
Jan Ellenberg – EMBL
EMBL IC Lecture Hall
12:50 – 13:50Conference lunch EMBL Canteen

Practical info

Registration Fees and Abstract Submission

Registration is for free. Places are limited.

Abstract submission deadline is 18th July 2024.  

Onsite Information


All meals and coffee breaks are included. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

Health and safety notes

Do not smoke in any EMBL building.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

  • The first aid room is located next to the ATC Registration Desk (room 10- 205).
  • Dial the Emergency number 222 from any EMBL internal phone only.
  • Where is the accident? What happened? How many injured?
  • Emergency number 06221-387 7821 from mobile phones.
  • Please report all accidents to the conference officer at the registration desk.

In case of fire …

  • Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
  • A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
  • Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg.


Wi-Fi is available onsite. The eduroam network (secure, world-wide roaming access service developed for the international research and education community) is also available.


During the conference an EMBL Photographer may be taking photographs. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Travel to and from the venue

There is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. More detailed information on travelling to EMBL can be found on our Travel Information page.

Address: EMBL, Meyerhofstraße 1, 69117 Heidelberg, Germany. For further information on getting to EMBL Heidelberg visit Public Transportation to the Venue. For information about accommodation and local transportation please refer to the FAQ page.


The EMBL Imaging Centre training activities are generously supported by the Boehringer Ingelheim Foundation.

Industry Workshops

Zeiss: Dynamics in Life: Analyse large 4D datasets seamlessly with ZEISS arivis Cloud

Understanding dynamic behaviour is vital to gaining insights into biological processes. Across all scales, dynamics provide a crucial insight, from movement of organisms, organs or cells, developmental changes in organisms or tissues to cell-cell interactions and intracellular molecular behaviour which one often cannot observe due to phototoxicity, slow acquisitions or too complicated software. ZEISS offers a wide range of systems & software to observe & analyse samples with minimal light exposure at high speed down to molecular resolution.

Get ready to dive into the exciting world of light sheet microscopy and image analysis with ZEISS! Join us for an upcoming workshop where we’ll demonstrate the incredible power of Deep Learning (DL) in segmenting light sheet image data.

In the field of microscopy, image segmentation is a crucial step in image analysis, and traditional methods can be time-consuming and require manual intervention. But with deep learning, we can simplify and automate the segmentation process, making it faster, more efficient than ever before and allow you to do research that was previously not possible!

During this workshop, we’ll explore a fascinating case study of C. elegans embryo development, where researchers leveraged the superior performance of ZEISS arivis Cloud platform to develop DL networks that could be executed in the true 3D environment of ZEISS arivis Pro. This allowed them to segment and track cell division in a C. elegans embryo during the very early stages of development.

Leica: With the user, for the user – Leica Labs at the EMBL Imaging Centre supporting IC users and driving innovation in visualization and analysis

With the user, for the user – Leica Labs at the EMBL Imaging Centre supporting IC users and driving innovation in visualization and analysis.”

Leica Microsystems has always developed close relationships with academic and scientific research institutions to advance scientific understanding through microscopy. The partnership with the EMBL Imaging Centre is a prime example of our mission to drive innovation in visualization and analysis through partnering with users. Now, thanks to our unique partnership with the European Molecular Biology Laboratory (EMBL) in Heidelberg, researchers can gain access to cutting edge sample preparation, widefield and confocal imaging, and image analysis technology. 

Location is key to understanding biological mechanisms, from the inner workings of subcellular components to how cells form and interact across normal and diseased tissues. Microscopy enables researchers to look at the bigger picture and track proteins and other biomarkers at a single cell level to better understand the whole tissue landscape. In this workshop, we will give you an overview of the Leica Microsystems solutions available at the EMBL Imaging Centre and how they can help to advance your research.

Among the advanced solutions that we will highlight in more detail UC Enuity, a cutting-edge ultramicrotome capable of fluorescent and 3D targeting that was developed in collaboration with the EMBL. With a high degree of automation, it enables automatic sample alignment and trimming. It helps and guides the user through tedious tasks in ultramicrotomy thus simplifying the process of sample preparation and making ultramicrotomy more accessible.

Sample preparation for downstream molecular biology analysis is enabled by isolating regions of interest (ROI) from entire areas of tissue down to single cells or even subcellular structures such as chromosomes by laser microdissection (LMD) with the LMD7. With the help of Aivia, our image visualization, analysis and interpretation platform, regions of interest (ROI) which are destined for laser microdissection (LMD) can be detected and imported directly into the LMD software for microdissection. This workflow saves time and results in more robust statistics thanks to high throughput and automation.

In addition, we will elaborate on the experimental design and considerations to perform high multiplexing imaging experiments beyond 10 fluorophores on a single sample on the STELLARIS confocal platform. STELLARIS is particularly well suited for high multiplexing strategies as it combines a freely tunable white light laser (WLL | 440nm -790 nm) excitation with up to 5 highly sensitive spectral detectors for complete flexibility of detection from 410 nm up to the NIR range. This unique combination allows to fit a large palette of fluorophores and to optimize any possible combination. We will discuss appropriate fluorophore panels and the details of sample preparation. Furthermore, we will cover the challenges and tools required for imaging. Finally, we will showcase how advanced image analysis tools can be used to harness the insights from high multiplexing imaging results accurately segmenting cells so you can spend less time on analyzing data and more time on the biology via AI-driven spatial insights.

Adjacent to the symposium schedule, you are welcome to schedule demonstrations of the highlighted products.

Date: 17-18 October 2024

Location: EMBL Heidelberg 

Time: 12:30

Venue: EMBL Imaging Centre


Abstract submission 18 July 2024

Registration: 5 September 2024

Contact: ic-contact@embl.de

Share this event