Ori Avinoam
Weizmann Institute of Science
Israel
Overview
Applications for this event are not open yet. If you are interested in receiving more information please register your interest.
Course overview
The course is designed to equip participants with both practical and hands-on skills in Correlative Light and Electron Microscopy (CLEM) in both room temperature and cryogenic conditions and provide a solid theoretical foundation. These advanced imaging modalities enable researchers to precisely locate structures of interest unambiguously within cellular ultrastructures. Such techniques were refined at the European Molecular Biology Laboratory (EMBL) and are still developed and applied here regularly.
Recognizing the increasing demand for in situ CLEM applications, the training is geared towards enabling attendees to create customized CLEM workflows to address their unique research questions and share this knowledge within their institutions. Our course delves into the specifics of these methods, emphasizing high-precision localization and cutting edge sample preparation techniques. Furthermore, it offers significant interaction with CLEM and EM experts, facilitating rich discussions and troubleshooting sessions. This ensures that participants not only learn the methodology but also gain insightful, actionable guidance to apply CLEM techniques effectively in their research endeavors. Networking activities will ensure an overall community strengthening environment.
What past participants say about the course
“The course provided an excellent balance of theory and hands-on training in CLEM, with expert guidance and valuable networking opportunities. I feel much more confident in applying these techniques to my research” – Deniz Başöz, Acibadem University, Turkey
“Fantastic course and trainers, would absolutely recommend it to anyone wanting to do CLEM, at any level of experience. It’s so comprehensive that you leave with the confidence you can apply everything you’ve seen to your own experiments.” – Emanuel Fertig, Victor Babes National Institute of Pathology, Romania
“The course was outstanding. There is lots of practical information and opportunity to talk with the trainers. I learned a lot of new workflows that I can bring to my home institution and directly apply. Thank you for having me!” – Gerben de Zwaan, Wageningen University and Research, The Netherlands
Sponsors
Sponsorship opportunities
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Warning
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Speakers
Speakers, trainers, and staff
Mandy Boermel
EMBL Heidelberg
Germany
Petr Chlanda
University Heidelberg
Germany
Charlotta Funaya
University of Heidelberg
Germany
Herman Fung Kar Ho
University of Michigan
United States
Steffen Klein
EMBL Heidelberg
Germnay
Wanda Kukulski
University of Bern
Switzerland
Mathilda Hjoerdis Lennart
Max Planck Institute of Molecular Cell Biology and Genetics
Germany
Pedro Machado
Human Technopole
Italy
Rachel Mellwig
EMBL Heidelberg
Germany
Perrine Paul-Gilloteaux
Nantes Université
France
Andreia Pinto
Leica Microsystems / EMBL
Germany
Paolo Ronchi
EMBL Heidelberg
Germany
Anna Steyer
EMBL Heidelberg
Germany
Léa Swistak
EMBL Heidelberg
Germany
Salo Veijo
Karolinska Institute
Sweden
Evgenia Zagoriy
EMBL Heidelberg
Germany
Zhengyi Yang
EMBL Heidelberg
Germany
Scientific organisers
Ori Avinoam
Weizmann Institute of Science
Israel
Mandy Börmel
EMBL Heidelberg
Germany
Rachel Mellwig
EMBL Heidelberg
Germany
Nadav Scher
EMBL Heidelberg
Germany
Evgenia Zagoriy
EMBL Heidelberg
Germany
Course organisers
Ecem Cayiroglu
EMBL Heidelberg
Germany
Lucía Rodriguez Minutta
EMBL Heidelberg
Germany
Michelle Steinhauer
EMBL Heidelberg
Germany
Preliminary programme
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- Some pre-course work (such as watching pre-recordings and protocol reading) with estimated time 0-10 hours will be required and will be shared in advance of the course
- Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change
- For registered participants, recorded talks will be accessible on demand for 4 weeks after the end of the event, unless indicated otherwise
Day 1: Sunday, 31 January 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 14:00 – 14:30 | Arrival and registration | ISG Hotel |
| 14:30 – 15:00 | Welcome and house notes and course overview | |
| 15:00 – 16:00 | Lecture 1: How to choose your CLEM approach Ori Avinoam – Weizmann Institute of Science, Israel | ISG Hotel |
| 16:00 – 16:30 | Coffee Break | ISG Hotel |
| 16:30 – 18:00 | Flashtalks | ISG Hotel |
| 18:00 – 19:00 | Lecture 2: In-situ CLEM workflow and best practices Rachel Mellwig – EMBL Heidelberg, Germany | ISG Hotel |
| 19:00 – 21:00 | Dinner and networking | ISG Hotel |
Day 2: Monday, 01 February 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 08:40 – 08:50 | Bus from the ISG Hotel to EMBL ATC | ISG Hotel |
| 08:50 – 09:00 | Overview of the day | Flex Lab A&B |
| 09:00 – 09:30 | Introduction | Flex Lab A&B |
| 09:30 – 10:30 | Lecture 3: Keynote Speaker: CLEM for structural cell biology: past, present and future Wanda Kukulski – University of Bern, Switzerland | Flex Lab A&B |
| 10:30 – 10:45 | Coffee Break + Meet the speaker | Flex Lab A&B |
| 10:45 – 11:30 | Lecture 4: Tips and tricks to adapt on-section CLEM to diverse biological questions Mandy Boermel – EMBL Heidelberg, Germany | Flex Lab A&B |
| 11:30 – 12:15 | Lecture 5: Strategies for cryoEM sample preparation Evgenia Zagoriy – EMBL Heidelberg, Germany | EMBL Canteen |
| 12:15 – 13:15 | Lunch | EMBL Canteen |
| 13:15 – 19:30 | Practical session 1 Practical session 1A – High pressure freezing High-pressure freezing of cell monolayers on sapphire discs and yeast using Leica EM-ICE freezing machine in the Imaging Centre. Anna Steyer – EMBL Heidelberg, Germany Andreia Pinto – Leica Microsystems, Germany Practical session 1B – Freeze substitution Demonstration on how the freeze substitution machine works and discussion of the protocol for CLEM. Paolo Ronchi – EMBL Heidelberg, Germany Ori Avinoam – The Weizmann Institute of Science, Israel Mathilda Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany Nadav Scher – EMBL Heidelberg, Germany Pedro Machado – Human Technopole, Italy Practical session 1C – Plunge freezing Plunge freezing cells onto EM grids using the Leica EM GP2 Zhengyi Yang – EMBL Heidelberg, Germany Léa Swistak – EMBL Heidelberg, Germany Veijo Salo – Karolinska Institutet, Sweeden Practical session 1D – Micropatterning Pre-patterning grids in preparation to seeding cells Evgenia Zagoriy – EMBL Heidelberg, Germany Herman Fung – University of Michigan, USA | EMCF and IC |
| 19:30 – 21:00 | Dinner with dissussion: Core facility management and career | RTL |
| 21:00 | Bus to ISG Hotel |
Day 3: Tuesday, 02 February 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 08:40 – 08:50 | Bus from the ISG Hotel to EMBL ATC | Flex Lab A&B |
| 08:50 – 09:00 | Overview of the day | Flex Lab A&B |
| 09:00 – 10:00 | Lecture 6: Cryo-CLEM to study viruses Petr Chlanda – Heidelberg University, Germany | Flex Lab A&B |
| 10:00 – 10:30 | Coffee Break + Meet the speaker | Flex Lab A&B |
| 10:30 – 11:15 | Lecture 7: Tricks and pitfalls in ultramicrotomy Andreia Pinto – EMBL Heidelberg, Germany | Flex Lab A&B |
| 11:15 – 11:45 | Lecture 8: In block fluorescence imaging for FIB-SEM imaging Paolo Ronchi – EMBL Heidelberg, Germany | Flex Lab A&B |
| 11:45 – 12:45 | Lunch | EMBL Canteen |
| 12:45 – 19:15 | Practical session 2 Practical session 2A – Ultramicrotomy at room temperature Trimming and sectioning of room temperature samples Viola Oorschot – EMBL Heidelberg, Germany Andreia Pinto – EMBL Heidelberg, Germany Nadav Scher – EMBL Heidelberg, Germany Practical session 2B – Light microscopy on plastic sections Fluorescence microscopy imaging of a thin section on an EM grid Paolo Ronchi – EMBL Heidelberg, Germany Mandy Boermel – EMBL Heidelberg, Germany Practical session 2C – Cryo light microscopy (LSM900 Zeiss) Fluorescence imaging of high-pressure frozen samples Anna Steyer – EMBL Heidelberg, Germany Zhengyi Yang – EMBL Heidelberg, Germany Veijo Salo – Karolinska Institutet, Sweeden Practical session 2D – Cryo light microscopy (Leica Stellaris) Fluorescence imaging of plunge frozen cells Steffen Klein – EMBL Heidelberg, Germany Léa Swistak – EMBL Heidelberg, Germany | EMCF and IC |
| 19:15 – 20:15 | Dinner | EMBL Canteen |
| 20:15 | Bus to ISG Hotel | EMBL ATC Entrance |
Day 4: Wednesday, 03 February 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 08:40 – 08:50 | Bus from the ISG Hotel to EMBL ATC | |
| 08:50 – 09:00 | Overview of the day | Flex Lab A&B |
| 09:00 – 09:30 | Lecture 9: On section clem to STEM workflow Pedro Machado – Human Technopole, Italy | Flex Lab A&B |
| 09:30 – 10:00 | Lecture 10: Different flavours of CLEM Charlotta Funaya – Heidelberg University, Germany | Flex Lab A&B |
| 10:00 – 11:00 | Practical session 3A: SerialEM demonstration with Remote TEM session Mandy Boermel – EMBL Heidelberg, Germany Ori Avinoam – Weizmann Institute of Science, Israel | Computer Training Lab |
| 11:00 – 11:15 | Coffee break + Meet the Speakers | Computer Training Lab |
| 11:15 – 12:15 | Practical session 3B: SerialEM hands-on Mandy Boermel – EMBL Heidelberg, Germany Ori Avinoam – Weizmann Institute of Science, Israel | Computer Training Lab |
| 12:15 – 13:15 | Lunch | EMBL Canteen |
| 13:15 – 13:45 | Lecture 11: Introductory talk: Icy and eC-CLEM Perrine Paul-Gilloteaux – University of Nantes, France | Computer Training Lab |
| 13:45 – 15:15 | Practical session 3C: Introductory talk and Computer practical: Icy and eC-CLEM: Perrine Paul-Gilloteaux – University of Nantes, France Nadav Scher – EMBL Heidelberg, Germany | Computer Training Lab |
| 15:15 – 15:30 | Coffee break + Meet the Speakers | Computer Training Lab |
| 15:30 – 16:00 | Debrief: Wrap up of first round of practicals, Q&A | Computer Training Lab |
| 16:00 – 17:00 | Transfer to Downtown (with a stop at ISG Hotel) | |
| 17:00 – 22:15 | Guided city tour and course dinner in old town Heidelberg |
Day 5: Thursday, 04 February 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 08:40 – 08:50 | Bus from the ISG Hotel to EMBL ATC | |
| 08:50 – 09:00 | Overview of the day | Flex Lab A&B |
| 09:00 – 09:30 | Lecture 12: Room temperature CLEM success story Mathilda Hjoerdis Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany | Flex Lab A&B |
| 09:30 – 10:00 | Lecture 13: Cryo-CLEM success story Léa Swistak – EMBL Heidelberg, Germany | Flex Lab A&B |
| 10:00 – 10:15 | Coffee break + Meet the Speakers | Flex Lab A&B |
| 10:15 – 13:00 | Practical session 4 – In depth practicles part 1 (See details below) | EMCF and IC |
| 13:00 – 14:00 | Lunch | EMBL Canteen |
| 14:00 – 20:00 | Practical session 4 – In depth practicles part 2 Practical 4A – Troubleshooting sample preparation – FS, HPF, PF Ori Avinoam – Weizamnn Institute of Science, Israel Mathilda Hjoerdis Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany Herman Fung – University of Michigan, USA Pedro Machado – Human Technopole, Italy Practical 4B – Demo – TFS Hydra pFIB on-lamella CLEM workflow Zhengyi Yang – EMBL Heidelberg, Germany Practical 4C – Software hands-on session (ICY, SerialEM) – Bring your own data Perrine Paul-Gilloteaux – University of Nantes, France Nadav Scher – EMBL Heidelberg, Germany Practical 4D – Demo – Plasma FIB Tescan Samuel Zachej – Tescan, Evegenia Zagoriy – EMBL Heidelberg, Germany Practical 4E – Managing an EM facility, interactive session and facility tour Rachel Mellwig – EMBL Heidelberg, Germany Charlotta Funaya – Heidelberg University, Germany Practical 4F – Demo – Meteor in-chamber CLEM Marit Smeets – Delmic, The Netherlands Evegenia Zagoriy – EMBL Heidelberg, Germany Practical 4G – Demo – Leica Enuity Andreia Pinto – Leica Microsystems, Germany Practical 4H – F30 correlative tomogram acquisition Mandy Boermel – EMBL Heidelberg, Germany Practical 4I – In-block confocal microscopy Manuel Gunkel – EMBL Heidelberg, Germany Paolo Ronchi – EMBL Heidelberg, Germany Practica 4J – Ultramicrotomy, including serial-sections Viola Oorschot – EMBL Heidelberg, Gemrany | EMCF and IC |
| 20:00 – 21:00 | Dinner | EMBL Canteen |
| 21:00 | Bus to the ISG Hotel | EMBL ATC Entrance |
Day 6: Friday, 05 February 2027
| Time (Europe/Berlin) | Speaker | Location |
|---|---|---|
| 08:40 – 08:50 | Bus from the ISG Hotel to EMBL ATC | |
| 08:50 – 09:00 | Overview of the day | Flex Lab A&B |
| 09:00 – 10:30 | Round table discussions on open questions, students explain implementations for their own projects | Flex Lab A&B |
| 10:30 – 11:00 | Lecture 14: Cryo-liftout workflow Zhengyi Yang – EMBL Heidelberg, Germany | Flex Lab A&B |
| 11:00 – 11:15 | Coffee break + Meet the Speakers | Flex Lab A&B |
| 11:15 – 11:45 | Lecture 15: Probes for Cryo-CLEM Herman Fung – University of Michigan, USA | Flex Lab A&B |
11:45 – 12:15 | Lecture 16: Efficient targeting in cryo-CLEM for in situ applications Anna Steyer – EMBL Heidelberg, Germany | Flex Lab A&B |
| 12:15 – 13:00 | Lunch | EMBL Canteen |
| 13:00 – 13:30 | Lecture 17: Visualizing Lipid Flux and Organelle Biogenesis by Cryo-Correlative Microscopy Veijo Salo – Karolinska Institute, Sweden | Flex Lab A&B |
| 13:30 – 14:00 | Lecture 18: 3D CLEM in Cryo Steffen Klein – EMBL Heidelberg, Germany | Flex Lab A&B |
| 14:00 – 14:15 | Closing remarks Feedback and Farewell | Flex Lab A&B |
| 14:30 | Departure to the train station |
Date: 31 Jan - 5 Feb 2027
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Organisers:
-
Ori Avinoam
Weizmann Institute of Science, Israel -
Mandy Börmel
EMBL Heidelberg, Germany -
Rachel Mellwig
EMBL Heidelberg, Germany -
Nadav Scher
EMBL Heidelberg, Germany -
Evgenia Zagoriy
EMBL Heidelberg, Germany
Contact: EMBL Events
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