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March 13 - 16, 2022

From 3D Light to 3D Electron Microscopy

Virtual 6th Joint Workshop and Symposium

Life happens in 3D – and understanding biological context in the three dimensions has been a major driver in the past decades in both light and electron microscopy. Today the trend towards 3D continues with large volume imaging and highest resolution with modern light and electron microscopy-based techniques now enabling previously impossible insights into functional and structural biology. Correlative microscopy can combine a large variety of different imaging techniques such as confocal microscopy, X-ray microscopy and different volume EM methods e.g. Array Tomography or Serial block face imaging. Comprehensive workflow solutions and automatisation have eased the path for the use of Correlative Microscopy and volumetric imaging.

An emerging challenge resulting from the improved connectivity between the individual imaging modalities is the handling of larger and thus more complex data. Workflow flexibility, file compatibility and big data handling are the new challenges to be tackled, not only from a hardware perspective but also for image processing and visualisation.

This meeting is centred on scientific sessions covering a broad range of correlative workflows, volume EM imaging, image processing techniques as well as segmentation and visualisation. The meeting will take place from 13 to 16 March 2022 – please save this date to your calendar! Don’t miss this exciting opportunity for exchange with researchers and industry to explore the new and emerging technologies and methods for correlative microscopy and volume EM in life sciences.

Due to the COVID-19 situation, we decided to offer the 6th Joint Workshop and Symposium ‘From 3D Light to 3D Electron Microscopy’ as an virtual event, only.
All participants are able to present their own scientific work in a poster presentation or an oral presentation. The organising committee will review abstracts for the oral presentations.

We look forward to meeting you virtually!

Further information about the event.

The event is jointly organised by EMBL, ZEISS, The Francis Crick Institute and The VIB Ghent.



Sunday 13 March 2022

Topic Time (CET) Speaker Title

Welcome and opening remarks

1.00 - 1.15 pm

Organisers and ZEISS


Keynote Session
Chair: Yannick Schwab & Rachel Mellwig

1.15 - 2.00 pm

Alexandra Pacureanu, European Synchrotron Radiation Facility, France

Keynote lecture 1: Multimodal and multiscale 3D imaging of cells, tissues and organisms with X-ray light

2.00 - 2.10 pm



2.10 - 2.55 pm

Jan Ellenberg, EMBL Heidelberg, Germany

Keynote lecture 2: Correlative imaging of cell division across scales


2.55 - 3.05 pm



Session 1: 
vCLEM insights into biological structure and function
Chairs: Lucy Collinson & Chris Guérin

3.05 - 3.35 pm

Andreas Müller, Paul-Langerhans-Institut Dresden, Germany

3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse ß-cells

3.35 - 4.05 pm

Carles Bosch, The Francis Crick Institute London, UK

From mammalian circuits to synapses: correlative multimodal imaging using hard x-rays

4.05 - 4.20 pm

Linda Wedemann, Centre for Structural Systems Biology; Hannover Medical School; Leibniz-Institute for Experimental Virology (HPI), Germany

Intermittent bulk release of human cytomegalovirus: identification of a novel egress pathway via whole-cell 3D CLEM

4.20 - 4.35 pm



4.35 - 5.05 pm

Rachel Lennon, The University of Manchester, UK

Investigating basement membranes with volume electron microscopy

5.05 - 5.20 pm

Alice Liang, NYU Grossman School of Medicine, USA

Structural and protein composition changes in plakophilin-2 deficient adult hearts revealed by volume electron microscopy

5.20 - 5.30



Panel Discussion
Hosted by Lucy Collinson & Yannick Schwab

5.30 - 6.30 pm


vCLEM community around the globe

Meet the speakers of Day 1

6.30 - 7.00 pm



Monday 14 March 2022

Topic Time (CET) Speaker Title

Social programme: speed networking

12.00 - 12.45 pm



Overview of the day

1.00 – 1.15 pm

Chris Guérin


Session 2: 
vEM and vCLEM on diverse sample types
Chair: Saskia Lippens & Evelien van Hamme

1.15 – 1.45 pm

Paolo Ronchi, EMBL Heidelberg, Germany

Integrating transcriptomics and volume EM to study the evolution of cell types

1.45 – 2.15 pm

Peijun Zhang, University of Oxford, UK

Correlative and multi-scale imaging of virus infection

2:15 – 2:30 pm

Chun So, Max Planck Institute for Biophysical Chemistry, Germany

Mechanism of spindle pole organization and instability in human oocytes

2.30 - 2.40 pm



2.40 – 3.10 pm

Kirk Czymmek, Danforth Plant Science Center, St. Louis, USA

Strategies for Multiscale and Multiplex Correlative Workflow in Plants

3.10 - 3.25 pm

Irene Pilar Ayuso Jimeno, EMBL Rome, Italy

Identifying long-range synaptic inputs using genetically encoded labels and volume electron microscopy


3.25 - 3.35 pm



Workshop 1

3.35 - 4.35 pm

Christel Genoud & Jean Daraspe & Olivia Muriel Lopez, UNIL, Switzerland

Sample preparation for volume EM and vCLEM

Poster Session

4.35 - 5.35 pm



Workshop 2

5.35 - 6.35 pm

Jemima Burden & Ian White, UCL London, UK
Raffaela Carzaniga, The Francis Crick Institute, London, UK

Breaking down the correlative workflow for Array Tomography: from section collection to image analysis


6.35 - 6.45 pm



Session 3: 
New vCLEM workflows - part 1
Chair: Anneke Kremer & Saskia Lippens

6.45 - 7.15 pm

Aaron Kuan, Harvard University, Cambridge, USA

Neural Cartography: Mapping Decision-Making Circuits with Light, X-ray, and Electron Microscopy

7.15 - 7.45 pm

Naomi Kamasawa, Max Planck Florida Institute for Neuroscience, Jupiter, USA

How to link brain function and synaptic ultrastructure

Meet the  speakers and workshop contributors of Day 2

7.45 - 8.15 pm



Tuesday 15 March 2022

Topic Time (CET) Speaker Title

Overview of the day

1.00 - 1.15 pm

Chris Guérin


Session 3: New vCLEM workflows – part 2
Chair: Paolo Ronchi & Marianne Sandvold Beckwith

1.15 - 1.45 pm

Alex De Marco, Monash University, Melbourne, Australia

Increasing throughput and efficiency in cryo-CLEM

1.45 - 2.15 pm

Wei Guan & Azumi Yoshimura, The Francis Crick Institute, London, UK

Hitting the target: cells, circles, sections, and the ultraLM2

2.15 - 2.30 pm

Marit de Beer, Radboudumc, The Netherlands

3D cryo-CLEM of a wall-deficient bacteria provides evidence for ancient mechanism of cellular uptake

2.30 - 2.45 pm



2.45 - 3.15 pm

Liz Duke, EMBL Hamburg, Germany

Can X-ray imaging contribute to the 3D Light to 3D electron microscopy workflow?

3.15 - 3.30 pm

Nadav Scher, Weizmann Institute of Science, Israel

3D correlative cryo-FM and cryo-FIB-SEM using lipid droplets as in-situ fiducial markers for correlation


3.30 - 3.40



Workshop 3

3.40 - 4.40 pm

Anneke Kremer & Saskia Lippens, VIB Ghent
Marianne Beckwith & Kimberly Meechan, EMBL Heidelberg

X-ray targeting of arabidopsis pollen tetrads for SBF-SEM


4.40 - 4.50 pm



Workshops 4

4.50 - 5.50 pm

Anna Steyer & Simone Mattei, EMBL Heidelberg
Andreas Schertel, ZEISS

Correlative cryo workflow


5.50 - 6.00 pm



Session 3: New vCLEM workflows - part 3
Chair: Anneke Kremer & Evelien van Hamme

6.00 - 6.30 pm

Thomas Templier, Collectome, Lausanne, Switzerland

MagC, magnetic collection of ultrathin sections for vCLEM

6.30 - 7.00 pm

Jacob Hoogenboom, University of Technology, Delft, The Netherlands

Faster CLEM with single and multi-beam SEMs

Meet the speakers and workshop contributors of Day 3

7.00 - 7.30 pm



Wednesday 16 March 2022

Topic Time (CET) Speaker Title

Overview of the day

1:00 -1:15 pm

Chris Guérin


Workshop 5

1:15 - 2:15 pm

Paolo Ronchi & Manuel Gunkel & Aliaksandr Halavatyi & Karel Mocaer, EMBL Heidelberg, Germany,
Giulia Mizzon, Heidelberg University, Germany

FIB-SEM acquisition of single cells in a large sample guided by fluorescence


2.15 - 2.25 pm



Workshop 6

2:25 - 3:25 pm

Anna Lena Eberle & Tomasz Garbowski & Stephan Nickell, Carl Zeiss MultiSEM GmbH

Introducing the high-throughput serial section acquisition workflow with ZEISS MultiSEM


3:25 - 3:35 pm



Session 4: New developments in vCLEM image processing
Chair: Anna Kreshuk & Julian Hennies

3:35 - 4:05 pm

Kedar Narayan, NIH National Cancer Institute Center for Cancer Research, USA

Taking the measure of cells with volume electron microscopy

4:05 - 4:35 pm

Christian Tischer, EMBL Heidelberg, Germany

CLEM data formats, visualisation and registration

4:35 - 5:05 pm

Aubrey Weigel, HHMI Janelia Research Campus, Ashburn, USA

Towards automatic whole cell organelle segmentation in volume electron microscopy

5:05 - 5:20 pm



5:20 - 5:50 pm

Matthew Hartley, EMBL-EBI, Cambridgeshire, UK

Archiving correlative imaging data: challenges and opportunities

5:50 - 6:05 pm

Martin Schorb, EMBL Heidelberg, Germany

A modular and generic framework for high-performance alignment of volume microscopy data

6:05 - 6:20 pm

Deniz Daviran, Radboudumc, The Netherlands

Image post-processing for 3D cryo-FIB-SEM: squeezing the information out!

Meet the speakers and workshop contributers of Day 4

6:20 - 6:50 pm




6:50 - 7:00 pm



Closing lecture

7:00 - 7:45 pm

Saskia Lippens, VIB Ghent, Belgium

CLEM: Consolidating Life scientists & Experts in Microscopy

Closing remarks

7:45 - 8:00 pm

Organizers & ZEISS



All times in CET

* Recorded talks will be accessible on demand for 2 weeks after the end of the event

Workshop #1

​Sample Preparation for volume EM and vCLEM

During this workshop, we will share with participants experiences about sample preparation for the different techniques presented during the conference. We will show tips and tricks for sample preparation and mounting on different supports for 3DEM and CLEM. We will cover the techniques for SBEM sample prep, FIBSEM sample prep (with and without fluorescence preservation) as well as array tomography.​

Contributing people: ​Christel Genoud (UNIL), Jean Daraspe (UNIL), Olivia Muriel Lopez (UNIL)

Workshop #2

Breaking down the correlative workflow for Array Tomography: from section collection to image analysis.

See how non-destructive ‘Array Tomography’ (AT) works: This workshop will cover different serial sectioning approaches, strategies for image acquisition, through to aligning the 2D images to be able to generate a 3D model. ​These volume EM datasets can be correlated with 3D light microscopy datasets of the same sample, acquired previously by either confocal imaging of the sample live or fixed, or widefield imaging of the serial sections.​

Contributing people: Jemima Burden (UCL London), Ian White (UCL London), Raffaela Carzaniga (The Francis Crick Institute, London)

Workshop #3

X ray targeting of arabidopsis pollen tetrads for SBF-SEM

We will show you how XRay images can be used to determine the position of pollen tetrads in the arabidopsis anther and how to use this data to trim the sample block to be able to relocate this position in SBF-SEM for imaging of specific pollen tetrads.​

​Contributing people: Anneke Kremer (VIB Ghent), Saskia Lippens (VIB Ghent), Marianne Beckwith (EMBL Heidelberg), Kimberly Meechan (EMBL Heidelberg)

Workshop #4

Correlative Cryo Workflow

Learn how you can combine cryo-confocal imaging, cryo-lamella preparation and cryo-electron tomography to get high-resolution information of your favorite structure. The correlative workflow connects a confocal fluorescence microscope, with a focused ion beam - scanning electron microscope for targeted lamella preparation and a high-end transmission electron microscope. You will learn about the hardware and software involved to investigate your samples in their native state.​

Contributing people: ​Anna Steyer (EMBL Heidelberg), Simone Mattei (EMBL Heidelberg), Andreas Schertel (ZEISS)

Workshop #5

FIB-SEM acquisition of single cells in a large sample guided by fluorescence.

This workshop will present a correlative 3D light and electron microscopy workflow that integrates in-resin confocal fluorescence microscopy, 2-photon branding and focused ion beam scanning electron microscopy (FIB-SEM), as described in Ronchi et al., 2021. We will discuss how to preserve fluorescence during sample preparation for volume EM and show how to target the FIB-SEM acquisition of specific cells of interest based on a fluorescence 3D map acquired by confocal imaging of the block.​

Contributing people: Paolo Ronchi (EMBL Heidelberg), Giulia Mizzon (Heidelberg University), Manuel Gunkel (EMBL Heidelberg), Aliaksandr Halavatyi (EMBL Heidelberg)

Workshop #6

Introducing the high-throughput serial section acquisition workflow with ZEISS MultiSEM

We will present the typical serial section acquisition workflow with a multibeam scanning electron microscope, where navigation and ROI definition is routinely done on a correlated wide-field light microscope overview image of the sample. A semi-automated Experiment Wizard guides the user step-by-step through the workflow setup, emphasizing the ease-of-use required for a true high-throughput imaging experience. Besides that, operation principle and image data structure of the ZEISS MultiSEM will be introduced.​

​Contributing people: ​Anna Lena Eberle, Tomasz Garbowski, Stephan Nickell (all Carl Zeiss MultiSEM GmbH)

Panel Discussion | March 14th 2022

vCLEM community around the globe | Hosted by Lucy Collinson & Yannick Schwab

  • The discussion will be moderated by international panellists all involved in community efforts around vCLEM. They will share their views and trigger feedback from the audience around 3 topics: how international communities organise access to infrastructures (open facilities, funding mechanisms); how they develop their training and outreach activities; how they help scientists with dealing with their data (standards, repositories).


Yannick Schwab | EMBL Heidelberg, Germany
Paolo Ronchi | EMBL Heidelberg, Germany
Lucy Collinson | The Francis Crick Institute London, UK
Raffaela Carzaniga | The Francis Crick Institute London, UK
Saskia Lippens | VIB Ghent, Belgium
Anneke Kremer VIB Ghent, Belgium
Chris Guérin | VIB Ghent, Belgium
Alexandra Elli | Carl Zeiss Microscopy GmbH