March 13 -16, 2022

From 3D Light to 3D Electron Microscopy

6th Joint Workshop and Symposium

The event is jointly organised by EMBL, ZEISS, The Francis Crick Institute and The VIB Ghent.
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 unpredictable COVID-19 situation, we are going to offer the 6th Joint Workshop and Symposium ‘From 3D Light to 3D Electron Microscopy’ as an onsite workshop at the EMBL in Heidelberg, Germany and for all of those who are not able to join in person we will broadcast parts of the event so you are able to join us remotely.
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 either virtually or in person at the EMBL in Heidelberg!

Further information on the registration fee and all about the event.

Preliminary Programme

Sunday 13 March 2022

Topic Time (CET) Speaker Title

Arrival and registration for on-site participants

2.00 - 3.30 pm




3.30 - 4.00 pm

Organizers and Bernhard Zimmermann

Keynote Session, Chair: Yannick Schwab

4.00 - 5.00 pm

Alexandra Pacureanu - European Synchrotron Radiation Facility, France


5.00 - 6.00 pm

Jan Ellenberg – EMBL Heidelberg, Germany

Correlative imaging of cell division across scales

Welcome reception for on-site participants

6.00 - 8.00 pm



Monday 14 March 2022


Time (CET) Speaker Title

Session 1:
vCLEM insights into biological structure and function
Chair: Lucy Collinson
9.00 – 11:30 am

9.00 - 9.30 am

Andreas Müller – Paul-Langerhans-Institut Dresden, Germany

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

9.30 – 10.00 am

Carles Bosch – The Francis Crick Institute, UK

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

10.00 – 10.15 am

Selected talk from abstracts


10.15 – 10.45 am



10.45 – 11.15 am

Rachel Lennon – The University of Manchester, UK

Investigating basement membranes with volume electron microscopy

11.15 – 11.30 am

Selected talk from abstracts


Workshops 1 - 6
Recordings available for virtual participants

11.30 – 1.00 pm



Lunch with posters
for on-site participants

1.00 – 2.15 pm



Workshops 1 - 6
Recordings available for virtual participants

2.15 – 3.45 pm




3:45 – 4:00 pm



Session 2:
vEM and vCLEM on diverse sample types
Chair: Saskia Lippens
4.00 – 6:15 pm

4.00 – 4.30 pm

Paolo Ronchi – EMBL Heidelberg, Germany

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

4.30 – 5.00 pm

Kirk Czymmek – Danforth Plant Science Center, USA

Strategies for Multiscale and Multiplex Correlative Workflow in Plants

5.00 – 5.15 pm


Selected talk from abstracts

5.15 – 5.30 pm



5.30 – 6.00 pm

Peijun Zhang – University of Oxford, UK

Correlative and multi-scale imaging of virus infection

6.00 – 6.15 pm


Selected talk from abstracts

Panel Discussion
Hosted by Lucy Collinson & Yannick Schwab

6.15 – 7:00 pm


Community initiatives around the globe


7.00 pm

Free evening


Tuesday 15 March 2022

Topic Time Speaker Title

Session 3: New vCLEM workflows –
part I
Chair: Paolo Ronchi
9.00 - 11.30 am

9.00 - 9.30 am

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

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

9.30 - 10.00 am

Jacob Hoogenboom – Delft University of Technology, The Netherlands

Faster CLEM with single and multi-beam SEMs

10.00 - 10.15 am

Selected talk from abstracts


10.15 - 10.45 am



10.45 - 11.15 am

Liz Duke – EMBL Hamburg, Germany

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

11.15 - 11.30 am

Selected talk from abstracts


Workshops 1-6
Recordings available for virtual participants

11.30 - 1.00 pm



Lunch with posters
for on-site participants

1.00 - 2.15 pm



Workshops 1-6
Recordings available for virtual participants

2.15 - 3.45 pm




3.45 - 4.00 pm



Session 3: New vCLEM workflows -
part II
Chair: Anneke Kremer
4.00 - 6.45 pm

4.00 - 4.30 pm

Aaron Kuan - Harvard University, USA

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

4.30 - 5.00 pm

Naomi Kamasawa– Max Planck Florida Institute for Neuroscience, USA

How to link brain function and synaptic ultrastructure

5.00 – 5.15 pm

Selected talk from abstracts


5.15 – 5.30 pm



5.30 – 6.00 pm

Thomas Templier – Collectome, Lausanne, Switzerland

MagC, magnetic collection of ultrathin sections for vCLEM

6.00 – 6.30 pm

Alex DeMarco – Monash University, Australia

Increasing throughput and efficiency in cryo-CLEM

6.30 – 6.45 pm

Selected talk from abstracts


Panel Discussion
Hosted by Lucy Collinson & Yannick Schwab

6.45 – 7.30 pm




7.30 – 10.00 pm

Conference dinner
for on-site participants

Conference dinner

Wednesday 16 March 2022

Topic Time (CET) Speaker Title

Session 4: New developments in vCLEM image processing
Chair: Anna Kreshuk
9.00 - 11.30 am

9.00 – 9.30 am

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

Taking the measure of cells with volume electron microscopy

9.30 – 10.00 am

Christian Tischer – EMBL Heidelberg, Germany

CLEM data formats, visualisation and registration

10.00 – 10.30 am

Aubrey Weigel – HHMI Janelia Research Campus, USA

Towards automatic whole cell organelle segmentation in volume electron microscopy

10.30 – 11.00 am



11.00 – 11.30 am

Matthew Hartley – EMBL-EBI, UK

Archiving correlative imaging data: challenges and opportunities


11.30 – 12.30 pm

Closing Keynote: Rob Parton – The University of Queensland, Australia

Exploring cellular membranes using multiscale microscopy (Chair: Yannick Schwab)


12.30 – 12.45 pm

Poster award + Closing Words


All times in CET

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

Workshop #1

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 #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

​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 #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 1 | 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).

Panel Discussion 2 | March 15th 2022

Trends in vCLEM and vEM | Hosted by tbd

  • tbd


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