5^th Joint Workshop and Scientific Meeting on Correlative Microscopy

Start: 22 March 2020
End: 24 March 2020
Location: The Francis Crick Institute

February 15-17, 2021

Virtual Correlative Microscopy Symposium | February 15-17, 2021

Workshop in collaboration with the Francis Crick Institute, the VIB Ghent and the EMBL Heidelberg

Due to the ongoing COVID-19 outbreak we would like to convert the 5th Joint Workshop and Symposium ‘From 3D Light to 3D Electron Microscopy’ into a virtual event.
The online meeting will take place from 15th to 17th February 2021 during three half days – please save this date to your calendar!
We are looking forward to meeting you virtually and to sharing this way your scientific research among the community!

Your Organisation Committee and Your ZEISS Team

From 3D Light to 3D Electron Microscopy

Joined virtual symposium for Correlative Microscopy

Life happens in 3D. In the race to truly understand biological samples and processes, 3D correlative light and electron microscopy (CLEM) is a key enabler, illuminating the link between function and structure. Correlative microscopy can combine a large variety of different imaging techniques, including confocal microscopy, superresolution imaging, light sheet fluorescence microscopy, X-ray microscopy, and volume electron microscopy.

CLEM can provide insights into biological processes with high spatial and temporal resolution. Dedicated CLEM workflow solutions and automation can change the way scientists approach volumetric imaging into the nanoscale. The improved connectivity between imaging modalities allows to acquire larger and more complex data. Thus, flexibility, file compatibility and big data handling become new challenges to be tackled, not only from a hardware perspective but also for data processing and visualization.

The Electron Microscopy Science Technology Platform at the Francis Crick Institute in London, UK and the Bioimaging facilities of the EMBL Heidelberg, Germany and VIB Ghent, Belgium together with ZEISS, are proud to host the 5^th joint symposium on Correlative Microscopy and volume EM - this time virtually. The whole meeting is centered on scientific sessions covering a broad range of correlative workflows, encompassing sample preparation, volume imaging, data management, visualization and analysis. In addition, participants will have the opportunity to join instrument workshops and round table discussions in a virtual way. Meet other researchers and your friends during the virtual get-together.

All participants are invited to present their own scientific work in poster presentations.

Don’t miss this exciting opportunity for exchange with researchers and industry to explore the new and emerging technologies and methods for 3D correlative microscopy and Volume EM in Life Sciences.

Agenda

Monday, 15^th February 2021

Time (CET)	Topic	Speaker	Details
2.00 – 2.15 pm	Welcome	Organisational Committee
2.15 – 3.45 pm	Session 1: Light and Electron Microscopy	Nalan Liv (Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Netherlands)	Correlative Light and Electron Microscopy of Single Organelles: Live-cell imaging meets three dimensional ultrastructure
		Antony Fearns (Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, London, UK)	CLEIMiT: Correlative Light Electron Ion Microscopy of antibiotics in tissue
		Dumisile Lumkwana (University of Stellenbosch, South Africa / UCL)	Investigating the role of spermidine on autophagosomes using 3D CLEM
		Marianne S. Beckwith (EMBL, Heidelberg, Germany)	Customized substrates for 3D CLEM of single cells
		Jemima Burden (MRC Laboratory for Molecular Cell Biology, London, UK)	3D CLEM saves the day
		all	Q&A Session
3.45 – 4.45 pm	Round table discussions (in parallel)	Anna Kreshuk (EMBL, Heidelberg, Germany) John Bogovic (HHMI, Janelia Research Campus, Ashburn, USA)	1: Image Analysis and Visualization
		Ejia Jokitalo (University of Helsinki, Finland) Paul Verkade (University of Bristol, UK)	2: Trends in Volume EM and Correlative Microscopy
		Jason Swedlow (School of Life Sciences, University of Dundee, UK)	3: Metadata Standards / File Formats / Data Archive
		Anna Steyer (EMBL Heidelberg, Germany) Martin Pilhofer (ETH Zürich, Switzerland)	4: Cryo Microscopy
4.45 –5.00 pm	Break
5.00 –6.30 pm	Session 2: Sample Diversity	Anna Steyer (EMBL Heidelberg, Germany)	Volume imaging: from HeLa cells to the human nervous system
		Ben Giepmans (UMC Groningen, Netherlands)	Multiscale Multimodal Multicolor Microscopy
		Marie-Charlotte Domart (The Francis Crick Institute, London, UK)	Toxoplasma gondii in zebrafish – A targeted correlative and multimodal imaging approach
		Einat Zelinger (The Hebrew University of Jerusalem, Israel)	Drosophila sperm storage: new insights using 3D correlative microscopy
		Johan Decelle (University Grenoble , Grenoble, France)	Unveiling the subcellular architecture and symbiotic interactions in the oceanic plankton using 3D electron microscopy
		all	Q&A Session
6.30 – 6.45 pm	Break
6.45 – 7.30 pm	Key Note	Kristina Micheva (Stanford University, Palo Alto, USA)	3D Light and 3D Electron Microscopy: The many ways of seeing inside the brain
7.30 – 8.15 pm	Virtual Get-Together & Poster Session

All times in CET

Tuesday, 16^th February 2021

Time (CET)	Topic	Speaker	Details
2.00 – 2.15 pm	Welcome	Organisational Committee
2.15 – 3.45 pm	Session 3: Many roads to CLEM	Andreas Walter (Bioimaging Austria (CMI), Vienna, Austria)	Austrian BioImaging & COMULIS: Correlated Multimodality Imaging Across Scales and Institutes
		Carles Bosch (The Francis Crick Institute, London, UK)	Subcellular context in multi-mm samples of functionally-images mammalian brain – new roads to correlation using X-rays
		Christopher Parmenter (Nanoscale Microscale Research Centre, University of Nottingham, UK)	Correlative Cryo Microscopy: Challenges and Progress
		Louise Hughes (Oxford Instruments NanoAnalysis, High Wycombe, UK)	Elemental segmentation: EDS as a method to segregate biological structure in 3D Volume electron microscopy
		Saskia Lippens (VIB Bioimaging Core, Ghent, Belgium)	The liver revisited: CLEM reveals the Kuppfer cell niche
		all	Q&A Session
3.45 – 4.45 pm	Workshop 1	The Francis Crick Institute (Catherine Maclachan, Chris Peddie, Raffa Carzaniga)	Volume X-ray and serial blockface microscopy
4.45 – 5.00 pm	Break
5.00 – 6.00 pm	Workshop 2	UCL in collaboration with ZEISS (Jemima Burden, Ian White / Alan Kidger, Stephen Furzeland)	Serial Section Tomography (Array Tomography)
6.00 – 6.15 pm	Break
6:15 – 7.15 pm	Round table discussions (in parallel)	Anna Kreshuk (EMBL Heidelberg, Germany) / John Bogovic (HHMI, Janelia Research Campus, Ashburn, USA)	1: Image Analysis and Visualization
		Ejia Jokitalo (University of Helsinki, Finland), Paul Verkade (University of Bristol, UK)	2: Trends in Volume EM and Correlative Microscopy
		Jason Swedlow (School of Life Sciences, University of Dundee, UK)	3: Metadata Standards / File Formats / Data Archive
		Anna Steyer (EMBL Heidelberg, Germany)/Martin Pilhofer (ETH Zürich, Switzerland)	4: Cryo Microscopy
7.15 – 8.00 pm	Key Note	Wah Chiu (Stanford University and SLAC National Accelerator Laboratory, Palo Alto, USA)	Multi-Scale 3D Cryogenic Microscopy and Tomography of Cells
8.00 – 8.45 pm	Virtual Get-Together & Poster Session

All times in CET

Wednesday, 17^th February 2021

Time (CET)	Topic	Speaker	Details
2.00 – 2.15 pm	Welcome	Organisational Committee
2.15 – 3.30 pm	Session 4: Image Processing	Perrine Paul-Gilloteaux, (SFR Santé F Bonamy, France Bioimaging, Nantes, France)	Correlation, Visualization and Analysis in CLEM
		John Bogovic (HHMI, Janelia Research Campus, Ashburn, USA)	Segmentation and Registration Methods for CLEM in Cell Biology
		Joris Roels (VIB Bio Imaging Core, Ghent, Belgium)	Scalable automatic segmentation of mitochondria in volume EM
		Ilja Belevich (University of Helsinki, Finland)	DeepMIB: User-friendly and open-source software for training of deep learning network for biological image segmentation
		all	Q&A Session
3.30 – 3.45 pm	Break
3.45 – 5.00 pm	Workshop 3	EMBL in collaboration with VIB (Paolo Ronchi, Yannick Schwab / Saskia Lippens, Anneke Kremer)	Correlative Microscopy in 3D: From LSM to FIB-SEM
5.00 – 6.00 pm	Workshop 4	ZEISS Microscopy Customer Center Europe (Endre Majorovits, Steffen Burgold)	The Correlative Cryo Workflow
6.00 – 6.30 pm	Break
6.30 – 7.00 pm	Closing Key Note	Yannick Schwab	From gene expression atlases to ultrastructure: the contribution of CLEM to study specific cell types in multicellular organisms
7.00 – 7.15 pm	Wrap-up & End	Organisational Committee

All times in CET

Workshop #1

Correlative light, X-ray, and serial blockface imaging: from preparation to execution

In this workshop, we will use a combination of light, X-ray, and serial blockface microscopy to correlate 3-dimensional volumes across scales, and link structure to function. Begin with a confocal laser scanning microscope to examine the localisation of fluorescent markers and identify target regions of interest. Verify and relocate each area using X-ray microscopy, and finally move to a scanning electron microscope equipped with a Focal Charge Compensation module and Gatan 3View2XP® to reveal the underlying ultrastructure of each target with nanometer resolution.

Workshop #2

Serial Section Tomography (Array Tomography)

See how non-destructive ‘Array Tomography’ (AT) works: after image acquisition, all single 2D images are computed into a 3D model. Volume EM datasets can be correlated with 3D light microscopy datasets of the same sample acquired with fluorescence contrast.

Workshop #3

Targeting FIBSEM acquisition of single cells in a large specimen guided by LSM

Learn how to preserve the fluorescence during sample preparation for 3D correlative microscopy. You will see how to link a laser scanning microscope and a focused ion beam scanning electron microscope (FIB-SEM) to acquire high quality 3D images of a biological sample – even when you are in different labs. Correlative 3D data sets will be produced at the end to identify fluorescent cells of interest within an homogeneous tissue.

Workshop #4

The Correlative Cryo Workflow

Learn more about the correlative cryo workflow and how recent technological developments have significantly improved the ease of this process. The correlative cryo workflow connects a widefield microscope or LSM with a FIB/SEM enabling volume imaging and streamlined production of TEM lamella without compromising the image quality. You will see all the features that simplify the workflow and experience first-hand the new possibilities for investigating your vitrified sample.

Round-Table Discussion 1

Image Analysis and Visualization | Chairs: Anna Kreshuk, John Bogovic

As enjoyable as microscopic images are - their real value is in the data they provide. What do you need to get the information out of the images? What are the challenges and the missing pieces? Discuss with other scientists the state of art in image analysis and the available visualization tools.

Round-Table Discussion 2

Trends in Volume EM and Correlative Microscopy | Chairs: Eija Jokitalo, Paul Verkade

Volume EM is getting more and more popular - especially in combination with correlative microscopy. What are trends in these areas? Where we are going and how we can get there are the topics of this round-table discussion.

Round-Table Discussion 3

Metadata Standards / File Formats / Data Archive | Chair: Jason Swedlow

Efficient and successful connected workflows require an aligned and robust data transfer. File formats and metadata have to be available at any time during the entire workflow to ensure a smooth transfer of all data and to get the most out of the experiment – even after months and years. Reliable and flexible data archiving is a must. Where and how can we save the data? Which data do we need and how can we handle the flood of data? Do we need a standard format for metadata and how can we make published data sets available to the scientific community and encourage data mining and re-use? This discussion will present options and help in developing community standards and best practices.

Round-Table Discussion 4

Cryo Microscopy | Chairs: Anna Steyer, Martin Pilhofer

Since the Nobel prize in 2017 cryo-electron microscopy has experienced a renaissance in Life Sciences. Ongoing developments and the linkage to other imaging modalities extend the scope of action in this evolving field. We would like to discuss, where you see the current hurdles and challenges when doing cryo microscopy, what is needed to do cryo microscopy successfully and where you see this technique in the future.