UPDATE March 5th 2020

Workshop will be postponed to Spring 2021 due to COVID 19

It is with regret that we have to inform you that the upcoming 5th Joint Workshop and Symposium ‘From 3D Light to 3D Electron Microscopy’ at the Francis Crick Institute in London needs to be postponed due to the COVID-19 outbreak.
Considering advice from Public Health England, the Francis Crick Institute has advised against travel and events at this time. We are also aware of the rising number of restrictions on guests, and have received a number of emails from colleagues advising that they can no longer travel. Given our responsibility towards the health and wellbeing of all attendees and colleagues (a total of 200 guests from around the globe) we have no choice but to postpone.

We will reschedule the meeting once the current travel restrictions are lifted, and will contact you with further details at that time.

We greatly appreciate your understanding and are very sorry for any inconvenience this will cause.

The Organisation Committee

From 3D Light to 3D Electron Microscopy

Workshop at the Francis Crick Institute in collaboration with ZEISS

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, micro CT 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 and ZEISS Microscopy, are proud to host the 5th joint workshop and symposium on Correlative Microscopy and volume EM. 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 and can learn more about special topics at talk tables supported by CLEM experts from ZEISS.

All participants are invited to present their own scientific work in poster or oral presentations. A scientific panel will review abstracts submitted for presentation.

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 in Life Sciences.

CRICK_Logo

Agenda

Sunday, 22nd March 2020

4:00 PM

Registration

4:30 PM

Welcome
Lucy Collinson (Francis Crick Institute) and Bernhard Zimmermann (ZEISS)

4:45 PM

1st Keynote:
Kristina Micheva, Stanford University, Palo Alto
3D Light and 3D Electron Microscopy: The Many Ways of Seeing Inside the Brain

5:30 PM

2nd Keynote:
Jan Ellenberg, EMBL, Heidelberg
Advanced Imaging of Cellular Processes Across Scales

6:15 – 7:15 PM

Reception

Monday, 23rd March 2020

Session 1: Many Roads to Correlation | Chair: Andreas Walter

9:00 AM

Andreas Walter (Bioimaging Austria (CMI), Vienna, Austria): Austrian BioImaging & COMULIS:
Correlated Multimodality Imaging Across Scales and Institutes

9:30 AM

Carles Bosch (The Francis Crick Institute, London, UK):
Subcellular Context in Multi-mm Samples of Functionally-Imaged Mammalian Brain – New Roads to Correlation using X-Rays

9:50 AM

Christopher Parmenter (Nanoscale Microscale Research Centre, University of Nottingham, UK):
Correlative Cryo Microscopy: Challenges and Progress

10:10 AM

Louise Hughes (Oxford Instruments NanoAnalysis, High Wycombe, UK):
Elemental Segmentation: EDS as a Method to Segregate Biological Structure in 3D Volume Electron Microscopy

10:25 AM

Coffee Break

Session 2: Correlative Light and Electron Microscopy | Chair: Nalan Liv

10:55 AM

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

11:25 AM

Antony Fearns (Host-pathogen interactions in tuberculosis laboratory, The Francis Crick Institute, London, UK):
CLEIMiT: Correlative Light Electron Ion Microscopy of Antibiotics in Tissue

11:45 AM

Dumisile Lumkwana (University of Stellenbosch, South Africa):
Investigating the Role of Spermidine on Autophagosomes Using 3D CLEM

12:05 PM

Marianne S. Beckwith (EMBL, Heidelberg, Germany):
Customized Substrates for 3D CLEM of Single Cells  

12:20 PM

Lunch Break + Posters

Workshop Session

1:30 PM

Workshop 1-4 (Rotation 1) /
Round Table Discussion 1: Image Analysis and Visualization
Chairs: Anna Kreshuk (EMBL, Heidelberg, Germany), John Bogovic (HHMI, Janelia Research Campus, Ashburn, USA)

3:00 PM

Workshop 1-4 (Rotation 2) /
Round Table Discussion 2: Trends in Volume EM and Correlative Microscopy
Chairs: Eija Jokitalo (University of Helsinki, Finland), Paul Verkade (University of Bristol, UK)

4:30 PM

Coffee Break

Session 3: Electron Microscopy in Life Sciences | Chair: Saskia Lippens 

5:00 PM

Saskia Lippens (VIB Bioimaging Core, Ghent, Belgium):
The Liver Revisited: CLEM Reveals the Kuppfer Cell Niche

5:30 PM

Errin Johnson (Sir William Dunn School of Pathology, Oxford, UK):
3D-CLEM Approaches to Better Understand the Interaction of Pathogenic and Commensal Neisseria Species with Each Other and with the Human Host

5:50 PM

Paolo Ronchi (EMBL, Heidelberg, Germany):
Fluorescence and X-Ray Based Targeting of FIB-SEM Acquisition  

6:10 - 6:25 PM

Jemima Burden (MRC Laboratory for Molecular Cell Biology, London, UK):
3D CLEM Saves the Day  

6:30 PM

Conference Dinner

Tuesday, 24th March 2020

Session 4: Sample Diversity | Chair: Anna Steyer

9:00 AM

Anna Steyer (Max-Planck-Institute of Experimental Medicine, Goettingen, Germany): Volume Imaging: From HeLa Cells to the Human Nervous System

9:30 AM

Giepmans, Ben N. G. (UMC Groningen, Netherlands):
Multiscale Multimodal Multicolor Microscopy

9:50 AM

Marie-Charlotte Domart (The Francis Crick Institute, London, UK):
Toxoplasma Gondii in Zebrafish – A Targeted Correlative and Multimodal Imaging Approach  

10:10 AM

Einat Zelinger (The Hebrew University of Jerusalem, Israel):
Drosophila sperm storage: new insights using 3D correlative microscopy. 

10:25 AM

Coffee Break

Session 5: Image Processing and Analysis | Chair: Perrine Paul-Gilloteaux

10:55 AM

Perrine Paul-Gilloteaux (SFR Santé F Bonamy, France Bioimaging, Nantes, France):
Correlation, Visualization and Analysis in CLEM

11:25 AM

John Bogovic (HHMI, Janelia Research Campus, Ashburn, USA):
Segmentation and Registration Methods for CLEM in Cell Biology

11:45 AM

Joris Roels (VIB Bio Imaging Core, Ghent, Belgium):
Scalable Automatic Segmentation of Mitochondria in Volume EM

12:05 PM

Ilya Belevich (University of Helsinki, Finland):
Protocol Organizer for Automated Image Processing Pipelines on MIB  

12:20 PM

Yannick Schwab (EMBL, Heidelberg, Germany):
From Gene Expression Atlases to Ultrastructures: the Contribution of CLEM to Study Specific Cell Types in Multicellular Organisms

1:00 PM

Lunch Break + Posters

Workshop Session and Round Table Discussions

2:15 PM

Workshop 1-4 (Rotation 3) /
Round Table Discussion 3: Metadata Standards / File Formats / Data Archive
Chairs: Jason Swedlow (School of Life Science, University of Dundee, Dundee, UK), Ardan Padwardhan (EMBL-EBI, Cambridgeshire, UK)

3:45 PM

Workshop 1-4 (Rotation 4)

5:15 PM

Closing Words: Lucy Collinson

Workshop #1

Sample Preparation

Profit from the knowledge of experts and learn how to optimize sample preparation for correlative and volume electron microscopy workflows under cryo and ambient conditions. See how you produce ultrathin serial sections for Array Tomography, and how to vitrify samples after live cell imaging. Tips and tricks for the sample preparation in correlative microscopy will be shown live in the lab.

Workshop #2

Volume X-ray and Serial block face Microscopy

Learn how combining an X-ray microscope (XRM) and serial block face imaging in the SEM can reveal more information about your biological samples. Start with the XRM for screening and identification of regions of interest, then move your sample to a SEM equipped with Gatan 3View® and Focal Charge Compensation to image your specimens ultrastructure with nanometer resolution.

Workshop #3

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 #4

Correlative Microscopy with ZEN Connect

Learn how to link a laser scanning microscope (LSM) and a focused ion beam scanning electron microscope (FIB-SEM) to acquire high quality 3D images of the same biological sample in different modalities. Learn how using an LSM and a FIB-SEM can help to target exactly the region of interest and how ZEN Connect makes image acquisition more efficient.

Round-Table Discussion 1

Image Analysis and Visualization | Chair: 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 | Chair: 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, Ardan Padwardhan

  • 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.

Talk Table 1

MultiSEM

ZEISS MultiSEM employs multiple parallel electron beams in a single instrument to increase the field of view while maintaining the high spatial resolution of scanning electron microscopes. Our experts are looking forward to explaining the mSEM® technology, discussing data throughput challenges and giving an outlook on further workflow developments.
Learn more

Talk Table 2

Correlative Cryo Microscopy

With the Nobel prize in 2017, cryo microscopy enjoyed a renaissance. Here, you have the opportunity to talk about the latest developments in cryo microscopy with our experts. Learn what are the benefits of ZEISS cryo LSM and ZEISS cryo FIB/SEM. Let us know, how ZEISS can support you.
Learn more

Talk Table 3

How to use the Power of Deep Learning to Easily Segment Images

Image segmentation is currently one of the biggest challenges in microscopy. Segmentation lays the foundation for all subsequent image analysis steps. ZEISS ZEN Intellesis uses deep learning and Python to easily create robust and reproducible segmentation results, even for non-experts. You can now train the software once and then ZEN Intellesis can segment a batch of hundreds of images automatically. You save time and minimize user bias.
Learn more

Talk Table 4

APEER – From image to information, optimize your workflow

Create your own imaging modules using the programming language of your choice. Combine private and public image processing modules into customized solutions. Automate the workflows for increased productivity and reproducibility. Save valuable research time by not reinventing code. Share work with your team or with the community. Work from anywhere using any device.
Learn more

Talk Table 1

MultiSEM

ZEISS MultiSEM employs multiple parallel electron beams in a single instrument to increase the field of view while maintaining the high spatial resolution of scanning electron microscopes. Our experts are looking forward to explaining the mSEM® technology, discussing data throughput challenges and giving an outlook on further workflow developments.
Learn more

Talk Table 2

Correlative Cryo Microscopy

With the Nobel prize in 2017, cryo microscopy enjoyed a renaissance. Here, you have the opportunity to talk about the latest developments in cryo microscopy with our experts. Learn what are the benefits of ZEISS cryo LSM and ZEISS cryo FIB/SEM. Let us know, how ZEISS can support you.
Learn more

Talk Table 3

How to use the Power of Deep Learning to Easily Segment Images

Image segmentation is currently one of the biggest challenges in microscopy. Segmentation lays the foundation for all subsequent image analysis steps. ZEISS ZEN Intellesis uses deep learning and Python to easily create robust and reproducible segmentation results, even for non-experts. You can now train the software once and then ZEN Intellesis can segment a batch of hundreds of images automatically. You save time and minimize user bias.
Learn more

Talk Table 4

APEER – From image to information, optimize your workflow

Create your own imaging modules using the programming language of your choice. Combine private and public image processing modules into customized solutions. Automate the workflows for increased productivity and reproducibility. Save valuable research time by not reinventing code. Share work with your team or with the community. Work from anywhere using any device.
Learn more

Registration closed

Thanks a lot for the overwhelming response. Unfortunately we are over capacity and we have closed fully registrations.

Location

The Francis Crick Institute

How to get there

By tube
The nearest London Underground stations are:
• King's Cross St Pancras: Northern, Piccadilly, Hammersmith and City, Circle and Metropolitan lines. Station has step-free access.
• Euston: Victoria, Northern, London Overground lines

By bus
The following bus routes pass near the Crick
• Bus routes 45, 46, 214 stop outside the Crick on Midland Road
• Bus routes 10, 30, 59, 73, 91, 205, 390, 476 stop on Euston Road outside the British Library

By car
There are a small number of disabled parking spaces for blue badge holders outside the Crick on Ossulston Street. The Francis Crick Institute does not have car parking facilities, and local parking is very limited. The nearest car parking is at Euston station and St Pancras station.

By train
The nearest railway stations are St Pancras International, King's Cross and Euston stations.

By air
• From London City Airport: take the DLR to Bank, then the Underground (Northern Line) to King's Cross St Pancras. Or take the DLR to West Ham, then the Underground (Hammersmith & City) to King's Cross St Pancras.
• From Heathrow airport: Heathrow Express, 15 mins to Paddington station, then the Underground (Circle line or Hammersmith & City) to King's Cross St Pancras. Or take the Underground (Piccadilly Line) to King's Cross St Pancras (1 hour travelling time).
• From Gatwick airport: take a national rail train to St Pancras International. Or take the Gatwick Express, 30 mins to Victoria station, then the Underground (Victoria) to King's Cross St Pancras.
• From Stansted airport: Stansted Express to Tottenham Hale station, and then the Underground (Victoria) to King's Cross St Pancras. Or take the Stanstead Express to Liverpool Street station, then the Underground (Circle) to King's Cross St Pancras.
• From Luton airport: take the Luton Airport Shuttle to Luton Airport Parkway station, then the Thameslink to St Pancras International.

Hotels

Recommended Hotels in walking distance to the symposium

Crowne Plaza London – Kings Cross

1 King's Cross Rd, Islington
London WC1X 9HX
Phone: +44 20 7833 3900

To guarantee a discounted rate please quote ZEISS / CRICK event.

22nd March 2020 - £130.00 B&B

23rd March 2020 - £190.00 B&B

24th March 2020 - £220.00 B&B

Organizers

Lucy Collinson | The Francis Crick Institute London, UK
Raffaela Carzaniga | The Francis Crick Institute London, UK
Chris Guérin | VIB Ghent, Belgium
Saskia Lippens | VIB Ghent, Belgium
Yannick Schwab | EMBL Heidelberg, Germany
Nicole Schieber | EMBL Heidelberg, Germany
Alexandra Elli | ZEISS Research Microscopy Solutions, Germany