5^th Joint Workshop and Scientific Meeting on Correlative Microscopy

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

London, UK | 22 - 24 March 2020

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.

Preliminary Agenda

Sunday, 22^nd March 2020

4:00 PM	Registration
4:30 PM	Welcome Lucy Collinson (Francis Crick Institute) and Michael Santilli (ZEISS)
4:45 PM	1st Keynote: Kristina Micheva, Stanford University, Palo Alto
5:30 PM	2nd Keynote: Jan Ellenberg, EMBL, Heidelberg
6:15 – 7:15 PM	Reception

Monday, 23^rd March 2020

Session 1: Many Roads to Correlation \| Chair: Andreas Walter
9:00 AM	Andreas Walter, Bioimaging Austria – Correlated Multimodal Imaging Node Austria
9:30 AM	Speaker 1
9:50 AM	Speaker 2
10:10 AM	Speaker 3
10:25 AM	Coffee Break

Session 2: Correlative Light and Electron Microscopy \| Chair: Nalan Liv
10:55 AM	Nalan Liv - University Medical Center, Utrecht
11:25 AM	Speaker 1
11:45 AM	Speaker 2
12:05 PM	Speaker 3
12:20 PM	Lunch Break + Posters

Workshop Session
1:30 PM	Workshop 1-4 (Rotation 1) / Round Table Discussion 1
3:00 PM	Workshop 1-4 (Rotation 2) / Round Table Discussion 2
4:30 PM	Coffee Break

Session 3: Electron Microscopy in Life Sciences \| Chair: Saskia Lippens
5:00 PM	Chair Talk: 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 Phathology): 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	Speaker 2
6:10 PM	Speaker 3
7:10 PM	Conference Dinner

Tuesday, 24^th March 2020

Session 4: Sample Diversity \| Chair: Johan Decelle
9:00 AM	Chair Talk: Johan Decelle (Université Grenoble Alpes, Grenoble, France): Unveiling the subcellular architecture and symbiotic interactions in the oceanic plankton using 3D electron microscopy
9:30 AM	Thomas Deerinck (NCMIR, San Diego, USA): The development of a charge-resistant embedded medium for SBEM
9:50 AM	Speaker 2
10:10 AM	Speaker 3
10:25 AM	Coffee Break

Session 5: Image Processing and Analysis \| Chair: Perrine Paul-Gilloteaux
10:55 AM	Chair Talk: Perrine Paul-Gilloteaux (Université de Nantes, Nantes, France): Correlation, visualisation and analysis in CLEM
11:25 AM	John Bogovic, (HHMI, Janelia Research Campus, Ashburn, USA) : tbd
11:45 AM	Speaker 2
12:05 PM	Speaker 3
12:25 PM	Closing Keynote: 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
2:15 PM	Workshop 1-4 (Rotation 3) / Round Table Discussion 3
3:45 PM	Workshop 1-4 (Rotation 4)
5:15 PM	Closing Words: Lucy Collinson

Registration

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 tube collapse

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 bus collapse

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.

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

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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.

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