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EMBO Practical Course

Volume Correlative Light Electron Microscopy

07 – 12 July 2024 | London, United Kingdom

  • Registration Deadline
  • 10 May 2024
  • Abstract Submission Deadline
  • 17 May 2024
  • Chosen Participants Will Be Notified By
  • 24 May 2024
  • Payment Deadline
  • 7 June 2024

Apply now!


Download calendar invitation



About the Practical Course

In 2023, volume Electron Microscopy (vEM) was named as one of the seven technologies to watch by Nature. vEM is a term that describes a group of techniques that reveal the 3D ultrastructure of cells and tissues through continuous depths greater than 1 micron. vEM techniques require correlative workflows using light and/ or X-ray microscopy to target the limited fields of view that can be imaged by EM. These workflows are known as volume Correlative Light and Electron Microscopy (vCLEM). This practical course on vCLEM is an evolution of the previous EMBO CLEM courses, taking into account the huge progress in the field in a very short space of time and with an updated programme that reflects the current state of the art in correlative and multimodal imaging. A critical aspect of the course will be the focus on software for image acquisition, processing and analysis, and FAIR data sharing through public image archives. Four workflows will be covered on the course:

Workflow 1: Correlative Array Tomography

Tissue containing fluorescent protein tags will be sliced using a vibratome, imaged using a Laser Scanning Confocal Microscope with enhanced resolution, embedded using the Ellisman/ Deerinck protocol, sectioned using an ultramicrotome with manual and semi-automated section retrieval, and imaged in the SEM with AT acquisition software.

Workflow 2: X-ray targeting for Block Face Imaging

Heavy metal-stained, resin-embedded tissue will be imaged by microCT to locate a region of interest, trimmed to the plane of interest using Crosshair software and a motorised ultramicrotome, and the ROI imaged using Serial Block Face Scanning Electron Microscopy with SBEMimage open-source image acquisition software.

Workflow 3: High pressure freezing to electron tomography and FIB-SEM

Cells expressing fluorescent proteins will be imaged live on sapphire discs in a Laser Scanning Confocal Microscope and vitrified using a high pressure freezer with fast transfer capabilities. Samples will be freeze substituted, sectioned and imaged by TEM tomography using a transmission electron microscope with serial EM acquisition software. In parallel, FS protocols that incorporate heavy metals for vEM workflows and FIB-SEM image acquisition will be discussed.

Workflow 4: Visual Proteomics CLEM Kit

A monolayer of cells labelled with fluorescent proteins, tracker dyes and/or Alexa dyes will be prepared using a non-HPF In-Resin Fluorescence (IRF protocol). The resulting resin blocks will be serial sectioned onto substrates, imaged using serial super resolution light microscopy, followed by array tomography in a scanning electron microscope, to produce high resolution volume CLEM overlays. We will also show an alternative workflow to target the florescent regions, where the block is imaged with a confocal microscope and the fluorescence 3D map is used to target a specific cell of interest for vEM imaging.

Workflow 5: Software

Experts in open-source software and public image archiving will train participants in how to: Understand and use AI methods for segmentation, including the use of manual annotation and citizen science to gather training data; align LM to EM data using CLEM-Reg software; handle multimodal image data in MOBIE; and deposit correlative image data into EMPIAR and the BioImage Archive.

About EMBO Courses and Workshops

EMBO Courses and Workshops are selected for their excellent scientific quality and timelines, provision of good networking activities for all participants and speaker gender diversity (at least 40% of speakers must be from the underrepresented gender).

Organisers are encouraged to implement measures to make the meeting environmentally more sustainable.







  • Registration Deadline
  • 10 May 2024
  • Abstract Submission Deadline
  • 17 May 2024
  • Chosen Participants Will Be Notified By
  • 24 May 2024
  • Payment Deadline
  • 7 June 2024



Registration includes:

  • Accommodation (hotels are pre-booked)
  • Lunches and refreshments
  • Dinners (apart from free evenings)
  • Social event
  • Course materials


The selected participants will pay using the Crick Moodle shop. They will be sent a link via email.

Selection criteria

Applicants are requested to submit a short abstract that puts forward a justification for their attendance at the course. The selection will be made by the course organisers.

Abstract guidelines

The abstract (200 words maximum) should include a brief career summary, a justification as to why the student wants to attend the course, how it will benefit their research, and any other reasons that they feel justify their attendance. Applicants will be selected based on scientific merit, and on the justification provided. Additional criteria will include equality and diversity considerations, including geographical distribution of attendees.

Travel grants and registration fee waivers

Travel grants and registration fee waivers are available for participants.

Selection of awardees is handled directly by the organizers. EMBO travel grants and registration fee waivers are allocated on the basis of the quality of the submitted abstract.

Applicants do not need to apply separately for these but should indicate on the registration form if they wish to be considered.

Additional travel grants are available for EMBC Associate Member States Chile, India, Singapore and Taiwan.

Special travel grants and registration fee waivers

A limited number of travel grants and registration fee waivers are availablefor scientists working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia and Turkey. Grants are allocated on the basis of the quality of the submitted abstract.

A maximum of 700 Euros per participant are available to cover registration fees, travel, and accommodation (no additional subsistence costs can be covered). To apply, please indicate the itemized amount requested in the travel grants section of the registration form.

Child care grants

EMBO Courses and Workshops offers grants to offset additional childcare costs incurred by participants or speakers when participating at any EMBO Courses and Workshop funded meeting. Eligible costs include fees for a caregiver or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please indicate on the registration form whether you would like to be considered for the grant. Please also describe how you intend to use the childcare grant and specify the sum that you will need.


Sustainability at the Crick means a conscientious way of working that incorporates being resourceful, reusing, and generating less waste. We have over 70 Sustainability Representatives running a behavioural change programme called Green Impact to encourage sustainable actions and are a member of the Laboratory Efficiency Assessment Framework (LEAF), with 19 labs involved so far. The Crick is also on advisory boards for the Laboratory Efficiency Action Network (LEAN), Camden Climate Change Alliance (CCCA), and Net Zero Carbon Knowledge Quarter Group. Our building has an excellent BREEAM rating with infrastructure including: 1700m2 photovoltaic panels on our building giving the Crick enough energy to power 10 domestic dwellings per year; a HVAC (heating ventilation and air conditioning) that recovers heat from the exhaust air of the building and uses it to preheat fresh air as it is brought in; a combine heat and power system produces a dynamic 2MW of electrical power for the building and also uses waste heat from the exhaust to pre heat water for steam generation. This is used in our HVAC system to humidify air and to operate our 22 autoclaves. We operate a Simmtronics Automated lighting system incorporating Building Management System Presence detectors that helps us to auto start/stop meeting room ventilation when not in use. We encourage biodiversity in our city space with a brown roof and wildflower garden and encourage cycling to work through provision of a safe, indoor, dedicated cycle park. The Crick is developing a sustainability strategy to reduce our impact on the environment from the materials we buy to the waste we create. A carbon reduction programme has been developed to meet our commitment of working towards a net zero carbon operation. We aim to reduce Scope 1 and 2 carbon emissions by 50% by 2030 compared to our 2019/2020 baseline and has set a target of achieving net zero carbon by 2040 with an ambition to accelerate this date if circumstances allow. Our waste streams are constantly reviewed to identify additional diversion routes or recycling areas. On average, the Crick generates just over 800 tonnes of waste per annum. Since 2017, our onsite recycling rate has increased by 26.3%, with 72% of this waste now being recycled or reused. This represents a significant recycling swing of around 215 tonnes in the last 4 years. We also work to reduce the number of vehicles that come to site for deliveries and waste removal and have a bespoke compactor on site to reduce the number of vehicles required to collect recycling.

Catering will include vegetarian days, locally sourced ingredients, and bottled water or single-use wares will be avoided.

Abstract books and programs will be shared in electronic form only.

Code of conduct

Anti-harassment and non-discrimination policy

At EMBO, we believe that harassment and discriminatory behaviour are unacceptable in any setting. EMBO's code of conduct is applicable for all participants of this EMBO meeting and can be found here.






The Francis Crick Institute

1 Midland Road




Students will stay in double rooms at the Hub by Premier Inn in King’s Cross. They won’t share a room and breakfast will be provided at the hotel.


The Crick is easily accessible by train, tube and bus.

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

The following bus routes pass near the Crick

  • Bus routes 46, 63, and 214 stop outside the Crick on Midland Road
  • Bus routes 30, 73, 91, 205 and 390 stop on Euston Road outside the British Library

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

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

Take the Heathrow Express (15 mins travelling time) or the Underground (Elizabeth Line, 30 mins travelling time) to Paddington, then the Underground (Circle or Hammersmith & City Line) 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 Line) to King's Cross St Pancras.

From Stansted airport

Take the Stansted Express to Tottenham Hale station, and then the Underground (Victoria Line) to King's Cross St Pancras. Or take the Stanstead Express to Liverpool Street station, then the Underground (Circle Line) to King's Cross St Pancras.

From Luton airport

Take the Luton Airport Shuttle to Luton Airport Parkway station, then the Thameslink train to St Pancras International.

About the Area

The Francis Crick Institute is located next to St Pancras railway station in the Camden area of Central London. The area offers a variety of activities. Delegates could visit the British Library and explore its vast collection of books and manuscripts, and explore the shops in St Pancras station and the surrounding area, including Coal Drops Yard. There are plenty of supermarkets, cafes, restaurants and bars for any budget, and you could visit the popular Harry Potter platform 9¾ at King’s Cross station. If you’re interested in a more relaxing activity, you could take a leisurely stroll along Regent's Canal and enjoy the picturesque scenery, or visit Camley Street Natural park. From St Pancras or Kings Cross stations, delegates can gain access to all of London and beyond, making this area an excellent base to explore from.

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