In situ CLEM at room temperature and in cryo – Course and Conference Office

EMBO Practical Course

In situ CLEM at room temperature and in cryo


Course overview

Correlative Light and Electron Microscopy (CLEM) allows precise localisation of an event of interest within cells and tissues. During this course, we will focus on a specific method that has been developed at EMBL that enables the localisation of fluorescent proteins with high accuracy at the ultrastructural level. The course will cover both the theory and practicals of high precision CLEM, as well as opportunities to discuss their research with CLEM experts and receive practical and troubleshooting advice.


This course is intended for scientists with experience in EM who want to further develop their skills in high-accuracy correlated microscopy.


The course will combine lectures and hands-on practical work covering all steps in the work flow including cryogenic sample preparation, ultramicroscopy, image registration and electron tomography.

Learning outcomes

Participants will gain hands-on experience with the CLEM methods and learn tips from the people who developed the methods.

Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.


Speakers, trainers, and staff

Scientific Organisers

Course Organisers

Lea Hohmann

EMBL Heidelberg


Irena Provaznikova

EMBL Heidelberg



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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – 12 February 2023
Time (Europe/Berlin)SpeakerLocation
14:00 – 14:30RegistrationISG Hotel
14:30 – 15:00Welcome and house notes and course overviewISG Hotel
15:00 – 16:00EMBO Young Investigator Lecture:
How to choose your CLEM approach
Ori Avinoam – Weizmann Institute of Science, Israel
ISG Hotel
16:00 – 16:30Coffee breakISG Hotel
16:30 – 19:00Flash talks by speakers, trainer, and participantsISG Hotel
19:00 – Open endDinnerISG Hotel
Day 2 – 13 February 2023
Time (Europe/Berlin)SpeakerLocation
09:00 – 09:15Safety briefing   Courtyard Room A & B
09:15 – 10:15Keynote lecture: History of Cryo-CLEM
Anna Sartori-Rupp – Institut Pasteur, France
Courtyard Room A & B
10:15 – 10:30Coffee breakCourtyard Room A & B
10:30 – 11:30Lecture: Strategies to culture cells for cryoEM
Ievgeniia Zagoriy – EMBL Heidelberg, Germany
Courtyard Room A & B
11:30 – 12:15Lecture: Technical aspects of the RT and Cryo CLEM workflow
Mandy Boermel – EMBL Heidelberg, Germany Martin Schorb – EMBL Heidelberg, Germany
Courtyard Room A & B
12:15 – 13:15LunchATC Foyer
13:15 – 18:30Practical: Sample preparation RT and cryo (parallel sessions for 3 sub-groups)  Training Lab A & B
18:30 – 19:40DinnerEMBL Canteen
Day 3 – 14 February 2023
Time (Europe/Berlin)SpeakerLocation
09:00 – 10:00Lecture: Tips and tricks to adapt on-section CLEM to diverse biological questions
Paolo Ronchi – EMBL Heidelberg, Germany
Courtyard Room A & B
10:00 – 11:00Lecture: Tricks and pitfalls in ultramicrotomy
Helmut Gnaegi – Diatome Ltd, Switzerland
Courtyard Room A & B
11:00 – 11:15Coffee breakCourtyard Room A & B
11:15 – 12:15Lecture: Site Specific Cryo-FIB Preparation
Julia Mahamid – EMBL Heidelberg, Germany
Courtyard Room A & B
12:15 – 13:00LunchEMBL Canteen
13:00 – 19:00Practicals: RT sectioning, light microscopy at RT and cryo (parallel sessions for 4 sub-groups)Training Lab A&B
19:00 – 20:00DinnerEMBL Canteen
Day 4 – 15 February 2023
Time (Europe/Berlin)SpeakerLocation
09:00 – 10:15Computer practical: SerialEM hands-on with Remote TEM session
Martin Schorb – EMBL Heidelberg, Germany
Computer Training Lab
10:15 – 10:30Coffee breakComputer Training Lab
10:30 – 12:00Computer practical: SerialEM hands-on
Martin Schorb – EMBL Heidelberg, Germany
Computer Training Lab
12:00 – 13:00LunchEMBL Canteen
13:00 – 14:30Introduction & Computer practical: Icy and ec-CLEM
Perrine Paul-Gilloteaux – University of Nantes, France
Computer Training Lab
14:30 – 15:00Coffee breakComputer Training Lab
15:00 – 16:30Computer practical: Icy and ec-CLEM
Perrine Paul-Gilloteaux – University of Nantes, France
Computer Training Lab
16:30 – 17:00Wrap up of first round of practicals that have introduced the entire workflow, Q&AComputer Training Lab
17:00 – open endSocial Event: Guided city tour and dinner in old town HeidelbergDowntown Heidelberg
Day 5 – 16 February 2023
Time (Europe/Berlin)SpeakerLocation
09:00 – 10:00Keynote Lecture: Cryo-CLEM to study viruses
Petr Chlanda – University of Heidelberg, Germany
Courtyard Room A & B
10:00 – 10:30Coffee breakCourtyard Room A & B
10:30 – 11:00Lecture: Practical considerations for 3D cryo-CLEM
Herman Fung – EMBL Heidelberg, Germany
Courtyard Room A & B
11:00-11:30Lecture: EasyGrid: Advancing cryo-EM sample preparation
Michael Hons – EMBL Grenoble, France
Courtyard Room A & B
11:30 – 12:15Lecture: Volume CLEM and 3DCLEM
Pedro Machado – Oxford Instruments NanoAnalysis, UK
Paolo Ronchi – EMBL Heidelberg, Germany
Courtyard Room A & B
12:15 – 13:00LunchEMBL Canteen
13:00 – 19:00Practicals: In-depth PRACTICALS on specific topics based on students’ selection (subgroups)Training Lab A & B
19:00 – 20:00DinnerEMBL Canteen
Day 6 – 17 February 2023
Time (Europe/Berlin)SpeakerLocation
09:00 – 09:45Lecture: Multimodal image data, handling, visualization etc.
Christian Tischer – EMBL Heidelberg, Germany
Courtyard Room A & B
09:45 – 10:30Roundtable discussion on open questions, students explain implementations for their own projectsCourtyard Room A & B
10:30 – 11:00Coffee breakCourtyard Room A & B
11:00 – 12:30Discussion – Call for Help – Discussion on specific questions concerning the participants’ projectsCourtyard Room A & B
12:30 – 12:45Lecture: Introduction to relevant networks, EuroBioImaging, access to imaging resources, EMBL IC
Aastha Mathur – EMBL Heidelberg, Germany
Virginia Pierini – EMBL Heidelberg, Germany
Courtyard Room A & B
12:45 – 13:00Wrap up – FeedbackCourtyard Room A & B
13:00 – 13:15Packed lunch / FarewellCourtyard Room A & B

Practical information

Registration fees and motivation letter

The course is limited to 20 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.


Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks.
This EMBO course includes accommodation and transportation to and from the ISG Hotel to the venue.

PhD Student€500

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.


  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.

Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses only)

For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant. 

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.

Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course

– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course


You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.


The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.


Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles


Accommodation has been pre-booked for you at the ISG Hotel for the default dates of 12 to 17 February (5 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG. In case you would like to have a single room, please let us know and please note that you will be required to pay an additional cost of 31€ per night. This should be paid by you directly to the ISG during your stay. Any additional nights need to be booked and paid for by you. We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. The bus schedule can be found here.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For further information on getting to EMBL Heidelberg visit our Travel Information page.

For enquiries about accommodation and local transportation please refer to the FAQ page.

Technical requirements and event software

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Additional information

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.


Event supporter:

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.


EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 12 - 17 Feb 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Application: Closed


  • Ori Avinoam

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