In situ CLEM at room temperature and in cryo

Time (Europe/Berlin)	Speaker	Location
14:00 – 14:30	Arrival and registration	ISG Hotel
14:30 – 15:00	Welcome and house notes and course overview
15:00 – 16:00	Lecture 1: How to choose your CLEM approach Ori Avinoam – Weizmann Institute of Science, Israel	ISG Hotel
16:00 – 16:30	Coffee Break	ISG Hotel
16:30 – 18:00	Flashtalks	ISG Hotel
18:00 – 19:00	Lecture 2: In-situ CLEM workflow and best practices Rachel Mellwig – EMBL Heidelberg, Germany	ISG Hotel
19:00 – 21:00	Dinner and networking	ISG Hotel

Time (Europe/Berlin)	Speaker	Location
08:40 – 08:50	Bus from the ISG Hotel to EMBL ATC	ISG Hotel
08:50 – 09:00	Overview of the day	Flex Lab A&B
09:00 – 09:30	Introduction	Flex Lab A&B
09:30 – 10:30	Lecture 3: Keynote Speaker: CLEM for structural cell biology: past, present and future Wanda Kukulski – University of Bern, Switzerland	Flex Lab A&B
10:30 – 10:45	Coffee Break + Meet the speaker	Flex Lab A&B
10:45 – 11:30	Lecture 4: Tips and tricks to adapt on-section CLEM to diverse biological questions Mandy Boermel – EMBL Heidelberg, Germany	Flex Lab A&B
11:30 – 12:15	Lecture 5: Strategies for cryoEM sample preparation Evgenia Zagoriy – EMBL Heidelberg, Germany	EMBL Canteen
12:15 – 13:15	Lunch	EMBL Canteen
13:15 – 19:30	Practical session 1 Practical session 1A – High pressure freezing High-pressure freezing of cell monolayers on sapphire discs and yeast using Leica EM-ICE freezing machine in the Imaging Centre. Anna Steyer – EMBL Heidelberg, Germany Andreia Pinto – Leica Microsystems, Germany Practical session 1B – Freeze substitution Demonstration on how the freeze substitution machine works and discussion of the protocol for CLEM. Paolo Ronchi – EMBL Heidelberg, Germany Ori Avinoam – The Weizmann Institute of Science, Israel Mathilda Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany Nadav Scher – EMBL Heidelberg, Germany Pedro Machado – Human Technopole, Italy Practical session 1C – Plunge freezing Plunge freezing cells onto EM grids using the Leica EM GP2 Zhengyi Yang – EMBL Heidelberg, Germany Léa Swistak – EMBL Heidelberg, Germany Veijo Salo – Karolinska Institutet, Sweeden Practical session 1D – Micropatterning Pre-patterning grids in preparation to seeding cells Evgenia Zagoriy – EMBL Heidelberg, Germany Herman Fung – University of Michigan, USA	EMCF and IC
19:30 – 21:00	Dinner with dissussion: Core facility management and career	RTL
21:00	Bus to ISG Hotel

Time (Europe/Berlin)	Speaker	Location
08:40 – 08:50	Bus from the ISG Hotel to EMBL ATC	Flex Lab A&B
08:50 – 09:00	Overview of the day	Flex Lab A&B
09:00 – 10:00	Lecture 6: Cryo-CLEM to study viruses Petr Chlanda – Heidelberg University, Germany	Flex Lab A&B
10:00 – 10:30	Coffee Break + Meet the speaker	Flex Lab A&B
10:30 – 11:15	Lecture 7: Tricks and pitfalls in ultramicrotomy Andreia Pinto – EMBL Heidelberg, Germany	Flex Lab A&B
11:15 – 11:45	Lecture 8: In block fluorescence imaging for FIB-SEM imaging Paolo Ronchi – EMBL Heidelberg, Germany	Flex Lab A&B
11:45 – 12:45	Lunch	EMBL Canteen
12:45 – 19:15	Practical session 2 Practical session 2A – Ultramicrotomy at room temperature Trimming and sectioning of room temperature samples Viola Oorschot – EMBL Heidelberg, Germany Andreia Pinto – EMBL Heidelberg, Germany Nadav Scher – EMBL Heidelberg, Germany Practical session 2B – Light microscopy on plastic sections Fluorescence microscopy imaging of a thin section on an EM grid Paolo Ronchi – EMBL Heidelberg, Germany Mandy Boermel – EMBL Heidelberg, Germany Practical session 2C – Cryo light microscopy (LSM900 Zeiss) Fluorescence imaging of high-pressure frozen samples Anna Steyer – EMBL Heidelberg, Germany Zhengyi Yang – EMBL Heidelberg, Germany Veijo Salo – Karolinska Institutet, Sweeden Practical session 2D – Cryo light microscopy (Leica Stellaris) Fluorescence imaging of plunge frozen cells Steffen Klein – EMBL Heidelberg, Germany Léa Swistak – EMBL Heidelberg, Germany	EMCF and IC
19:15 – 20:15	Dinner	EMBL Canteen
20:15	Bus to ISG Hotel	EMBL ATC Entrance

Time (Europe/Berlin)	Speaker	Location
08:40 – 08:50	Bus from the ISG Hotel to EMBL ATC
08:50 – 09:00	Overview of the day	Flex Lab A&B
09:00 – 09:30	Lecture 9: On section clem to STEM workflow Pedro Machado – Human Technopole, Italy	Flex Lab A&B
09:30 – 10:00	Lecture 10: Different flavours of CLEM Charlotta Funaya – Heidelberg University, Germany	Flex Lab A&B
10:00 – 11:00	Practical session 3A: SerialEM demonstration with Remote TEM session Mandy Boermel – EMBL Heidelberg, Germany Ori Avinoam – Weizmann Institute of Science, Israel	Computer Training Lab
11:00 – 11:15	Coffee break + Meet the Speakers	Computer Training Lab
11:15 – 12:15	Practical session 3B: SerialEM hands-on Mandy Boermel – EMBL Heidelberg, Germany Ori Avinoam – Weizmann Institute of Science, Israel	Computer Training Lab
12:15 – 13:15	Lunch	EMBL Canteen
13:15 – 13:45	Lecture 11: Introductory talk: Icy and eC-CLEM Perrine Paul-Gilloteaux – University of Nantes, France	Computer Training Lab
13:45 – 15:15	Practical session 3C: Introductory talk and Computer practical: Icy and eC-CLEM: Perrine Paul-Gilloteaux – University of Nantes, France Nadav Scher – EMBL Heidelberg, Germany	Computer Training Lab
15:15 – 15:30	Coffee break + Meet the Speakers	Computer Training Lab
15:30 – 16:00	Debrief: Wrap up of first round of practicals, Q&A	Computer Training Lab
16:00 – 17:00	Transfer to Downtown (with a stop at ISG Hotel)
17:00 – 22:15	Guided city tour and course dinner in old town Heidelberg

Time (Europe/Berlin)	Speaker	Location
08:40 – 08:50	Bus from the ISG Hotel to EMBL ATC
08:50 – 09:00	Overview of the day	Flex Lab A&B
09:00 – 09:30	Lecture 12: Room temperature CLEM success story Mathilda Hjoerdis Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany	Flex Lab A&B
09:30 – 10:00	Lecture 13: Cryo-CLEM success story Léa Swistak – EMBL Heidelberg, Germany	Flex Lab A&B
10:00 – 10:15	Coffee break + Meet the Speakers	Flex Lab A&B
10:15 – 13:00	Practical session 4 – In depth practicles part 1 (See details below)	EMCF and IC
13:00 – 14:00	Lunch	EMBL Canteen
14:00 – 20:00	Practical session 4 – In depth practicles part 2 Practical 4A – Troubleshooting sample preparation – FS, HPF, PF Ori Avinoam – Weizamnn Institute of Science, Israel Mathilda Hjoerdis Lennartz – Max Planck Institute of Molecular Cell Biology and Genetics, Germany Herman Fung – University of Michigan, USA Pedro Machado – Human Technopole, Italy Practical 4B – Demo – TFS Hydra pFIB on-lamella CLEM workflow Zhengyi Yang – EMBL Heidelberg, Germany Practical 4C – Software hands-on session (ICY, SerialEM) – Bring your own data Perrine Paul-Gilloteaux – University of Nantes, France Nadav Scher – EMBL Heidelberg, Germany Practical 4D – Demo – Plasma FIB Tescan Samuel Zachej – Tescan, Evegenia Zagoriy – EMBL Heidelberg, Germany Practical 4E – Managing an EM facility, interactive session and facility tour Rachel Mellwig – EMBL Heidelberg, Germany Charlotta Funaya – Heidelberg University, Germany Practical 4F – Demo – Meteor in-chamber CLEM Marit Smeets – Delmic, The Netherlands Evegenia Zagoriy – EMBL Heidelberg, Germany Practical 4G – Demo – Leica Enuity Andreia Pinto – Leica Microsystems, Germany Practical 4H – F30 correlative tomogram acquisition Mandy Boermel – EMBL Heidelberg, Germany Practical 4I – In-block confocal microscopy Manuel Gunkel – EMBL Heidelberg, Germany Paolo Ronchi – EMBL Heidelberg, Germany Practica 4J – Ultramicrotomy, including serial-sections Viola Oorschot – EMBL Heidelberg, Gemrany	EMCF and IC
20:00 – 21:00	Dinner	EMBL Canteen
21:00	Bus to the ISG Hotel	EMBL ATC Entrance

Time (Europe/Berlin)	Speaker	Location
08:40 – 08:50	Bus from the ISG Hotel to EMBL ATC
08:50 – 09:00	Overview of the day	Flex Lab A&B
09:00 – 10:30	Round table discussions on open questions, students explain implementations for their own projects	Flex Lab A&B
10:30 – 11:00	Lecture 14: Cryo-liftout workflow Zhengyi Yang – EMBL Heidelberg, Germany	Flex Lab A&B
11:00 – 11:15	Coffee break + Meet the Speakers	Flex Lab A&B
11:15 – 11:45	Lecture 15: Probes for Cryo-CLEM Herman Fung – University of Michigan, USA	Flex Lab A&B
11:45 – 12:15	Lecture 16: Efficient targeting in cryo-CLEM for in situ applications Anna Steyer – EMBL Heidelberg, Germany	Flex Lab A&B
12:15 – 13:00	Lunch	EMBL Canteen
13:00 – 13:30	Lecture 17: Visualizing Lipid Flux and Organelle Biogenesis by Cryo-Correlative Microscopy Veijo Salo – Karolinska Institute, Sweden	Flex Lab A&B
13:30 – 14:00	Lecture 18: 3D CLEM in Cryo Steffen Klein – EMBL Heidelberg, Germany	Flex Lab A&B
14:00 – 14:15	Closing remarks Feedback and Farewell	Flex Lab A&B
14:30	Departure to the train station

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

Your registration for the event includes:

• Admission to the event
• Possibility to submit an abstract (if applicable)
• Meals and coffee breaks
• Course materials
• Access to the e-learning platform
• A letter to support your visa application (for more information, check the ‘Travel and accommodation’ tab)

For this EMBO course, the fees include accommodation and transportation to and from the Hotel to the venue

Academia	€500
PhD Student	€500
Industry	€1000

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.

Cancellation policy

If you are no longer able to take part in the course, please inform your course contact responsible for this event. Your registration and the submitted motivation letter will be deleted.

Please also check our Terms and Conditions for the cancellation policy.

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.

Instructions

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 2,000 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.

Please note it is not possible to apply after the motivation letter deadline!

Selection

The selection results will be announced by email to all applicants. We aim to announce 3 weeks (21 days) after the motivation letter submission deadline but delays may occur.

Further details

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

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of travel grants, childcare grants, and accessibility grants.

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

Travel grant

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

• 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.

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 grants

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers, and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter, child-care facility, or travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

EMBO accessibility grant

For EMBO Practical Course participants with accessibility needs, there is the possibility to apply for an accessibility grant to offset costs incurred by participants or speakers when participating at a course. Eligible costs include costs incurred for equipment or adaptations to the course environment, or travel costs for an event companion to assist the participant or speaker during the course where necessary. While we do our best to accommodate needs, please note that extensive changes to the course environment might not be possible. Priority will be given to early-stage researchers.

A maximum amount of €500 can be awarded per participant applying for an EMBO accessibility grant. In order to apply for this grant for EMBO Practical Courses, you must be registered by the application deadline. 

Application

Whether you are attending onsite or virtually, to apply for financial assistance, please follow the steps in the application system. During the process of submitting your motivation letter to the system, you will be asked which type of grant you want to apply for.

Applications for financial support will not influence the outcome of the selection results.

Results

Grant allocations are announced by email to all applicants after the selection results.

Selection for financial assistance 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.

Please note that for childcare grants, priority will be given to early-stage researchers.

Further details

Check out this list of external funding opportunities. 

For further information about financial assistance please refer to the FAQ page.

Visa

We can send you a registration confirmation to support your visa procedure (not an official invitation letter). Please contact the Conference Officer responsible for your event. Read our FAQ for more information.

Travel

If you are travelling to Heidelberg via aeroplane, train, car, or long-distance bus, you can find useful information on our travel information page.

Accommodation

Accommodation information is currently being finalized and will be available soon.

Please note that as of 1 October 2025, Heidelberg City Council is introducing an overnight stay tax for tourists visiting Heidelberg (including work related trips). The cost will be 3.50 EUR per night for the first five nights of a consecutive stay and will be added to the hotel’s nightly rate. Please contact the individual hotel directly if you have any questions.

Local transportation

Course shuttle buses

Shuttle buses will go from the Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Other local transportation

In addition to the shuttle busses, there is also the public bus 28 that serves the EMBL campus and taxis can be easily booked at any time. For more information, please refer to the local transportation (RNV) website.

You may also walk from the ISG Hotel to EMBL (takes up to 30 minutes)

Map to walk from ISG Hotel to EMBL

Further details

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

For more information about accommodation and travel, please refer to the FAQ page.

Here you will find useful information for when you are onsite at the event.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the computer training lab or wet labs.

Internet

Wi-Fi is available on campus using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Charging stations

There are lockers available next to the stairs leading down into the Auditorium. You will find some of those equipped with sockets to charge your smartphone/tablet etc.

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the course.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the course.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Room for prayers, meditation, and yoga

There is a room for prayer, yoga, and meditation, located on level E0 behind the Auditorium. Please be respectful of others using the room.

EMBL campus map

Health and safety notes

Please take a moment to read our health and safety policy.

• Do not smoke in any EMBL building.
• Eating and drinking is prohibited in the Auditorium and all laboratories.
• Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required

• The first aid room is located next to the ATC Registration Desk (room 10- 205).
• Dial the Emergency number 222 from any EMBL internal phone only.
• Be prepared to answer the following questions: Where is the accident? What happened? How many injured?
• Emergency number 06221-387 7821 from mobile phones.
• Please report all accidents to the conference officer at the registration desk.

In case of fire

• Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
• A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
• Do not use the lifts.

Beyond first aid

The Heidelberg University Hospital or ‘Universitätsklinikum‘ has a 24 hour accident and emergency facility and is at ‘Im Neuenheimer Feld 672’. It is a 8km or a 20 minute taxi ride away from EMBL. In a medical emergency, the ambulance service generally transports patients to this hospital.

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg.

The EMBL course and conference office team are able to advise you on where to turn for emergency or non-emergency medical treatment in Heidelberg and can assist you in making appointments and / or arranging transport to get to the pharmacy or a doctor of your choice if necessary. Please note, we are not however permitted to personally accompany you off-campus.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

(delete if no technical requirements for this course!)

Technical requirements

Below you will find the software and technical requirements for this course. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.

Add your software name here

Add a descritpion about your software here and any other important info

Additional 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. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

DELETE THIS TAB IF COURSE IS NOT HYBRID!!

Guidelines

• Do not broadcast the course to unregistered participants.
• Do not share your login details with others.
• You are encouraged to post on social media about the event. Post unless the speaker specifically says otherwise, but be mindful of unpublished data. 
• Please do not capture, transmit or redistribute data presented at the meeting.
• Video library of the recorded talks during the event and for 4 weeks afterwards. Please note: at the request of individual speakers, some talks are not recorded.

Additional information can be found in our Code of Conduct.

How to ask questions

Questions during and after the talks can be asked in the live streaming platform. If time runs out or you think of a question later, you can use the EMBL eCampus forum or send a direct message to the speaker/trainer.

Time zone

The programme is planned based on the Europe/Berlin time zone, unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accommodate as many time zones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Please find additional information including FAQs and terms and conditions on our Information for Participants page.