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Advances in cryo-electron microscopy and 3D image processing – Course and Conference Office

EMBO Practical Course

Advances in cryo-electron microscopy and 3D image processing

Overview

Proof of COVID-19 vaccination or recovery is required to attend this on-site course. Please see EMBL’s COVID-19 safety policy for on-site events.

Course overview

Cryo-electron microscopy (cryoEM) has become the method of choice for determining atomic-level structures of large and flexible macromolecular assemblies that are notoriously difficult to study by other techniques. In addition, it has unique capabilities for obtaining structural information in situ, within complex (cellular) environments, and to deal with biologically heterogeneous samples. With the advent of the cryoEM “resolution revolution”, the method has undergone a tremendous growth in user base. Yet, the underlying methods are complex and under constant development. Therefore, in depth advanced training is essential to ensure future generations can adapt emerging technologies to expand into new areas of biological research. This course provides the theoretical and practical foundations of advanced cryoEM techniques, from sample preparation to data collection to image processing.

Audience

To meet the exceptional demand of the field for advanced training, this course is aimed at PhD students and Post Docs with experience in cryoEM and 3D image processing. It will enable them to better apply cryoEM to their cutting-edge research, disseminate their gained expertise to colleagues at their home institution and, eventually, to develop cryoEM methods beyond the state-of-the-art.

Modules/resources

During this course we will focus on the following aspects:

  • Single particle reconstruction (cisTEM, Relion, cryoSPARC)
  • Subtomogram averaging
  • Atomic models (model building and integrative modeling)
  • Session at the microscopes (cryo-EM/ET and cryo-FIB)
  • Latest developments in instrumentations

Learning outcomes

After this course, students should have learned advanced topics of cryo-EM/ET data collection and image processing and be able to apply and adapt these techniques for challenging research projects.

What past participants say about the course

“This a world-class course. The access to experts and cutting-edge techniques is incredible.” – Corbin Black, McGill University, Canada

 

The EMBL Imaging Centre training activities are generously supported by the Boehringer Ingelheim Foundation.

Speakers

Speakers, trainers, and staff

Hui Guo

The Hospital for Sick Children

Canada

Wim Hagen

EMBL Heidelberg

Germany

Thomas Hoffman

EMBL Heidelberg

Germany

Sagar Khavnekar

Max Planck Institute of Biochemistry

Germany

Dari Kimanius

MRC Laboratory of Molecular Biology

UK

Eva Nogales

Howard Hughes Medical Institute and University of California, Berkeley

USA

Yi Sun

EMBL Heidelberg

Germany

Scientific organisers

Course organisers

Programme

Got something to say? Tweet it with #EMBOCryoEM

  • Some pre-course work will be required and will be shared in advance of the course.
  • All times in the programme below are shown as the time in Europe/Berlin.
  • Programme is preliminary and subject to change
Day 1 – Sunday 21 August 2022
TimeSpeakersLocation
13:45 – 14:00 Shuttle to EMBLISG bus stop
14:00 – 15:00Registration and light refreshmentsATC registration
15:00 – 15:15Introduction and housenote slides
Julia Mahamid – EMBL Heidelberg, Germany 		Courtyard Room
15:15 – 15:30 Course overview
Simone Mattei – EMBL Heidelberg, Germany		Courtyard Room
15:30 – 16:30Cutting edge research with Single Particle Analysis
Eva Nogales – Howard Hughes Medical Institute and University of California, Berkeley, USA		Courtyard Room
16:30 – 17:00Coffee breakFlex Lab
17:00 – 18:00Cutting edge research with Tomography
Giulia Zanetti – Birkbeck College, UK		Courtyard Room
18:00 – 19:00An overview of the past and future of cryoEM
Richard Henderson – MRC Laboratory of Molecular Biology, UK		Courtyard Room
19:00 – 19:45Pizza dinnerRooftop lounge
19:45 – 21:45Student presentations IRooftop lounge
22:00Shuttle to ISG Hotel Bus stop
Day 2 – Monday 22 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBL ISG
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Cryo-EM image formation and optics
Chris Russo – MRC Laboratory of Molecular Biology, UK		Courtyard Room
10:00 – 11:00Introduction to the microscope
Radostin Danev – The University of Tokyo, Japan		Courtyard Room
11:00 – 12:00 Fundamentals of image processing and Maximum likelihood approaches
Nikolaus Grigorieff – University of Massachusetts Medical School, USA		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 14:00Specimen preparation: vitrification and sample supports
Lori Passmore – MRC Laboratory of Molecular Biology, UK		Courtyard Room
14:00 – 15:00Handling heterogeneity in cryoEM sample preparation
Kelly Nguyen – MRC Laboratory of Molecular Biology, UK		Courtyard Room
15:00 – 15:30Coffee breakFlex Lab
15:30 – 17:00Forces in vitrification, beam damage and
phase plates: past and future of cryoEM II
Robert Glaeser – Lawrence Berkeley National Laboratory, USA (remote)		Courtyard Room
17:00 – 18:00Panel discussion
Discussion leader: Lori Passmore, MRC Laboratory of Molecular Biology, UK		Courtyard Room
18:00 – 19:00DinnerCanteen
19:00 – 21:00Student presentations IIRooftop lounge
21:15Shuttle to ISG HotelBus stop
Day 3 – Tuesday 23 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBL ISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00AI for cryoEM image processing
Sjors Scheres – MRC Laboratory of Molecular Biology, UK		Courtyard Room
10:00 – 11:00Handling heterogeneity in cryoEM image processing
Sjors Scheres – MRC Laboratory of Molecular Biology, UK		Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Sebastian Eustermann – EMBL Heidelberg, Germany		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 15:30Practical
Session 1: Single Particle Analysis | Relion
Session 2: Single Particle Analysis | cisTEM
Session 3: Single Particle Analysis | cryoSPARC
Session 4: Subtomo Analysis
IC 15-104
IC 15-125
IC 15-114

Computer training lab
15:30 – 16:00Coffee break Flex Lab
16:00 – 18:00Practical
Session 1 (continued): Single Particle
Analysis | Relion
Session 2 (continued): Single Particle
Analysis | cisTEM
Session 3 (continued): Single Particle
Analysis | cryoSPARC
Session 4 (continued): Subtomo Analysis
IC 15-104

IC 15-125

IC 15-114

Computer training lab
18:00 – 19:00Vegetarian dinnerCanteen
19:00 – 21:00Student presentations IIIRooftop lounge
21:15Shuttle to ISG HotelBus stop
Day 4 – Wednesday 24 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBL ISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Best practices of microscopy for data collection for Single Particle Analysis and Tomography
Wim Hagen – EMBL Heidelberg, Germany		Courtyard Room
10:00 – 11:00Practical considerations of initial image processing: on the fly processing
Henning Stahlberg – EPFL, Switzerland		Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Simone Mattei – EMBL Heidelberg, Germany 		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 15:30Practical
Session 1 (continued): Single Particle
Analysis | Relion
Session 2 (continued): Single Particle
Analysis | cisTEM
Session 3 (continued): Single Particle
Analysis | cryoSPARC
Session 4 (continued): Subtomo Analysis
IC 15-125

IC 15-114

IC 15-104

Computer training lab
15:30 – 16:00Coffee breakFlex Lab
16:00 – 18:00Practical
Session 1 (continued): Single Particle
Analysis | Relion
Session 2 (continued): Single Particle
Analysis | cisTEM
Session 3 (continued): Single Particle
Analysis | cryoSPARC
Session 4 (continued): Subtomo Analysis
IC 15-125

IC 15-114

IC 15-104

Computer training lab
18:00 – 19:00DinnerCanteen
19:00 – 21:00Student presentations IVRooftop lounge
21:15Shuttle to ISG HotelBus stop
Day 5 – Thursday, 25 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBL ISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Automation of single particle EM
Bridget Carragher – New York Structural Biology Center, USA		Courtyard Room
10:00 – 11:00Atomic model building and validation
Frank DiMaio – University of Washington, USA		Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader – Henning Stahlberg,
EPFL, Switzerland		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 15:30Practical
Session 1 (continued): Single Particle
Analysis | Relion
Session 2 (continued): Single Particle
Analysis | cisTEM
Session 3 (continued): Single Particle
Analysis | cryoSPARC
Session 4 (continued): Subtomo Analysis
IC 15-114

IC 15-104

IC 15-125

Computer training lab
15:30 – 16:00Coffee breakFlex Lab
16:00 – 18:30Practical
Session 1 (continued): Single Particle
Analysis | Relion
Session 2 (continued): Single Particle
Analysis | cisTEM
Session 3 (continued): Single Particle
Analysis | cryoSPARC
Session 4 (continued): Subtomo Analysis
IC 15-114

IC 15-104

IC 15-125

Computer training lab
18:30 – 19:30Preparation for practicals discussion /
Pizza dinner		Rooftop lounge
19:30-20:00CryoEM in Pharma
Alexis Rohou – Genentech, USA 		Rooftop lounge
20:00-21:00Discussion round: Career Paths in academia, facilities and industryRooftop lounge
21:00Walk to ISG Hotel
Day 6 – Friday 26 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBLISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Sample preparation for in situ cryo
-electron tomography: FIB technology
Phillip Erdmann – Human Technopole, Italy		Courtyard Room
10:00 – 11:00Particle localization and extraction in
cryo-electron tomograms
Beata Turonova – Max Planck Institute
of Biophysics, Germany (remote)		Courtyard Room
11:00 – 12:00 High resolution subtomogram analysis
William Wan – Vanderbilt University, USA		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 13:15Group photo
13:15 – 14:00Preparation for practical presentationCourtyard Room
14:00 – 16:00Practical discussion
Comparing methods, tips and tricks and
data interpretation
Discussion leader: Sebastian Eustermann
– EMBL Heidelberg, Germany		Courtyard Room
16:00 – 19:00City tour and free time
19:30 – 21:00Downtown dinner
Day 7 – Saturday 27 August 2022
TimeSpeakersLocation
08:35Shuttle to EBMLISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Correlative light and electron microscopy for Structural Cell Biology
Wanda Kukulski – University of Bern, Switzerland		Courtyard Room
10:00 – 10:30Sponsor presentations – Thermo Fisher Scientific
Christopher Schmid, Martin Obr: High-Resolution and High-Throughput Structural Biology with Electron Cryo-Tomography		Courtyard Room
10:30-11:00Sponsor presentations – CryoSol
Giulia Weissenberger: VitroJet: Moving sample preparation into a new era		Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Julia Mahamid – EMBL Heidelberg, Germany 		Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 15:30Practical
Session 5: Single Particle Analysis | Relion
Session 6: Single Particle Analysis |cisTEM
Session 7: Single Particle Analysis | cryoSPARC
Session 8: Subtomo Analysis

Session 9: Model Building

Session 10: Microscopy and Demos
IC 15-104
IC 15-114
IC 15-125

Computer training lab
Helix seminar room B01
Imaging centre
15:30 – 16:00Coffee breakFlex Lab
16:00 – 18:00Practical
Session 5 (continued): Single Particle
Analysis | Relion
Session 6 (continued): Single Particle Analysis | cisTEM
Session 7 (continued): Single Particle
Analysis | cryoSPARC
Session 8 (continued): Subtomo Analysis

Session 9 (continued): Model Building

Session 10 (continued): Microscopy and Demos
IC 15-104

IC 15-114

IC 15-125

Computer training lab
Helix seminar room B01
Imaging centre
18:00 – 18:30Coffee break Flex Lab
18:30 – 19:30Practical
Session 5 (continued): Single Particle
Analysis | Relion
Session 6 (continued): Single Particle Analysis | cisTEM
Session 7 (continued): Single Particle
Analysis | cryoSPARC
Session 8 (continued): Subtomo Analysis

Session 9 (continued): Model Building
IC 15-104

IC 15-114

IC 15-125

Computer training lab
Helix seminar room B01
19:30 – 20:00Walk to ISG Hotel
20:00-21:30Dinner and continued discussionISG hotel
Day 8 – Sunday 28 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBLISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 09:30Sponsor presentations – Oxford InstrumentsCourtyard Room
09:30 – 10:00Sponsor presentations – GatanCourtyard Room
10:00 – 10:30Coffee breakFlex lab
10:30 – 12:30Practical
Session 5 (continued): Single Particle
Analysis | Relion
Session 6 (continued): Single Particle
Analysis |cisTEM
Session 7 (continued): Single Particle
Analysis | cryoSPARC
Session 8 (continued): Subtomo Analysis

Session 9 (continued): Model Building

Session 10 (continued): Microscopy
and Demos
IC 15-104

IC 15-114

IC 15-125

Computer training lab
Helix seminar room B01
Imaging centre
12:30 – 13:30Lunch breakCanteen
13:30 – 16:00Practical
Session 5 (continued): Single Particle
Analysis | Relion
Session 6 (continued): Single Particle
Analysis |cisTEM
Session 7 (continued): Single Particle
Analysis | cryoSPARC
Session 8 (continued): Subtomo Analysis
Session 9 (continued): Model Building
Session 10 (continued): Microscopy
and Demos
IC 15-104

IC 15-114

IC 15-125

Computer training lab
Helix seminar room B01
Imaging centre
16:00 – 16:30Coffee break Flex Lab
16:30 – 18:30Practical
Session 5 (continued): Single Particle
Analysis | Relion
Session 6 (continued): Single Particle
Analysis |cisTEM
Session 7 (continued): Single Particle
Analysis | cryoSPARC
Session 8 (continued): Subtomo Analysis
Session 9 (continued): Model Building		Courtyard Room
Computer training lab
Meeting room B11
Helix seminar room B01
Helix seminar room A01
18:30 – 19:30DinnerCanteen
19:30 – 20:30Discussion round: Recent breakthroughs and emerging technologiesCourtyard Room
20:30Walk to ISG
Day 9 – Monday 29 August 2022
TimeSpeakersLocation
08:35Shuttle to EMBLISG bus stop
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 09:30Sponsor presentation – KleindiekCourtyard Room
09:30 – 10:30Fitting of low-resolution EM maps and integrative structure determination
Jan Kosinski – EMBL Hamburg, Germany 		Courtyard Room
10:30- 11:30In-cell Structural Biology
Julia Mahamid – EMBL Heidelberg, Germany		Courtyard Room
11:30 – 12:00Coffee breakFlex lab
12:00 – 13:00 Importance of Data Sharing, structural databases and FAIR principles
Ardan Patwardhan – EMBL-EBI Hinxton, UK (remote)		Courtyard Room
13:00 – 14:00Wrap up with emphasis on the future of cryoEM, responsible practice, reporting and validation standardsCourtyard Room
14:00 – 14:30Packed lunch and departure
14:30Bus to train stationBus stop

Practical information

Registration fees and motivation letter

The course is limited to up to 24 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

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.

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.

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.

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 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 more detailed information, follow the instructions provided in 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

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 events in Heidelberg and will be indicated during the abstract or motivation letter submission process.

Your place in the meeting 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 or conference.

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, EMBL Conference or EMBO|EMBL Symposium from within Europe.
– up to €1000 for participants travelling to an EMBL Course, EMBL Conference or EMBO|EMBL Symposium from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

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 and workshops only)

For EMBO Practical Course or EMBO Workshop 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 or conference. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, 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 EUR can be awarded per participant applying for an EMBO Childcare Grant. In order to apply for this grant for EMBO Workshops, you must be registered by the abstract submission deadline.

Application

You may apply for financial assistance when submitting your motivation letter for courses, and abstract for conferences. 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.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter or abstract 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 meeting. Selection is based on your current work or study location, the reasons for needing financial support and the impact this event will have on your career.

Reimbursement

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

Further details

View our list of external funding opportunities and information on attending a conference as an event reporter.

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 21 to 29 August (8 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfasts, for your stay at the ISG but that you will be required to pay an additional cost of 21 EUR per night for a single room. 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. A bus schedule and location of the bus stops will be made available prior to the meeting.

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.

Sponsors

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 conferences, 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.

Date: 21 - 29 Aug 2022

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre and EMBL Imaging Centre

Deadline(s):

Application: Closed

Organisers:

  • Julia Mahamid
    EMBL Heidelberg, Germany
    • Sebastian Eustermann
      EMBL Heidelberg, Germany
      • Simone Mattei
        EMBL Heidelberg, Germany
        • Lori Passmore
          Cambridge Biomedical Campus, UK
          • Henning Stahlberg
            École Polytechnique Fédérale de Lausanne, Switzerland

          Contact: Iva Gavran

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          #EMBOCryoEM

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