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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.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

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 basic 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.

Speakers and Trainers

Hui Guo

The Hospital for Sick Children

Canada

Wim Hagen

EMBL Heidelberg

Germany

Dari Kimanius

MRC Laboratory of Molecular Biology

UK

Eva Nogales

Lawrence Berkeley National Laboratory

USA

Scientific Organisers

Course Organisers

Iva Gavran

Course and Conference Officer

EMBL Heidelberg

Germany

Programme

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  • 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
14:00 – 14:30Arrival to EMBL
14:30 – 15:00Safety introductionsCourtyard Room
15:00 – 15:15Introduction and housenote slides
Julia Mahamid, EMBL Heidelberg
Courtyard Room
15:15 – 15:30 Course overview
Simone Mattei, EMBL Heidelberg
Courtyard Room
15:30 – 16:30Cutting edge research with Single
Particle Analysis

Eva Nogales, Lawrence Berkeley
National Laboratory
Courtyard Room
16:30 – 17:30Cutting edge research with Tomography
Giulia Zanetti, Birkbeck College
Courtyard Room
17:30 – 18:00Coffee breakFoyer
18:00 – 19:00An overview of the past and future
of cryoEM
Richard Henderson, MRC Laboratory
of Molecular Biology
Courtyard Room
19:00 – 19:30Tapas dinnerFoyer
19:30 – 21:00Student presentations IFoyer
21:00Shuttle to ISG HotelATC entrance
Day 2 – Monday, 22 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Cryo-EM image formation and optics
Chris Russo, MRC Laboratory of
Molecular Biology
Courtyard Room
10:00 – 11:00Introduction to the microscope
Radostin Danev, The University of Tokyo
Courtyard Room
11:00 – 12:00 Specimen preparation: vitrification
and sample supports

Lori Passmore, MRC Laboratory of
Molecular Biology
Courtyard Room
12:00 – 13:00Lunch breakFoyer
13:00 – 14:00Fundamentals of image processing
and Maximum likelihood approaches

Nikolaus Grigorieff, University of
Massachusetts Medical School
Courtyard Room
14:00 – 15:00AI for cryoEM image processing
Sjors Scheres, MRC Laboratory of
Molecular Biology
Courtyard Room
15:00 – 15:30Coffee breakFoyer
15:30 – 17:00Forces in vitrification, beam damage and
phase plates: past and future of cryoEM II
Robert Glaeser, Lawrence Berkeley
National Laboratory
Courtyard Room
17:00 – 18:00Panel discussion
Discussion leader: Lori Passmore
Courtyard Room
18:00 – 18:30Group photo
18:30 – 19:00DinnerFoyer
19:00 – 21:00Student presentations IFoyer
21:00Shuttle to ISG HotelATC entrance
Day 3 – Tuesday, 23 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the dayCourtyard Room
09:00 – 10:00Handling heterogeneity in cryoEM
sample preparation

Kelly Nguyen, MRC Laboratory of
Molecular Biology
Courtyard Room
10:00 – 11:00Handling heterogeneity in cryoEM
image processing

Sjors Scheres, MRC Laboratory of
Molecular Biology
Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Sebastian Eustermann
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
Courtyard Room
15:30 – 16:00Coffee breakFoyer
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
Courtyard Room
18:00 – 19:00DinnerFoyer
19:00 – 21:00Student presentations IIIFoyer
21:00Shuttle to ISG HotelATC entrance
Day 4 – Wednesday, 24 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00Best practices of microscopy for data
collection for Single Particle Analysis

and Tomography
Wim Hagen, EMBL Heidelberg
Courtyard Room
10:00 – 11:00Practical considerations of initial
image processing: on the fly processing

Henning Stahlberg, EPFL
Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Simone Mattei
Courtyard Room
12:00 – 13:00Lunch breakFoyer
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
Courtyard Room
15:30 – 16:00Coffee breakFoyer
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
Courtyard Room
18:00 – 19:00DinnerCanteen
19:00 – 21:00Student presentations IVCanteen
21:00Shuttle to ISG HotelATC entrance
Day 5 – Thursday, 25 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00High-resolution single-particle analysis:
how to reach 2.5 Å routinely?
Bridget Carragher, New York
Structural Biology Center
Courtyard Room
10:00 – 11:00Atomic model building and validation
Frank DiMaio, University of Washington
Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Henning Stahlberg
Courtyard Room
12:00 – 13:00Lunch breakFoyer
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
Courtyard Room
15:30 – 16:00Coffee breakFoyer
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
Courtyard Room
18:30 – 20:30Preparation for practicals discussion /
Pizza dinner
Canteen
20:30Shuttle to ISG HotelATC entrance
Day 6 – Friday, 26 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00Sample preparation for in situ cryo
-electron tomography: FIB technology
Phillip Erdmann, Human Technopole
Courtyard Room
10:00 – 11:00Particle localization and extraction in
cryo-electron tomograms

Beata Turonova, Max Planck Institute
of Biophysics
Courtyard Room
11:00 – 12:00 High resolution subtomogram
analysis

William Wan, Vanderbilt University
Courtyard Room
12:00 – 13:00Lunch breakFoyer
13:00 – 14:00Preparation for practical presentationCourtyard Room
14:00 – 16:00Practical discussion
Comparing methods, tips and tricks and
data interpretation
Discussion leader: Sebastian Eustermann
Courtyard Room
16:00 – 19:00Free time
19:00 – 21:00Downtown dinner
Day 7 – Saturday, 27 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00Correlative light and electron microscopy
for Structural Cell Biology

Wanda Kukulski, University of Bern
Courtyard Room
10:00 – 11:00Sponsors talks (2×30 min)Courtyard Room
11:00 – 12:00 Panel discussion
Discussion leader: Julia Mahamid
Courtyard Room
12:00 – 13:00Lunch breakFoyer
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
Courtyard Room
15:30 – 16:00Coffee breakFoyer
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
Session10 (continued): Microscopy
and Demos
Courtyard Room
18:00 – 19:00Discussion round: Career Paths in
academia, facilities and industry
Courtyard Room
19:00 – 21:00Dinner and continued discussion Canteen
21:00Shuttle to ISG HotelATC entrance
Day 8 – Sunday, 28 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00Fitting of low-resolution EM maps
and integrative structure determination
Jan Kosinski, EMBL Hamburg
Courtyard Room
10:00 – 12:00Practical
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
Session10 (continued): Microscopy
and Demos
Courtyard Room
12:00 – 13:00Lunch breakCanteen
13:00 – 15:30Practical
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
Courtyard Room
15:30 – 16:00Coffee breakFoyer
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
18:00 – 18:15Bus to ISG hotelATC entrance
18:30 – 19:30Discussion round: recent breakthroughs
and emerging technologies
ISG hotel
19:30 – 20:30DinnerISG hotel
Day 9 – Monday, 29 August 2022
TimeSpeakersLocation
08:50 – 09:00Overview of the day
09:00 – 10:00CryoEM in Pharma
Alexis Rohou, Genentech
Courtyard Room
10:00 – 11:00In-cell Structural Biology
Julia Mahamid, EMBL Heidelberg
Courtyard Room
11:00 – 11:30 Importance of Data Sharing,
structural databases and FAIR principles

Ardan Patwardhan, EMBL-EBI Hinxton
Courtyard Room
11:30 – 12:30Wrap up with emphasis on the future of
cryoEM, responsible practice, reporting
and validation standards
Courtyard Room
12:30 – 14:00Lunch and Departure

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

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.

Boehringer Ingelheim Fonds Travel Grant

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

This grant covers costs related to your attendance to 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

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.

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

Organisers:

  • Julia Mahamid
    EMBL Heidelberg, Germany
    • Sebastian Eustermann
      EMBL Heidelberg, Germany
      • Simone Mattei
        EMBL Heidelberg, Germany

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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