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Advanced fluorescence imaging techniques – Course and Conference Office

EMBL Course

Advanced fluorescence imaging techniques

Overview

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

Course overview

This practical course will cover advanced light microscopy techniques and participants will learn how to derive qualitative and quantitative insights on molecular mechanisms in cells and developing organisms. Invited guest researchers together with microscopy experts from EMBL will foster an intense information flow with a balance of lectures and practical workshops. The focus of the course will be on the use of fluorescence microscopy to obtain information about localisation and functions of proteins and other bio-molecules at different spatial scales.

Audience

This course is directed towards researchers in the life sciences with access to light microscopy equipment, who have an immediate need to apply the techniques they will learn to solve biological problems at the cellular and molecular level in vivo. As the course will be primarily focused on the advanced techniques, we expect participants to have basic knowledge of light microscopy.

Modules/resources

The topics will include fluorescence microscopy techniques such as fast time-lapse microscopy of living cells, spinning disk and point-scanning confocal microscopy, light sheet microscopy of cleared samples, photo-manipulation as a tool, multicolour single-molecule localization microscopy (SMLM) with spectral demixing, expansion microscopy, FRET-based techniques. For demanding applications, we will cover the aspects of image processing and analysis and the possibilities of microscope automation. The modules will cover all necessary knowledge and demonstrate tools to conduct similar pipelines at your home lab enabling you to answer emerging biological questions.

Learning outcomes

  • Get an overview of advanced fluorescence imaging techniques.
  • Obtain hands-on experience setting up and running advanced experiments on modern fluorescence microscopes.
  • Discuss the possibilities and drawbacks of experiment planning and data interpretation with experts in the field.

This course is kindly supported by the EMBL Advanced Light Microscopy Facility.

This course is organised in cooperation with Evident.

What past participants say

“I highly recommend this course if you are looking to take your fluorescence microscopy experiments to the next level.” – Josefina Marin-Rojas, Universidad de Chile, Chile

Speakers

Speakers, trainers, and staff

Manuel Alexander Peter Gunkel

EMBL Heidelberg

Germany

Mark Hink

University of Amsterdam

The Netherlands

Ines Höfer

Evident

Germany

Robert Kasper

Evident

Germany

Simone Köhler

EMBL Heidelberg

Germany

Marko Lampe

EMBL Heidelberg

Germany

Stefan Marawske

Stefan Marawske

Evident

Germany

Pedro Pereira

ITQB NOVA

Portugal

Stefan Terjung

EMBL Heidelberg

Germany

Urs Ziegler

University of Zurich

Switzerland

Scientific organisers

Manuel Alexander Peter Gunkel

EMBL Heidelberg

Germany

Stefan Marawske

Stefan Marawske

Evident

Germany

Course Organisers

Lea Hohmann

Course and Conference Manager

EMBL Heidelberg

Germany

Preliminary programme

Day 1 – 7 May 2023
Time (Europe/Berlin)SpeakerLocation
16:00 – 16:30WelcomeISG Hotel
16:30 – 19:30Flash talks by participantsISG Hotel
19:30 – 21:00DinnerISG Hotel
Day 2 – 8 May 2023
Time (Europe/ Berlin)SpeakerLocation
09:00 – 10:00Lecture + Q&A: Concepts in Light microscopy
Urs Ziegler – University of Zurich, Switzerland
Courtyard Room A & B
10:00 – 11:00Lecture + Q&A: DIY super-resolution: Expanding biology above diffraction
Pedro Matos Pereira- ITQB, Portugal
Courtyard Room A & B
11:00 – 11:30Coffee BreakCourtyard Room A & B
11:30 – 12:30Practical: Preparation of expansion microscopy samples
Pedro Matos Pereira- ITQB, Portugal
Flex Lab A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Hands-on practical 1:
Live cell imaging

Joana Delgado – University of Zurich, Switzerland
Urs Ziegler – University of Zurich, Switzerland
(Groups 1+2)

3D imaging of model organisms with CLSM
Stefan Terjung – EMBL, Heidelberg, Germany
Stefan Marawske – Evident
(Groups 3+4)
Microscopy rooms
16:00 – 16:15Coffee breakCourtyard Room A & B
16:15 – 18:45Hands-on practical 2:

3D imaging of model organisms with CLSM
Stefan Terjung – EMBL, Heidelberg, Germany
Stefan Marawske – Evident
(Groups 1+2)

Deconvolution
Urs Ziegler – University of Zurich, Switzerland
(Groups 3+4)


Microscopy rooms





Computer training lab
18:45 – 19:45DinnerEMBL Canteen
19:45 – 20:45Departure to HotelATC Entrance
Day 3 – 9 May 2023
Time (Europe/ Berlin)SpeakerLocation
09:00 – 10:00Lecture + Q&A: Adaptive Feedback Microscopy
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Courtyard Room A & B
10:00 – 11:00Lecture + Q&A: Light sheet microscopyCourtyard Room A & B
11:00 – 11:30Coffee breakCourtyard Room A & B
11:30 – 12:30Practical: Setting and debugging adaptive feedback microscopy pipelines
Manuel Gunkel – EMBL Heidelberg, Germany
Computer training lab
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Hands-on practical 3:

Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
(Groups 1+2)

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 3)

Live cell imaging
Joana Delgado – University of Zurich, Switzerland
(Group 4)
Microscopy rooms
16:00 – 16:15Coffee breakCourtyard Room A & B
16:15 – 18:45Hands-on practical 4:

Deconvolution
Urs Ziegler – University of Zurich, Switzerland
(Groups 1+2)


Live cell imaging

Joana Delgado – University of Zurich, Switzerland
(Group 3)

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 4)
Computer training lab





Microscopy rooms
18:45 – 20:00Dinner
Day 4 – 10 May 2023
Time (Europe/ Berlin)SpeakerLocation
09:00 – 10:00Lecture + Q&A: Single Molecule Localisation MicroscopyCourtyard Room A & B
10:00 – 11:00Lecture + Q&A: Courtyard Room A & B
11:00 – 11:30Coffee break
11:30 – 12:30Lecture + Q&A: Measuring interactions and biosensors using FRET
Mark Hink – University of Amsterdam, The Netherlands
Courtyard Room A & B
12:30 – 13:30LunchEMBL Canteen
Hands-on practical 5:

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Debora Keller-Olivier – Abbelight, France
(Group 1)

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 2)

FRET
Mark Hink – University of Amsterdam, The Netherlands
(Group 3)

Imaging expanded samples
Pedro Matos Pereira- ITQB, Portugal
(Group 4)
Microscopy rooms
Coffee breakCourtyard Room A & B
Hands-on practical 6:

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 1)

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Debora Keller-Olivier – Abbelight, France
(Group 2)

Imaging expanded samples
Pedro Matos Pereira- ITQB, Portugal
(Group 3)

FRET
Mark Hink – University of Amsterdam, The Netherlands
(Group 4)
Microscopy rooms
18:45 – 21:45Dinner downtown
Day 5 – 11 May 2023
Time (Europe/ Berlin)SpeakerLocation
09:00 – 10:00Lecture + Q&A: Visualizing chromosomes during meiosis
Simone Köhler – EMBL Heidelberg, Germany+ Q&A:
Courtyard Room A & B
10:00 – 11:00Lecture + Q&A: Courtyard Room A & B
11:00 – 11:30Coffee breakCourtyard Room A & B
11:30 – 12:30Lecture + Q&A: Courtyard Room A & B
12:30 – 13:30LunchEMBL Canteen
Hands-on practical 7:

FRET
Mark Hink – University of Amsterdam, The Netherlands
(Group 1)

Imaging expanded samples
Pedro Matos Pereira- ITQB, Portugal
(Group 2)

Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
(Group 3)

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Debora Keller-Olivier – Abbelight, France
(Group 4)
Microscopy rooms
Coffee breakCourtyard Room A & B
Hands-on practical 8:

Imaging expanded samples
Pedro Matos Pereira- ITQB, Portugal
(Group 1)

FRET
Mark Hink – University of Amsterdam, The Netherlands
(Group 2)

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Debora Keller-Olivier – Abbelight, France
(Group 3)


Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
(Group 4)
Microscopy rooms
18:45 – 20:00DinnerEMBL Canteen
Day 6 – 12 May 2023
Time (Europe/ Berlin)SpeakerLocation
09:00 – 10:30Practical: FRET data analysis
Mark Hink – University of Amsterdam, The Netherlands
Computer training lab
10:30 – 11:00Coffee breakoutside Computer training lab
11:00 – 12:30Practical: SMLM data analysis?Computer training lab
12:30 – 13:45LunchEMBL Canteen
13:45 – 15:00Preparation of student presentationsComputer training lab
15:00 – 16:30Student presentationsComputer training lab
16:30 – 17:00Wrap up of course and departure

Practical information

Registration fees and motivation letter

The course is limited to 16 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. Participants are expected to book and pay their own accommodation and travel expenses. 

Academia€550
PhD Student€550
Industry€1100

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.

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 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.

Accommodation and shuttles

Hotel

Single rooms have been reserved for 5 nights (7-12 May 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code MIC23-02). 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.

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.

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

Application

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.

Selection

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.

Reimbursement

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.

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 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.

Warning

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: 7 - 12 May 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Registration: 12 Feb 2023


Organisers:

  • Joana Delgado Martins
    University of Zurich, Switzerland
    • Manuel Gunkel
      EMBL Heidelberg, Germany
      • Aliaksandr Halavatyi
        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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