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Advanced Fluorescence Imaging Techniques – Course and Conference Office

EMBL Course

Advanced Fluorescence Imaging Techniques

Overview

EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

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 experts from the EMBL and microscopy professionals 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 quantitative information about protein dynamics in living samples.

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.

Modules/Resources

The topics will include fluorescence microscopy techniques such as fast time-lapse microscopy, spinning disk and point-scanning confocal microscopy, photo-manipulation as a tool, multicolor single molecule localization microscopy (SMLM) with spectral demixing. For the demanding applications we will cover the aspects of image analysis and 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

Participants will get an overview about advanced fluorescence imaging techniques.

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

This course is organised in cooperation with Olympus.

Speakers and Trainers

Michel Biocco

abbelight

France

Mark Hink

University of Amsterdam

the Netherlands

Pavel Tomancak

Max Planck Institute of Molecular Cell Biology and Genetics

Germany

Scientific Organisers

Course Organisers

Programme

Programme



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  • The virtual course will start with an onboarding session on 18 and 19 August. It is mandatory to attend on one of the days, participants can choose the day. The course will continue on Monday 23 August with the regular programme. Full-time attendance is required for the course duration.
  • Participants will be required to view the pre-recorded talks and study the pre-course material prior to the main start of the course on Monday 23 August.
  • The course will include live and pre-recorded talks, interactive discussion sessions, online practicals, hands on exercises and networking.
  • Information on the live stream and access to the course platform will be provided shortly before the start of the event.
  • Participants will be divided into 4 groups for the practicals and are required to stay in the same group throughout the entire course.
  • All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and date along with your city into the Time Zone Converter.

This programme may be subject to change.

Day 0 – Wednesday, 18 August 2021
TimeSession
13:00-16:00Onboarding and technical troubleshooting
Day 0 – Thursday, 19 August 2021
TimeSession
13:00-16:00Onboarding and technical troubleshooting
Day 1 – Monday, 23 August 2021
TimeSession
12:00-12:30Check-in
12:30-13:00Welcome and course overview
13:00-13:30Concepts in Light microscopy
Urs Ziegler – University of Zurich, Switzerland
Live talk
13:30-13:45Q&A session: Concepts in Light microscopy
Urs Ziegler – University of Zurich, Switzerland
13:45-14:30Flash talk presentations
by participants
14:30-15:00Principles in single molecule localization microscopy
Sandrine Lévêque-Fort – University of Paris Saclay, France
Live talk
15:00-15:15Q&A session: Principles in single molecule localization microscopy
Sandrine Lévêque-Fort – University of Paris Saclay, France
15:30-16:00Break
16:00-19:00Introduction into Imaging Concepts
Stefan Marawske, Heiko Gaethje – Olympus Europa SE & Co.KG, Germany
Hands-on microscopy practical
(Groups 3+4)
Day 2 – Tuesday, 24 August 2021
TimeSession
09:00-12:00Introduction into Imaging Concepts
Stefan Marawske, Heiko Gaethje – Olympus Europa SE & Co.KG, Germany
Hands-on microscopy practical
(Groups 1+2)
12:00-13:00Break
13:00-13:45Flash talk presentations
by participants
13:45-14:15Single phenotype transcriptomics as a platform to identify networks regulating Golgi structure
Sanjana Singh – EMBL Heidelberg, Germany
Live talk
14:15-14:30Q&A session: Single phenotype transcriptomics as a platform to identify networks regulating Golgi structure
Sanjana Singh – EMBL Heidelberg, Germany
14:30-15:15Principles and applications of photomanipulation techniques (FRAP, photoactivation and others)
and
Adaptive feedback microscopy for high-content imaging and beyond
Aliaksandr Halavatyi, Manuel Gunkel – EMBL Heidelberg, Germany
Live Q&A (based on material in pre-recorded talks)
15:30-16:00Break
16:00-19:00 Live cell imaging
Joana Delgado, Urs Ziegler – University of Zurich, Switzerland
(Group 3)

Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes 
Aliaksandr Halavatyi, Manuel Gunkel – EMBL Heidelberg, Germany
(Group 4)

Hands-on microscopy practicals
Day 3 – Wednesday, 25 August 2021
TimeSession
09:00-12:00Live cell imaging
Joanna Delgado, Urs Ziegler – University of Zurich, Switzerland
(Group 1)

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

Hands-on microscopy practicals
12:00-13:00Break
13:00-13:30SPIM and its applications in developmental biology
Pavel Tomancak – Max Planck Institute of Molecular Cell Biology and Genetics, Germany
Live talk
13:30-13:45 Q&A session: SPIM and its applications in developmental biology
Pavel Tomancak – Max Planck Institute of Molecular Cell Biology and Genetics, Germany
13:45-14:15The brain under surveillance: Neural-immune interactions in the development and repair of the CNS
Francesca Peri – University of Zurich, Switzerland
Live talk
14:15-14:30Q&A session: The brain under surveillance: Neural-immune interactions in the development and repair of the CNS
Francesca Peri – University of Zurich, Switzerland
14:30-15:15Social event
15:30-16:00Break
16:00-19:00Live cell imaging
Joanna Delgado, Urs Ziegler – University of Zurich, Switzerland
(Group 4)

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Paul Barthelemy – abbelight, France
(Group 3)

Hands on microscopy practicals

Day 4 – Thursday, 26 August 2021
TimeSession
09:00-12:00Live cell imaging
Joanna Delgado, Urs Ziegler – University of Zurich, Switzerland
(Group 2)

Multicolor Single molecule Localization Microscopy with Spectral Demixing
Paul Barthelemy – abbelight, France
(Group 1)

Hands on microscopy practicals
12:00-13:00Break
13:00-13:45Measuring interactions and biosensors using FRET
Mark Hink – University of Amsterdam, The Netherlands
Live Q&A (based on material in pre-recorded talks)
13:45-14:15Using light to measure biophysical properties of subcellular organelles
Simone Reber – Humboldt-Universität zu Berlin, Germany
Live talk
14:15-14:30Q&A session: Using light to measure biophysical properties of subcellular organelles
Simone Reber – Humboldt-Universität zu Berlin, Germany
14:30-15:15DIY super-resolution: Expanding biology above diffraction
Pedro Matos Pereira- ITQB, Portugal
Live Q&A (based on material in pre-recorded talks)
15:30-16:00Break
16:00-19:00Multicolor Single molecule Localization Microscopy with Spectral Demixing
Paul Barthelemy – abbelight, France
(Group 4)

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

Hands on microscopy practicals
Day 5 – Friday, 27 August 2021
TimeSession
09:00-12:00Multicolor Single molecule Localization Microscopy with Spectral Demixing
Paul Barthelemy – abbelight, France
(Group 1)

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

Hands on microscopy practicals
12:00-13:00Break
13:00-15:30Student presentations
presentation of learning outcomes by participants
15:30-16:00Wrap up and end of course

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 and all course materials):

Academia125 Euro
PhD Student125 Euro
Industry520 Euro

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:

Motivation letter length: 
The maximum limit of 2000 characters (ca. 200 words) refers to manually typed text (spaces included).

Free field text length: The maximum characters for your answers in the free field text boxes is 255 (spaces included).Text only: If you copy-paste the text, hidden formatting might still be included and you will be informed that your text exceeds the character limit. We recommend either:

  1. saving your text as text only in your editor or Email programme, OR
  2. copy-pasting it into Notepad and then onto the website.

Symbols: If you have special symbols in your text make sure you are using Unicode characters, otherwise these will not be recognised by the tool.

Further Details

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

Financial Assistance

Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. Attendance at the event is required in order to be eligible to receive the reimbursement. In order to apply for this grant, 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

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal. Read the instructions on how to apply for financial assistance.

Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons 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 some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

Check out this list of external funding opportunities or get more information on attending the conference as an event reporter.

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

Virtual Participation Guidelines

Guidelines

Please do:

  • Use the event-specific hashtag as communicated during the event for any related tweets
  • Tweet unless the speaker specifically says otherwise
  • Be mindful of unpublished data
  • Be respectful in tone and content

Please don’t:

  • Broadcast the course to unregistered participants
  • Capture, transmit or redistribute data presented at the meeting unless presenter gives explicit consent
  • Use offensive language in your posts
  • Engage in rudeness or personal attacks

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos on the event platform for you to enjoy during the event.

How to ask questions

Questions during and after the talks can be asked in live streaming platform. The chair moderates the questions and shares them with the speaker. If time runs out or you think of a question later, you can use the EMBL eCampus forum to ask your questions in the dedicated session channels or via direct message.

Time zone

The programme is planned based on Central European Time (Berlin, Amsterdam, Paris), unless otherwise stated. As many virtual participants are attending from around the world, we do our best to accomodate as many timezones as possible when creating the programme. Please take your time zone into consideration when planning your attendance.

Technical requirements

Hardware

During the course practicals we aim to broadcast the microscope software having many graphical elements. Therefore following minimum hardware setup is recommended:

  • Minimum screen resolution – Full HD (1920×1080)
  • Use external screens. Bigger screens (>22 inch) are beneficial.
  • Please use two screens if possible. We will provide recommendations to participants how to set up VC software on two screens.
  • Headsets will improve audio quality and voice clarity.

Internet Requirements

Client computer with fast and stable internet access for the live virtual sessions:

  • Minimum: 50 mbit download and 10 mbit upload
  • Preferred: 100 mbit download and upload (at your host institute)
  • While using the software during the course, please make sure you have nothing else using your bandwidth.
  • We recommend using a wired connection.

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 and other VC packages will be used for the live talks, discussions and virtual practicals. 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.

Sponsors

This course is organised in cooperation with Olympus.

Olympus logo

Olympus logo

Date: 23 - 27 Aug 2021

Location: Virtual


Deadline(s):

Application: Closed


Organisers:

  • Paul Barthelemy
    Abbelight, France
    • Joana Delgado
      University of Zurich, Switzerland

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

Founder partners

Corporate partners

Associate partners

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