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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 information about protein localisation, dynamics, and functions 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.

Modules/Resources

The topics will include fluorescence microscopy techniques such as fast time-lapse microscopy, spinning disk and point-scanning confocal microscopy, light sheet microscopy of cleared samples, 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.

Course Format Information

The entire course, including hands-on practicals, will happen virtually. 

All participants will attend lectures and live Q&A sessions together each day between 13:00 and 16:00 (times might vary slightly depending on the day).

Some lectures will happen live, other lectures and tutorials will be prerecorded and provided to participants in advance. Each prerecorded module will be associated with live Q&A sessions to discuss with the speaker. For practicals, participants will be subdivided into four smaller groups. Two groups will attend the practicals each day between 16:00 and 19:00, two other groups will attend the practicals from 9:00 to 12:00.

Online practical sessions will run on four high-end microscopes located at four different sites. Practical providers will set up the audio-visual equipment, including cameras, to explain and discuss the hardware with participants. Then the screens of microscope computers will be shared with participants via Zoom. In some practicals participants will get an opportunity to control the software remotely to configure new experiments and adjust experiment settings.

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

Speakers and Trainers

Mark Hink

University of Amsterdam

The Netherlands

Scientific Organisers

Stefan Marawske

Stefan Marawske

Olympus Europa SE & Co.KG

Germany

Irina Rakotoson

Irina Rakotoson

PhaseView-Olympus

France

Course Organisers

Maryann Heck

Course and Conference Officer

EMBL Heidelberg

Germany

Yvonne Yeboah

Yvonne Yeboah

Training Laboratory Manager

EMBL Heidelberg

Germany

Programme

Got something to say? #EMBLFluorImaging

  • The virtual course will start on Monday 9 May with an onboarding session and access to the pre-recorded talks from invited speakers and trainers. The course will continue on  Monday 16 May with the regular programme.
  • Participants will be required to view the pre-recorded talks (7 h) prior to the main start of the course on Monday 16 May. During the 5-day course duration, full-time attendance is required.  

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 – Monday 9 May 2022
TimeSession
13:00-16:00Onboarding and technical troubleshooting
Day 1 – Monday 16 May 2022
TimeSession
12:30-13:00Welcome and course overview
13:00-13:30Lecture: Concepts in light microscopy
Urs Ziegler – University of Zurich, Switzerland
13:30-13:45Q&A session: Concepts in light microscopy
Urs Ziegler – University of Zurich, Switzerland
13:45-14:30Flash talk presentations by participants
14:30-15:30Q&A session (based on material in pre-recorded talks):
Concepts of image acquisition and processing
Heiko Gaethje – Olympus Europa SE & Co.KG
15:30-16:00Break
16:00-19:00Hands-on microscopy practicals:

Multicolor single molecule localization microscopy with spectral demixing
Debora Keller-Olivier – Abbelight, France
(Group 3)

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 4)
Day 2 – Tuesday 17 May 2022
TimeSession
09:00-12:00Hands-on microscopy practicals:

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)
12:00-13:00Break
13:00-13:45Flash talk presentations by participants
13:45-14:45Q&A session (based on material in pre-recorded talks):
Principles and applications of photomanipulation techniques (FRAP, photoactivation and others)
and
Adaptive feedback microscopy for high-content imaging and beyond
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
14:45-15:30Q&A session (based on material in pre-recorded talks):
DIY super-resolution: Expanding biology above diffraction
Pedro Matos Pereira- ITQB, Portugal
15:30-16:00Break
16:00-19:00 Hands-on microscopy practicals:

Live cell imaging
Joana Delgado – University of Zurich, Switzerland
Urs Ziegler – University of Zurich, Switzerland
(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)
Day 3 – Wednesday 18 May 2022
TimeSession
09:00-12:00Hands-on microscopy practicals:

Live cell imaging
Joana Delgado – University of Zurich, Switzerland
Urs Ziegler – University of Zurich, Switzerland
(Group 1)

Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
(Group 2)
12:00-13:00Break
13:00-13:30Lecture: The brain under surveillance: Neural-immune interactions in the development and repair of the CNS
Francesca Peri – University of Zurich, Switzerland
13:30-13:45 Q&A session: The brain under surveillance: Neural-immune interactions in the development and repair of the CNS
Francesca Peri – University of Zurich, Switzerland
13:45-14:15Lecture: To diffraction limit and beyond: using spectral demixing multicolor 3D-dSTORM to study synapses organisation
Benjamin Compans – King’s College London, UK
14:15-14:30Q&A session: To diffraction limit and beyond: using spectral demixing multicolor 3D-dSTORM to study synapses organisation
Benjamin Compans – King’s College London, UK
14:30-15:00Lecture: Light sheet imaging for live and cleared specimens France Lam – IBPS, France
15:00-15:15 Q&A session: Light sheet imaging for live and cleared specimens
France Lam – IBPS, France
15:15-16:00Break
16:00-19:00Hands on microscopy practicals:

Multicolor single molecule Localization Microscopy with Spectral Demixing
Debora Keller-Olivier – Abbelight, France
(Group 4)

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

Day 4 – Thursday 19 May 2022
TimeSession
09:00-12:00Hands on microscopy practicals:

Multicolor single molecule localization microscopy with spectral demixing
Debora Keller-Olivier – Abbelight, France
(Group 2)

Ultra-thin light sheet microscope with automated multi-scale imaging capabilities
Irina Rakotoson – PhaseView, France
(Group 1)
12:00-13:00Break
13:00-14:00Q&A session (based on material in pre-recorded talks):
Measuring interactions and biosensors using FRET
Mark Hink – University of Amsterdam, The Netherlands
14:00-14:30Lecture: Single phenotype transcriptomics as a platform to identify networks regulating Golgi structure
Sanjana Singh – EMBL Heidelberg, Germany
14:30-14:45Q&A session: Single phenotype transcriptomics as a platform to identify networks regulating Golgi structure
Sanjana Singh – EMBL Heidelberg, Germany
14:45-15:45Social event: Quiz Time
15:45-16:00Break
16:00-19:00Hands on microscopy practicals:

Live cell imaging
Joana Delgado – University of Zurich, Switzerland
Urs Ziegler – University of Zurich, Switzerland
(Group 4)

Applying adaptive feedback microscopy for high-throughput photoactivation of specific cell phenotypes
Aliaksandr Halavatyi – EMBL Heidelberg, Germany
Manuel Gunkel – EMBL Heidelberg, Germany
(Group 3)
Day 5 – Friday 20 May 2022
TimeSession
09:00-12:00Hands on microscopy practicals:

Live cell imaging
Joana Delgado – University of Zurich, Switzerland
Urs Ziegler – University of Zurich, Switzerland
(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 1)
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):

Academia€125
PhD Student€125
Industry€250

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

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.

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 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.

Additional Information

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

Sponsors

This course is organised in cooperation with Olympus.

Date: 16 - 20 May 2022

Location: Virtual


Deadline(s):

Application: Closed


Organisers:

  • Joana Delgado
    University of Zurich, Switzerland
    • Manuel Gunkel
      EMBL Heidelberg, Germany
      • Aliaksandr Halavatyi
        EMBL Heidelberg, Germany
        • Debora Keller-Olivier
          Abbelight, France

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