Super-Resolution Microscopy: Time-Resolved STED Nanoscopy – Course and Conference Office

EMBL Course

Super-Resolution Microscopy: Time-Resolved STED Nanoscopy


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 five-day comprehensive online microscopy course focuses on stimulated emission depletion microscopy (STED) and its application to biological questions.

Through lectures, tutorials, demonstrations and practical workshops, the course provides in-depth knowledge on all aspects of STED Nanoscopy.

It covers the fundamentals of STED microscopy, different technical implementations and has a strong emphasis on sample preparation – including choice of fluorophores and refractive index matching, as well as image acquisition strategies for fixed samples and living cells. Students will have the opportunity for exercises on state-of-the-art STED microscopes in which they will acquire high quality nanoscopy data.

The faculty consists of Invited guest researchers, experts from the EMBL and Leica Microsystems.

In order to adapt to different time zones, the practical sessions will be run in 2 individual corridors:

  • 2 groups in the morning (10:00 – 12:00 CEST)
  • 2 groups in the late afternoon (16:30 – 18:30 CEST)

Presentations, tutorials and other activities for all participants will take place in a shared slot in-between the practicals: 13:00 – 16:00 (CEST).


This course is designed for researchers at the early stages of their career in the life sciences (e.g. pre or postdoctoral level), ideally with access to a STED microscope. The participants should have an immediate need to apply the trained skills for their biological questions. The course is strongly centered on practical aspects of STED microscopy and is therefore especially suited for people who rely on STED nanoscopy for their research.


The course will cover the entire range of skills needed to apply STED nanoscopy in biology. The following topics will be covered in lectures, tutorials as well as in practical workshops:

  • Sample preparation for STED microscopy, including choice of fluorophores and refractive index matching
  • Technical implementations – CW-STED, pulsed-STED, gated-STED, time-resolved STED (tauSTED)
  • Multi-Color 2D and 3D STED microscopy
  • Image acquisition strategies for live-cell STED
  • STED Fluorescence Correlation Spectroscopy (STED-FCS)

Learning Outcomes

At the end of the course, the participants will be able to design experiments using STED microscopy, prepare high-quality microscopy samples and acquire state-of-the-art nanoscopy images.

What Past Participants Say About the Course

“The course was well organised, extremely motivating and valuable. The course gave me the right tools and understanding to optimise super-resolution microscopy for my project.” – Ida Jentoft, Max Planck Institute for Biophysical Chemistry, Germany

“A very well designed course for both beginners as well as for people who have prior experience working on STED/STORM imaging. It has a good balance of theory and practical sessions, and offers a unique chance to image your own samples after the course. Overall a great experience!” – Rukmini Mukherjee, Goethe University, Germany

“My research focus is on understanding Centrioles and Centrosomes in Drosophila. I actively employ SRM techniques in my research and was just learning about STED microscopy so the course supplemented and helped in my understanding and learning of this new microscopy technique.” – Pallavi Panda, University of Cambridge, UK

Speakers and Trainers


Kai Johnsson

Max Planck Institute for Medical Research



Scientific Organisers

Course Organisers


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  • The virtual course will start on Monday 28 June with an onboarding session. The course will continue on Monday 12 July with the regular programme.

The following times are used in the programme below:

  • Central European Summer Time (CEST): eg. Berlin, Amsterdam Paris
  • Eastern Standard Time (EDT): eg. New York, Quebec

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

In order to accommodate different time zones, the Workshop Groups 1+2 will always be scheduled in the afternoon (CEST) and Groups 3+4 always in the morning (CEST).

Day 0 – Monday 28 June 2021
Time (EDT)Time (CEST)Session
TBATBAOnboarding and technical troubleshooting

Day 1 – Monday 12 July 2021
Time (EDT)Time (CEST)Session
06:45-07:0012:45-13:00Welcome and course overview
07:00-08:3013:00-14:30Flash talks of participants’ projects (with break)
08:45-09:4514:45-15:45Studying the structure of chromosomes in single human cell by super-resolution microscopy
Jan Ellenberg – EMBL Heidelberg, Germany
09:45-10:0015:45-16:00Introduction to Workshops

Group 1: WS STED-imaging of fixed cells

Group 2: WS STED-imaging of thick samples
and tissues

Day 2 – Tuesday 13 July 2021

Time (EDT)Time (CEST)Session
04:00-06:0010:00-12:00Group 3: WS STED-imaging of fixed cells

Group 4: WS STED-imaging of
thick samples and tissues
06:45-07:0012:45-13:00Check-in of the day
07:00-07:0513:00-13:05Overview of the day
07:05-07:5013:05-13:50Presentation Title: TBA
Christian Eggeling – University of Oxford, UK
08:00-08:4514:00-14:45Investigating cellular logistics with live-cell STED
Francesca Bottanelli – Freie Universität Berlin,
09:15-10:0015:15-16:00Tutorial: Sample Preparation 1 –
Refractive Index Matching and Optics
10:30-12:3016:30-18:30Group 1: WS STED-imaging of thick samples
and tissues

Group 2: WS STED-imaging of fixed cells
Day 3 – Wednesday 14 July 2021
Time (EDT)Time (CEST)Session
04:00-06:0010:00-12:00Group 3: WS STED-imaging of thick
samples and tissues

Group 4: WS STED-imaging of fixed cells
06:45-07:0012:45-13:00Check-in of the day
07:00-07:0513:00-13:05Overview of the day
Mike Heilemann – Goethe University Frankfurt, Germany
08:00-08:4514:00-14:45New fluorescent probes for live-cell imaging
Kai Johnsson – Max Planck Institute for Medical Research, Germany
09:15-10:0015:15-16:00Tutorial: Sample Preparation 2 – Fluorophores
and staining
10:30-12:3016:30-18:30Group 1: WS Live cell STED imaging

Group 2: WS STED-FCS

Day 4 – Thursday 15 July 2021

Time (EDT)Time (CEST)Session
04:00-06:0010:00-12:00Group 3: WS Live cell STED imaging

Group 4: WS STED-FCS
06:45-07:0012:45-13:00Check-in of the day
07:00-07:0513:00-13:05Overview of the day
07:05-07:3013:05-13:30Contextual super-resolution imaging – Fine structure preservation for light and electron microscopy
Jana Döhner – University of Zurich, Switzerland
07:30-07:5513:30-13:55Studying the nanoscale architecture of the kidney filter using high- and super-resolved microscopy
David Unnersjö-Jess – University of Cologne, Germany
08:00-08:4514:00-14:45Presentation Title: TBA
Speaker: TBA
09:15-10:0015:15-16:00Tutorial: Discussion of selected participants projects and experimental planning
10:30-12:3016:30-18:30Group 1: WS STED-FCS

Group 2: WS Live-cell STED imaging

Day 5 – Friday 16 July 2021

Time (EDT)Time (CEST)Session
04:00-06:0010:00-12:00Group 3: WS STED-FCS

Group 4: WS Live cell STED imaging
06:45-07:0012:45-13:00Check-in of the day
07:00-07:0513:00-13:05Overview of the day
07:05-07:5013:05-13:50Presentation Title: TBA
Speaker: TBA
08:00-09:0014:00-15:00Social activity
09:15-10:0015:15-16:00Live Q&A Session based on pre-recorded talk
Sophie Allart – INSERM, France
10:00-10:2016:00-16:20Closing remarks, comments, farewell

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 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.


  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. 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


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 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.


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 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.


This course is organised in cooperation with Leica Microsystems.

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Technical Requirements

Below you will find the software and technical requirements for this course.


  • Headsets is highly recommended for improved voice clarity and better audio quality

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)

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.

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Date: 12 - 16 Jul 2021

Location: Virtual


Application: Closed


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

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