Fundamentals of widefield and confocal microscopy and imaging – Course and Conference Office

EMBL Course

Fundamentals of widefield and confocal microscopy and imaging


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

Course overview

Light microscopy is the most widely used form of microscopy for life science research. The correct handling of the microscope and optimising image quality (e.g. contrast, resolution) as well as experimental design according to different applications are crucial to obtain the best results.

This course will provide the participants with an overview of the basics of microscopy (light and optics, contrast techniques and imaging). The confocal part will include multicolour, 3D, and time-lapse imaging as well as spectral imaging, introduction to photobleaching and photoactivation techniques. Basic image analysis tools including measurement functions, colocalisation, and spectral unmixing as well as 3D/4D image processing will be covered, both in theory and practice. The course will combine lectures with intense daily hands-on practices followed by discussions.


This course is directed towards PhD students and faculty searching for instruction on light microscopy and basic image processing, with basic level on microscopy.

Learning outcomes

Participants will get an overview of the basics of microscopy.

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

This course is organised in cooperation with Evident-Olympus.


Speakers, trainers, and staff

Heiko Gaethje

Evident Scientific


Stefan Marawske

Evident Scientific


Jens Marquardt

Evident Scientific


Peter Vander

Evident Scientific


Scientific organisers

Heiko Gaethje

Evident Scientific


Stefan Marawske

Evident Scientific


Jens Marquardt

Evident Scientific


Stefan Terjung

EMBL Heidelberg


Course organisers

Catherine Casas

Catherine Casas-Saavedra

Course and Conference Officer

EMBL Heidelberg


Irena Provaznikova

Training Laboratory Officer

EMBL Heidelberg


Preliminary programme

Are you on social media? Post using #EMBLWidefieldConfocal and don’t forget to tag @EMBLEvents

Day 1 – Monday 22 April 2024
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceB&B Hotel
09:00 – 09:15Arrival and welcome, house notesCourtyard Room A & B
09:15 – 13:00Basics of optics and microscopy
Theoretical basics of light and optics
• Types of microscope frames – and types of optics
• Set up bright field microscopes and the appropriate optics for different needs
• Cleaning, centering adjusting and operating a microscope
• Basic set-up and use of imaging devices

Hands-on session 1
Courtyard Room A & B
13:00 – 14:00LunchEMBL Canteen
14:00 – 15:00Contrast methods
• Introduction into contrast methods
(phase contrast and differential interference contrast/DIC)
Courtyard Room A & B
15:00 – 17:30Contrast methods – set up and alignment
• Set up and use of contrast methods:
phase contrast and differential interference contrast/DIC

Hands-on session 2
Courtyard Room A & B
17:30 – 18:00Discussing open questionsCourtyard Room A & B
18:00 – 19:00DinnerEMBL Canteen
19:00Departure to HotelATC Entrance
Day 2 – Tuesday 23 April 2024
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceB&B Hotel
08:50 – 09:00Arrival and coffeeCourtyard Room A & B
09:00 – 12:30Basics of digital imaging
• Adaptation of digital cameras and their
• Interpretation of image content, histogram and digital filter functions
• Improving digital image contrast
Courtyard Room A & B
12:30 – 13:30LunchEMBL Canteen
13:30 – 16:00Fluorescence microscopy I
• Introduction to fluorescence microscopy
• Setting up of microscopes and cameras for fluorescence observation
• The different types of illumination sources (e.g. mercury, xenon, metal halide or LED)
• Cubes, filters and objectives
• Find the appropriate filter combination for a given fluorochrome and application

Hands-on session 3
Courtyard Room A & B
16:00 – 17:30Discussing open questionsCourtyard Room A & B
17:30 – 18:30Pizza dinnerATC Rooftop Lounge
18:30Departure to HotelATC Entrance
Day 3 – Wednesday 24 April 2024
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceB&B Hotel
08:50 – 09:00Arrival and coffeeCourtyard Room A & B
09:00 – 11:30Fluorescence microscopy II
• Auto-fluorescence – a source for noise
• Digital imaging for fluorescence microscopy
• Specific needs of digital cameras
• Digital multicolor handling
• Acquisition of multidimensional images (3D, time)

Hands-on session 3 (continued)
Courtyard Room A & B
11:30 – 11:35Group picture
11:35 – 12:30Guided tour of the EMBL Advanced light microscopy facility (ALMF)ALMF
12:30 – 13:30LunchEMBL Canteen
13:30 – 15:00Lecture: Introduction to the confocal microscopeCourtyard Room A & B
15:00 – 18:00Hands on session (Group work)
Different applications will be covered in small groups.

Module 1: Multicolor imaging
Module 2: Photomanipulation techniques – FRAP, FLIP and Photoconversion
Module 3: 3D image collection and enhancement – zooming, resolution, SNR, z-stacks, IMARIS basic
Module 4: Time-lapse imaging, bleaching and viability; Multi-Area Time-Lapses and Stitching
Microscopy rooms
18:00 – 18:30EMBL Bus via ISG Hotel to downtownATC Entrance
18:30 – 20:00Free time
20:00 – 22:00Dinner downtownOskar Restaurant u. Vinothek
Day 4 – Thursday 25 April 2024
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceB&B Hotel
08:50 – 09:00Arrival and coffeeCourtyard Room A & B
09:00 – 10:00FRAP and Photoconversion (Talk)Courtyard Room A & B
10:00 – 13:00Hands-on session (Group work)
Work in Modules
Microscopy rooms
13:00 – 14:00LunchEMBL Canteen
14:00 – 18:00Hands-on session (Group work)
Comparative time-lapse overnight experiment on three different setups
Microscopy rooms
18:00 – 19:00DinnerEMBL Canteen
19:00Departure to HotelATC Entrance
Day 5 – Friday 26 April 2024
Time (Europe/Berlin)SessionLocation
08:40Bus from hotel to EMBL ATC EntranceB&B Hotel
08:50 – 09:00Arrival and coffeeCourtyard Room A & B
09:00 – 09:30Evaluation and summary
of overnight timelapse acquisition
Courtyard Room A & B
09:30 – 12:30Hands on session (Group work)
Work in Modules
Microscopy rooms
12:30 – 13:00Tips and tricks for data presentationCourtyard Room A & B
13:00 – 13:10Closing remarksCourtyard Room A & B
13:10 – 13:25Packed lunchATC Foyer
13:25EMBL Bus via Hotel to main train stationATC Entrance

Practical information

Registration fees and motivation letter

The course is limited to 12 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.


Registration fees include admission, course materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

PhD Student€525

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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:

  • 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.

Financial assistance

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers, travel grants and childcare grants

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.

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.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.


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.


The scientific organisers will select the recipients of registration fee waivers and travel grants 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 for registration fee waivers and travel grants 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.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). 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 (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.

Accommodation and travel

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.


Accommodation is not included in the registration fee. Participants are expected to book and pay for their own accommodation. Single rooms have been reserved for 5 nights (21 – 26 April) at B&B Hotel. After the selection process, selected participants should contact the hotel directly (heidelberg@hotelbb.com) to make a booking with the booking code (MIC24-01) by the deadline of Monday, 25 March. We recommend that all course participants stay in 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 more information about accommodation and travel, please refer to the FAQ page.

On-site information


All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

EMBL Merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order or get in contact with your Course Organiser.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

  • The first aid room is located next to the ATC Registration Desk (room 10- 205).
  • Dial the Emergency number 222 from any EMBL internal phone only.
  • Where is the accident? What happened? How many injured?
  • Emergency number 06221-387 7821 from mobile phones.
  • Please report all accidents to the conference officer at the registration desk.

In case of fire …

  • Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
  • A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
  • Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.


Wi-Fi is available on campus. Log in using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.


There are lockers available on-site to store your luggage, which require a 2 EUR coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.


During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.


We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.


A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Additional information

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.

Technical requirements and event software

Technical requirements

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

  • Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
  • You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
  • If you have a non-standard HDMI port (other than type A), you need to bring an adaptor.
  • Keyboard and PC mouse are available for use with a standard USB port. If you have a different port type, such as USB-C, you will need to bring your own.

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.

COVID-19 related questions

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.


Media partners

Imaging and Microscopy, a Wiley magazine

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.


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: 22 - 26 Apr 2024

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Application: Closed


  • Heiko Gaethje

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