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

EMBL Course

Fundamentals of widefield and confocal microscopy and imaging


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, photobleaching (FRAP, FLIP, FLAP) 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.


  • Basics of optics and microscopy
  • Contrast methods
  • Basics of digital imaging
  • Fluorescence microscopy
  • Hands-on sessions

Learning outcomes

Participants will get an overview about the basics of microscopy.


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


This course is organised in cooperation with Evident-Olympus.


Speakers, trainers and staff

Scientific organisers

Course organisers

Preliminary programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with an estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Monday 4th December 2023
Time (Europe/Berlin)SessionLocation
08:20 – 08:35Bus from hotel to EMBL ATC EntranceISG Hotel
08:40 – 09:00Arrival and welcome, house notesFlex Lab A & B
09:00 – 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
Flex Lab A & B
13:00 – 14:00LunchEMBL Canteen
14:00 – 15:00Contrast methods
• Introduction into contrast methods
(phase contrast and differential interference
Flex Lab A & B
15:00 – 17:30Contrast methods – set up and alignment
• Set up and use of contrast methods:
phase contrast and differential interference

Hands-on session 2
Flex Lab A & B
17:30 – 18:00Discussing open questionsFlex Lab A & B
18:00 – 19:00DinnerEMBL Canteen
19:00 – 19:10Departure to HotelATC Entrance
Day 2 – Tuesday 5th December 2023
Time (Europe/Berlin)SessionLocation
08:20 – 08:35Bus from hotel to EMBL ATC EntranceISG Hotel
08:40 – 09:00Arrival and coffeeFlex Lab 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
Flex Lab 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
Flex Lab A & B
16:00 – 17:30Discussing open questionsFlex Lab A & B
17:30 – 18:40DinnerEMBL Canteen
18:40 – 18:50Departure to HotelATC Entrance
Day 3 – Wednesday 6th December 2023
Time (Europe/Berlin)SessionLocation
08:20 – 08:35Bus from hotel to EMBL ATC Entrance
08:40 – 09:00Arrival and coffeeFlex Lab 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)
Flex Lab A & B
11:30 – 11:35Group pictureFlex Lab A & B
11:35 – 12:30Guided tour of the EMBL Advanced light microscopy facility (ALMF)ALMF
12:30 – 13:30LunchEMBL Canteen
13:30 – 15:00Introduction to the confocal microscope (Talk)Flex Lab 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 – 19:00EMBL Bus via ISG Hotel to Restaurant TBCATC Entrance
19:00 – 22:00Dinner in downtown HeidelbergRestaurant TBC
Day 4 – Thursday 7th December 2023
Time (Europe/Berlin)SessionLocation
08:20 – 08:35Bus from hotel to EMBL ATC EntranceISG Hotel
08:40 – 09:00Arrival and coffeeFlex Lab A & B
09:00 – 10:00FRAP and Photoconversion (Talk)Flex Lab A & B
10:00 – 13:00Hands-on session (Group work)
Work in Modules
Microscopy rooms
13:00 – 14:00LunchEMBL Canteen
14:00 – 17:00Hands-on session (Group work)
Work in Modules
Microscopy rooms
17:00 – 18:00Comparative time-lapse overnight experiment
on three different setups
Microscopy rooms
18:00 – 18:40DinnerEMBL Canteen
18:40 – 18:50Departure to HotelATC Entrance
Day 5 – Friday 8th December 2023
Time (Europe/Berlin)SessionLocation
08:20 – 08:35Bus from hotel to EMBL ATC EntranceISG Hotel
08:40 – 09:00Arrival and coffeeFlex Lab A & B
09:00 – 09:30Evaluation and summary
of overnight timelapse acquisition
Flex Lab A & B
09:30 – 12:30Hands on session (Group work)
Work in Modules
Microscopy rooms
12:30 – 13:00Tips and tricks for data presentationFlex Lab A & B
13:00 – 13:05Closing remarksFlex Lab A & B
13:05 – 13:15Packed lunchATC Foyer
13:15 – 00:00EMBL Bus via ISG Hotel to main train stationATC Main 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, COVID-19 safety measures, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses. 

PhD Student€500

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 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


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 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.


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 shuttles


Single rooms have been reserved for 5 nights (Sunday 3rd December – Friday 8th December 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code MIC23-01). 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 the 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.

Event software

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.


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: 4 - 8 Dec 2023

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Application: 11 Sep 2023


  • Heiko Gaethje
    Evident Scientific, Germany

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