Specialist Course on Light and Fluorescence Microscopy edition 2020

Target Group

PhD students who (will) make extensive use of microscopic visualization techniques for biomedical research applications. No prior experience or training is required.


All PhD students

Organizing & Scientific Committee

  • Prof. Dr. Kevin Braeckmans (Ghent University - Faculty of Pharmaceutical Sciences),
  • Prof. Dr. Stefaan De Smedt (Ghent University - Faculty of Pharmaceutical Sciences),
  • Prof. Dr. Luc Leybaert (Ghent University - Faculty of Medicine and Health Sciences),
  • Prof. Dr. Els Van Damme (Ghent University - Faculty of Bioscience Engineering),
  • Prof. Dr. Andre Skirtach (Ghent University - Faculty of Bioscience Engineering),
  • Prof. Dr. Winnok De Vos (University of Antwerp - Faculty of Veterinary Sciences),
  • Prof. Dr. Wilfried Philips (Ghent University - Faculty of Engineering & Architecture),
  • Prof. Dr. Ward De Spiegelaere (Ghent University - Faculty of Veterinary Medicine),
  • Prof. Dr. Filip Van Nieuwerburgh(Ghent University - Faculty of Pharmaceutical Sciences),
  • Dr. Herlinde De Keersmaecker (Ghent University - Centre for Advanced Light Microscopy),
  • Dr. Toon Brans (Ghent University - Faculty of Pharmaceutical Sciences/ Centre for Advanced Light Microscopy)


Light microscopy, and especially fluorescence microscopy, is an essential tool to investigate and characterize biological specimen in the life sciences. Modern microscopes offer an increasing range of technical capabilities, but thereby become gradually more complex and require appropriate training for correct scientific use. This specialist course provides doctoral students with limited experience in microscopic imaging with the understanding and skills that are needed to perform light and confocal imaging at a research-grade level.

Topic and Objectives

This course covers topics which are essential to perform light and confocal imaging at a research-grade level. An introduction to the basic principles in light microscopy will be given followed by an overview and explanation of the most frequently employed light and fluorescence microscopy techniques. Application of these microscopy principles and techniques in life science research will be demonstrated in hands-on demonstration sessions, complemented by an introduction to image processing. The course will be taught by several experts in the field and offers both theoretical lectures and practical demonstrations.

Theoretical lectures during the morning of day 1 and day 2 will offer the participants the background that is needed to perform light microscopy studies in a correct scientific way. Theory will be put into practice in a three- to four-hour demonstration session in the afternoon of day 1 and 2. The demonstration sessions naturally complement the theoretical lectures and allow the participants to become familiar with the different imaging techniques. Using real-world examples, the participants are given practical guidelines on correct instrument usage and obtaining optimal data quality. The last half day comprises a guided computer session that introduces the fundamentals of image processing. Focus will be on good practice in image processing and methods to extract quantitative data. This session will provide the participants with a basic knowledge allowing to implement image analysis through FIJI in their research.

Dates and Venue

  • Wednesday to Friday noon, 2-3-4th September 2020

Campus Heymans + Campus UZ

Program and Time schedule

  • Day 1: Theoretical session (September 2 2020, 9-12 a.m.) - Seminariezaal 4, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium

Lecture 1: Fundamentals of light and imaging – prof. Kevin Braeckmans

The main physical principles involved in image formation are explained. After reviewing concepts as light refraction, diffraction, resolution, etc., the basics of image formation are addressed. The differences between the types of objective lenses are discussed and attention is drawn to correct sample illumination.

Lecture 2: Transmitted light microscopy and digital imaging – Dr. Toon Brans

The visualization of cells often proves to be difficult. The use of dedicated illumination techniques can enhance the image quality significantly. This lecture furthermore focuses on contrast-enhancing techniques such as DIC and phase contrast microscopy that help to reveal the smallest details in a cell. Concepts as resolution and noise are explored further and  guidelines involving correct camera use and the impact of digital imaging are offered.

  • Day 1: Demonstration sessions (September 2  2020, 1 – 5 p.m.) - Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium

Transmitted light microscopy – Dr. Toon Brans, Dr. Herlinde De Keersmaecker, representatives from Industry

In the first demonstration session cell visualization with transmitted light microscopy is covered. The participants will set the correct sample illumination and explore different transmitted light microscopy techniques. The advantages of contrast-enhancing techniques will be demonstrated and the principles of digital imaging are put into practice.

  • Day 2: Theoretical session (September 3 2020, 9 – 12 a.m ) - Seminariezaal 1, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium

Lecture 1-2: Epi-fluorescence and confocal imaging – prof. Winnok De Vos

Fluorescence microscopy allows to image specific parts of a specimen with unrivalled contrast. In this session the basic concepts underlying fluorescence imaging are reviewed. It is explained how, with the use of various confocal techniques, optical slicing and three-dimensional imaging is achieved. Furthermore it is pointed out that the combination of confocal imaging and spectral detection is an excellent way to differentiate between different subunits in a sample. Special attention is drawn to practical considerations that are inherent to confocal microscopy, such as photobleaching and bleed-through.

Lecture 3: Cell labelling and considerations for live cell imaging – Dr. Herlinde De Keersmaecker

This lecture explores the different properties of fluorescent labels and discusses the practical considerations when used for life science research. Different techniques used to introduce fluorescent dyes into a specific structure of both fixed and living cells are discussed. Attention is given to creating optimal conditions for live cell imaging.

  • Day 2: Demonstration session (September 3 2020, 1 – 5 p.m.) - Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium
    Campus UZ Gent, 90.53 - Blok B

Fluorescence and confocal imaging – Dr. Toon Brans, Dr. Herlinde De Keersmaecker, Geert Meesen

The concepts of epi-fluorescence microscopy and confocal imaging will be shown on basis of several case studies. These case studies will demonstrate the capabilities and caveats of fluorescence imaging methods covered during the theoretical lectures with as goal to develop a correct scientific way of microscopic imaging. With each case study the participants will be guided through the design of a microscopy experiment and the best practices for obtaining high-quality microscopic images.

  • Day 3: Guided computer session (September 4 2020, 9 – 12 a.m.) - PC-lokaal, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium

Principles of image processing – Dr. Toon Brans, Dr. Herlinde De Keersmaecker

Using the images from the previous demonstration sessions, the fundamentals of image processing and quantitative image analysis are explained through a guided computer session. The session also provides the basic understanding of FIJI, an open source image processing platform widely used in biomedical research.


Please follow this link: https://eventmanager.ugent.be/SpecialistCourseLFM

If the course is fully booked, you can ask to be added to the waiting list by sending an e-mail to . In case of cancellations, you can take the open place.

Registration fee

Free of charge for Doctoral School members of Life Sciences and Medicine, (Bioscience) Engineering and Natural Sciences of Ghent University

Teaching material

Print outs of all theoretical lectures and a sharepoint platform for all digital documents (data set for pc session, handouts of theoretical lectures, additional documentation) will be provided. Instrumentation of the Centre for Advanced Light Microscopy and microscopy demonstration samples will be available during demonstration sessions.

Number of participants




Evaluation methods and criteria (doctoral training programme)

100 % participation during all sessions