Specialist Course on Light and Fluorescence Microscopy

Target Group

This course is primarily intended for 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 Committee

The partners of the UGent Centre for Advanced Light Microscopy are the main organizer of this course. The Centre is a recognized university-wide Centre of Expertise that acts as a microscopy core directed to researchers from the Life Sciences. Offering expert training in microscopic imaging is a core duty of the Centre and fits directly in its overall aim to promote high-quality scientific research in the life sciences in which advanced light microscopy plays a pivotal role.


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. The course will be taught by several experts in the field and offers both theoretical lectures and practical courses. The most frequently employed light microscopy techniques will be discussed, complemented by an introduction to image processing. The instrumentation of the UGent Centre for Advanced Light Microscopy will be available for the practical sessions, allowing the participants to become acquainted with the instrumentation that is available at UGent and which may be of use in their research projects.


The course will run over two and a half days. Theoretical lectures are offered in the morning of day 1 and 2. They introduce the core principles of microscopic imaging, tailored to the needs of a researcher in life sciences. These theoretical sessions offer the participants the essential knowledge 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 practical session in the afternoon of day 1 and 2. The practical sessions naturally complement the theoretical lectures and allow the participants to become familiar with the different imaging techniques. The demonstrations and hands-on training sessions take place on the instrumentation of the UGent Centre for Advanced Light Microscopy.

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 course is organized in series with the workshop “Imaging interactions with fluorescence: from the nano-to-macro scale” in which more in-depth topics such as fluctuation spectroscopy, super-resolution and light sheet microscopy are covered. The workshop is organized by Hasselt University from September 5 to 7, 2018 (immediately following this specialist course). More information can be found on https://www.uhasselt.be/NanoMacroImaging-2018

Dates and Venue

Monday to Wednesday noon, 3 + 4 + 5th September 2018

Campus Heymans + Campus UZ:

September 3 2018, 9-12 a.m: Leslokaal 0.23 (0 BlokB), Campus UZ Gent, 90.53 - Blok B
September 3 2018, 1 – 4 p.m: Room 009, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium
September 4 2018, 9 – 12 a.m: Seminariezaal 1, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium
September 4 2018, 1 – 4 p.m: Room 009, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium & Campus UZ Gent, 90.53 - Blok B
September 5 2018, 9 – 12 a.m: PC-lokaal, Campus Heymans, 91.03 - Farmacie Practica/Hoogbouw/Auditorium


  • September 3 2018, 9-12 a.m: Theoretical session

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 reveal the smallest details in a cell. Concepts as resolution and noise are explored further and  guidelines involving correct camera use are offered.

  • September 3 2018, 1 – 4 p.m: Practical session

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

In the first hands-on microscopy 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.


  • September 4 2018, 9 – 12 a.m: Theoretical session

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 techniques used to introduce fluorescent dyes into a specific structure inside a cell. Specific staining protocols and practical guidelines are presented for both fixed and living cells. Attention is given to creating the optimal conditions for live cell imaging.

  • September 4 2018, 13 – 17 p.m: Practical session

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

The concepts of epi-fluorescence microscopy and confocal imaging will be shown. After a demonstration of the capabilities and caveats of both imaging methods, participants start a hands-on part in which a correct scientific way of microscopic imaging will be developed.

  • September 5 2018, 9 – 12 a.m

Principles of image processing – TBA

Using the images from the previous practical 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 ImageJ, an open source image processing platform widely used in biomedical research.


Please follow this link: https://webappsx.ugent.be/eventManager/events/microscopy

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 of Ghent University.

Number of participants




Evaluation methods and criteria (doctoral training programme)

100 % participation during all sessions