Specialist Course on Light and Fluorescence Microscopy edition 2021

Target Group

PhD students with limited experience in light microscopy who (will) make extensive use of microscopic visualization techniques for biomedical research applications (in the near future). No prior experience or training is required.


All PhD students

Organizing & Scientific Committee

    Prof. Dr. Kevin Braeckmans
    Faculty: Pharmaceutical Sciences - Department: Pharmaceutics
    E-mail: Kevin.Braeckmans@UGent.be

    Other members of the organising & scientific committee

    Prof. Dr. Luc Leybaert (Ghent University - Faculty of Medicine and Health Sciences)
    Prof. Dr. Winnok De Vos (University of Antwerp - Faculty of Veterinary Sciences)
    Prof. Dr. Andre Skirtach (Ghent University - Faculty of Bioscience Engineering)
    Prof. Dr. Els Van Damme (Ghent University - Faculty of Bioscience Engineering)
    Prof. Dr. Stefaan De Smedt (Ghent University - Faculty of Pharmaceutical Sciences)
    Dr. Herlinde De Keersmaecker (Ghent University - Centre for Advanced Light Microscopy)
    Geert Meesen (Ghent University - Faculty of Bioscience Engineering)


    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 that is 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 and fluorescence microscopy will be given followed by an overview and explanation of the most frequently employed light and fluorescence microscopy techniques. These microscopy principles and techniques in life science research will be demonstrated during the afternoon 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 demonstrations. The course gives the participants an excellent basis for receiving more in-depth individual training afterwards as offered by the Centre for Advanced Light Microscopy on the use of its instruments. Note that these individual trainings are not included in the specialist course, but can be optionally selected on a fee-for-service basis afterwards depending on the participant’s needs and specific research questions.

    Theoretical lectures during the morning of day 1 and day 2 will offer the participants the background 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 are intended to provide insight in the theoretical principles. In small groups of 5-7 students the theoretical principles are demonstrated and different imaging techniques are shown. Using real-world examples, the participants are given practical guidelines on correct data acquisition and obtaining optimal data quality. These sessions form a solid basis for further individual hands-on training offered by the Centre for Advanced Light Microscopy. The last half day comprises a guided computer session that introduces 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

    • 1 - 3 September 2021 (Wed to Fri)

    Campus Heymans + Campus UZ

    Program and Time schedule

      • Day 1: Theoretical session (September 1, 2021 from 9-12 a.m.)

      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.Day 1: 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 – Geert Meesen
      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 1,  2021 from 1 – 5 p.m.)

      Transmitted light microscopy – Dr. Herlinde De Keersmaecker, Geert Meesen
      In the first demonstration session cell visualization with transmitted light microscopy is covered. The participants will learn in groups of 7 to 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 2, 2021 from – 12 a.m )

      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 2, 2021 from 1 – 5 p.m.)

      Fluorescence and confocal imaging – Dr. Herlinde De Keersmaecker, Geert Meesen, representative industry (Nikon)
      The concepts of epi-fluorescence microscopy and confocal imaging will be shown. Each session will demonstrate and focus on a specific capability and the related caveats of fluorescence imaging methods covered during the theoretical lectures with as goal to develop a correct scientific way of microscopic imaging.

      • Day 3: Guided computer session (September 3, 2021 from 9 – 12 a.m.)

      Basics of image processing – Geert Meesen, Dr. Herlinde De Keersmaecker
      Using a set of microscopy images, the fundamentals of image processing and quantitative image analysis are explained through a guided computer session. The session provides basic understanding and application of FIJI, an open source image processing platform widely used in biomedical research.


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

      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

      Access to a sharepoint platform for all digital documents (data sets 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

      Max 20 participants to guarantee sufficient availability of equipment for the demonstration sessions. A selection procedure will be used to select applicants which will apply light microscopy on a short time base to assure optimal use of time and resources. Therefore we will ask students a short motivation letter containing their expectations, experience level and a description of the (planned) application of light microscopy in their research.



      Evaluation methods and criteria (doctoral training programme)

      100 % participation during all sessions