CLB-30306 Cell Biology and Advanced Imaging Technologies


Credits 6.00

Teaching methodContact hours
Individual Paper2
Course coordinator(s)dr. ir. MJ Ketelaar
Lecturer(s)dr. ing. JW Borst
dr. KJ van 't Klooster
dr. ir. MJ Ketelaar
Examiner(s)dr. ir. MJ Ketelaar
dr. ing. JW Borst

Language of instruction:


Assumed knowledge on:

CBI-10306 Cell Biology, MAT-15403 Statistics 2, PCC-12803 General Chemistry for the Life Sciences, MAT-14903 Mathematics 2 or equivalent courses. Basic knowledge of optics (lens equation) and electromagnetic waves (wavelength, phase, photons and absorption).

Continuation courses:

Thesis CLB, BIC, PPH or MIB; MOB-30806 Regulation of Plant Development.


Note: This course has a maximum number of participants. The deadline for registration is one week earlier than usual. See Academic Year ( -> Registration for Courses.
Advanced light microscopy and reporter gene techniques are indispensable for mechanistic studies on the functioning and organisation of cells. New microscopy technologies and digital imaging allow us to study dynamic processes at shorter time scales and with higher spatial resolution in living cells. In this practical course the principles and cell biological application of different microscopy techniques will be taught. Topics include (green) fluorescent proteins (GFP), luciferase reporter assays, widefield and confocal fluorescence microscopy, differential interference contrast microscopy (DIC), fluorescence lifetime imaging microscopy (FLIM), Förster resonance energy transfer (FRET), fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), digital image analysis, image noise, and microscope construction. These techniques and concepts will be applied to study promoter activity; dynamics of intracellular organisation; protein diffusion; and intermolecular interactions. An important aspect of the course is data acquisition, reduction and analysis. How can quantitative data be extracted from digital images for comparison with quantitative models of cellular mechanisms?
The course has a maximal capacity of 40 students. Students are accepted in the order of: 1) students for which this course is compulsory; 2) students for which this course is restricted optional in their programme; 3) students for which the course is part of their minor; 4) students for which this is a free choice course. The last open spots are given to students in order of their registration.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- explain principles of light microscopy techniques and reporter methods;
- identify the components of advanced light microscopes and know the basics of their operation;
- operate light microscopes based on a knowledge of their design and capabilities;
- extract quantitative data from digital images;
- process data and compare results with provided quantitative models on molecular and cell biological processes;
- adapt a critical attitude towards the presentation of microscopy data in literature papers;
- write a short research paper on a conducted cell biological experiment and present the work orally;
- explain the presented cell biological processes in a mechanistic manner;
- select appropriate microscopy techniques for cell biological work.


Lectures. Conduct experiments on cells and biochemical reconstitution assays using advanced light microscopes (experiments are compulsory since acquired skills are part of the learning outcome). Use a computer module to actively simulate the use of fluorescence microscopes. Use computer programs (Excel, imageJ/Fiji) for data handling and processing. Study cell biological research papers that apply light microscopy and participation in literature discussion groups. Write a report in the form of a research paper and present the work with an oral presentation.


- written exam with open questions assessing your understanding of the topics and concepts of the lectures, tutorials and practical experiments (70%). The written exam needs a minimal mark of 5.5 to pass this course;
- a report on one of the performed practical experiments, written in teams of 2 students, is assessed for clarity of writing, report structure / line of argumentation, critical reflection on research performed (discussion), and data handling and presentation in figures (20%);
- An oral presentation of the reported findings is judged for verbal presentation and use of appropriate terminology, structure of the presentation and layout of slides, and interaction with the public (5%);
- participation and achievements during the experiments and literature discussions are judged (5%).


A syllabus will be provided at the first day of the course. Blackboard pages contain lecture slides, test questions and student reports on the conducted experiments.

Compulsory for: BBIBiologyBScA: Cell and Molecular Biology2AF
Restricted Optional for: MBIBiologyMScA: Cell and Molecular Biology2AF
MBTBiotechnologyMScA: Cellular/Molecular Biotechnology2AF
MPBPlant BiotechnologyMScA: Functional Plant Genomics2AF
Restricted Optional for: WUBNTBSc Minor Bionanotechnology2AF