Kies de Nederlandse taal
Course module: B-MLMIC
Light Microscopy
Course info
Course codeB-MLMIC
ECTS Credits1.5
Category / LevelM (Master)
Course typeCourse
Language of instructionEnglish
Offered byFaculty of Science; Graduate School of Life Sciences; Graduate School of Life Sciences;
Contact persondr. L.C. Kapitein
dr. L.C. Kapitein
Feedback and availability
Other courses by this lecturer
Contactperson for the course
dr. L.C. Kapitein
Other courses by this lecturer
Teaching period
W16A  (08/04/2019 to 03/05/2019)
Teaching period in which the course begins
Time slot-: Not in use
Study mode
RemarkDate course: 8 - 12 April 2019. Send an e-mail to for enrollment.
Course application processadministratie onderwijsinstituut
Enrolling through OSIRISNo
Enrolment open to students taking subsidiary coursesNo
Waiting listNo
Course placement processdocent
After completion the course, the student:
  1. knows the fundamentals of light microscopy, and fluorescence microscopy in particular
  2. knows the basics of advanced, current techniques in fluorescence microscopy as well as their applications
  3. is be able to understand and evaluate current cell biological literature employing these techniques
  4. is able to perform live-cell imaging on advanced microscope setups
  5. is able to perform basic image analysis
  6. is able to design experimental approaches to biological questions using these techniques
About 25 students will acquire basic and advanced knowledge on optical microscopy, with an emphasis on fluorescence microscopy. Four two-hour technology lectures will guide the students through the field of optical microscopy, covering a large array of topics ranging from fundamental principles of image formation and fluorescence to modern techniques such as superresolution microscopy (see detailed program). Three one-hour applications lectures from different cell biologists/neuroscientists will demonstrate how these techniques can be employed to solve important biological problems. In addition, four afternoons will be devoted to hands-on practical work, during which students can directly see modern microscopy at work at state-of-the-art facilities (featuring spinning-disk confocal microscopy, TIRFM, single-molecule fluorescence, photo-ablation, superresolution microscopy, STED) and will be trained in quantitative image analysis.

This part will be complemented by training in reading and interpretation of scientific literature, illustrating employment of microscopic imaging techniques. The precise organization of the practical part will strongly depend on the number of participating students.
This one week is meant to be dedicated to this course and students are encouraged to work together as a group and support each other.

Send an e-mail to the course coordinator (Lukas Kapitein, The mail should contain 1) your name; 2) student number; 3) e-mail address; 4) telephone number; 5) current Master track. Please note: the number of participants is limited to 25. Only the first registrations can be accepted.

Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS: CSnD. Neuroscience and Cognition, especially the tracks Experimental and Clinical Neuroscience and any other master programme with relevant basal courses.

The exam (1 hour)
There will be an exam on the material covered in the lectures (50% of the final mark).
In addition, each technology lecture will be preceded by a short examination to test understanding of the basic concepts of the previous lecture. Questions and answers will be directly discussed after the test to support deeper understanding. The average score with contribute 30% of the final mark. The average score should be above a 5 to gain access to the final examination.

20% of the grade will be based on the short examinations, 50% on the final exam, and 30% on participation and presentations.
Topic covered in the technology lectures

Zooming in on microscopes - basics of light microscopy 
-  Light and matter
-  Geometrical optics
-  Image formation and contrast generation
-  Koehler illumination, outline of a microscope
-  Objectives, numerical aperture and resolution
-  Aberrations 
On windows and wine
-  Fluorescence microscopy
-  Basics of fluorescence
-  Outline of a fluorescence microscope
-  Special fluorescent probes
-  Confocal microscopy
-  TIRF microscopy 
-  Multiphoton microscopy
-  Light-sheet microscopy

Light at work
- Active-illumination techniques
- Live-cell microscopy
- Active illumination microscopy (FRAP, FLIP, Photoactivation/ablation)
- FRET microscopy (FLIM)
Breaking the barriers
-  Supersensitive and superresolved microscopy
-  Single-molecules fluorescence microscopy
-  Superresolution techniques (PALM, STORM, STED)
-  Basics of (EM)CCD and CMOS technology
-  Understanding photon counts, noise and grey values
-  Comparison of different cameras
-  Image processing

Entry requirements
You must have a valid study entrance permit
Prerequisite knowledge
Bachelor of science in the same field.
Prerequisite knowledge can be obtained through
Required Material:\par None, slide handouts will be available.
Useful link:\par.
Required materials
Additional materials will be sent by email before the course
Fiji (ImageJ variant)
Instructional formats
Computer practical

Guest lecture




Final result
Test weight100
Minimum grade-

Kies de Nederlandse taal