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Image Analysis with Applications in Microscopy


Admission requirements

Not applicable.


Microscopy images are typically good material to learn about image processing and analysis. In this course the origin and analysis of images acquired through microscopy is the leading theme. Images play a major role in understanding of biological processes. Bio-molecular processes are visualized by a range of microscopical techniques and modalities. From images coherent visualizations and models are derived. The characteristic sequence of image analysis starts with the acquisition, proceeds to restoration and segmentation to conclude with analysis. This sequence will be the skeleton of this course. Image acquisition in microscopy will be dealt with on a theoretical as well as practical level. In a series of lectures all important aspects of imaging along the line of the characteristic sequence of image analysis are dealt with. Concepts of image processing will be introduced and it will be discussed how set of image features is compiled in measurements. Subjects will use the 2D imaging as a means of explaining the principles and switch to multi-dimensional imaging to illustrate the implications of imaging in research and connect to current topics in bio-medical research. Presenting results through visualization and modeling is an ingredient found in applications that are discussed. The course consists of a series of lectures, practical assignments using programmable image analysis software environments and “hands-on” experience with microscopes (i.e. image acquisition). Short written exams are used to probe the knowledge from the lectures, the practical work is assessed with report of the assignments.

Course objectives

At completion of the course, the student should be able to:

  • Understand the basic theory of Image Processing and Analysis.

  • Understand the principles of microscopy imaging and how to process and analyze images originating from a microscope.

  • Understand the basic algorithms for image processing and how to get to a measurement

  • Have gained insight in the conditions which should be fulfilled to obtain reliable measurements from images, especially microscope images

  • Have been exposed to software systems for image processing and analysis and understand the basic operational flow.

  • Solve problems within a programmable software environment.

  • Have gained understanding of the mode of operation of a (automated) microscope and the meaning of the images it produces.


The most recent timetable can be found at the students' website.

Mode of instruction

  • Lectures en online lectures

  • Practical Software

  • Practical Image Acquisition/Microscopy

  • Site Visits

  • Assignments

Course load

Total hours of study: 168 hrs. (= 6 EC)
Lectures: 30:00 hrs.
Practical work 100:00 hrs.
Tutoring: 18:00 hrs.
Examination: 4:00 hrs.
Exam preparation: 16:00 hrs.

Assessment method

  • Written exam (Divided over 4 (or more) tests)

  • Report on Assignments

  • Mark = 50% Written Exam + 50% Report


See Blackboard.

Reading list

  • Digital Image Processing, 3rd edition, Rafael C. Gonzalez & Richard E. Woods, Publisher Prentice Hall, ISBN 0201180758

  • Papers made available on the website

  • Handouts from the lectures made available on the website.


  • You have to sign up for classes and examinations (including resits) in uSis. Check this link for more information and activity codes.

  • Please also register for the course in Blackboard.

Contact information

Lecturer: Fons Verbeek
Website: Image Analysis with Applications in Microscopy