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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 Computer Science (MSc) student website.

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

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For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

Mode of instruction

  • Lectures and 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; as agreed with the students in class)

  • Report on Assignments

  • Mark = 50% Written Exam + 50% Report

The teacher will inform the students how the inspection of and follow-up discussion of the exams will take place.

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.


From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.

Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.

Extensive FAQ's on MyStudymap can be found here.


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