Admission requirements
Not applicable.
Description
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 all kind of processes and phenomena. The principles of image formation, processing and analysis are however generic. For biomedical research 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 (python) "ands-on” experience with microscopes (i.e. image acquisition). Short written exams (4) are used to probe the knowledge from the lectures, the practical work is assessed with reports of the practical assignments (6).
Course objectives
At completion of the course, the student should be able to:
Explain the principles of image formation and its relation to signal processing.
Transfer the principles of image formation to microscopy, resolution and sampling.
Explain the principles of electronic sensors and imaging.
Process and analyze images originating from a microscope.
Apply the basic theory of Image Processing and Analysis.
Apply the basic algorithms for image processing
Apply the basic algorithms for measurement
Explain the conditions for reliable measurements from images, especially microscope images
Apply software systems for image processing and analysis.
Solve problems image analysis problema with a prorammable software environment.
Report results from experimental sets of images.
Timetable
The most recent timetable can be found at the Computer Science (MSc) student website.
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Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
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.
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Lecturer: Prof.dr.ir. Fons Verbeek
Website: Image Analysis with Applications in Microscopy
Remarks
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.