Course Personnel

Lecturer
 [071 - 527 5773]
Assistants
[071 - 527 2727]
[071 - 527 2727]
[071 - 527 2727]
Microscopy
[071 - 527 4986]

Latest News

(25-01-2020) Content upgraded, tentative schedule can be seen in Lecture notes section.

(26-01-2020) First lecture Image Analysis 2020, February 3rd 2020, Room 312 Snellius. Course structure will be explained in this lecture.

(01-02-2020) BlackBoard Subscription will be available as of 03-02-2020, as will be announced in the first lecture.

(04-02-2020) Lecture slides Lecture 01, available, see Lecture Notes section.
(06-02-2020) Lecture slides Lecture 02, available, see Lecture Notes section.
(10-02-2020) Lecture slides Lecture 03 (partially), available, see Lecture Notes section.
(13-02-2020) Lecture slides Lecture 03 available.
(13-02-2020) Lecture slides Lecture 04 available.
(22-02-2020) Lecture slides Lecture 05 available.
(24-02-2020) Lecture slides Lecture 06 available.
(27-02-2020) Lecture slides Lecture 07 available.
(02-03-2020) Lecture slides Lecture 08 available.
(05-03-2020) Lecture slides Lecture 09 available.
(12-03-2020) Lecture slides Lecture 10 available.

(21-03-2020) Video Lecture 11 available.
(21-03-2020) Lecture slides Lecture 11 available.

(25-03-2020) Video Lecture 12 available.
(25-03-2020) Lecture slides Lecture 12 available.

(02-04-2020) Video Lecture 13 available.
(02-04-2020) Lecture slides Lecture 13 available.

(15-04-2020) Video Lecture 14 available.
(15-04-2020) Lecture slides Lecture 14 available.

(08-05-2020) Video Lecture 15 available.
(08-05-2020) Lecture slides Lecture 15 available.

(08-06-2020) Assignment 2 - 5 available.
See Course Documents Section of this URL for links ...

(08-06-2020) Data Assignment 5, about 500 Mb!.

(17-06-2020) Assignment 6 available.
(19-06-2020) Assignment 6 (updata) & Assignment 6 data (update).

(24-06-2020) Please check you mailbox (BB-address) to read instructions on the written exam 25-06-2020, 15.00 hrs.

(24-06-2020) List of topics for test 1 -4 can be found in the lecture schedule, link in last item on retakes.

Course Information

Code: 4343MMAV6
ECTS: 6.0
Level: 500
Language: English
Schedule: cf. section Lectures Content
Prerequisite:
BSc in Computer Science, Biology, Chemistry, LST, BPS or ...
Target audience:
Master BioInformatics, CS, MT, Biology, Chemistry, Math, LST, BPS and ...

Course Description

This course is on image analysis and how to extract useful information from images. The perspective taken is that of the use of image analysis in scientific research. In his 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 microscope 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 and pattern recognition. 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 the switch to multidimensional 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). The theoretical part is concluded with two written exams. The course is concluded with a report on the practical work.

This course is formally known as Microscopy, Modelling and Visualization. The course is targeted for master students as well as for those PhD students for whom knowledge of imaging and image processing is beneficial to their research projects.

This course will be lectured by Prof. Dr. Ir. F.J. Verbeek
Assistance in the practical part will be given by Xiaoqin Tang and Mehrdad Jahanbanifard, Shima Javanmardi & Laduona Dai
The microscopy will be assisted by G. Lamers (head microscopy unit, IBL).