Syllabus database for doctoral courses

  • Syllabus database for doctoral courses


Swedish title Basal bildanalys: fokus på applikationer inom mikroskopi.
English title Basic image analysis: focused on microscopy applications.
Course number 2783
Credits 3.0
Responsible KI department Department for Clinical Science, Intervention and Technology
Specific entry requirements None.
Grading Passed /Not passed
Established by The Board of Doctoral Education
Established 2014-03-04
Purpose of the course
Intended learning outcomes After the completion of the course, the student will be able to:
- understand basic concepts and methods in computerized image analysis
- practically use image analysis software
- choose and apply suitable image analysis methods to extract quantitative information from images in real applications
Contents of the course The course covers key concepts in basic image analysis. This includes general overviews and fundamental techniques in image analysis, tutorials and practical computer exercises with focus on microscopy images from biomedical reseach. The free and open-source image analysis programs CellProfiler and ImageJ will be used. State-of-the art methods and current advances in the field will be discussed. The student will be required to take an active part and contribute to discussions and apply their knowledge in computer exercises as well as a project related to their own research.
Teaching and learning activities The pedagogic framing of this course is based on lectures with corresponding review papers and practical computer exercises. The course will run over 3 weeks with course days 2 days each week. The students will perform practical exercises in-between the course days.
Students have to bring a laptop (PC or Mac) with preinstalled softwares (free open source) to all course days and also have to have access to a computer for the practical exercises.
Compulsory elements The lectures and practical sessions are mandatory as well as the examination. Compensation according to the instructions of the course director.
Examination Short written and oral report with image analysis approach, implementation, and conclusion on own problem (using own material if possible).
Literature and other teaching material The course literature will consist of recent original and review papers on selected topics within the field. Handouts from the lecturers will also be included.

V. Ljosa and A.E. Carpenter. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening.
PLoS Comput Biol. 2009 Dec;5(12):e1000603. doi: 10.1371/journal.pcbi.1000603.

Optional textbook: R. C. Gonzalez and R. E. Woods, ""Digital Image Processing"", 3rd. ed.: Upper Saddle River, N.J. : Prentice Hall, cop. 2008, ISBN: 9780131687288.
Course responsible Cecilia Gotherstrom
Department for Clinical Science, Intervention and Technology

Klinisk Immunologi F79
Karolinska Universitetssjukhuset Huddinge
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