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SGN-3606 LIGHT MICROSCOPY IN FOUR DIMENSIONS, 3 cr
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Person responsible
Professor Ulla Ruotsalainen
Lecturers
Jussi Tohka, Senior Researcher, jussi.tohka@tut.fi
Implementation rounds
Implementation 1
| Period 1 | Period 2 | Period 3 | Period 4 | Period 5 | Summer | Language of instruction | |
| Lecture | - | - | - | - | - | 16 h/week | In English only |
| Exam | In English only | ||||||
Objectives
The aim of the course is to introduce the basic properties of light microscopy with 3D and dynamic options together with the most relevant 3D image processing techniques. This course in intended for students and researchers with some basic knowledge of microscopy and image processing.
Contents
| Content | Core content | Complementary knowledge | Specialist knowledge |
| 1. | Physics of light microscopes
concept of resolution and contrast different imaging modes limits of operation |
Application areas
fixed sample imaging live sample imaging video-microscopy |
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| 2. | Confocal microscopy from principles to practice:
Principles of confocal optics theoretical and practical considerations Practical confocal microscopy |
Techniques behind the curtain - preparing the biological samples for imaging.
Specific labelling of biological targets Fluorescence resonance energy transfer Application examples |
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| 3. | Special techniques utilising confocal optics
Fluorescence correlation spectroscopy Single molecule detection Two-photon excitation of fluorescence Resolution enhancement 4Pi confocal microscopy STED-microscopy |
On fluorescent labeling. | |
| 4. | Automatic analysis of 3-D images
filtering in 3 dimensions (gaussian, anisotropic diffusion) image segmentation by thresholding imaging artefacts motivation for spatial information modeling |
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| 5. | Spatial prior information in 3-D image segmentation
Markov random fields deformable models level sets and gradient flows |
Requirements for completing the course
Exam and written review of one of the topics of the course.
Assessment criteria
To pass the course the student has to pass the exam based on the lectures and make a short written review of the given literature material related to the topics of the course.
Prerequisites
| Number | Name | Credits | M/R |
| SGN-1106 | Introductory Signal Processing | 3 | Recommendable |
| SGN-1200 | Signal Processing Methods | 4 | Recommendable |
| SGN-1250 | Signal Processing Applications | 4 | Recommendable |
| SGN-3010 | Digital Image Processing I | 5 | Recommendable |
| SGN-3016 | Digital Image Processing I | 5 | Recommendable |
Other comments
Additional lectures are given by Prof. Pekka Hänninen, Laboratory of Biophysics, University of Turku and Juhani Soini, Ph. D., ArcDia Ltd.
| Last modified | 06.02.2006 |
| Modified by | Antti Niemistö |