Introduction to Biological Imaging

The course gives the fundamental engineering background on methods of image formation with focus on image reconstruction approaches (tomography). It presents the hardware, physical principles and algorithmic implementations of mainstream imaging approaches such as microscopy and Magnetic Resonance Imaging and of emerging imaging methods such as optical and opto-acoustic imaging poised to shape the biological and medical paradigm. Examples from real life biological and medical applications are showcased. The course includes hands-on practical exercises using Matlab, reading of state-of-the-art research papers and a field trip to an imaging facility.

After successful completion of this course, students will be able to:
- name and understand physical and hardware components of all major imaging techniques,
- understand wave propagation in tissues for non-diffracted and diffracted sources,
- apply principles of forward modelling and inversion / image reconstruction,
- conduct own inversion programming in Matlab,
- understand application regimes of anatomical, functional and molecular imaging, and
- identify emerging, next generation imaging technologies.

knowledge in linear algebra, Fourier-transforms, computer-based numerical solutions, and electronics
(corresponding modules: Linear Algebra (EI) [MA9409], Analysis 3 [MA9413] , Signal Theory [EI00330]).
Knowledge in Matlab is also helpful but not required.

The course is a mixture of presentations of several scientific topics by the lecturer and staff members as well as practical exercises (especially programming with standard-software), where the learned theory is applied and further expanded. Another component is literature work, where the students make themselves familiar with current research topics through papers and are to practise their preparation / summary for a presentation. Also planned is the visit of a research institution for a further practical demonstration.

- EDV-based presentation of topics by lecturers and students
- "paper" publications
- the students solve exercises on mostly provided computers with suitable software (Matlab)

recommended:
- Ntziachristos, Vasilis, Anne Leroy-Willig, and Bertrand Tavitian, eds. Textbook of in vivo Imaging in Vertebrates. John Wiley & Sons, 2007.
- Kak, A. C., and M. Slaney. "Principles of computerized tomography (piscataway, nj: Ieee)." (1987).

The exam consists of a 90 minutes exam (to be taken without auxiliary tools).

Here, the competencies gained through this module will be tested. For example, it will be tested, if the physical components of all major imaging techniques can be named and are understood, if wave propagation in tissues for non-diffracted and diffracted sources is understood, if the principles of forward modelling and inversion / image reconstruction can be applied, if own inversion programming in Matlab can be conducted etc.
The answers need to be given in own words as well as by ticking given multiple choice questions.