M.Sc./M.Ed. Seminar: Systems Control in Biophysics

Dynamics of Biophysical Systems


Summer term 2016, Begin: Apr. 19.

Times: Tuesday 15:45-17:15,
Place: IMB Mainz, Ackermannweg 4, Meeting room 1.624 (1st floor)

Seminar available through video conferencing at KIP, Uni Heidelberg
Lecturers: Dr. Udo Birk, Prof. Dr. Christoph Cremer
The language used throughout the course will be English, unless otherwise specified.
This course will be taught at the post-baccalaureate level. A basic knowledge in electromagnetics/optics and in digital image processing could be very helpful. These are subject of our course on Basics of Biomedical Optics and on Modelling with Matlab in Optical Imaging.

In this seminar, some of the apparently obvious but on closer look not so trivial questions related to modelling and control of complex biophysical systems, i.e. dynamics of biomechanical and biochemistry in solid state biophysics will be discussed. Discussions will be stimulated and augmented by regular presentations of recent research papers.

Students actively participating will give a presentation focusing on one of the particular problems encountered in "real" optical imaging, i.e. in the presence of factors deteriorating the image quality from the ideal, mathematical point-image. For example, the interaction of light and tissue, and also influence of noise on quantitative imaging, of motion, of fluctuating light output etc. will be discussed. Since the aim of optical imaging is (at least in a physics environment) to obtain quantitative data, problems related to image quantization and image digitization (pixelated digital images), as well as to image processing are a further important focus of this seminar.

These general topics will be amended by more specialized presentations on problems related to fluorescence imaging such as e.g. photophysics of fluorophores, and to superresolution microscopy.

Aim of this seminar is to provide the students with the opportunity to prepare for oral examinations by providing a discussion forum for state-of-the art optical imaging methods. At the same time, topics of the seminar presentations will illustrate the enormous potential that photonics and in particular optical imaging has for your future career.

M.Sc. Physics course

Please register at Jogustine

Course material

Will be handed out during the lectures/course

Preliminary program

Date 1. Technical Presentation by 2. Journal Article by
19.04. General outline of the course
Registration for seminar talks
UB --- ---
27.04. Discussion NN NN
04.05. Polymer models UB NN
11.05. How to efficiently make molecules blink AS NN
18.05. Effects of Illumination in Fluorescence Microscopy: Forces, Damage, and Polarization NN NN
25.05. Out-of-focus suppression in SMLM NN NN
01.06. Structured Illumination Microscopy FS NN
08.06. Photoswitching AS NN
15.06. Multiblinking in Localization Microscopy AG NN
22.06. Winter break

29.06. Winter break

06.07. Discussion

13.07. Focus field distribution JvH NN
20.07. Multi-photon absorption and fluorescence JvH NN
27.07. Motion artefacts in biomedical imaging FS NN
03.08. Discussion

Additional topics for the talks could be:
- Spatially Modulated Illumination
- Optical Tomography
- Superresolution in biology
- Sampling and digitization
- How to construct a microscope objective lens
- Interaction of light and biological tissue
- Effects of Illumination in Fluorescence Microscopy: Forces, Damage, and Polarization
- Stimulated Emission in real experiments
- Numerical Aperture: How it defines image quality