Basics of Biomedical Optics / Grundlagen der Biomedizinischen Optik

Lecture / Tutorial / Lab

Winter term 2013/2014, Begin: Oct. 22.

Lectures: Tuesday 14:15-15:45, IMB Mainz, Ackermannweg 4, Seminar room 2nd floor
Tutorial: Wednesday 14:15-15:00, Institut für Physik, Staudingerweg 7, CIP pool 03.423
Lab: Block course March 10-12, three full days.
Lecturers: Dr. Udo Birk, Prof. Dr. Christoph Cremer
Teaching language will be English, unless otherwise specified.

In the tutorials, a general introduction to the concept of image processing will be given, based on the programming environment MATLAB. Students will be given exercises to model the physical processes discussed during the lectures, and to evaluate the potential of the corresponding imaging / illumination / detection techniques.

In the lectures to Basics of Biomedical Optics 1 (winter term 2013/2014), i.e. in the first half of this two semester course, the main optical concepts of imaging and general technical aspects for realization of optical imaging devices are in focus. After an introduction to the electromagnetic concepts of light and its interaction with tissue, we will discuss recent development in technical optics (e.g. light sources, detectors) making possible the huge progress that biomedical imaging has recently seen. Several conceptual models representing (and simplifying) the optical image formation process will be discussed. Reasons for limitations in image resolution will be given, and means to overcome the technical problems will be presented. Contrasting mechanisms of optical imaging will be discussed and first approaches to enhance the 3D resolution in microscopy. The course will be complemented by a brief historical outline.

In the labcourse, several examples of high- and super-resolution microscopes will be worked with in hands-on experiments. These microscopes will be applied to image biological specimens from ongoing research collaborations. Students will perform image analysis to reconstruct represenations of the biological structures at hand.
The aim is to provide the students with access to state-of-the art far field optical microscopy setups, illustrating the enormous progress that far field optical microscopy has recently made.

M.Sc. Physics course

Jogustine entry for this course at the University of Mainz

Course lecture material and exercises

available here ...

Preliminary program

Date Content Lecturer
22.10. General outline of the course
A short history of optics (glass, lenses, microscopes, telescopes, ...)
29.10. What is color, what is scattering?
The electromagnetic spectrum and the statistical nature of light
05.11. Classical optics, from ray optics to wave optics to beam optics, some quantum optics
Gaussian beam propagation
12.11. Fourier Optics UB
19.11. EM Dipole: near field, far field
near field imaging
26.11. Lasers: Theory, conditions, and technical realization UB
03.12. History 1: The Advent of Microscopy CC
10.12. Detectors
Optical Design
17.12. Radiometry
Interaction of light and tissue: effects of laser power, pulse parameters
24.12. Winter break
31.12. Winter break
07.01. White light generation
Fluorescence and other contrasting mechanisms
14.01. Optical Imaging 1: Image formation and Point Spread Function UB
21.01. Optical Imaging 2: Limitations in imaging
Apodization, Vectorial Diffraction Theory
28.01. Confocal Laser Scanning Microscopy CC
04.02. Axial Imaging: Micro-Axial Tomography, Theta Microscopy UB