Optics in Medicine

Dr. Kleinsasser, 5 ECTS

• Biological Systems
• Trunk System
• Nervous System
• Respiration
• Circulation
• Heart
• Digestion
• Neuroscience
• Functional cardiology
• Advanced endoscopy
• Advanced neuroimaging

Students learn to

• describe relevant structures of the human anatomy and basic physiological processes
• understand features of biological systems when applying optical technologies to them
• describe exemplarily applications of optical technologies in medicine

Dr. Klämpfl, 5 ECTS

• Repetition of important topics of optics
• Scattering of light
• Basics of laser tissue interaction
• Diagnostics applications of Light and lasers
• Therapeutics applications of light and lasers
• Theoretical and practical exercises

Prof. Dr. Maier, 5 ECTS

(also offered in winter term)

• Medical imaging helps physicians to take a view inside the human body and therefore allows better treatment and earlier diagnosis of serious diseases. However, as straightforward as the idea itself is, so diversified are the technical difficulties to overcome when implementing a clinically useful imaging device. We begin this module by discussing all available modalities and the actual imaging goals which highly affect the imaging result.
• Some modalities produce very noisy results, but there are multiple other artifacts that show up in raw acquisition data and have to be dealt with. We address these issues in the chapter preprocessing and show how to compensate for image distortions, how to interpolate defect pixels, and finally correct bias fields in magnetic resonance images.
• The largest portion of this course covers the theory of medical image reconstruction. Here, from a set of projections from different viewing angles a 3-D image is merged that allows a definite localization of anatomical and pathological features. Following roughly the historical development of CT devices, we study the process from parallel beam to fan beam geometry and include a discussion of phantoms as a tool for calibration and image quality assessment. We then move forward and learn about reconstruction in 3-D. Since the system matrix often grows in dimensions such that many direct solvers become infeasible, we also discuss pros and cons of iterative methods.
• In the final chapter, image registration is introduced as the concept of computing the mapping that maps the content of one image to another. Two different acquisitions usually result in images that are at least rotated and translated against each other. Image registration forms the set of tools that we need to match certain image features in order to align both images for further processing, image improvement or image overlays.

Prof. Dr. Maier, 5 ECTS

(also offered in winter term)

This module focuses on recent developments in image processing driven by medical applications. All algorithms are motivated by practical problems. The mathematical tools required to solve the considered image processing tasks will be introduced. In addition to the lectures, we also offer exercise classes. The exercises consist of theoretical parts where you immerse in lecture topics. But we also set emphasis on the practical implementation of the methods.

Comment: The two courses about Magnetic Resonance Imaging are not offered in the order which would be ideal for MAOT students, but in opposite order. Students with some prior knowledge in the field might consider to join Magnetic Resonance Imaging 2 directly. Other options are: attending part one during the fundamental courses in the first semester; starting with the part one in the third semester (maybe only attending part one); working on part 1 based on recordings from previous semesters and only attend part 2 in the actual course.

Prof. Dr. Fredrik Laun, 5 ECTS

• Echo-planar imaging
• Functional magnetic resonance imaging
• Parallel imaging: SENSE
• Parallel imaging: GRAPPA
• Balanced steady state sequences
• UHF MRI and non-proton MRI
• Multiple RF-pulses – coherence pathways – time-of-flight MRI
• Flow-motion
• Perfusion – diffusion
• Diffusion: Susceptibility weighted imaging & Quantitative Susceptibility Mapping

Dr. Klämpfl, 5 ECTS

• Selected topics of optics
• Light sources for medical applications and medical engineering
• Optical components and systems for medical engineering
• Interaction mechanisms of laser and biological tissue
• Photonics in diagnostics
• Photonics in therapeutics

Prof. Dr. Friedrich, PD Dr. Schürmann, 5 ECTS

• Application of optical methods in the field of cell biology and medicine
• Microscopy: Basic concepts, methods to enhance contrast, optical resolution and limits, components and setup of light microscopes, fluorescence microscopy
• Applications of fluorescence microscopy in life sciences, methods for labeling of biological structures and cellular processes´
• Epi-fluorescence, confocal and multiphoton microscopy, concepts and application examples
• Optical endoscopy and endomicroscopy in research and clinics
• Super-resolution microscopy, concepts and applications for optical Imaging beyond the diffraction Limit of Resolution

Prof. Dr. Fredrik Laun, 5 ECTS

• The basics of image formation
• Some basic pulse sequences
• About contrast generation
• A bit about artefacts
• A bit about acceleration techniques

Prof. Sandoghdar, Dr. Möckl 5 ECTS

In winter term 2022/23 the course for this module is called „Microscopy approaches to study biological systems„

Microscopy has become an indispensable tool to investigate biological systems – from viruses to whole animals. In this seminar, we will explore this fascinating research area by studying and discussing key publications from the field. Each participant is assigned to a couple of important publications that employed a microscopy approach to study a biological question in a creative, impactful, and instructive way. Examples include optical microscopy methods such as light-sheet microscopy, super-resolution approaches, and scattering-based techniques; electron microscopy; or mass spectrometry imaging. Furthermore, important image analysis strategies will be considered. Each participant will discuss the publications with the seminar instructors and subsequently present the approach and the key findings to the whole seminar.

Dr. Singh, 5 ECTS

• Confocal microscopy: Confocal microscopy is an imaging technique which provides improved resolution and contrast compared to full field imaging by using a pin hole which helps reducing the out of focus light. Confocal microscopes are backbone for most of biological labs and are used frequently to study cellular mechanics.
• Optical coherence tomography imaging (OCT): OCT is an imaging technique which can provide axial resolution better than 1 micron using broadband low coherence light source. This has allowed to perform optical biopsies for several biological samples in vivo.
• Raman microscopy: Raman microscopy is a technique within vibrational spectroscopy, which is based on the inelastic scattering of light. It provides information on the chemical composition of the sample based on its vibrational spectra. Since the development of the first commercial Raman spectrometer in 1953, advances in lasers and detectors and the discovery of new phenomena have expanded the use of this technique in several research fields
• Stochastic optical reconstruction microscopy (STORM): STORM is one of the most ubiquitously employed super-resolution imaging techniques. It utilizes sequential activation and time-resolved localization of photoswitchable fluorophores to create high resolution images. During imaging, only an optically resolvable subset of fluorophores is activated to a fluorescent state at any given moment, such that the position of each individual fluorophore can be determined with high precision.
• Stimulated emission depletion (STED): STED creates super-resolution images by the selective deactivation of fluorophores, minimising the area of illumination at the focal point, and thus enhancing the achievable resolution for a given system.
• Multi-photon excitation (MPE): MPE microscopy is an imaging technique which operates in non linear regime that combines point scanning methods with multiphoton fluorescence to create high-resolution, three-dimensional images of biological samples. Several forms of MPE such as 2 photon, 3 photon microscopy etc, are available. MPE is particularly useful in biology because it can be used to probe delicate living cells and tissues without damaging the sample.
• Phase contrast microscopy (PCM): Several cells offer very low contrast when visualized with standard microscope. PCM provides improved contrast and is a label-free imaging technique allowing visualization of transparent cells. The quantitative phase contrast image provides information about the optical path length change introduced by the sample because of its refractive index and thickness.
• Polarization sensitive optical coherence tomography (ps-OCT): ps-OCT is gaining attention because of its ability to diagnose certain pathological conditions at an early stage. Several pathological conditions such as cancer can be detected at an early stage by measuring birefringent properties of the tissue. ps-OCT uses low coherence polarized light to probe the birerefregence of the tissue.
• Brillouin Microscopy: Brillouin microscopy is an emerging optical technique that enables non- contact measurement of viscoelastic properties of a material with diffraction-limited resolution in 3D.