Search result: Catalogue data in Autumn Semester 2016
MAS in Medical Physics  | ||||||
 Specialization: General Medical Physics and Biomedical Engineering | ||||||
| Major in Bioimaging | ||||||
| Core Courses | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 227-0386-00L | Biomedical Engineering | W | 4 credits | 3G | J. Vörös, S. J. Ferguson, S. Kozerke, U. Moser, M. Rudin, M. P. Wolf, M. Zenobi-Wong | |
| Abstract | Introduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The focus is on learning the concepts that govern common medical instruments and the most important organs from an engineering point of view. In addition, the most recent achievements and trends of the field of biomedical engineering are also outlined. | |||||
| Objective | Introduction into selected topics of biomedical engineering as well as their relationship with physics and physiology. The course provides an overview of the various topics of the different tracks of the biomedical engineering master course and helps orienting the students in selecting their specialized classes and project locations. | |||||
| Content | Introduction into neuro- and electrophysiology. Functional analysis of peripheral nerves, muscles, sensory organs and the central nervous system. Electrograms, evoked potentials. Audiometry, optometry. Functional electrostimulation: Cardiac pacemakers. Function of the heart and the circulatory system, transport and exchange of substances in the human body, pharmacokinetics. Endoscopy, medical television technology. Lithotripsy. Electrical Safety. Orthopaedic biomechanics. Lung function. Bioinformatics and Bioelectronics. Biomaterials. Biosensors. Microcirculation.Metabolism. Practical and theoretical exercises in small groups in the laboratory. | |||||
| Lecture notes | Introduction to Biomedical Engineering by Enderle, Banchard, and Bronzino AND https://www1.ethz.ch/lbb/Education/BME | |||||
| 227-0447-00L | Image Analysis and Computer Vision | W | 6 credits | 3V + 1U | L. Van Gool, O. Göksel, E. Konukoglu | |
| Abstract | Light and perception. Digital image formation. Image enhancement and feature extraction. Unitary transformations. Color and texture. Image segmentation and deformable shape matching. Motion extraction and tracking. 3D data extraction. Invariant features. Specific object recognition and object class recognition. | |||||
| Objective | Overview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises. | |||||
| Content | The first part of the course starts off from an overview of existing and emerging applications that need computer vision. It shows that the realm of image processing is no longer restricted to the factory floor, but is entering several fields of our daily life. First it is investigated how the parameters of the electromagnetic waves are related to our perception. Also the interaction of light with matter is considered. The most important hardware components of technical vision systems, such as cameras, optical devices and illumination sources are discussed. The course then turns to the steps that are necessary to arrive at the discrete images that serve as input to algorithms. The next part describes necessary preprocessing steps of image analysis, that enhance image quality and/or detect specific features. Linear and non-linear filters are introduced for that purpose. The course will continue by analyzing procedures allowing to extract additional types of basic information from multiple images, with motion and depth as two important examples. The estimation of image velocities (optical flow) will get due attention and methods for object tracking will be presented. Several techniques are discussed to extract three-dimensional information about objects and scenes. Finally, approaches for the recognition of specific objects as well as object classes will be discussed and analyzed. | |||||
| Lecture notes | Course material Script, computer demonstrations, exercises and problem solutions | |||||
| Prerequisites / Notice | Prerequisites: Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C. The course language is English. | |||||
| Practical Work | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 465-0800-00L | Practical Work  Only for MAS in Medical Physics | O | 4 credits | external organisers | ||
| Abstract | The practical work is designed to train the students in the solution of a specific problem and provides insights in the field of the selected MAS specialization. Tutors propose the subject of the project, the project plan, and the roadmap together with the student, as well as monitor the overall execution. | |||||
| Objective | The practical work is aimed at training the student’s capability to apply and connect specific skills acquired during the MAS specialization program towards the solution of a focused problem. | |||||
| Electives | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 151-0605-00L | Nanosystems | W | 4 credits | 4G | A. Stemmer, J.‑N. Tisserant | |
| Abstract | From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles. Intermolecular forces, their macroscopic manifestations, and ways to control such interactions. Self-assembly and directed assembly of 2D and 3D structures. Special emphasis on the emerging field of molecular electronic devices. | |||||
| Objective | Familiarize students with basic science and engineering principles governing the nano domain. | |||||
| Content | The course addresses basic science and engineering principles ruling the nano domain. We particularly work out the links between topics that are traditionally taught separately. Special emphasis is placed on the emerging field of molecular electronic devices, their working principles, applications, and how they may be assembled. Topics are treated in 2 blocks: (I) From Quantum to Continuum From atoms to molecules to condensed matter: characteristic properties of simple nanosystems and how they evolve when moving towards complex ensembles. (II) Interaction Forces on the Micro and Nano Scale Intermolecular forces, their macroscopic manifestations, and ways to control such interactions. Self-assembly and directed assembly of 2D and 3D structures. | |||||
| Literature | - Kuhn, Hans; Försterling, H.D.: Principles of Physical Chemistry. Understanding Molecules, Molecular Assemblies, Supramolecular Machines. 1999, Wiley, ISBN: 0-471-95902-2 - Chen, Gang: Nanoscale Energy Transport and Conversion. 2005, Oxford University Press, ISBN: 978-0-19-515942-4 - Ouisse, Thierry: Electron Transport in Nanostructures and Mesoscopic Devices. 2008, Wiley, ISBN: 978-1-84821-050-9 - Wolf, Edward L.: Nanophysics and Nanotechnology. 2004, Wiley-VCH, ISBN: 3-527-40407-4 - Israelachvili, Jacob N.: Intermolecular and Surface Forces. 2nd ed., 1992, Academic Press,ISBN: 0-12-375181-0 - Evans, D.F.; Wennerstrom, H.: The Colloidal Domain. Where Physics, Chemistry, Biology, and Technology Meet. Advances in Interfacial Engineering Series. 2nd ed., 1999, Wiley, ISBN: 0-471-24247-0 - Hunter, Robert J.: Foundations of Colloid Science. 2nd ed., 2001, Oxford, ISBN: 0-19-850502-7 | |||||
| Prerequisites / Notice | Course format: Lectures and Mini-Review presentations: Thursday 10-13, ML F 36 Homework: Mini-Reviews Students select a paper (list distributed in class) and expand the topic into a Mini-Review that illuminates the particular field beyond the immediate results reported in the paper. | |||||
| 227-0391-00L | Medical Image Analysis | W | 3 credits | 2G | P. C. Cattin, M. A. Reyes Aguirre | |
| Abstract | It is the objective of this lecture to introduce the basic concepts used in Medical Image Analysis. In particular the lecture focuses on shape representation schemes, segmentation techniques, and the various image registration methods commonly used in Medical Image Analysis applications. | |||||
| Objective | This lecture aims to give an overview of the basic concepts of Medical Image Analysis and its application areas. | |||||
| Prerequisites / Notice | Basic knowledge of computer vision would be helpful. | |||||
| 227-0965-00L | Micro and Nano-Tomography of Biological Tissues | W | 4 credits | 3G | M. Stampanoni, P. A. Kaestner | |
| Abstract | The lecture introduces the physical and technical know-how of X-ray tomographic microscopy. Several X-ray imaging techniques (absorption-, phase- and darkfield contrast) will be discussed and their use in daily research, in particular biology, is presented. The course discusses the aspects of quantitative evaluation of tomographic data sets like segmentation, morphometry and statistics. | |||||
| Objective | Introduction to the basic concepts of X-ray tomographic imaging, image analysis and data quantification at the micro and nano scale with particular emphasis on biological applications | |||||
| Content | Synchrotron-based X-ray micro- and nano-tomography is today a powerful technique for non-destructive, high-resolution investigations of a broad range of materials. The high-brilliance and high-coherence of third generation synchrotron radiation facilities allow quantitative, three-dimensional imaging at the micro and nanometer scale and extend the traditional absorption imaging technique to edge-enhanced and phase-sensitive measurements, which are particularly suited for investigating biological samples. The lecture includes a general introduction to the principles of tomographic imaging from image formation to image reconstruction. It provides the physical and engineering basics to understand how imaging beamlines at synchrotron facilities work, looks into the recently developed phase contrast methods, and explores the first applications of X-ray nano-tomographic experiments. The course finally provides the necessary background to understand the quantitative evaluation of tomographic data, from basic image analysis to complex morphometrical computations and 3D visualization, keeping the focus on biomedical applications. | |||||
| Lecture notes | Available online | |||||
| Literature | Will be indicated during the lecture. | |||||
| 227-0967-00L | Computational Neuroimaging Clinic Prerequisite: Successful completion of course "Methods & Models for fMRI Data Analysis" (227-0969-00L). | W | 3 credits | 2V | K. Stephan | |
| Abstract | This seminar teaches problem solving skills for computational neuroimaging, based on joint analyses of neuroimaging and behavioural data. It deals with a wide variety of real-life problems that are brought to this meeting from the neuroimaging community at Zurich, e.g. mass-univariate and multivariate analyses of fMRI/EEG data, or generative models of fMRI, EEG, or behavioural data. | |||||
| Objective | 1. Consolidation of theoretical knowledge (obtained in the following courses: 'Methods & models for fMRI data analysis', 'Translational Neuromodeling', 'Computational Psychiatry') in a practical setting. 2. Acquisition of practical problem solving strategies for computational modeling of neuroimaging data. | |||||
| Content | This seminar teaches problem solving skills for computational neuroimaging, based on joint analyses of neuroimaging and behavioural data. It deals with a wide variety of real-life problems that are brought to this meeting from the neuroimaging community at Zurich, e.g. mass-univariate and multivariate analyses of fMRI/EEG data, or generative models of fMRI, EEG, or behavioural data. | |||||
| Prerequisites / Notice | The participants are expected to have successfully completed at least one of the following courses: 'Methods & models for fMRI data analysis', 'Translational Neuromodeling', 'Computational Psychiatry' | |||||
| 227-0969-00L | Methods & Models for fMRI Data Analysis | W | 6 credits | 4V | K. Stephan | |
| Abstract | This course teaches methods and models for fMRI data analysis, covering all aspects of statistical parametric mapping (SPM), incl. preprocessing, the general linear model, statistical inference, multiple comparison corrections, event-related designs, and Dynamic Causal Modelling (DCM), a Bayesian framework for identification of nonlinear neuronal systems from neurophysiological data. | |||||
| Objective | To obtain in-depth knowledge of the theoretical foundations of SPM and DCM and of their application to empirical fMRI data. | |||||
| Content | This course teaches state-of-the-art methods and models for fMRI data analysis. It covers all aspects of statistical parametric mapping (SPM), incl. preprocessing, the general linear model, frequentist and Bayesian inference, multiple comparison corrections, and event-related designs, and Dynamic Causal Modelling (DCM), a Bayesian framework for identification of nonlinear neuronal systems from neurophysiological data. A particular emphasis of the course will be on methodological questions arising in the context of studies in psychiatry, neurology and neuroeconomics. | |||||
| 376-1279-00L | Virtual Reality in Medicine Does not take place this semester. | W | 3 credits | 2V | R. Riener | |
| Abstract | Virtual Reality has the potential to support medical training and therapy. This lecture will derive the technical principles of multi-modal (audiovisual, haptic, tactile etc.) input devices, displays and rendering techniques. Examples are presented in the fields of surgical training, intra-operative augmentation, and rehabilitation. The lecture is accompanied by practical courses and excursions. | |||||
| Objective | Provide theoretical and practical knowledge of new principles and applications of multi-modal simulation and interface technologies in medical education, therapy, and rehabilitation. | |||||
| Content | Virtual Reality has the potential to provide descriptive and practical information for medical training and therapy while relieving the patient and/or the physician. Multi-modal interactions between the user and the virtual environment facilitate the generation of high-fidelity sensory impressions, by using not only visual and auditory modalities, but also kinesthetic, tactile, and even olfactory feedback. On the basis of the existing physiological constraints, this lecture will derive the technical requirements and principles of multi-modal input devices, displays, and rendering techniques. Several examples are presented that are currently being developed or already applied for surgical training, intra-operative augmentation, and rehabilitation. The lecture will be accompanied by several practical courses on graphical and haptic display devices as well as excursions to facilities equipped with large-scale VR equipment. Target Group: Students of higher semesters and PhD students of - D-HEST, D-MAVT, D-ITET, D-INFK, D-PHYS - Robotics, Systems and Control Master - Biomedical Engineering/Movement Science and Sport - Medical Faculty, University of Zurich Students of other departments, faculties, courses are also welcome! | |||||
| Literature | Book: Virtual Reality in Medicine. Riener, Robert; Harders, Matthias; 2012 Springer. | |||||
| Prerequisites / Notice | The course language is English. Basic experience in Information Technology and Computer Science will be of advantage More details will be announced in the lecture. | |||||
| 402-0674-00L | Physics in Medical Research: From Atoms to Cells | W | 6 credits | 2V + 1U | B. K. R. Müller | |
| Abstract | Scanning probe and diffraction techniques allow studying activated atomic processes during early stages of epitaxial growth. For quantitative description, rate equation analysis, mean-field nucleation and scaling theories are applied on systems ranging from simple metallic to complex organic materials. The knowledge is expanded to optical and electronic properties as well as to proteins and cells. | |||||
| Objective | The lecture series is motivated by an overview covering the skin of the crystals, roughness analysis, contact angle measurements, protein absorption/activity and monocyte behaviour. As the first step, real structures on clean surfaces including surface reconstructions and surface relaxations, defects in crystals are presented, before the preparation of clean metallic, semiconducting, oxidic and organic surfaces are introduced. The atomic processes on surfaces are activated by the increase of the substrate temperature. They can be studied using scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The combination with molecular beam epitaxy (MBE) allows determining the sizes of the critical nuclei and the other activated processes in a hierarchical fashion. The evolution of the surface morphology is characterized by the density and size distribution of the nanostructures that could be quantified by means of the rate equation analysis, the mean-field nucleation theory, as well as the scaling theory. The surface morphology is further characterized by defects and nanostructure's shapes, which are based on the strain relieving mechanisms and kinetic growth processes. High-resolution electron diffraction is complementary to scanning probe techniques and provides exact mean values. Some phenomena are quantitatively described by the kinematic theory and perfectly understood by means of the Ewald construction. Other phenomena need to be described by the more complex dynamical theory. Electron diffraction is not only associated with elastic scattering but also inelastic excitation mechanisms that reflect the electronic structure of the surfaces studied. Low-energy electrons lead to phonon and high-energy electrons to plasmon excitations. Both effects are perfectly described by dipole and impact scattering. Thin-films of rather complex organic materials are often quantitatively characterized by photons with a broad range of wavelengths from ultra-violet to infra-red light. Asymmetries and preferential orientations of the (anisotropic) molecules are verified using the optical dichroism and second harmonic generation measurements. These characterization techniques are vital for optimizing the preparation of medical implants and the determination of tissue's anisotropies within the human body. Cell-surface interactions are related to the cell adhesion and the contractile cellular forces. Physical means have been developed to quantify these interactions. Other physical techniques are introduced in cell biology, namely to count and sort cells, to study cell proliferation and metabolism and to determine the relation between cell morphology and function. 3D scaffolds are important for tissue augmentation and engineering. Design, preparation methods, and characterization of these highly porous 3D microstructures are also presented. Visiting clinical research in a leading university hospital will show the usefulness of the lecture series. | |||||
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