Search result: Catalogue data in Autumn Semester 2014

Biomedical Engineering Master Information
Master Programme According to Programme Regulations 2013
Track Courses
Recommended Elective Courses
These courses are particularly recommended for the Bioelectronics track. Please consult your track advisor if you wish to select other subjects.
227-0166-00LAnalog Integrated Circuits Information W6 credits2V + 2UQ. Huang
AbstractThis course provides a foundation in analog integrated circuit design based on bipolar and CMOS technologies.
ObjectiveIntegrated circuits are responsible for much of the progress in electronics in the last 50 years, particularly the revolutions in the Information and Communications Technologies we witnessed in recent years. Analog integrated circuits play a crucial part in the highly integrated systems that power the popular electronic devices we use daily. Understanding their design is beneficial to both future designers and users of such systems.
The basic elements, design issues and techniques for analog integrated circuits will be taught in this course.
ContentReview of bipolar and MOS devices and their small-signal equivalent circuit models; Building blocks in analog circuits such as current sources, active load, current mirrors, supply independent biasing etc; Amplifiers: differential amplifiers, cascode amplifier, high gain structures, output stages, gain bandwidth product of op-amps; Stability; Comparators; Second-order effects in analog circuits such as mismatch, noise and offset; A/D and D/A converters; Introduction to switched capacitor circuits.
The exercise sessions aim to reinforce the lecture material by well guided step-by-step design tasks. The circuit simulator SPECTRE is used to facilitate the tasks. There is also an experimental session on op-amp measurments.
Lecture notesHandouts of presented slides. No script but an accompanying textbook is recommended.
LiteratureGray, Hurst, Lewis, Meyer, "Analysis and Design of Analog Integrated Circuits", 5th Ed. Wiley, 2010.
227-0447-00LImage Analysis and Computer Vision Information W6 credits3V + 1UG. Székely, O. Göksel, L. Van Gool
AbstractLight 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.
ObjectiveOverview of the most important concepts of image formation, perception and analysis, and Computer Vision. Gaining own experience through practical computer and programming exercises.
ContentThe 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 notesCourse material Script, computer demonstrations, exercises and problem solutions
Prerequisites / NoticePrerequisites:
Basic concepts of mathematical analysis and linear algebra. The computer exercises are based on Linux and C.
The course language is English.
227-0963-00LStatistical Parametric Mapping (SPM)W2 credits1VK. Stephan
AbstractThis course provides a comprehensive coverage of state-of-the-art statistical methods for fMRI data analysis, focusing on tools provided by the open source software package SPM
ObjectiveKnowledge of modern statistical methods for fMRI data analysis
ContentSpatial preprocessing & physiological noise correction
Voxel-based morphometry
Mass-univariate & multivariate analyses of fMRI
'Resting state' fMRI
Bayesian analysis methods
Effective connectivity analyses (Dynamic Causal Modeling)
227-0981-00LCross-Disciplinary Research and Development in Medicine and Engineering Restricted registration - show details
A maximum of 8 medical degree students and 8 (biomedical) engineering degree students can be admitted, their number should be equal.
W4 credits2V + 2AV. Kurtcuoglu, D. de Julien de Zelicourt, M. Meboldt, M. Schmid Daners, O. Ullrich
AbstractCross-disciplinary collaboration between engineers and medical doctors is indispensable for innovation in health care. This course will bring together engineering students from ETH Zurich and medical students from the University of Zurich to experience the rewards and challenges of such interdisciplinary work in a project based learning environment.
ObjectiveThe main goal of this course is to demonstrate the differences in communication between the fields of medicine and engineering. Since such differences become the most evident during actual collaborative work, the course is based on a current project in physiology research that combines medicine and engineering. For the engineering students, the specific aims of the course are to:

- Acquire a working understanding of the anatomy and physiology of the investigated system;
- Identify the engineering challenges in the project and communicate them to the medical students;
- Develop and implement, together with the medical students, solution strategies for the identified challenges;
- Present the found solutions to a cross-disciplinary audience.
ContentAfter a general introduction to interdisciplinary communication and detailed background on the collaborative project, the engineering students will receive tailored lectures on the anatomy and physiology of the relevant system. They will then team up with medical students who have received a basic introduction to engineering methodology to collaborate on said project. In the process, they will be coached both by lecturers from ETH Zurich and the University of Zurich, receiving lectures customized to the project. The course will end with each team presenting their solution to a cross-disciplinary audience.
Lecture notesHandouts and relevant literature will be provided.
227-1033-00LNeuromorphic Engineering I Information W6 credits2V + 3UT. Delbrück, G. Indiveri, S.‑C. Liu
AbstractThis course covers analog circuits with emphasis on neuromorphic engineering: MOS transistors in CMOS technology, static circuits, dynamic circuits, systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions.
ObjectiveUnderstanding of the characteristics of neuromorphic circuit elements and their interaction in parallel networks.
ContentNeuromorphic circuits are inspired by the structure, function and plasticity of biological neurons and neural networks. Their computational primitives are based on physics of semiconductor devices. Neuromorphic architectures often rely on collective computation in parallel networks. Adaptation, learning and memory are implemented locally within the individual computational elements. Transistors are often operated in weak inversion (below threshold), where they exhibit exponential I-V characteristics and low currents. These properties lead to the feasibility of high-density, low-power implementations of functions that are computationally intensive in other paradigms. The high parallelism and connectivity of neuromorphic circuits permit structures with massive feedback without iterative methods and convergence problems and real-time processing networks for high-dimensional signals (e.g. vision). Application domains of neuromorphic circuits include silcon retinas and cochleas, real-time emulations of networks of biological neurons, and the development of autonomous robotic systems. This course covers devices in CMOS technology (MOS transistor below and above threshold, floating-gate MOS transistor, phototransducers), static circuits (differential pair, current mirror, transconductance amplifiers, multipliers, power-law circuits, resistive networks, etc.), dynamic circuits (linear and nonlinear filters, adaptive circuits), systems (silicon neuron, silicon retina, motion circuits) and an introduction to multi-chip systems. The lectures are accompanied by weekly laboratory sessions on the characterization of neuromorphic circuits, from elementary devices to systems.
LiteratureS.-C. Liu et al.: Analog VLSI Circuits and Principles; various publications.
Prerequisites / NoticeParticular: The course is highly recommended for those who intend to take the spring semester course 'Neuromorphic Engineering II', that teaches the conception and layout of such circuits with a set of inexpensive software tools, ending with an optional submission of a mini-project for CMOS fabrication.

Prerequisites: Background in basics of semiconductor physics helpful, but not required.
227-2037-00LPhysical Modelling and Simulation Information W5 credits4GC. Hafner, J. Smajic
AbstractPhysical modelling plays an important role in the analysis and design of new structures, especially for micro and nano devices where fabrication and measurement are difficult. After the fundamentals of electromagnetics, mechanics, and thermodynamics, an introduction to the main concepts and most widely used codes for physical modelling is given and commercial codes are applied.
ObjectiveBasic knowledge of the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics. Knowledge of the main concepts of numerical methods for physical modelling and simulation. Ability 1) to select appropriate software, 2) to apply it for solving given problems, 3) to validate the results, 4) to interactively improve the models until sufficiently accurate results are obtained.
ContentSince the fabrication and characterization of micro- and nanostructures is difficult, expensive, and time-consuming, numerical modelling drastically reduced the design process. Although many commercial software packages are available, it is important to know the drawbacks and difficulties of the numerical methods behind them and to be able to validate the results obtained with such packages.
First, an introduction to the fundamental equations and effects of electromagnetics, mechanics, and thermodynamics is given. This is important for understanding the problems to be analyzed and for validating results obtained from software packages. After this, the main concepts of numerical methods and of the most widely used codes for physical modelling are outlined and compared, which is essential for the adequate selection of software for solving given problems. After this, prominent commercial software packages are applied to various types of problems, ranging from electrodynamics to multiphysics. For becoming able to select appropriate software and to validate the results obtained, different commercial software packages will be used and compared during the exercises in form of small projects.
151-0255-00LEnergy Conversion and Transport in Biosystems
Does not take place this semester.
W4 credits2V + 1UD. Poulikakos, A. Ferrari
AbstractTheory and application of thermodynamics, energy conversion and fluid dynamics in biological systems and biomedicine at the macro scale and the cellular level.
ObjectiveTheory and application of energy conversion at the macro scale and the cellular level. Understanding of the basic features governing fluid transport in the principal fluidic systems of the human body. Connection of characteristics and patterns from other fields of engineering to biofluidics. Heat and mass transport processes within the human body and relation to biomedical technologies.
ContentHeat and mass transfer models for the transport of thermal energy and chemical species in the human body. Physiology, pathology and biomedical intervention based on extreme temperatures (medical radio frequency therapy, tissue freezing and cryotherapy). Introduction to the main fluidic systems of the human body (cardiovascular, cerebrospinal etc.). Description of the functionality of these systems and of analytical experimental and computational techniques for understanding of their operation. Introduction to bioengineering approaches for the treatment of common pathogenic conditions of these systems. Introduction to cell metabolism, cellular energy transport and cellular thermodynamics.
Lecture notesScript as well as additional material in the form of hand-outs will be distributed.
LiteratureLecture notes and references therein.
252-0523-00LComputational Biology Information W6 credits3V + 2UG. H. Gonnet
AbstractStudy of computational techniques, algorithms and data structures used to solve problems in computational biology. Topics: basic biology, string alignment, phylogeny (distance, character, parsimony), molecular evolution, multiple sequence alignment, probabilistic and statistical models, Markov models, microarrays, dynamic programming, maximum likelihood and specialized DNA and protein analysis.
ObjectiveFamiliarize the students with the basic concepts of molecular biology and the models and algorithms used to understand, classify and predict behaviour of living organism. This course is at the most basic level, where the main issues, mostly of molecular sequences, are studied.
ContentThis course lies in the intersection between Computer Science and Molecular Biology. The main purpose is to study computational techniques, algorithms and data structures which are usually applied to solve problems in Molecular Biology and Biochemistry.
The following topics are likely to be covered: Introduction, mathematical models of evolution, protein and DNA sequence alignment and its meaning, phylogenetic tree construction, multiple sequence alignments, secondary structure prediction, molecular dynamics, threading, role of bioinformatics in drug design, etc. From the computer science point of view we concentrate our attention in practical solutions for the above problems. Biological knowledge is an asset but not a prerequisite.
376-1219-00LRehabilitation Engineering II: Rehabilitation of Sensory and Vegetative Functions Information W3 credits2VR. Riener, R. Gassert
AbstractRehab. Engineering is the application of science and technology to ameliorate the handicaps of individuals with disabilities to reintegrate them into society.The goal is to present classical and new rehabilitation engineering principles applied to compensate or enhance motor, sensory, and cognitive deficits. Focus is on the restoration and treatment of the human sensory and vegetative system.
ObjectiveProvide knowledge on the anatomy and physiology of the human sensory system, related dysfunctions and pathologies, and how rehabilitation engineering can provide sensory restoration and substitution.
ContentIntroduction, problem definition, overview
Rehabilitation of visual function
- Anatomy and physiology of the visual sense
- Technical aids (glasses, sensor substitution)
- Retina and cortex implants
Rehabilitation of hearing function
- Anatomy and physiology of the auditory sense
- Hearing aids
- Cochlea Implants
Rehabilitation and use of kinesthetic and tactile function
- Anatomy and physiology of the kinesthetic and tactile sense
- Tactile/haptic displays for motion therapy (incl. electrical stimulation)
- Role of displays in motor learning
Rehabilitation of vestibular function
- Anatomy and physiology of the vestibular sense
- Rehabilitation strategies and devices (e.g. BrainPort)
Rehabilitation of vegetative Functions
- Cardiac Pacemaker
- Phrenic stimulation, artificial breathing aids
- Bladder stimulation, artificial sphincter
Brain stimulation and recording
- Deep brain stimulation for patients with Parkinson, epilepsy, depression
- Brain-Computer Interfaces
LiteratureIntroductory Books:

An Introduction to Rehabilitation Engineering. R. A. Cooper, H. Ohnabe, D. A. Hobson (Eds.). Taylor & Francis, 2007.

Principles of Neural Science. E. R. Kandel, J. H. Schwartz, T. M Jessell (Eds.). Mc Graw Hill, New York, 2000.

Force and Touch Feedback for Virtual Reality. G. C. Burdea (Ed.). Wiley, New York, 1996 (available on NEBIS).

Human Haptic Perception, Basics and Applications. M. Grunwald (Ed.). Birkhäuser, Basel, 2008.

The Sense of Touch and Its Rendering, Springer Tracts in Advanced Robotics 45, A. Bicchi et al.(Eds). Springer-Verlag Berlin, 2008.

Interaktive und autonome Systeme der Medizintechnik - Funktionswiederherstellung und Organersatz. Herausgeber: J. Werner, Oldenbourg Wissenschaftsverlag 2005.

Neural prostheses - replacing motor function after desease or disability. Eds.: R. Stein, H. Peckham, D. Popovic. New York and Oxford: Oxford University Press.

Advances in Rehabilitation Robotics - Human-Friendly Technologies on Movement Assistance and Restoration for People with Disabilities. Eds: Z.Z. Bien, D. Stefanov (Lecture Notes in Control and Information Science, No. 306). Springer Verlag Berlin 2004.

Intelligent Systems and Technologies in Rehabilitation Engineering. Eds: H.N.L. Teodorescu, L.C. Jain (International Series on Computational Intelligence). CRC Press Boca Raton, 2001.

Selected Journal Articles and Web Links:

Abbas, J., Riener, R. (2001) Using mathematical models and advanced control systems techniques to enhance neuroprosthesis function. Neuromodulation 4, pp. 187-195.

Bach-y-Rita P., Tyler M., and Kaczmarek K (2003). Seeing with the brain. International journal of human-computer-interaction, 15(2):285-295.

Burdea, G., Popescu, V., Hentz, V., and Colbert, K. (2000): Virtual reality-based orthopedic telerehabilitation, IEEE Trans. Rehab. Eng., 8, pp. 430-432
Colombo, G., Jörg, M., Schreier, R., Dietz, V. (2000) Treadmill training of paraplegic patients using a robotic orthosis. Journal of Rehabilitation Research and Development, vol. 37, pp. 693-700.

Hayward, V. (2008): A Brief Taxonomy of Tactile Illusions and
Demonstrations That Can Be Done In a Hardware Store. Brain Research Bulletin, Vol 75, No 6, pp 742-752

Krebs, H.I., Hogan, N., Aisen, M.L., Volpe, B.T. (1998): Robot-aided neurorehabilitation, IEEE Trans. Rehab. Eng., 6, pp. 75-87

Levesque. V. (2005). Blindness, technology and haptics. Technical report, McGill University. Available at:

Quintern, J. (1998) Application of functional electrical stimulation in paraplegic patients. NeuroRehabilitation 10, pp. 205-250.

Riener, R., Nef, T., Colombo, G. (2005) Robot-aided neurorehabilitation for the upper extremities. Medical & Biological Engineering & Computing 43(1), pp. 2-10.

Riener, R. (1999) Model-based development of neuroprostheses for paraplegic patients. Royal Philosophical Transactions: Biological Sciences 354, pp. 877-894.

The vOICe.

VideoTact, ForeThought Development, LLC.
Prerequisites / NoticeTarget Group:
Students of higher semesters and PhD students of
- Biomedical Engineering, Robotics, Systems and Control
- Medical Faculty, University of Zurich
Students of other departments, faculties, courses are also welcome
376-1351-00LMicro/Nanotechnology and Microfluidics for Biomedical ApplicationsW2 credits2VE. Delamarche
AbstractThis course is an introduction to techniques in micro/nanotechnology and to microfluidics. It reviews how many familiar devices are built and can be used for research and biomedical applications. Transistors for DNA sequencing, beamers for patterning proteins, hard-disk technology for biosensing and scanning microfluidics for analyzing tissue sections are just a few examples of the covered topics.
ObjectiveThe main objective of the course is to introduce micro/nanotechnology and microfluidics to students having a background in the life sciences. The course should familiarize the students with the techniques used in micro/nanotechnology and show them how micro/nanotechnology pervades throughout life sciences. Microfluidics will be emphasized due to their increasing importance in research and medical applications. The second objective is to have life students less intimidated by micro/nanotechnology and make them able to link instruments and techniques to specific problems that they might have in their projects/studies. This will also help students getting access to the ETHZ/IBM Nanotech Center infrastructure if needed.
ContentMostly formal lectures (2 × 45 min), with a 2 hour visit and introduction to cleanroom and micro/nanotechnology instruments, last 3 sessions would be dedicated to the presentation and evaluation of projects by students (3 students per team).
Prerequisites / NoticeNanotech center and lab visit at IBM would be mandatory, as well as attending the student project presentations.
529-0837-00LBiomicrofluidic EngineeringW7 credits3GA. de Mello
AbstractMicrofluidics describes the behaviour, control and manipulation of fluids that are geometrically constrained within sub-microliter environments. The use of microfluidic devices offers an opportunity to control physical and chemical processes with unrivalled precision, and in turn provides a route to performing chemistry and biology in an ultra-fast and high-efficiency manner.
ObjectiveIn the course students will investigate the theoretical concepts behind microfluidic device operation, the methods of microfluidic device manufacture and the application of microfluidic architectures to important problems faced in modern day chemical and biological analysis. A design workshop will allow students to develop new microscale flow processes by appreciating the dominant physics at the microscale. The application of these basic ideas will primarily focus on biological problems and will include a treatment of diagnostic devices for use at the point-of-care, advanced functional material synthesis, DNA analysis, proteomics and cell-based assays. Lectures, assignments and the design workshop will acquaint students with the state-of-the-art in applied microfluidics.
ContentSpecific topics in the course include, but not limited to:

1. Theoretical Concepts
Features of mass and thermal transport on the microscale
Key scaling laws
2. Microfluidic Device Manufacture
Conventional lithographic processing of rigid materials
Soft lithographic processing of plastics and polymers
Mass fabrication of polymeric devices
3. Unit operations and functional components
Analytical separations (electrophoresis and chromatography)
Chemical and biological synthesis
Sample pre-treatment (filtration, SPE, pre-concentration)
Molecular detection
4. Design Workshop
Design of microfluidic architectures for PCR, distillation & mixing
5. Contemporary Applications in Biological Analysis
Cellular analyses (single cells, enzymatic assays, cell sorting)
6. System integration
Applications in radiochemistry, diagnostics and high-throughput experimentation
Lecture notesLecture handouts will be provided
Prerequisites / NoticeThis lecture will be recorded for Students of Basel (BSSE), details will be announced later.
636-0003-00LBiological Engineering and BiotechnologyW6 credits3GM. Fussenegger
AbstractBiological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market.
Objective1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development.
Lecture notesHandsout during the course.
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