"Sensing and Actuating Life"
42-611/27-709 Engineering Biomaterials | 12 units | Fall
This course will cover structure-processing-property relationships in biomaterials for use in medicine. This course will focus on quantitative aspects of biomaterials design. Topics of study include surfaces, thermodynamics, receptor-binding kinetics, quantitative analysis of cell behavior, and transport phenomena. This course will discuss practical applications of these materials in medical devices, drug delivery, tissue engineering, biosensors, etc. This course is a project-based option for graduate students that is taught concurrently with 42-411.
Pre-requisite: 06-221, 24-221, 27-215 or equivalent; Graduate student in CIT or permission of instructor.
42-620 Engineering Molecular Cell Biology | 12 Units | Fall
Cells are not only basic units of living organisms but also fascinating engineering systems that exhibit amazing functionality, adaptability, and complexity. Applying engineering perspectives and approaches to study molecular mechanisms of cellular processes plays a critical role in the development of contemporary biology. At the same time, understanding the principles that govern biological systems provides critical insights into the development of engineering systems, especially in the micro- and nano-technology. The goal of this course is to provide basic molecular cell biology for engineering students with little or no background in cell biology, with particular emphasis on the application of quantitative and system perspectives to basic cellular processes. Course topics include the fundamentals of molecular biology, the structural and functional organization of the cell, the cytoskeleton and cell motility, the mechanics of cell division, and cell-cell interactions.
Pre-requisite: Differential Equations. knowledge of modern biology is suggested but not required. Proficiency in basic computation such as MATLAB programming is expected.
42-622/06-622 Bioprocess Design | 9 units | Spring, intermittent
This course is designed to link concepts of cell culture, bioseparations, formulation and delivery together for the commercial production and use of biologically-based pharmaceuticals; products considered include proteins, nucleic acids, and fermentation-derived fine chemicals. Associated regulatory issues and biotech industry case studies are also included. The format of the course is a mixture of equal parts lecture, open discussion and participant presentation. Course work consists of team-oriented problem sets of an open ended nature and individual-oriented industry case studies. The goals of the course are to build an integrated, technical knowledge base of the manufacture of biologically based pharmaceuticals and the US biotechnology industry. Working knowledge of basic cell and modern biology, biochemistry, and differential equations/partial differential equations is assumed.
Pre-requisite: 42-321 Cellular and Molecular Biotechnology, or both 03-232 Biochemistry and 06-422 Chemical Reaction Engineering, or instructor permission.
42-624 Biological Transport and Drug Delivery | 9 units | Spring
Analysis of transport phenomena in life processes on the molecular, cellular, organ and organism levels and their application to the modeling and design of targeted or sustained release drug delivery technologies. Coupling of mass transfer and reaction processes will be a consistent theme as they are applied to rates of receptor-mediated solute uptake in cells, drug transport and biodistribution, and drug release from delivery vehicles. Design concepts underlying new advances in nanomedicine will be described.
Pre-requisite: 06-262 Mathematical Methods of Chemical Engineering or 21-260 Differential Equations [Top]
42-631 Neural Data Analysis | 9 units | Fall
The vast majority of behaviorally relevant information is transmitted through the brain by neurons as trains of action potentials. How can we understand the information being transmitted? This class will cover the basic engineering and statistical tools in common use for analyzing neural spike train data, with an emphasis on hands-on application. Topics will include neural spike train statistics, estimation theory (MLE, MAP), signal detection theory (d-prime, ROC analysis), information theory (entropy, mutual information, neural coding theories, spike-distance metrics), discrete classification (naïve Bayes), continuous decoding (PVA, OLE, Kalman), and white-noise analysis. Each topic covered will be linked back to the central ideas from undergraduate probability, and each assignment will involve actual analysis of neural data, either real or simulated, using Matlab. This class is meant for upper-level undergraduates or beginning graduate students, and is geared to the engineer who wants to learn the neurophysiologist's toolbox and the neurophysiologist who wants to learn new tools.
Pre-requisites: undergraduate probability (36-217 or 36-225, or equivalent). [Top]
42-632 (formerly 42-590/18-699A) Neural Signal Processing | 12 units | Spring
The brain is among the most complex systems ever studied. Underlying the brain's ability to process sensory information and drive motor actions is a network of 10^11 neurons, each making 10^3 connections with other neurons. Modern statistical and machine learning tools are needed to interpret the plethora of neural data being collected, both for (1) furthering our understanding of how the brain works, and (2) designing biomedical devices that interface with the brain. This course will cover a range of statistical methods and their application to neural data analysis. The statistical topics include latent variable models, dynamical systems, point processes, dimensionality reduction, Bayesian inference, and spectral analysis. The neuroscience applications include neural decoding, firing rate estimation, neural system characterization, sensorimotor control, spike sorting, and field potential analysis.
Pre-requisites: Introductory probability theory and random variables; introductory linear algebra. No prior knowledge of neuroscience is needed. [Top]
42-640/24-658 Computational Bio-Modeling and Visualization | 12 units | Spring
Biomedical modeling and visualization play an important role in mathematical modeling and computer simulation of real/artificial life for improved medical diagnosis and treatment. This course integrates mechanical engineering, biomedical engineering, computer science, and mathematics together. Topics to be studied include medical imaging, image processing, geometric modeling, visualization, computational mechanics, and biomedical applications. The techniques introduced are applied to examples of multi-scale biomodeling and simulations at the molecular, cellular, tissue, and organ level scales.
Pre-requisite: None. [Top]
42-641/24-676 Bio-Inspired Robotics | 12 units | Fall
This course investigates animal locomotion principles such as ground locomotion, flapping flight, swimming, and water surface locomotion and adapting those principles to bio-inspired robotic platforms. It uses the ‘Principles of Animal Locomotion’ book as the main course textbook while adding many recent updates and robotic content from research articles and news. Besides the basic biomechanics, locomotion dynamics, and mechanism design knowledge, it includes the current trends in literature, detailed case studies and discussions, and guest lecturer talks. Course final projects involve theoretical and hands-on topics on design, analysis, manufacturing, and control of bio-inspired robots with various locomotion capabilities. In addition to a final project presentation and report, the course requires a literature survey report and weekly or biweekly homework, and involves several quizzes.
Pre-requisite: None. [Top]
42-642 Biological Fluid Mechanics | 12 units | Spring, every other year
Fluid dynamics and transport phenomena associated with biological and biomedical problems are studied through selected topics from cardiovascular fluid dynamics, swimming/flying in nature and biomimetic technologies. Course objectives are to prepare students to design and perform contemporary research in physiological, biological and biomedical fluid mechanics, and to understand emerging biomimetic engineering methods, emphasizing quantitative understanding and fundamental engineering concepts. Computational and experimental techniques (CFD, flow visualization, PIV, LDV, POD, confocal microscopy) will be studied with hands-on research projects. Principles of interdisciplinary (biologist/clinician/engineer) collaboration are emphasized. The course is intended for advanced undergraduate and entering graduate students. Familiarity with elementary fluid mechanics and introductory Matlab programming is expected. Students who have not previously taken a fluid dynamics class should consult with the instructor.
Pre-requisites: Basic fluid mechanics. [Top]
42-643/24-615 Microfluidics | 12 units | intermittent
This course offers an introduction to the emerging field of microfluidics with an emphasis on chemical and life sciences applications. During this course students will examine the fluid dynamical phenomena underlying key components of “lab on a chip” devices. Students will have the opportunity to learn practical aspects of microfluidic device operation through hands-on laboratory experience, computer simulations of microscale flows, and reviews of recent literature in the field. Throughout the course, students will consider ways of optimizing device performance based on knowledge of the fundamental fluid mechanics. Students will explore selected topics in more detail through a semester project. Major course topics include pressure-driven and electrokinetically-driven flows in microchannels, surface effects, micro-fabrication methods, micro/nanoparticles for biotechnology, biochemical reactions and assays, mixing and separation, two-phase flows, and integration and design of microfluidic chips.
Pre-requisites: Basic fluid mechanics or instructor permission. [Top]
42-645/24-655 Cellular Biomechanics | 9 units | Spring, every other year
This course discusses how mechanical quantities and processes such as force, motion, and deformation influence cell behavior and function, with a focus on the connection between mechanics and biochemistry. Specific topics include: (1) the role of stresses in the cytoskeleton dynamics as related to cell growth, spreading, motility, and adhesion; (2) the generation of force and motion by moot molecules; (3) stretch-activated ion channels; (4) protein and DNA deformation; (5) mechanochemical coupling in signal transduction. If time permits, we will also cover protein trafficking and secretion and the effects of mechanical forces on gene expression. Emphasis is placed on the biomechanics issues at the cellular and molecular levels; their clinical and engineering implications are elucidated. 3 hours lecture.
Pre-requisite: None. [Top]
42-646 Molecular Biomechanics | 9 units | Spring, every other year
This class is designed to present concepts of molecular biology, cellular biology and biophysics at the molecular level together with applications. Emphasis will be placed both on the biology of the system and on the fundamental physics, chemistry and mechanics which describe the molecular level phenomena within context. In addition to studying the structure, mechanics and energetics of biological systems at the nano-scale, we will also study and conceptually design biomimetic molecules and structures. Fundamentals of DNA, globular and structured proteins, lipids and assemblies thereof will be covered.
Pre-requisite: Thermodynamics or instructor permission. [Top]
42-647/24-659 (formerly 42-752) Introduction to Continuum Biomechanics | 12 units | Spring
This course provides a general survey of the application of continuum mechanics to biomechanics. The objective of this course is to provide the basic ideas of continuum mechanics for engineering and science students with little or no background in biomechanics, with particular emphasis on the application of quantitative and system perspectives to fluid and solid mechanics problems. The course begins with a historical review of the subject followed by a review of vector and tensor analysis, before discussing various measures of deformation and stress formulations. The development and understanding of appropriate constitutive models for particular problems are emphasized. Both analytical and experimental results are presented through readings from recent literature and the relevance of these results to the solution of unsolved problems is highlighted. The course encourages class participation and discussion in a seminar fashion and includes individually-crafted research projects that will be discussed in class.
Pre-requisites: 21-260 Differential Equations or 06-262 Mathematical Methods of Chemical Engineering or permission of instructor. Knowledge in mechanics of deformable solids (24-202) and fluid mechanics desirable but not required. [Top]
42-660 Surgery for Engineers | 12 units | Spring
This course explores the impact of engineering on surgery. Students will interact with clinical practitioners and investigate the technological challenges that face these practitioners. A number of visits to the medical center are anticipated for hands on experience with a number of technologies utilized by surgeons to demonstrate the result of advances in biomedical engineering. These experiences are expected to include microvascular surgery, robotic surgery, laparoscopic, and endoscopic techniques. Tours of the operating room and shock trauma unit will be arranged. If possible observation of an operative procedure will be arranged (if scheduling permits). Invited surgeons will represent disciplines including cardiovascular surgery, plastic and reconstructive surgery, surgical oncology, trauma surgery, minimally invasive surgery, oral and maxillofacial surgery, bariatric surgery, thoracic surgery, orthopedic surgery, and others. Specific engineering topics which may be relevant to each of these specialties as well as topics which span many specialties (for example imaging, biomaterials, biomechanics, etc) will be presented by various faculty members of the CMU Biomedical Engineering dept. Students will self-select into teams and present a broad topic overview that will augment the clinical speaker’s presentation. The topics and teams will be finalized on the first day of class and can be tailored to reflect the specific interests of the class but might include topics such as: pump functions of the heart, compliance of the vascular system, electrical map and function of the heart, surgical approaches to cancer, etc. A final paper/presentation will identify an unsolved surgical problem and a potential bioengineered solution for the problem. The possibility to extend this effort into an independent research endeavor will be discussed.
The Primary Instructor is Howard Edington, M.D., MBA System Chairman of Surgery, Allegheny Health Network. This course meets once a week for 3 hours. Several sessions will be held at the Medical Center, transport provided.
Pre-requisite: Physiology. [Top]
42-662 Basic Statistics for Biomedical Research | 9 units | Fall
This is a lecture/seminar course designed to cover medical experimental design, types of statistical error and the mechanics of commonly used statistical methods. Emphasis will be placed on use of appropriate statistical tools as opposed to the mathematical underpinnings of the statistical tests themselves. Students will be expected to solve statistical problems derived from clinical practice as well as the medical literature. Web-based resources as well as a statistical software package will be provided.
There is no textbook for the course. The biostatistics software package to be used for the course is Medcalc which is available as a free download for 25 uses (PC platform only) at www.medcalc.be. Students will also be directed to public-domain web sites which run Java applets capable of performing most of the problems presented in class.
The instructor is Matthew R Quigley, MD., Associate Professor of Neurosurgery, Drexel University and staff neurosurgeon at Allegheny General Hospital. Dr Quigley has taught the Graduate Medical Education Biostatistics course at Allegheny General Hospital for the last 5 years and obtained extensive hands-on experience with experimental design and data analysis as the Chair of the Institutional Review Board, the oversight committee for all human research performed at the hospital. [Top]
42-698A Bioinstrumentation | 9 units | Fall
(Not for Students in BSIP Track, Who May Take This Course as a Track Elective)
This course aims to build the foundation of basic principles, applications and design of bioinstrumentation. Topics covered include biosignals recording, transducers for biomedical application, action potentials EMG, EEG, ECG, amplifiers and signal processing, blood flow and pressure measurements, data acquisition and signal conditioning, spectral analysis of data, filtering, and safety aspects of electrical measurements. Ultimately, students will learn (1) how to apply basic circuit theory to perform measurement of biosignals, (2) be familiar and use common measurement devices, such as multimeter and oscilloscope, (3) be familiar with Op-amps circuits, (4) how to acquire and analyze a signal using time and frequency techniques, and (5) how to filter a signal to remove noise.
Pre-requisite: Basic physics of electricity and magnetism. [Top]
42-698B Stem Cell Engineering | 9 units | Spring
This course will give an overview over milestones of stem cell research and will expose students to current topics at the frontier of this field. It will introduce students to the different types of stem cells as well as environmental factors and signals that are implicated in regulating stem cell fate. The course will highlight techniques for engineering of stem cells and their micro-environment. It will evaluate the use of stem cells for tissue engineering and therapies. Emphasis will be placed on discussions of current research areas and papers in this rapidly evolving field. Students will pick a class-related topic of interest, perform a thorough literature search, and present their findings as a written report as well as a paper review and a lecture. Lectures and discussions will be complemented by practical lab sessions, including: stem cell harvesting and culture, neural stem cell transfection, differentiation assays, and immunostaining, polymeric microcapsules as advanced culture systems, and stem cell integration in mouse brain tissue. The class is designed for graduate students and upper undergraduates with a strong interest in stem cell biology, and the desire to actively contribute to discussions in the class.
Pre-requisites: None. [Top]
42-698C Introduction to Biomedical Signal Processing | 9 units | Spring
This course is geared towards graduate students who have not been exposed to signal processing before. The aim is to introduce the basic signal processing tools for analysis and mining of biomedical signals. These will include an introduction to digital sequences (1D and multiD), systems, and analysis tools (Fourier and wavelet). We will cover some basic tasks used in various biomedical processing applications. Students will team up in semester-long projects.
Pre-requisite: This course is open to graduate students only. Basic knowledge of Matlab is recommended but not required. Basic mathematics for engineers including basic linear algebra, or permission of the instructor, is required. [Top]
42-698D Engineering in Medicine | 9 units | Fall
The main objective of this course is to bring together the principles of medical device innovation with the details of medical practice in the Intensive Care Unit (ICU). This will be achieved by: (1) a review of selected acute illnesses, and a recounting of patient cases seen in the ICU with each condition, (2) a brief description of currently used technologies and (3) study of the course textbook, “Biodesign”. Another objective is familiarizing the students with the skills needed by entrepreneurs. This will include concise writing, slide preparation for presentations, market and technology research (use of resources at the Pittsburgh Life Sciences Greenhouse is suggested), description of the Small Business Innovation Research (SBIR) program, and information on technology startup companies. Interaction in class will also be encouraged. Guest speakers will give some of the classes.
Pre-requisite: Physiology. [Top]
42-698F Technological Innovation in Biomedical Engineering | 9 units | Fall, every other year
Developing innovative technologies in biomedical engineering requires understanding patents and intellectual property as well as understanding patient needs and market pull. This course will introduce students to technological innovation through discussion of case studies across biomedical engineering. Students will learn to read patents and analyze patent landscapes as well as discuss approaches to developing creative solutions that meet product and regulatory requirements. A team-based project will allow students to apply their skills in biomedical engineering and the tools in this course to proposing novel therapeutics, devices, or diagnostics that meet critical patient needs and have market potential.
Pre-requisites: Graduate status in CIT or MCS, or permission of the instructor. [Top]
42-698G/27-570 Molecular and Micro-Scale Polymeric Biomaterials in Medicine | 9 units | Spring, every other year
This course will cover aspects of polymeric biomaterials in medicine from molecular principles to device scale design and fabrication. Topics include the chemistry, characterization, and processing of synthetic polymeric materials; cell-biomaterials interactions including interfacial phenomena, tissue responses, and biodegradation mechanisms; aspects of polymeric micro-systems design and fabrication for applications in medical devices. Recent advances in these topics will also be discussed.
Pre-requisite: None. [Top]
42-699E/27-520 Tissue Engineering | 12 units | Spring
This course will train students in advanced cellular and tissue engineering methods that apply physical, mechanical and chemical manipulation of materials in order to direct cell and tissue function. Students will learn the techniques and equipment of bench research including cell culture, immunofluorescent imaging, soft lithography, variable stiffness substrates, application/measurement of forces and other methods. Students will integrate classroom lectures and lab skills by applying the scientific method to develop a unique project while working in a team environment, keeping a detailed lab notebook and meeting mandated milestones. Emphasis will be placed on developing the written and oral communication skills required of the professional scientist. The class will culminate with a poster presentation session based on class projects. May count as practicum for practicum-option MS.
Pre-requisite: Cell biology and biomaterials, or permission of instructor. [Top]
42-699G Computational Methods in Biomedical Engineering | 12 units | Spring
This goal of this course is to enable students with little or no programming background to solve simple computational problems in science and engineering. Emphasis will be placed on enabling students to use currently available numerical methods (rather than developing anew) to solve engineering problems. Upon completing the course, the successful student will be able to use basic knowledge regarding computer architecture, data types, binary arithmetic, and programming, to solve sample quantitative problems in engineering. Topics will include: solving linear systems of equations, model fitting using least squares techniques (linear and nonlinear), data interpolation, numerical integration and differentiation, solving differential equations, and data visualization. Specific example computations in each topic above will be drawn from problems in physics, chemistry, as well as signal and image processing, and biomedical engineering. Students will work independently in groups for a final project. Matlab will be used as the programming language/environment for this class, although different languages such as C, Java, and Python will be briefly discussed (time permitting). May count as practicum for practicum-option MS.
Pre-requisite: Calculus, multivariate calculus, linear algebra, and differential equations [Top]
42-699L Inventive Problem Solving in Biomedical Engineering | 12 units | Fall
This course is aimed at discovering inventive solutions to some of medicine’s most difficult problems. It involves a theory of inventive problem solving known as “Triz” that teaches the student how to “invent on demand.” The structure of the course will follow a “flipped classroom” model: with reading assignments and pre-recorded lectures assigned before class and “homework” performed in-class. This will allow students to learn the material at their own pace, and to translate theory to practice in a group setting with mentorship of the course instructor and teaching assistant, and teamwork of classmates. Throughout the semester, specific problems will be assigned to the entire class on topics emphasizing cost saving (affordable health care act), medicine for under-resourced settings, and global health. A final project will be required of each student on a topic of choice (with instructor approval.) Each project will have an associated “client” from industry or healthcare who will serve as outside reviewer. The composition of the class will emphasize biomedical engineering students, but will also invite a limited enrollment of students from the School of Design, Tepper, and Heinz. Accordingly, there will be emphasis on multi-disciplinary teamwork, and networking. In summary, the goals of this course are to: develop formal skills in inventive problem solving, gain proficiency in teamwork and networking, and to actually solve real-world problems in medicine. May count as practicum for practicum-option MS.
Pre-requisite: Graduate standing for MCS and CIT students. For non- MCS or CIT graduate students, a degree in a science or engineering. For all other students, permission of the instructor. [Top]
42-699M Cardiovascular Biomechanics | 12 units | Spring
Sample Syllabus: 42-699M
The primary objective of the course is to teach how to model blood flow and mechanical forces in the cardiovascular system and medical devices. After a brief review of cardiovascular physiology and fluid mechanics, the course will progress from modeling blood flow and mechanical forces in a.) small-scale steady flow applications to b.) small-scale pulsatile applications to c.) large-scale or complex pulsatile flow applications. The course will also discuss how to calculate mechanical forces on cardiovascular tissue (blood vessels, the heart) and cardiovascular cells (endothelial cells, platelets, red and white blood cells), and the effects of those forces. Lastly, the course will focus on the biomechanical issues present in selected medical devices (heart valves, ventricular assist devices, artificial lungs).
Pre-requisite: Physiology and basic solid and fluid mechanics. [Top]
42-702 Advanced Physiology | 12 units | Spring
This course is an introduction to human physiology and includes units on all major organ systems. Particular emphasis is given to the musculoskeletal, cardiovascular, respiratory, digestive, excretory, and endocrine systems. Modules on molecular physiology, tissue engineering, and physiological modeling are also included. Due to the close relationship between structure and function in biological systems, each functional topic will be introduced through a brief exploration of anatomical structures. Basic physical laws and principles will be explored as they relate to physiologic function. (This course is designed to bring graduate students without prior undergraduate courses in physiology to a level of understanding suitable for various graduate research projects. It is not recommended for undergraduate students and cannot be counted toward the BME additional major).
Pre-requisite: Graduate standing. Modern Biology or permission of the instructor. [Top]
42-721 Biotechnology & Environmental Processes | 12 units | Fall, intermittent
This course presents the theory of microbiological processes relevant to environmental systems. Fundamental microbiology, kinetics of suspended-growth and fixed film systems, and processes in environmental biotechnology are the major topics. The microbiological theory presented is applicable to biological processes in engineered and natural systems. The major applications discussed in this course focus on pollution prevention and waste water treatment including: activated sludge, biofilm process, tertiary nutrient removal and menthanogenesis.
Pre-requisites: Modern Biology or Biochemistry or permission of instructor. [Top]
42-731/18-795 Bioimage Informatics | 12 units | Spring
The goals of this course are to provide students with the following: the ability to use mathematical techniques such as linear algebra. Fourier theory and sampling in more advanced signal processing settings; fundamentals of multiresolution and wavelet techniques; and in-depth coverage of some bioimaging applications such as compression and denoising. Upon successful completion of this course, the student will be able to: explain the importance and use of signal representations in building more sophisticated signal processing tools, such as wavelets; think in basic time-frequency terms; describe how Fourier theory fits in a bigger picture of signal representations; use basic multirate building blocks, such as a two-channel filter bank; characterize the discrete wavelet transform and its variations; construct a time-frequency decomposition to fit a given signal; explain how these tools are used in various applications; and apply these concepts to solve a practical bioimaging problem through an independent project.
Pre-requisite: Digital Image Processing, or permission of instructor. [Top]
42-732 Wavelets and Multiresolution Techniques | 12 units | Fall
The goal of this course is to expose students to multiresolution signal processing methods and their use in real applications as well as to guide them through the steps of the research process. All the necessary mathematical tools are introduced with an emphasis on extending Euclidean geometric insights to abstract signals; the course uses Hilbert space geometry to accomplish that. With this approach, fundamental concepts---such as properties of bases, Fourier representations, sampling, interpolation, approximation, and compression---are often unified across finite dimensions, discrete time, and continuous time, thus making it easier to focus on the few essential differences. The course covers signal representations on sequences, specifically local Fourier and wavelet bases and frames. It covers the two-channel filter bank in detail, and uses this signal-processing device as the implementation vehicle for all sequence representations that follow. The local Fourier and wavelet methods are presented side-by-side, without favoring any one in particular. Through the project, students will learn how to choose an appropriate representation and apply it to the specific problem at hand.
There will be 2-3 hours of pre-recorded video per week that can be viewed online at any time. There will also be two 1-hour sessions in person that are not mandatory and can be viewed later online. The instructor will also be available for meetings in person or online as needed. The total amount of work per week is expected to be around 12 hours on average.
The students are expected to have a good background in basic engineering mathematics, signal processing and linear algebra.
Pre-requisite: Signal Processing (18-491 or equivalent), or permission of instructor [Top]
42-735/16-725/18-791 Medical Image Analysis | 12 units | Spring
Students will gain theoretical and practical skills in medical image analysis, including skills relevant to general image analysis. The fundamentals of computational medical image analysis will be explored, leading to current research in applying geometry and statistics to segmentation, registration, visualization, and image understanding. Student will develop practical experience through projects using the new v4 of the National Library of Medicine Insight Toolkit (ITK), a popular open-source software library developed by a consortium of institutions including Carnegie Mellon University and the University of Pittsburgh. In addition to image analysis, the course will include interaction with clinicians at UPMC. ITKv4 includes a new simplified interface and many new features, several of which will be explored in the class. Extensive expertise with C++ and templates is no longer necessary (but still helpful). Some or all of the class lectures may be videoed for public distribution. May count as practicum for practicum-option MS. See Class Web Site.
Pre-requisites: Knowledge of vector calculus, basic probability, and C++ or python (most lectures will use C++). Required textbook, "Machine Vision", ISBN: 052116981X; Optional textbook, "Insight to Images", ISBN: 9781568812175. [Top]
42-744 Medical Devices | 12 units | Fall
This course is an introduction to the engineering, clinical, legal and regulatory aspects of medical device performance and failure. Topics covered include a broad survey of the thousands of successful medical devices in clinical use, as well as historical case studies of devices that were withdrawn from the market. In-depth study of specific medical devices will include: cardiovascular medicine (pacemakers, heart valves, vascular grafts, heart-assist pumps..), orthopedics (fixation devices, prostheses…), and general medicine (defibrillators, blood pressure cuffs, stethoscopes…) We will study the principles of operation (with hands-on examples), design evolution, and modes of failure. Additional lectures will provide basic information concerning biomaterials used for implantable medical devices (metals, polymers, ceramics) and their biocompatibility, mechanisms of failure (wear, corrosion, fatigue, fretting, etc.). Guest lectures will be provided by practicing engineers from regional medical device companies to provide real-world perspective of the development process.
In addition to a mid-term and final exam covering topics presented in class, students will prepare a written report that critically investigates a particular medical device that has been recalled by the FDA, of the student’s choosing. The report will include the design history, engineering analysis, and recommendations for future improvements (re-design). [Students enrolled in 42-744 will also be required to produce a lo-fi prototype, which they will present in class at the end of the semester.]
The ultimate objectives of this course are to (1) provide students with a broad understanding of the medical device industry, (2) stimulate critical analysis of medical device design, and (3) convey practical knowledge and skills that are valuable for a future career in the medical device industry.
Pre-requisites: Graduate standing for MCS and CIT students. For non- MCS or CIT graduate students, a degree in a science or engineering. For all other students, permission of the instructor. [Top]
42-747 Rehabilitation Engineering | 12 units | Fall
Rehabilitation engineering involves the application of engineering principles to design, develop, adapt, and apply assistive technologies to problems confronted by individuals with disabilities. This course considers not only technical issues in device development, but also the human factors and market forces that make some innovative technologies successful and others commercial failures. Engineering innovation by itself - without considering other factors leading to product acceptance – may mean that some innovative technologies don’t become or remain available to aid their intended beneficiaries.
This course surveys assistive technologies designed for a variety functional limitations - including mobility, communication, hearing, vision, and cognition - as they apply to activities associated with employment, independent living, education, and integration into the community. It differs from classical biomedical engineering by its focus on improving the quality of people’s lives, rather than improving their medical treatment. This course requires participation in day-long simulations of disabilities that may impact enrolled students’ participation in their other courses on the days they simulate a disability (e.g. blindness or paraplegia)
Pre-requisite: Completion of any engineering course with a grade of “B” or better, or permission of the instructor for students without any engineering background. [Top]
42-760 Graduate Surgery for Engineer Seminar | 3 units | Fall and Spring
This seminar course explores the impact of engineering on surgery. Students will interact with clinical practitioners and investigate the technological challenges that face these practitioners. A comprehensive version of this course, with surgical practicum, is listed as 42-660.
This course meets 3 hours weekly in the CMU campus for seminars and discussions, as part of the course 42-660 Surgery for Enginerrs. Students are encouraged to take the complete course with practicum 42-660, however those with a more peripheral interest may take this course as an option.
Primary Instructor: Jim Burgess, MD, Department of Neruosurgery, Allegheny General Hospital.
Pre-requisites: Graduate standing. Physiology. [Top]
Many courses that count toward BME degree requirements are offered by other Departments in the Carnegie Institute of Technology, the Mellon College of Science, the School of Computer Science, and the School of Humanities and Social Sciences. Some of these courses are listed below. Descriptions of these courses may be found through Schedule Finder or the web site of the respective department.
02-730 Cell and Systems Modeling | 12 units
02-750 Automation of Biological Research | 12 units
03-534 Biological Imaging and Fluorescence Spectroscopy | 9 units
03-712 Computational Methods for Biological Modeling and Simulation | 12 units
03-741 Advanced Cell Biology | 12 units
03-620 Techniques in Electron Microscopy | 9 units
03-762 Advanced Cellular Neuroscience | 12 units
03-815 Magnetic Resonance Imaging in Neuroscience | 12 units
03-871 Structural Biophysics | 12 units
06-607 Physical Chemistry of Colloids and Surfaces | 9 units
06-609 Physical Chemistry of Macromolecules | 9 units
06-610 Rheology and Structure of Complex Fluids | 9 units
09-707 Nanoparticles | 12 units
09-741 Organic Chemistry of Polymers | 12 units
09-801 Special Topics: Molecular Biophysics and Biochemistry | 12 units
10-701 Machine Learning | 12 units
10-702 Statistical Machine Learning | 12 units
10-708 Probabilistic Graphical Models | 12 units
15-853 Algorithms in the Real World | 12 units
15-883 Computational Models of Neural Systems | 12 units
16-711 Kinematics, Dynamic Systems and Control | 12 units
16-720 Computer Vision | 12 units
16-722 Sensing and Sensors | 12 units
16-764 Ethnography: Analyzing How Context Affects Technology Use | 12 units
16-868 Biomechanics and Motor Control | 12 units
18-491 Digital Signal Processing | 12 units
18-614 Microelectromechanical Systems | 12 units
18-669 Computing and Biology: Theory and Practice | 12 units
18-751 Applied Stochastic Process | 12 units
18-752 Estimation, Detection and Identification | 12 units
18-792 Advanced Digital Signal Processing | 12 units
18-793 Optical Image and Radar Processing | 12 units
18-794 Pattern Recognition Theory | 12 units
18-798 Image, Video, and Multimedia | 12 units
18-799K Special Topics in Cognitive Video | 12 units
18-819E Neural Technology, Sensing, and Stimulation | 12 units
21-690 Methods of Optimization | 12 units
24-614 Microelectromechanical Systems | 12 units
24-674 Design of Biomechatronic Systems for Humans | 12 units
24-703 Numberical Methods in Mechanical Engineering | 12 units
24-735 Heat Transfer in Biology and Medicine | 12 units
24-757 Nano / Micro Manufacturing | 12 units
24-778 Mechatronic Design | 12 units
24-787 Artificial Intelligence and Machine Learning for Design | 12 units
27-715 Applied Magnetism and Magnetic Materials | 12 units
27-718 Soft Materials | 12 units
27-764 Special Topics: Nanostructured Materials | 12 units
33-441 Introduction to BioPhysics | 10 units
33-767 Biophysics: From Basic Concepts to Current Research | 12 units
33-784 Physical Virology | 12 units
36-625/36-700 Probability and Mathematical Statistics I | 12 units
36-712 Statistical Approaches to Learning and Discovery | 12 units
36-746 Statistical Methods for Neuroscience | 12 units
36-747 Statistics for Lab Science | 12 units
39-800 Preparation for a Faculty Career | 0 units
86-675 Computational Perception | 12 units
Carnegie Mellon graduate students are permitted to register for one course per semester at the University of Pittsburgh (see Enrollment page), where offerings in the Department of Bioengineering and the School of Medicine may be of particular interest. Students who plan to register for a course at the University of Pittsburgh must apply through the CMU Hub, which will process the application form in advance. This must be done during the week of CMU Registration although the semester at University of Pittsburgh usually begins earlier. All the paper work goes through Carnegie Mellon.
BIOENG 1633 Biomechanics IV: Tissues, Organs, and Cells | 9 units | Fall | 9 units | Fall
This course at the 42-4xx level is an integral part of a joint CMU-Pitt T32 Ph.D. training program. Modern biomechanics is an increasingly diverse field that encompasses the mechanics of the whole human body and all the way to the cellular and molecular levels. This comprehensive course covers the application of biosolid mechanics to describe the mechanical behavior of soft and hard biological tissues, both native and engineered. The course will include a review of fundamental concepts and techniques of mechanics (e.g. stress, strain, constitutive relations), and of the structure and composition of tissues and cells. The course will then focus on the mechanical properties of specific tissues, e.g. bone, tendon, heart, vascular. [Top]
BIOENG 2330 Biomedical Imaging | 9 units | Spring
Taught by a BME adjunct professor, this graduate course introduces the major imaging modalities (x-ray, CAT-scan, MRI, ultrasound) used in clinical medicine and biomedical research, as well as the fundamentals of images, from a signals and systems standpoint. After completing the course, the student should be able to use imaging modalities to determine anatomical or physiological function and apply physics and signal processing in medical imaging for particular research applications. [Top]
42-701 Biomedical Engineering Seminar | 0 units | Fall and Spring
The Biomedical Engineering Seminar is required each semester for all students in residence. It provides opportunities to learn about research in various and related fields being conducted at other universities and in industry. All graduate students must register for this course during each semester of full-time study. Attendance is mandatory. [Top]
42-790 Practicum in Biomedical Engineering | 1-12 units | Fall and Spring
Students will work with a faculty member, local biomedically-oriented company or local clinical researcher on a technical research, development or outreach project. A faculty member affiliated with the Department of Biomedical Engineering will either serve as the advisor for an internal project or as a liaison for an external industrial/clinical project. This course may count as an elective for MS and PhD students if taken at a medical center.
Pre-requisite: Graduate standing and consent of faculty advisor/liaison. [Top]
42-792 Extramural Practicum | 3-36 units | Fall, Spring, and Summer
This course is for graduate students to gain experience in the real-world practice of biomedical engineering through extramural work. Students should register for Section A during the academic year and Section R during the summer.
Pre-requisite: Graduate standing, require special arrangement through the advisor and approval of the department, and approval of the Office of International Education for foreign students. [Top]
42-798 Current Readings in Biomedical Engineering | 1 or 2 units | Fall or Spring, intermittent
This course takes the "Journal Club" format involving at least three interacting research groups. Students are required to participate regularly and actively in discussing current literatures and make at least one presentation. The number of units is determined by the weekly or biweekly frequency. Students may receive at most 2 units over the entire period of training in each of the following broad areas - fundamental principles of biomedical engineering, technologies for biomedical research, technologies at the interface of biological and artificial materials, and clinical applications of biomedical engineering.
Pre-requisite: Students must obtain consent of the instructor before registering. Limited to graduate students and advanced undergraduate students. [Top]
42-799 Directed Study | 1-48 units | Fall and Spring
Students work with a faculty member affiliated with the Program at the University. Emphasizing resourcefulness and initiative, the students with their advisors evolve a project with both research and development aspects. By permission only.
Pre-requisite: Consent of advisor. [Top]
42-890 M.S. Research | 9-48 units | Fall, Spring, and Summer
Research culminating in a M.S. thesis. [Top]
42-899 M.S. Project Report | 0 units [Top]
42-990 Ph.D. Thesis Research | 9-48 units | Fall, Spring and Summer
Research culminating in a Ph.D. thesis. [Top]
42-996 Teaching Assistantship | 2 units | Fall and Spring
The 2-unit course is the vehicle for PhD students serving teaching assignments. PhD students must register for this course upon notification of the assignment as a teaching assistant (TA). MS students should not register for this course regardless of TA appointment. The units received for this course are not counted toward M.S. or Ph.D. degree requirements. Assignments are made by the department office and announced at the beginning of each semester. The duties generally consist of grading problem sets and holding office hours. An instructor may ask a TA to fill for a lecture in a lecture if the instructor is unavoidably away from campus during the class period. This might occur for no more than a couple lectures for a given class. This course is a requirement for graduation and must be taken by all PhD students for a total of three semesters. [Top]
42-997 Ph.D. Qualifying Examination | 0 unit
A qualifying examination is given to determine the student's general knowledge of the fields of engineering appropriate to the individual's program, and to assess the student’s ability to use this knowledge in the solution of problems and in the execution of original research. The examination comprises written and/or oral parts. The student will be considered to have passed the qualifying examination when he or she has successfully completed all of the required parts. A candidate must take the qualifying examination at the time specified by the department, generally within the first three semesters of study. Upon satisfactorily passing the examination, the student will be accepted as a candidate for the degree of Doctor of Philosophy. If the student has not already received a Master's Degree, upon application and provided that all other requirements have been met, he or she may be granted the degree of Master of Science at the next commencement.
Passing the Ph.D. qualifying examination admits a student to candidacy for the Ph.D. degree for a period of no longer than six calendar years. If, at the end of this six-year period, the Ph.D. has not been awarded, the student must reapply for admission to the graduate program and will be judged competitively with other students applying at the same time. If the student is re-admitted, he or she may, at the discretion of the department, be requested to pass the qualifying examination again before the Ph.D. is awarded. A student may petition for extension of the six-year limit under extenuating circumstances such as a forced change of advisor, military service, or prolonged illness. Note that the time limits on the duration of Ph.D. candidacy outlined here are more restrictive than those of the general university policy. [Top]
42-998 Ph.D. Proposal Examination | 0 units
Ph.D. students should register for Ph.D. Research Proposal during the semester scheduled for the proposal examination, which includes a written proposal for thesis research and an oral examination. The grade is pass/fail depending on the outcome of the proposal examination. [Top]
42-999 Ph.D. Thesis Defense | 0 units
Biomedical Engineering thesis defense examination. [Top]
ABD Status (All But the Dissertation)
After completion of all formal degree requirements other than the completion of an approval of the doctoral dissertation, and the public final examination, doctoral candidates shall be regarded as ABD (all but dissertation).
ABD Students in absentia (Registrar code: ABS), as opposed to ABD Students with student status, is a special status that, upon departmental certification thereof, may be regarded as being in absentia and not required to pay tuition. The In Abstentia staus applies when and, so long as, the following three conditions concur: 1) The candidate has been enrolled as a full-time doctoral candidate at Carnegie Mellon University for at least one academic year. Part-time graduate enrollment may, at the Department’s discretion, be counted pro rata towards this total. 2) The candidate does not receive a stipend predicated on his or her status as a graduate student or doctoral candidate and paid by or administered by the University (whether teaching or research assistantship, scholarship, or fellowship). 3) The student does not require substantial use of university resources. Note that Departmental certification of this condition shall be subject to guidelines established by the School or College. Typically, substantial use shall include office space other than desk space, if available; all but minimal use of laboratory space or university-furnished laboratory equipment and expendables; and all use of computer resources that is not specifically exempted for thesis text preparation. In absentia candidates shall be permitted use of the libraries or consultation with faculty or students (in particular, with a thesis advisor or members of the advising committee.) [Top]
Campus Office for Student Affairs and Graduate Admissions
Department of Biomedical Engineering
Carnegie Mellon University
Doherty Hall 2100
5000 Forbes Avenue
Pittsburgh, PA 15213
Ph: (412) 268-3955
Fax: (412) 268-1173
Department of Biomedical Engineering
Carnegie Mellon University
700 Technology Drive
Pittsburgh, PA 15219
Ph: (412) 268-6222
Fax: (412) 268-9807