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Department of Biomedical Engineering Courses

Note on Course Numbers

Each Carnegie Mellon course number begins with a two-digit prefix which designates the department offering the course (76-xxx courses are offered by the Department of English, etc.). Although each department maintains its own course numbering practices, typically the first digit after the prefix indicates the class level: xx-1xx courses are freshmen-level, xx-2xx courses are sophomore level, etc. xx-6xx courses may be either undergraduate senior-level or graduate-level, depending on the department. xx-7xx courses and higher are graduate-level. Please consult the Schedule of Classes each semester for course offerings and for any necessary pre-requisites or co-requisites.

42-101 Introduction to Biomedical Engineering
Fall and Spring: 12 units
This course will provide exposure to basic biology and engineering problems associated with living systems and health care delivery. Examples will be used to illustrate how basic concepts and tools of science & engineering can be brought to bear in understanding, mimicking and utilizing biological processes. The course will focus on four areas: biotechnology, biomechanics, biomaterials and tissue engineering and biosignal and image processing and will introduce the basic life sciences and engineering concepts associated with these topics. Pre-requisite OR co-requisite: 03-121 Modern Biology.
Corequisite: 03-121
42-200 Sophomore BME Research Project
Fall and Spring
Research projects for sophomores under the direction of a regular or adjunct BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects provided that a regular or adjunct BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units, and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a two-page project description with sign-off by the research advisor and a copy submitted for review and filing with the BME Department. A final written report of the results is required. Units may vary from 9 to 12 according to the expected time commitment, with one unit corresponding to 1 hour of research per week. One (but not more than one) semester of research, if registered for at least 9 units, may be counted as a restricted elective course toward the BME additional major.
42-201 Professional Issues in Biomedical Engineering
Fall and Spring: 3 units
This course exposes students to many of the issues that biomedical engineers face. It provides an overview of professional topics including bioethics, regulatory issues, communication skills, teamwork, and other contemporary issues. Outside speakers and case studies will describe real world problems and professional issues in biotechnology and bioengineering, and progress toward their solution. Prerequisite or co-requisite: 42-101 Introduction to Biomedical Engineering
42-202 Physiology
Fall and Spring: 9 units
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 interrelationship between structure and function in biological systems, each functional topic will be introduced through a brief exploration of anatomical structure. Basic physical laws and principles will be explored as they relate to physiologic function. Prerequisite or co-requisite: 03-121 Modern Biology, or permission of instructor.
Corequisite: 03-121
42-203 Biomedical Engineering Laboratory
Fall and Spring: 9 units
This laboratory course is designed to provide students with the ability to make measurements on and interpret data from living systems. The experimental modules reinforce concepts from 42-101 Introduction to Biomedical Engineering and expose students to four areas of biomedical engineering: biomedical signal and image processing, biomaterials, biomechanics, and cellular and molecular biotechnology. Several cross-cutting modules are included as well. The course includes weekly lectures to complement the experimental component. Prerequisites: 42-101 Introduction to Biomedical Engineering and 03-121 Modern Biology. Pre-med students should register for 03-206. Priority for enrollment will be given to students who have declared the Additional Major in Biomedical Engineering.
42-300 Junior BME Research Project
Fall and Spring
Research projects for sophomores under the direction of a regular or adjunct BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects provided that a regular or adjunct BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units, and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a two-page project description with sign-off by the research advisor and a copy submitted for review and filing with the BME Department. A final written report of the results is required. Units may vary from 9 to 12 according to the expected time commitment, with one unit corresponding to 1 hour of research per week. One (but not more than one) semester of research, if registered for at least 9 units, may be counted as a restricted elective course toward the BME additional major.
42-302 Biomedical Engineering Systems Modeling and Analysis
Fall and Spring: 9 units
This course will prepare students to develop mathematical models for biological systems and for biomedical engineering systems, devices, components, and processes and to use models for data reduction and for system performance analysis, prediction and optimization. Models considered will be drawn from a broad range of applications and will be based on algebraic equations, ordinary differential equations and partial differential equations. The tools of advanced engineering mathematics comprising analytical, computational and statistical approaches will be introduced and used for model manipulation.
42-341 Introduction to Biomechanics
Fall: 9 units
This course covers the application of solid and fluid mechanics to living tissues. This includes the mechanical properties and behavior of individual cells, the heart, blood vessels, the lungs, bone, muscle and connective tissues as well as methods for the analysis of human motion.
42-400 Senior BME Research Project
Fall and Spring
Research projects for sophomores under the direction of a regular or adjunct BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects provided that a regular or adjunct BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units, and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a two-page project description with sign-off by the research advisor and a copy submitted for review and filing with the BME Department. A final written report of the results is required. Units may vary from 9 to 12 according to the expected time commitment, with one unit corresponding to 1 hour of research per week. One (but not more than one) semester of research, if registered for at least 9 units, may be counted as a restricted elective course toward the BME additional major.
42-401 Foundation of BME Design
Fall: 6 units
This course sequence introduces Biomedical Engineering students to the design of useful biomedical products to meet a specific medical need. Students will learn to identify product needs, how to specify problem definitions and to use project management tools. Methods to develop creativity in design will be introduced. The course sequence is comprised of two parts: 42-401 is offered in the Fall semester and provides the students the opportunity to form project teams, select and define a project, create a development plan, and complete an initial prototype. 42-402 is offered in the Spring semester is a full semester course and completes the plan that was developed in the fall semester. This course culminates in the completion of multiple prototypes, a poster presentation, and a written report. Prerequisite: Senior standing in Biomedical Engineering. Co-requisite: 42-101.
Corequisite: 42-101
42-402 BME Design Project
Spring: 9 units
This course sequence introduces Biomedical Engineering students to the design of useful biomedical products to meet a specific medical need. Students will learn to identify product needs, how to specify problem definitions and to use project management tools. Methods to develop creativity in design will be introduced. The course sequence is comprised of two parts: 42-401 is offered in the Fall semester and provides the students the opportunity to form project teams, select and define a project, create a development plan, and complete an initial prototype. 42-402 is offered in the Spring semester is a full semester course and completes the plan that was developed in the fall semester. This course culminates in the completion of multiple prototypes, a poster presentation, and a written report. Prerequisite: 42-401
42-411 Engineering Biomaterials
Fall: 9 units
This course will cover structure-processing-property relationships in biomaterials for use in medicine. This course will focus on a variety of materials including natural biopolymers, synthetic polymers, and soft materials with additional treatment of metals and ceramics. Topics include considerations in molecular design of biomaterials, understanding cellular aspects of tissue-biomaterials interactions, and the application of bulk and surface properties in the design of medical devices. This course will discuss practical applications of these materials in drug delivery, tissue engineering, biosensors, and other biomedical technologies. Cross-listed with 27-411
42-426 Biosensors and BioMEMS
Intermittent: 9 units
This course emphasizes the principles of biomolecule-based sensing, including molecular recognition, biomolecular binding kinetics and equilibrium; methods of detection and signal transduction, including optical, colorimetric, fluorescence, potentiometric, and gravimetric techniques; statistical principles of high throughout screening; microfluidic and microarray device design principles and fabrication technologies; molecular motors. Prerequisites: 03-231 OR 03-232 Biochemistry.
42-431 Introduction to Biomedical Imaging and Image Analysis
Fall: 12 units
This course gives an overview of tools and tasks in various biological and biomedical imaging modalities, such as microscopy, magnetic resonance imaging, x-ray computed tomography, ultrasound and others. Students will be exposed to the major underlying principles in modern imaging systems as well as state of the art methods for processing biomedical images such as deconvolution, registration, segmentation, pattern recognition, etc. The discussion of these topics will draw on approaches from many fields, including physics, statistics, signal processing, and machine learning. As part of the course, students will be expected to complete an independent project. Students will have the opportunity to visit laboratory to see real biomedical imaging devices in action. Prerequisites: 18-290 Signals and Systems or permission of the instructor, working knowledge of Matlab, and some image processing experience. Cross-listed courses: 18-496
42-444 Medical Devices
Fall: 9 units
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, orthopedics, and general medicine. 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.). The level of technical content will require junior standing for MCS and CIT students, a degree in science or engineering for non-MCS or non-CIT graduate students, or permission of the instructor for all other students.
42-447 Rehabilitation Engineering
Fall: 9 units
Rehabilitation engineering is the systematic application of engineering sciences to design, develop, adapt, test, evaluate, apply, and distribute technological solutions to problems confronted by individuals with disabilities. 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. This course considers not only technical issues in device development, but also the psychosocial factors and market forces that influence device acceptance by individuals and the marketplace.
42-474 Special Topics: Introduction to Biophotonics
Fall: 9 units
Biophotonics, or biomedical optics, is a field dealing with the application of optical science and imaging technology to biomedical problems, including clinical applications. The course introduces basic concepts in electromagnetism and light tissue interactions, including optical properties of tissue, absorption, fluorescence, and light scattering. Imaging methods will be described, including fluorescence imaging, Raman spectroscopy, optical coherence tomography, diffuse optical spectroscopy, and photoacoustic tomography. The basic physics and engineering of each imaging technique are emphasized. Their relevance to human disease diagnostic and clinical applications will be included, such as breast cancer imaging and monitoring, 3D retinal imaging, ways of non-invasive tumor detection, as well as functional brain imaging in infants. NOTE: 42-474 is intended for undergraduates only. Pre-requisite: 33-107 Physics II for Engineering Students or permission of the instructor.
42-612 Tissue Engineering
Spring: 12 units
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. Pre-requisite: Knowledge in cell biology and biomaterials, or permission of instructor
42-613 Molecular and Micro-scale Polymeric Biomaterials in Medicine
Spring: 9 units
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.
42-620 Engineering Molecular Cell Biology
Fall: 12 units
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-requisites: 21-260 Differential Equations, or 06-262 Mathematical Methods of Chemical Engineering, or 18-202 Mathematical Foundations of Electrical Engineering. Advanced undergraduate or graduate student standing is required. Prior completion of 03-121 Modern Biology is suggested but not required. Proficiency in basic computation such as MATLAB programming is expected.
42-622 Bioprocess Design
Spring: 9 units
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 indivudual-oriented industry case studies. The goals of the course work are to build an integrated technical knowledge base of the manufacture of biologically based pharmaceuticals and U.S. biotechnology industry. Working knowledge of cell culture and modern biology, biochemistry and 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.
42-623 Cellular and Molecular Biotechnology
Fall: 9 units
This course will provide students with an introduction to biotechnology in an engineering context. The focus will be on using microorganisms to prepare therapeutically and technologically relevant biochemicals. Topics to be covered include cellular and microbial metabolism, recombinant DNA methodologies, bioreactor design, protein separation and purification, and systems approaches to biotechnology. Prerequisites: (42-202 Physiology OR 03-121 Modern Biology OR 03-232 Biochemistry) AND (06-262 Mathematical Methods of Chemical Engineering OR 21-260 Differential Equations) OR permission of instructor.
42-624 Biological Transport and Drug Delivery
Spring: 9 units
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 advances in nanomedicine will be described.
42-630 Introduction to Neuroscience for Engineers
Intermittent: 12 units
The first half of the course will introduce engineers to the neurosciences from the cellular level to the structure and function of the central nervous system (CNS) and include a study of basic neurophysiology; the second half of the course will review neuroengineering methods and technologies that enable study of and therapeutic solutions for diseases or damage to the CNS. A goal of this course is provide a taxonomy of neuroengineering technologies for research or clinical application in the neurosciences.
42-631 Neural Data Analysis
Fall: 9 units
The vast majority of behaviorally relevant information is transmitted through the brain by neurons as trains of actions 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 may include neural spike train statistics (Poisson processes, interspike intervals, Fano factor analysis), estimation (MLE, MAP), signal detection theory (d-prime, ROC analysis, psychometric curve fitting), information theory, discrete classification, continuous decoding (PVA, OLE), and white-noise analysis.
42-632 Neural Signal Processing
Fall: 12 units
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 roughly 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. Prerequisites: 18-290; 36-217, or equivalent introductory probability theory and random variables course; an introductory linear algebra course; senior or graduate standing. No prior knowledge of neuroscience is needed.
42-640 Computational Bio-Modeling and Visualization
Spring: 12 units
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.
42-643 Microfluids
Intermittent: 12 units
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: 24-231 or 06-261 or 12-355 or instructor permission.
42-645 Cellular Biomechanics
Intermittent: 9 units
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 hrs. lec. Prerequisite: Instructor permission. Prerequisites: None. Corequisites: None. Cross Listed Courses: 24-655 Notes: None. Reservations:
42-646 Molecular Biomechanics
Spring: 9 units
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.
42-647 Continuum Biomechanics: Solid and Fluid Mechanics of Physiological Systems
Spring: 12 units
This course provides a general survey of the solid and fluid mechanics of physiological systems, within the framework of continuum mechanics. The main objective of the course is to understand mathematical modeling of solid materials such as bone and tissues, and fluid mechanics of blood and other biofluids such as synovial fluid, etc. The course as a whole encourages class participation and discussion in a seminar-type fashion. 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 at the core of this course. Both analytical and to some extent experimental results are presented through readings from reports in recent journals and the relevance of these results to the solution of unsolved problems is highlighted. The intent is to provide the basic ideas of continuum mechanics for engineering and science students with little or no background in biomechanics or mathematical modeling, with particular emphasis on the application of quantitative and system perspectives to fluid and solid mechanics problems. In addition to looking at various examples with physiological applications, the last few weeks of the course are dedicated to discussing individually-crafted research projects for the students.
Corequisites: 24-262 and 24-231 and 21-260
42-648 Cardiovascular Mechanics
Spring: 12 units
The primary objective of the course is to learn to model blood flow and mechanical forces in the cardiovascular system. After a brief review of cardiovascular physiology and fluid mechanics, the students will progress from modeling blood flow in a.) small-scale steady flow applications to b.) small-scale pulsatile applications to c.) large-scale or complex pulsatile flow applications. The students will also learn 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 students will learn various methods for modeling cardiac function. When applicable, students will apply these concepts to the design and function of selected medical devices (heart valves, ventricular assist devices, artificial lungs).
42-661 Surgery for Engineers
Spring: 9 units
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. 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.
42-663 Computational Methods in BME
Spring: 12 units
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
42-664 Bioinstrumentation
Intermittent: 9 units
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: Physics II (E&M)
42-670 Special Topics: Biomaterial Host Interactions in Regenerative Medicine
Fall: 12 units
Special Topics: This course will provide students with hands-on experience in investigating host responses to synthetic and naturally biomaterials used in regenerative medicine applications. Students will gain experience in the analysis of host responses to these biomaterials as well as strategies to control host interaction. Biomaterial biocompatibility, immune interactions, tissue healing and regeneration will be addressed. Students will integrate classroom lectures with laboratory skills evaluating host-material interactions in a laboratory setting. Laboratory characterization techniques will include cell culture techniques, microscopic, cytochemical, immunocytochemical and histological analyses. Prerequisite: junior or senior standing in Biomedical Engineering or consent of the instructor.
42-671 Precision Medicine for Biomedical Engineers
Intermittent: 9 units
This course explores the opportunities for engineers in precision medicine of complex medical disorders. Students will interact with clinical practitioners and investigate the technological challenges that face these practitioners. The course will focus on common complex conditions and diseases such as inflammatory bowel disease (IBD), pancreatitis, diabetes mellitus and obesity, rheumatoid arthritis, multiple sclerosis, pain syndrome and pharmacogenetics. Improvement in care of these conditions requires a reverse engineering approach, and new tools because of the complexity and unpredictability of clinical course and best treatments on a case-by-case basis. Currently, the cost of medications for these conditions in Pittsburgh alone is >$1 billion, with a large percent of patients being miss-treated because of lack of precision medicine tools. The course includes introduction to medical genetics, biomarkers of disease, health records, disease modeling, outcome predictions, therapies, remote monitoring and smart applications. Special lectures on health economics and career opportunities are also planned. Each session will include an hour of didactic lectures, followed by an hour-long workshop of applications. Specific engineering topics which may be relevant to each of these specialties as well as topics which span many specialties (for example biodetectors, computational biology, bioinformatics, integrated applications) will be presented by various faculty members of the CMU biomedical engineering and other dept. Students will gain experience exploring genetic variants associated with common diseases, including the opportunity to explore their own DNA. Instructors David C. Whitcomb, MD, PhD (UPMC) Philip Empey, PharmD, PhD (UPMC)
42-672 Fundamentals of Biomedical Imaging and Image Analysis
Spring: 12 units
This course introduces fundamentals of biological and medical imaging modalities and related image analysis techniques. It is organized into three units. The first unit introduces fundamental principles of biological imaging modalities, such as fluorescence microscopy, super-resolution microscopy, and electron microscopy. These modalities are used to visualize and record biological structures and processes at the molecular and cellular levels. The second unit introduces fundamental principles of imaging modalities, such as magnetic resonance imaging, x-ray computed tomography, and ultrasound. These modalities are used to visualize and record medical structures and processes at the tissue and organ levels. Recent developments in convergence of biological and medical imaging are briefly discussed. The third section introduces fundamentals of computational techniques used for analyzing and understanding biological and medical images, such as deconvolution, registration, segmentation, tracking, and pattern recognition. The introduction to these topics will draw on concepts and techniques from several related fields, including physics, statistics, signal processing, computer vision, and machine learning. As part of the course, students will complete several independent projects. Students will also have the opportunity to visit laboratories to see some of the actual biomedical imaging devices in action. Prerequisites: 18-290 Signals and Systems or permission of the instructor. Proficiency in basic programming is expected. Knowledge of image processing, computer vision, and/or MATLAB is helpful but not essential.
42-673 Special Topics: Stem Cell Engineering
Intermittent: 9 units
Special Topics: 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.
42-674 Special Topics: Engineering for Survival: ICU Medicine
Intermittent: 9 units
Special Topics: Engineering for Survival: ICU Medicine
42-698 Special Topics
Fall and Spring: 9 units
42-698A Bioinstrumentation (Spring), 42-698C Introduction to Biomedical Signal Processing (Fall) 42-698D Engineering in Medicine (Fall), 42-698E Surgery for Engineers (Spring), 42-698G Molecular and Micro-scale Polymeric Biomaterials in Medicine (Spring), 42-698H BME Systems Modeling and Analysis (Fall), 42-698I Biofluid Mechanics (Fall), and 42-698P Introduction to Biophotonics (Fall) Please see http://www.bme.cmu.edu/ugprog/catalog.html for detailed course descriptions.
42-699 Special Topics
Fall and Spring: 12 units
42-699G Computational Methods in Biomedical Engineering (Spring), 42-699L Inventive Problem Solving in Biomedical Engineering (Fall), 42-699N Applied Nanoscience and Nanotechnology (Fall), and 42-699P Introduction to Biophotonics (Fall) Please see http://www.bme.cmu.edu/ugprog/catalog.html for detailed course descriptions.
42-735 Medical Image Analysis
Spring: 12 units
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 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. It is possible that a few class lectures may be videoed for public distribution. Prerequisites: Knowledge of vector calculus, basic probability, and either C++ or python. Required textbook, "Machine Vision", ISBN: 052116981X; Optional textbook, "Insight to Images", ISBN: 9781568812175.

Course Website: http://www.cs.cmu.edu/~galeotti/methods_course/
42-772 Special Topics: Applied Nanoscience and Nanotechnology
Fall: 12 units
Have you ever wondered what is nanoscience and nanotechnology and their impact on our lives? In this class we will go through the key concepts related to synthesis (including growth methodologies and characterizations techniques) and chemical/physical properties of nanomaterials from zero-dimensional (0D) materials such as nanoparticles or quantum dots (QDs), one-dimensional materials such as nanowires and nanotubes to two-dimensional materials such as graphene. The students will then survey a range of applications of nanomaterials through problem-oriented discussions, with the goal of developing design strategies based on basic understanding of nanoscience. Examples include, but are not limited to, biomedical applications such as nanosensors for DNA and protein detection, nanodevices for bioelectrical interfaces, nanomaterials as building blocks in tissue engineering and drug delivery, and nano materials in cancer therapy. Pre-requisite: Graduate standing. College level chemistry or physical chemistry, and thermodynamics.
42-773 Special Topics: Inventive Problem Solving in Biomedical Engineering
Fall: 12 units
This course is aimed at discovering inventive solutions to some of medicines 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.
42-774 Special Topics: Introduction to Biophotonics
Fall: 12 units
Biophotonics, or biomedical optics, is a field dealing with the application of optical science and imaging technology to biomedical problems, including clinical applications. The course introduces basic concepts in electromagnetism and light tissue interactions, including optical properties of tissue, absorption, fluorescence, and light scattering. Imaging methods will be described, including fluorescence imaging, Raman spectroscopy, optical coherence tomography, diffuse optical spectroscopy, and photoacoustic tomography. The basic physics and engineering of each imaging technique are emphasized. Their relevance to human disease diagnostic and clinical applications will be included, such as breast cancer imaging and monitoring, 3D retinal imaging, ways of non-invasive tumor detection, as well as functional brain imaging in infants. Pre-requisite: Graduate standing. College level physics covering electromagnetism and optics or permission of the instructor.