Courses and Study Notes

BIOE 8700/8701 − Bioinstrumentation/Labs


  • 3 credits
  • Instructors: Tong Ye, PhD
  • Previously offered: Fall 2014, Fall 2015, Spring 2017, Fall 2017, Fall 2018, Fall 2019, Fall 2020, and Fall 2021
  • Description: Bioinstrumentation is a discipline in which devices are designed and implemented for measurement of biological and medical signals. In this course, we will examine the fundamental concepts of signal measurement and processing and discuss the technologies that convert specific biologic and medical signals into meaningful quantities. The process of instrument prototyping will be introduced through lab sessions. Students will use LabVIEW (National Instrument) as a platform to learn data acquisition and signal processing and to build front-end circuits for prototyping instruments using the virtual instrumentation approach.
  • Textbook or References: Medical Instrumentation: Application and Design, by John G. Webster (Editor), Amit J. Nimunkar (Editor)


  • BIOE 4310/6310 – Introduction to Medical Imaging


  • 3 credits
  • Instructors: Tong Ye, PhD
  • Previously offered: Spring 2018, Spring 2019, Spring 2020, and Spring 2021
  • Description: Medical Imaging is the technology invented to create visual representations of the interior of a body. Since the discovery of x-ray in 1895, Medical Imaging has become one of most exciting research and application areas that attract scholars from many disciplines, such as Physics, Chemistry, Engineering, and Medicine. Nowadays, we can not only see bone fractures (Radiography) but also locate molecules inside our bodies (PET), and map brain activities in response to audio and visual information (fMRI). In medicine, Medical Imaging routinely provides the structural and functional information of the subsurface tissue of patients so that clinicians can make decisions on the treatment plan. This course will introduce the major imaging modalities in Medical Imaging. Focusing on principles, we will learn physics that governs each imaging modality, instrumentation that acquires signals, theory and engineering that forms images, and, last but least, some basic information that medical imaging machines can provide in medicine. Engineering approaches will be emphasized; computer software will be used to aid the learning process.
  • Textbook or References: Medical Imaging Signals and Systems 2nd Edition, by Jerry Prince (Author), Jonathan Links (Author)


  • BIOE 4910(H) − Bioengineering Research and Clinical Summer Immersion at Charleston (BEACH Program)


  • 3 credits/summer session
  • Instructors: Drs. Tong Ye (Course Director), Ann Foley, and Yongren Wu
  • Previously offered: Summer of 2018, 2019, and 2021
  • Description: Founded in 2018, this summer program targets students who are committed to advancing their engineering expertise in graduate school or a health profession after graduation. Hosted by the Clemson-MUSC Bioengineering Program, through hands-on work in research labs and shadowing experiences in clinics at MUSC in Charleston, students will develop a first-hand perspective about the skills necessary to succeed in graduate or health professional schools. The program will be held over 12 weeks (Summer I and Summer II per Clemson Academic Calendar). For each summer session, students spend at least 15 hours/week in research labs and clinics. On Friday mornings, all participants will meet in the classroom for seminars given by Clemson or MUSC faculty; postdoctoral scientists; PhD and medical students; and discussions led by an instructor. Research projects will typically focus on but not limited to the following topics: orthopedics, biomaterials, bioimaging, and stem cell-based tissue engineering. Please visit the BEACH program page for more information.


  • BIOE 8500-003/843 − Selective Topics in Advanced Biomedical Optics


  • 3 credits
  • Instructors: Drs. Bruce Gao and Tong Ye
  • Previously offered: Fall 2019
  • Description: Optical Microscopy have become an indispensable tool in biomedical research. The course will focus on the physics and mathematics of light propagation and detection. Light-tissue interaction will be also formulated mathematically. Through the course work, a solid theoretical foundation of biomedical optics will be laid out for students who want to develop novel optical imaging methods in biomedical research. The format of the class will be either lectures given by instructors or in-class discussion led by students.
  • Textbook or References: Introduction to Optical Microscopy 2nd Edition, by Jerome Mertz (Author)


  • BIOE 8500-402 − Selective Topics in Molecular and Functional Bioimaging


  • 3 credits
  • Instructors: Tong Ye, PhD
  • Previously offered: Fall 2015
  • Description: : “Imaging specific molecules and their interactions in space and time will be essential to understand how genomes create cells, how cells constitute organisms and how errant cells cause disease.”(Roger Tsien, Imagining imaging's future. Nature Reviews Molecular Cell Biology 4: SS16-SS21, 2003) In this course we focus on principles and applications of microscopic imaging modalities that can provide molecular contrasts in studying biological structures and functions. The course activities include lectures, in-class discussion, and tour of imaging facilities.
  • Textbook or References: Bioimaging: Current Concepts In Light & Electron Microscopy 1st Edition , by Douglas Chandler (Author), Robert W. Roberson (Author)