Methods In Medical Image Analysis - Spring 2018

16-725 (CMU RI) : BioE 2630 (Pitt)

John Galeotti
Usually meets with students after class
Peiyun Hu
By email or appointment

Course Website:
You should check the course website daily for announcements and handouts.

Course Goals

Students will gain theoretical and practical skills in 2D, 3D, and 4D biomedical image analysis, including skills relevant to general image analysis. Emphasis will be placed on understanding and effectivey combining existing algorithms in novel ways to solve specific proglems, rather than programming complex algoriths from scratch. 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. Additional and related covered topics include de-noising/restoration, morphology, level sets, and shape/feature analysis. Students will develop practical experience through projects using the latest version of the National Library of Medicine Insight Toolkit ( ITK ) and SimpleITK, 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, students will visit UPMC to interact with radiologists, pathologist(s), and possibly other clinicians via the Shadow Program.

Subject to change: 16-725 is a graduate class, and 16-425 is a cross-listed undergraduate section. 16-425 is new this year, and has substantially reduced requirements for the final project and for the larger homework assignments, nor does it require shadowing the clinicians.

Important Note about Videoing of Lectures

A few of the class lectures may be videoed for public distribution.  The camera would be in the back of the room, and we would attempt to point it over your heads. However, some students may at times be seen (usually only partially) by the camera. If you object to this, please see the instructor to discuss seating options to avoid ever being seen by the camera. Also, during video recording any audio in the classroom may be picked up and recorded by either the camera or the instructor's microphone. If on a particular occasion you want your voice removed from some part of the recording, then please inform the instructor after class that day.


Knowledge of  vector calculus,  basic probability,  and C++ or python,  including basic command-line familiarity and how to pass arguments to your own command-line programs

Extensive expertise with C++ and templates is not necessary, but some students may find it helpful.

Requirements and Grading



Posted online at
The lecture schedule (and some topics) are subject to change, depending in part on class interest and involvement.

Communication & Presentation Help

For assistance with the written or oral communication assignments in this class, visit CMU's Global Communication Center (GCC). GCC tutors can provide instruction on a range of communication topics and can help you improve your papers and presentations. The GCC is a free service, open to all (CMU?) students, and located in Hunt library. You can make tutoring appointments directly on the GCC website: You may also visit the GCC website to find out about communication workshops offered throughout the academic year.

Academic Integrity & Cheating:

The standard CMU Policies apply:

Students with Disabilities

If you have a disability for which you are or may be requesting an accommodation, you are encouraged to contact both your instructor and your university's appropriate office as early as possible in the term. For students at the University of Pittsburgh, this would be Pitt's Disability Resources and Services, 216 William Pitt Union, 412-648-7890 (412-383-7355 TTY),, which will verify your disability and determine reasonable accommodations for this course.

Take care of yourself.

Do your best to maintain a healthy lifestyle this semester by eating well, exercising, avoiding drugs and alcohol, getting enough sleep and taking some time to relax. This will help you achieve your goals and cope with stress.

All of us benefit from support during times of struggle. You are not alone. There are many helpful resources available on campus and an important part of the college experience is learning how to ask for help. Asking for support sooner rather than later is often helpful.

If you or anyone you know experiences any academic stress, difficult life events, or feelings like anxiety or depression, we strongly encourage you to seek support. Counseling and Psychological Services is here to help. Consider reaching out to a friend, faculty or family member you trust for help getting connected to the support that can help.

If you or someone you know is feeling suicidal or in danger of self-harm, call someone immediately, day or night:

If the situation is life threatening, call the police:

If you have questions about this or your coursework, please let me know.