Methods In Medical Image Analysis - Spring 2016

BioE 2630 (Pitt) : 18-791 (CMU ECE) : 42-735 (CMU BME)

John Galeotti
Usually meets with students after class
Teaching Assistant

Srivignesh Rajendran

Time TBD, Location TBD
And by appointment

Course Goals

To gain broad theoretical and practical skills in 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. Students 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 via the Shadow Program.

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.

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.