Topics in Mathematical Biology: biological image data and shape analysis

Khanh Dao Duc (University of British Columbia)

Sep 3, 2024 — Dec 6, 2024

About the course

Advances in imaging techniques have enabled the access to 3D shapes present in a variety of biological structures: organs, cells, organelles, and proteins. Since biological shapes are related to physiological functions, biological studies are poised to leverage such data, asking a common statistical question: how can we build mathematical and statistical descriptions of biological morphologies and their variations? In this course, we will review recent attempts to use advanced mathematical concepts to formalize and study shape heterogeneity, covering a wide range of imaging methods and applications. The main mathematical focus will be on basics of image processing (segmentation, skeletonization, meshing), Diffeomorphisms and metrics over shape space, optimal transport theory with application for image analysismanifold learning, with some other concepts covered in specific applications (e.g. quasiconformal mapping theory for shape representation, 3D reconstruction in Fourier space…). Students will be encourage to work in groups to present research papers and do a small project to pass the course. This course will also build on the recent BIRS workshop, Joint Mathematics Meetings, and the upcoming SIAM workshops (LSI 2024, SIMODS 2024) on this topic, with some participants to these events invited to contribute to this course and present their research.


This course is available for registration under the Western Dean's Agreement. To register, you must obtain the approval of the course instructor and you must complete the Western Dean's agreement form , using the details below. The completed form should be signed by your home institution department and school of graduate studies, then returned to the host institution of the course.

Enrollment Details

Course Name
Topics in Mathematical Biology: biological image data and shape analysis
Sep 3, 2024 — Dec 6, 2024
Course Number
MATH 612
Section Number
Section Code


For help with completing the Western Dean’s agreement form, please contact the graduate student program coordinator at your institution. For more information about the agreement, please see the Western Dean's Agreement website

Other Course Details

Lecture Schedule

Remote Access

Remote access will be via zoom. A combination of pre-pared slides and hand written notes will be used. The hand written notes will be on a blackboard or tablet depending on room availability. The lecturer will distribute lecture notes online.