BME 396: Studying Animal Behavior with High Speed Video

Quarter Offered

Fall : MW 12-12:50 ; Hartmann
Winter : MW 12-12:50 ; Hartmann


Permission of Instructor. Hours to be determined based on student schedules. Students must take both fall and winter quarters in succession.


High speed video has rapidly become an important tool for quantifying animal (including human) movement and behavior. In this course you will learn to train laboratory rats in a tactile discrimination task and gain experience analyzing high speed video of their behavior. We will discuss problems in lighting, depth of field, and how to merge two or more camera views into a single 3D image. Students will learn basic image processing techniques to track animals and their movements.

Who Takes It

Typically juniors and seniors. Permission of the instructor is required to take the course BME. Familiarity with Matlab is important and good calculus skills are helpful.


  • Responsible conduct of research with animals
  • An introduction to experiment for the quarter and why it is important
  • The difference between tasks that involve discrimination, determination, localization, identification.
  • The basics of operant conditioning, "clicker" training, and behavioral shaping
  • Basics of high-speed videography and lighting
  • Matlab video tracking and 3D video merging
  • How to organize data for a complex experiment.

Required class materials

Laptop computer with Matlab installed

Teaching methods

This is a laboratory course that is based around student schedules.  We will meet twice a week for the first 2 – 3 weeks of the quarter, and then meet only once a week in weeks 4 - 10.

Evaluation Methods

Grades will be based on class participation and a presentation at the end of each quarter