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Department of Computer Science College of Arts and Sciences

John K. Johnstone

John Johnstone. Associate Professor (joint appointment in Ophthalmology)
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University Hall 4161
(205) 975-5633

Research and Teaching Interests: Shape Modeling, Morphometry, Matrix Algorithms, Formal Languages

Office Hours: By appointment

Education:

  • B.S., University of Saskatchewan, Mathematics
  • M.S., Cornell University, Computer Science
  • Ph.D., Cornell University, Computer Science

As an undergraduate at the University of Saskatchewan, I began as a piano performance major but graduated with a degree in mathematics. I did undergraduate research every summer in the CS department, including work on twofold triple systems. During my Ph.D. studies I worked in John Hopcroft’s robotics lab at Cornell, and my dissertation involved analysis of algebraic curves, implemented in Common Lisp on a Lisp machine.

Before joining UAB in 1994 I was on the faculty at Johns Hopkins University. There I developed my present interest in biomedical modeling, drawn to the beautiful geometry of our anatomy. My Ph.D. students have gone on to places like Google, MIT Lincoln Laboratory, and Siemens Research, and to start companies like DeepMap.


  • Research Interests

    A recent research focus is computation of the morphology and morphometry of the optic nerve head, in collaboration with colleagues in the Department of Ophthalmology led by Dr. Christopher Girkin. A study of the shape of the optic nerve head, across populations and across time, is fundamental to a better understanding and prevention of glaucoma and other optic neuropathies. My research involves the construction of shape models of various regions of the optic nerve head to allow key measurements such as cup and laminar cup depth, choroidal thickness, and cup and laminar cup volume. Another recent interest is segmentation of the optic nerve head from OCT images or histology, a stage upstream from shape modeling.

    A long-term research interest is the modeling and analysis of smooth curves and surfaces, including the construction of smooth Bezier and B-spline curves and surfaces from point clouds and the study of their tangent space and scale space, motivated by problems in visibility analysis, grasping, and the semantics of shape. I am also interested in the development of open-source code for shape modeling.

  • Recent Courses
    • Introduction to Computer Science in Python
    • Automata and Formal Languages
    • Computer Graphics
  • Select Publications
    • Massimo A. Fazio, John K. Johnstone, Brandon Smith, Lan Wang, and Christopher A. Girkin. Displacement of the Lamina Cribrosa in Response to Acute Intraocular Pressure Elevation in Normal Individuals of African and European Descent, Investigative Ophthalmology and Visual Science, 57(7), June 2016, 3331-3339.
    • John K. Johnstone, Lindsay Rhodes, Massimo Fazio, Brandon Smith, Lan Wang, J. Crawford Downs, Cynthia Owsley, and Christopher Girkin. Measuring Mean Cup Depth in the Optic Nerve Head, Computer Aided Design and Applications, 13 (5), March 2016, 693-700.
    • John K. Johnstone, Massimo Fazio, Kulawan Rojananuangnit, Brandon Smith, Mark Clark, Crawford Downs, Cynthia Owsley, Michael J.A. Girard, Jean Martial Mari, and Christopher A. Girkin. Variation of the Axial Location of Bruch’s Membrane Opening with Age, Choroidal Thickness and Race. Investigative Ophthalmology and Visual Science 55, 3 (March 2014), 2004-9.
    • Lindsay A. Rhodes, Carrie Huisingh, John K. Johnstone, Massimo Fazio, Brandon Smith, Mark Clark, J. Crawford Downs, Cynthia Owsley, Michael J.A. Girard, Jean Martial Mari, and Christopher Girkin. Variation of Laminar Depth in Normal Eyes with Age and Race. Investigative Ophthalmology and Visual Science 55, 12 (December 2014), 8123–33.
    • G. Elber, J.K. Johnstone, M.-S. Kim and J.-K. Seong. The Kernel of a Freeform Surface and Its Duality with the Convex Hull of its Tangential Surface. International Journal of Shape Modeling 12, 2 (December 2006), 129-42.
    • John K. Johnstone. The Bezier Tangential Surface System: a Robust Dual Representation of Tangent Space. Computing 72 (special issue dedicated to papers from the Dagstuhl Seminar on Geometric Modeling, April 2004), 105-15.
    • J.P. Williams, J.K. Johnstone and L.B. Wolff. 1997. Rational Discrete Generalized Cylinders and their Application to Shape Recovery in Medical Images. In IEEE Conference on Computer Vision and Pattern Recognition. Puerto Rico, 387-392.
    • R.T. Farouki and J.K. Johnstone. The Bisector of a Point and a Plane Parametric Curve. Computer Aided Geometric Design 11, 2 (1994), 117-53.
    • John K. Johnstone and C. Bajaj. Sorting Points along an Algebraic Curve. SIAM Journal on Computing 19, 5 (October 1990), 925–967.