CS 384R (#56767), CAM 395T (#67597), BME 385J (#14608)
FALL
2007 TTH 9:30 – 11:00am
TAY 3.114
Geometric Modeling and Visualization
Image consists of Ribosome, Virus, Human body, Brain, NMJ(Neuromuscular junction), and Universe
|
Name |
|
|
Office |
ACES 2.324 |
|
|
|
|
Phone |
512-471-8870 |
|
Office hours |
Wed 9:00 am - 12:00 am or by appt. via suzanne@ices.utexas.edu |
CS384R, CAM395T, BME385J Course Outline
The course will teach you the basic algorithms, techniques and tools of geometric modeling and
visualization with applications in the biomedical sciences and engineering. Bio-medical modeling (or Biomodeling)
and visualization has roots in medical illustration and communication for the health sciences,
with branches of application to mathematical modeling and computer simulation of artificial life. In this
course we shall emphasize computational image processing, computational topology, computational
algebraic and differential geometry, polynomial spline approximations, computer graphics, together with
aesthetic choices involved in producing effective scientific animations. The emphasis shall be on spatial
realism, and the programmatic use of physiological simulation and visualization to quantitatively depict
"how things work" at the molecular, cellular, tissue, and organ level scales.
Exercises on domain and physiological modeling and visualization at multiple scales, shall be drawn from
virology (viral envelopes, capsids, proteins, nucleic acids), and neurology (brain, hippocampus, neuropil,
axons, dendrites, glial cells, ion-channels, neurotransmitters), and their interactions (molecular energetics
and force fields, molecular flexibility, synaptic transmission, synaptic spillover).
Lecture Topics
Maps2Models: filtering, contrast enhancement, classification, symmetry detection, segmentation, skeletonization, subunit identification, clustering, matching, compression, reconstruction
Models2Analytics I: surfaces, finite element meshing, spline representations, feature identification, symmetry detection, shape segmentation, matching & complementary docking, flexibility
Models2Analytics II: bonded and non-bonded energetics, forces, torques, dynamics, cubature, discrete differential operators, integral equations, sparsifiers, preconditioners, solvers.
Analytics2Informatics/Visualization I: differential/integral/topological/combinatorial properties, active sites, pockets, tunnels, regions of interest, contour trees, comparative structural analysis.
Analytics2Informatics/Visualization II: multi-dimensional transfer functions, visible surface and volume rendering, function on surface, capturing uncertainity, VisPortal, MolSignatureDB.
Grading
You will be graded on weekly homework assignments (70%) and a final exam (30%).
Lectures
| DATE |
LECTURES |
| August 30 |
|
| September 4 |
|
| September 6 |
|
| September 18 |
|
| October 23 |
|
| October 30 |
|
| November 6 |
Boundary & Finite Element Meshed Models III: Topologically Accurate Non-Linear Elements |
| November 12 |
Finite Elements from Imaging I & II: Active Contouring, Segmentation, Reconstruction |
| November 27 |
Geometric Partial Differential Equations: Non-Linear Surface & Volume Diffusion |
| December 12 |
Integrals & Integral Equations: Molecular Energetics & Forces |
Exercises:
|
1 |
Exercise 1 Algebraic Curve, Surface Splines - I Solution 1 |
|
2 |
Exercise 2 Algebraic Curve, Surface Splines - II Solution 2 |
|
3 |
Exercise 3 Algebraic Curve, Surface Splines - III Solution 3 |
|
4 |
Exercise 4 Algebraic Curve, Surface Splines - IV: Molecular Models Solution 4 |
|
5 |
Exercise 5 Finite Element Meshing - I: Linear Elemen Solution 5 |
|
6 |
Exercise 6 Finite Element Meshing II - Non-Linear Elements Solution 6 |
|
7 |
Exercise 7 Geometric Modeling and Visualization Final Solution 7 |
Pictures and Animations
Suggested Reading
Links