Sept 12
Speaker: Rachael Brady, Visualization Technology Group
Title: Visualization at Duke (Lecture in .ppt-2.45MB)

Visualization applies the algorithms of computer graphics with the fields of perception and representation to communicate digital information visually. Visualization is used for presentations, art creation, data analysis, model validation, illustration, data exploration, entertainment, and cognitive studies. The Friday forum is an opportunity for individuals to share their expertise and experiences in using visualization in their research. This talk will introduce the fall semester series of lectures and discuss resources for doing visualization at Duke.

Sept 19
Speaker: Martin McKeown, Neurology
Title: Brain Response to Dynamically Varying Visual Stimuli

Up to now, many talks in the Vis Forum have described the use of advanced visualization techniques to express (often high-dimensional) data in an interpretable way. This seminar will describe a complementary approach; we use relatively simple, dynamically varying visual stimuli, and determine the brain responses to these stimuli with high-dimensional measurements such as the Electroencephalogram (EEG) and functional Magnetic Resonance Imaging (fMRI). We argue that appropriately-designed visual stimuli have the potential to broadly impact diagnosis and therapeutics for a range of neurologic diseases. For example, in Parkinson's disease, visual deficits at certain spatial frequencies and contrasts may occur independently of other symptoms, and may respond poorly to treatment. Rare, target stimuli intermixed with frequent distracter stimuli (e.g. virtual balls moving towards the subject), may invoke diffuse arousal mechanisms in the brain which may be therapeutic for patients recovering from stroke. Continuous visual stimuli requiring ongoing input may provide an assay for detecting deficits in sustained attention, an under-recognized contributor to overall disability in Alzheimer's and other dementias, stroke, and Multiple Sclerosis (MS). A continuous performance task, involving tracking a circle following a Lissajous trajectory with a joystick-controlled cursor, will be described. We will demonstrate that, after processing with Independent Component Analysis (ICA), different EEG rhythms show distinct, time-locked spectral perturbations in response to the target changing size, tracking errors and movements of the joystick. When the same task is performed by chronic pain patients in an fMRI magnet, activity in the Anterior Cingulate Cortex demonstrates modulation by a painful stimulus distinctly different from normal controls.

Sept 6
Speaker: John Hatten, Chemistry
Title: Molecular Docking for Lead Discovery

Three bacterial enzymes are responsible for the synthesis of rhamnose, an unusual carbohydrate that plays a key structural role in the cell wall of many pathogens. 250,000 small molecules from the National Cancer Institute database were computationally screened as potential inhibitors to these enzymes. A number of the most promising compounds were then confirmed as inhibitors in the laboratory.

Oct 3
Speaker: David Schwartz, Center for Cognitive Neuroscience
Title: The Statistical Structure of Speech Sounds Predicts Musical Universals

The similarity of musical scales and consonance judgments across human populations has no generally accepted explanation. Work conducted in the Purves Lab over the past two years suggests that these 'musical universals' reflect the human brain's embodiment of the statistical structure of periodic sound energy in the natural world. An analysis of speech sounds, the principal source of periodic sound energy in the human auditory environment, shows that the probability distribution of amplitude/frequency combinations in human utterances predicts both the structure of the chromatic scale and consonance ordering. The presentation should be of interest to people working in signal processing, acoustics, speech, hearing, music, perception, machine learning and neuroscience.

Oct 10
Speaker: Paul Bell and Rachael Brady, Visualization Technology Group
Title: Introducing the Color 3D Printer (Lecture)

The visualization technology lab houses a Zcorp color 3D printer. This
printer was purchased with research funds from Herbert Edelsbrunner, who
is generously allowing this to be a shared resource to the Duke research
community. This Friday Forum will introduce the Zcorp printer's
capabilities, review the file formats that work well with the printer
software, and explain policies and fees associated with using the
printer. We will also illustrate the mechanics of printing a 3D model.

Oct 17
Speaker: Thom LaBean, Computer Science
Title: Looking at Self-assembling DNA Nanostructures -- Models and Molecules

DNA-based nanotechnology makes use of the extraordinarily programmable molecular recognition properties of complementary DNA sequences as "smart glue" in the self-assembly of complex nanostructures. Assembled nanostructures can contain DNA, metallic nanocrystals, proteins, carbon nanotubes, or other materials. Future applications of DNA self-assembly may include nanoelectronics, nanorobotics, sensors, and programmable molecular medicine. Visualization techniques are used during many stages of the design and analysis including physical and computer molecular models as well as imaging techniques such as scanning probe microscopy and electron microscopy.

Oct 24
Speaker: John Bower, Music
Title: Data Representation through Sound (Lecture in .ppt format, music sample 1, music sample 2)

Sonification, or aural display, is the representation of data through sound. Although computer users frequently encounter sound as signifiers of some event (startup chime, mail alert, etc.), the sonification of data remains a little or ill-exploited means of conveying information. Introductory material includes an overview of several available commercial and open-source application frameworks and aspects of sound design and perception/reception to be considered during tool development. This overview will be related to current and recent research in the field with wide-ranging applications found in the financial, I.T., military, biological, and musical disciplines.

Oct 31
St 31peaker: Tom Heil, Hearing Research Laboratories, Otolaryngology
Title: The Bionic Ear: Multimodal Approaches to Visualizing Intracochlear Electrode Arrays

Cochlear implants, known popularly as "bionic ears," are an increasingly common and costly clinical intervention for deafness. Their effectiveness, however, varies greatly, for reasons that are not clear. Researchers in the Hearing Research Laboratories are addressing the contribution of variations in intracochlear electrode array position to inter-subject performance with imaging techniques such as conventional x-rays, Tuned Aperture Computed Tomography (TACT®), and magnetic resonance microscopy. The resulting data are analyzed and combined with software tools that include ImageJ and Amira. The ultimate objective is to relate perceptual thresholds with the implant to electrode position relative to the target neural tissues.

Nov 7
Speaker: Kathy Nightingale, Biomedical Engineering
Title: The Duke Medical Imaging Laboratory: Integrating Research Tools into the Classroom and the Web

For the past several years we have developed and maintained a website in which some of the simulation tools used for medical imaging research are provided via a website to the internet community. In addition to our simulation tools, the notes from an advanced ultrasonic imaging course are provided, along with some sample homework exercises, and some useful links to other imaging websites. This presentation will discuss how we currently use this website, in addition to our experiences (successes and challenges) associated with providing such tools to the internet community.

Nov 14
Speaker: Fuhui Long, Center for Cognitive Neuroscience
Title: Color Perception and Modeling

Understanding how humans perceive color is important for imaging, graphics and visualization applications. In this talk I will first demonstrate some interesting human color perceptual phenomena. Then I will show that these perceptual phenomena can be explained by the statistics of natural scenes. Finally, I will introduce CIE color-appearance model for engineering applications.

Nov 21
Speaker: Tom Kepler, Center for Bioinformatics and Computational Biology
Title: 3D Simulation Studies of the Immune Response

The vertebrate immune system of consists of a great diversity of motile cells whose activities become coordinated during infection. This orchestration is mediated by signaling molecules either secreted (cytokines) or engaged by direct cell-cell contact. Pathogenic microorganism (and other stimuli) induce internal changes in the responding immune cells which, in turn, lead to spatial reorganization of these cells in a process arguably akin to a phase transition. We explore this perspective on immunity using PDE-embedded agent (PDEEA) models. In these models, the microorganisms and host leukocytes are represented computationally as agents with non-trivial internal structure, while the soluble factors are treated as continua described by reaction-diffusion equations. A substantial advantage of this approach comes from the ability to viusalize interactions in 3D space, as they might appear in real systems. At the same time, one would very much like to track additional dynamic information regarding the internal states of the cells. I will discuss our attempts to do these things.