VisLunch/Fall2009

November 6, 2009

- Structuring Feature Space: A Non-Parametric Method for Volumetric Transfer Function Generation (VIS paper discussion)

- Speaker: Evrard Ohou (SCI), http://www.sci.utah.edu/people/eohou.html

- Where: Conference Room 3760

- When: Friday noon (11/06)

October 30, 2009

- Volume Ray Casting with Peak Finding and Differential Sampling (VIS paper discussion)

- Speaker: Carson Brownlee (SCI), http://www.cs.utah.edu/~brownlee/grapes/Welcome.html

- Where: Conference Room 3760

- When: Friday noon (10/30)

October 30, 2009

- Depth Dependent Halos (VIS paper discussion)

- Speaker: Mark Kim (SCI), http://www.cs.utah.edu/~mbk/

- Where: Conference Room 3760

- When: Friday noon (10/30)

October 9, 2009

- An Interactive Visualization Tool for Multi-channel Confocal Microscopy Data in Neurobiology Research (VIS practice talk)

Confocal microscopy is widely used in neurobiology for studying the
three-dimensional structure of the nervous system.
Confocal image data are often multi-channel, with each channel resulting
from a different fluorescent dye or fluorescent protein; one channel may
have dense data, while another has sparse; and there are often structures at
several spatial scales: subneuronal domains, neurons, and large groups of
neurons (brain regions). Even qualitative analysis can therefore require
visualization using techniques and parameters fine-tuned to a particular
dataset. Despite the plethora of volume rendering techniques that have been
available for many years, the techniques standardly used in neurobiological
research are somewhat rudimentary, such as looking at image slices or
maximal intensity projections. Thus there is a real demand from
neurobiologists, and biologists in general, for a flexible visualization
tool that allows interactive visualization of multi-channel confocal data,
with rapid fine-tuning of parameters to reveal the three-dimensional
relationships of structures of interest. Together with neurobiologists, we
have designed such a tool, choosing visualization methods to suit the
characteristics of confocal data and a typical biologist's workflow. We use
interactive volume rendering with intuitive settings for multidimensional
transfer functions, multiple render modes and multi-views for multi-channel
volume data, and embedding of polygon data into volume data for rendering
and editing. As an example, we apply this tool to visualize confocal
microscopy datasets of the developing zebrafish visual system.

- Speaker: Yong Wan (SCI), http://www.sci.utah.edu/people/wanyong.html

- Where: Conference Room 3760

- When: Friday noon (10/09)

October 9, 2009

- Loop Surgery for Volumetric Meshes: Reeb Graphs Reduced To Contour Trees (VIS practice talk)

This paper introduces an efficient algorithm for computing the Reeb graph of a scalar function f defined on a volumetric
mesh M in R^3. We introduce a procedure called loop surgery that transforms M into a mesh M' by a sequence of cuts and guarantees
the Reeb graph of f (M') to be loop free. Therefore, loop surgery reduces Reeb graph computation to the simpler problem of
computing a contour tree, for which well-known algorithms exist that are theoretically efficient (O(n log n)) and fast in practice.
Inverse cuts reconstruct the loops removed at the beginning.
The time complexity of our algorithm is that of a contour tree computation plus a loop surgery overhead, which depends on the
number of handles of the mesh. Our systematic experiments confirm that for real-life volumetric data, this overhead is comparable
to the computation of the contour tree, demonstrating virtually linear scalability on meshes ranging from 70 thousand to 3.5 million
tetrahedra. Performance numbers show that our algorithm, although restricted to volumetric data, has an average speedup factor of
6,500 over the previous fastest techniques, handling larger and more complex data-sets.
We demonstrate the versatility of our approach by extending fast topologically clean isosurface extraction to non-simply connected
domains. We apply this technique in the context of pressure analysis for mechanical design. In this case, our technique produces
results in matter of seconds even for the largest models. For the same models, previous Reeb graph techniques do not produce a
result.

- Speaker: Julien Tierny (SCI), http://www.sci.utah.edu/~jtierny

- Where: Conference Room 3760

- When: Friday noon (10/09)

October 2, 2009

- VisMashup: Streamlining the Creation of Custom Visualization Applications (VIS practice talk)

- Authors: Emanuele Santos, Lauro Lins, James P. Ahrens, Juliana Freire, and Claudio T. Silva

Visualization is essential for understanding the increasing
volumes of digital data. However, the process required to create
insightful visualizations is involved and time consuming. Although
several visualization tools are available, including tools with
sophisticated visual interfaces, they are out of reach for users who
have little or no knowledge of visualization techniques and/or who
do not have programming expertise. In this paper, we propose
VisMashup, a new framework for streamlining the creation of
customized visualization applications. Because these applications
can be customized for very specific tasks, they can hide much of the
complexity in a visualization specification and make it easier for
users to explore visualizations by manipulating a small set of
parameters. We describe the framework and how it supports the
various tasks a designer needs to carry out to develop an
application, from mining and exploring a set of visualization
specifications (pipelines), to the creation of simplified views of
the pipelines, and the automatic generation of the application and
its interface. We also describe the implementation of the system
and demonstrate its use in two real application scenarios.

- Speaker: Emanuele Santos (SCI), http://www.sci.utah.edu/~emanuele/

- Where: Conference Room 3760

- When: Friday noon (10/02)

September 18, 2009

- First steps towards quantifying confidence (Summer internship)

Whenever a decision is made, circuitry of the brain is engaged based on
the difficulty of the task at hand. By carefully monitoring the neural
circuit responsible for error detection and handling, we have shown the
ability to determine whether the response given is correct or
incorrect. However, preliminary results indicate that based on the
spectral dynamics generated by the brain circuit involved, an objective
measure of a person's confidence in their answer can be derived.

- Speaker: Erik Anderson (SCI), http://www.sci.utah.edu/~eranders/

- Where: Conference Room 3760

- When: Friday noon (09/18)

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September 18, 2009

- Stratified representation scheme for subsurface modeling (Summer internship)

The steps involved in oil reservoir modeling are similar to the traditional scientific pipeline:
a model has to be updated each time new data comes in; afterwards, the new model is used for simulations
which in turn help scientists with the decision-making process. Current tools cannot easily handle
model updates due to limitations of the underlying framework – often the model must be rebuilt from scratch.
In this talk we will present a flexible framework for domain decomposition and surface manipulation.
During last summer, we have built a prototype of a modeling tool based on this flexible framework
providing a few key functionalities for geologists and geophysicist to perform surfaces updates.

- Speaker: Tiago Etienne Queiroz (SCI), http://www.sci.utah.edu/~etiene/

- Where: Conference Room 3760

- When: Friday noon (09/18)

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September 11, 2009

- Topological Analysis of 2D Steady Vector Fields

Vector fields arise widely in various
engineering applications. Topological analysis extracts
the qualitative information (i.e. structure) of a provided
vector field. The topology of a vector field consists of a
set of features of interest and their connectivity which
forms a graph called topological graph. This graph
segments the data domain into a number of sub-regions in
each of which the flow behavior possesses the same nature.
Therefore, topological analysis provides an efficient
means for the engineers to investigate the behaviors of
their data. In this talk, I will focus on the topology of
2D steady vector fields which is well defined. I will
briefly explain why engineers are interested in certain
features in 2D steday vector fields. Also, I will review
some techniques of extracting these features and
constructing the topological graphs with the focus on my
PhD work including ECG and MCG computation. To learn more
about what they are, please come to the talk.

- Speaker: Guoning Chen (SCI), http://oregonstate.edu/~cheng/

- Where: Conference Room 3760

- When: Friday noon (09/11)

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September 4, 2009

- Delaunay Methods for Approximating Geometric Domains

The Delaunay triangulation is used extensively for representing geometric
domains. In this talk, I consider the use of the Delaunay triangulation for
approximating two different domains. First, I present an algorithm, DelIso,
for building Delaunay meshes to approximate smooth surfaces defined by the
isosurfaces of volume datasets. DelIso employs a two stage algorithm which
discards the need to maintain the full 3D Delaunay triangulation in the second
stage. Implementation results have shown that by using this optimization we
can obtain a 2-3 times speedup over its one stage counterpart.

The second domain investigated is piecewise smooth complexes (PSCs). One of
the limitations of past meshing algorithms is that they could only be applied
to either smooth surfaces or polyhedral domains. PSCs are a more general
class where the shape is modeled as a collection of smooth patches that can
meet sharp corners as well as non-manifolds. We have designed DelPSC, an
algorithm to build Delaunay meshes that approximate PSCs. DelPSC was designed
to be easily implementable, removing the need for many of the expensive
computations that previously made Delaunay meshing for PSCs impractical. Its
meshing strategy employs a novel protection scheme to preserve sharp features
throughout the refinement. We can also guarantee that by reducing a single
scale parameter, the correct topology is achieved for the output mesh. The
approach used in DelPSC allows for meshing a wide variety of objects such as
non-smooth CAD parts and non-manifold objects.

- Speaker: Joshua A. Levine (Ohio State University), http://www.cse.ohio-state.edu/~levinej/

- Where: Conference Room 3760

- When: Friday noon (09/04)

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August 28, 2009

- Topology-based systems for data analysis and visualization

Topological techniques have become popular for the analysis of scalar
functions, for example, for automatic feature detection and
extraction. In this informal talk, I will present an overview of the
various software solutions we are developing to solve data analysis
and visualization problems. Some topological methods currently in
development at SCI utilize Reeb graphs, Morse-Smale complexes and
Jacobi sets. Some motivation and basic background for these techniques
will be presented in the talk. In particular, the main focus of the
talk will be covering the breadth of techniques that are currently
being developed here, and an overview of the state of the software
implementations.

- Speaker: Attila Gyulassy (SCI), http://idav.ucdavis.edu/~jediati/

- Where: Conference Room 3760

- When: Friday noon (08/28)

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Open Discussion and Semester Planning

A common practice for VisLunch is to use some of its
sessions as a mean to let people know about the work
of the new people around: new faculties, new post docs,
new PhD. students . As there are lots of new faces
around, we hope to schedule some of these presentations
in this session.

- Summer Internships

Hurrah! It's back to school time!

PhD. Students are strongly invited to schedule a VisLunch talk (~ 30 minutes)
to present the work they accomplished during their summer internship.

- IEEE VIS talks

Wow! SCI rocked once again at IEEE VIS this year!

If you're the presenter of an accepted VIS paper, please let
us know and we'll schedule a session for you so you can practice your talk.

This semester Julien Tierny and Attila Gyulassy will be responsible
for organizing the VisLunch sessions. Please feel free to contact them
for any question regarding VisLunch or for scheduling a talk:

Julien Tierny
Attila Gyulassy
Room: 4660
Phone: 585-3911
jtierny@sci.utah.edu, aggyulassy@ucdavis.edu

Information regarding the VisLunch sessions will posted on this wiki page (http://www.vistrails.org/index.php/VisLunch/Fall2009)

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