VistrailsWiki - User contributions [en]

VisLunch/Fall2009

2010-02-01T04:22:59Z

Jtierny: /* Open Discussion and Semester Planning */

== December 11, 2009 ==
- '''Photo-based Industrial Augmented Reality Registration And Navigation Methods'''

This talk will briefly introduce an industrial project for discrepancy
check using augmented reality. Construction companies employ CAD
software during the planning phase. Unfortunately what is finally
built often does not match the original plan. The procedure of
validating the model is called "discrepancy check". The system
proposed here allows the user to easily obtain an augmentation in
order to find differences between the planned 3D model and the built
items. The main difference to previous body of work in this field is
the emphasis on usability and acceptance of the solution. We will
demonstrates some user interaction techniques that ease the navigation
in the augmented CAD documentation and briefly present the different
algorithms developed to registered still images to a CAD coordinates
systems. The talk will also describe a registration approach based on
keyframe. Registration is at the core of every photo-based AR software
such as ours. This alignment of the image to the 3D model coordinate
system is usually achieved with fiducial markers. When a single
keyframe is used, the unknown baseline length has to be estimated in
order to superimpose virtual models onto the image. In this present, I
will present an automatic algorithm to augment the relative pose,
estimated using a single keyframe, into a full pose that will permit
superimposition.

- ''Speaker:'' Pierre Georgel (Technical University of Munich), http://campar.in.tum.de/Main/PierreGeorgel

- ''Where:'' Conference Room 3760

- ''When:'' Friday 10am (12/11)

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 13, 2009 ==
- '''Ensemble-Vis: A Framework for the Statistical Visualization of Ensemble Data'''

Scientists are increasingly using "ensemble data sets"
to explore relationships present in dynamic systems. Ensemble data
sets combine spatio-temporal simulation results generated using
multiple numerical models, sampled input conditions and perturbed
parameters. While ensemble data sets are a powerful tool for
mitigating uncertainty, they pose significant visualization and
analysis challenges due to their complexity. We present
"Ensemble-Vis", a framework consisting of a collection of overview
and statistical displays linked through a high level of interactivity
for gaining key scientific insight into the distribution of the
simulation results as well as the uncertainty associated with the
data. In contrast to methods that present large amounts of diverse
information in a single display, we argue that combining multiple
linked statistical displays yields a clearer presentation of the data
and facilitates a greater level of visual data analysis. We
demonstrate this approach using driving problems from climate modeling
and meteorology and discuss generalizations to other fields.

- ''Speaker:'' Kristi Potter (SCI), http://www.sci.utah.edu/~kpotter/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/13)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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 at sci dot utah dot edu, aggyulassy at ucdavis dot edu

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

----

VisLunch/Fall2009

2009-12-11T14:23:45Z

Jtierny: /* December 11, 2009 */

== December 11, 2009 ==
- '''Photo-based Industrial Augmented Reality Registration And Navigation Methods'''

This talk will briefly introduce an industrial project for discrepancy
check using augmented reality. Construction companies employ CAD
software during the planning phase. Unfortunately what is finally
built often does not match the original plan. The procedure of
validating the model is called "discrepancy check". The system
proposed here allows the user to easily obtain an augmentation in
order to find differences between the planned 3D model and the built
items. The main difference to previous body of work in this field is
the emphasis on usability and acceptance of the solution. We will
demonstrates some user interaction techniques that ease the navigation
in the augmented CAD documentation and briefly present the different
algorithms developed to registered still images to a CAD coordinates
systems. The talk will also describe a registration approach based on
keyframe. Registration is at the core of every photo-based AR software
such as ours. This alignment of the image to the 3D model coordinate
system is usually achieved with fiducial markers. When a single
keyframe is used, the unknown baseline length has to be estimated in
order to superimpose virtual models onto the image. In this present, I
will present an automatic algorithm to augment the relative pose,
estimated using a single keyframe, into a full pose that will permit
superimposition.

- ''Speaker:'' Pierre Georgel (Technical University of Munich), http://campar.in.tum.de/Main/PierreGeorgel

- ''Where:'' Conference Room 3760

- ''When:'' Friday 10am (12/11)

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 13, 2009 ==
- '''Ensemble-Vis: A Framework for the Statistical Visualization of Ensemble Data'''

Scientists are increasingly using "ensemble data sets"
to explore relationships present in dynamic systems. Ensemble data
sets combine spatio-temporal simulation results generated using
multiple numerical models, sampled input conditions and perturbed
parameters. While ensemble data sets are a powerful tool for
mitigating uncertainty, they pose significant visualization and
analysis challenges due to their complexity. We present
"Ensemble-Vis", a framework consisting of a collection of overview
and statistical displays linked through a high level of interactivity
for gaining key scientific insight into the distribution of the
simulation results as well as the uncertainty associated with the
data. In contrast to methods that present large amounts of diverse
information in a single display, we argue that combining multiple
linked statistical displays yields a clearer presentation of the data
and facilitates a greater level of visual data analysis. We
demonstrate this approach using driving problems from climate modeling
and meteorology and discuss generalizations to other fields.

- ''Speaker:'' Kristi Potter (SCI), http://www.sci.utah.edu/~kpotter/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/13)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-12-08T16:25:36Z

Jtierny:

== December 11, 2009 ==
- '''Photo-based Industrial Augmented Reality Registration And Navigation Methods'''

This talk will briefly introduce an industrial project for discrepancy
check using augmented reality. Construction companies employ CAD
software during the planning phase. Unfortunately what is finally
built often does not match the original plan. The procedure of
validating the model is called "discrepancy check". The system
proposed here allows the user to easily obtain an augmentation in
order to find differences between the planned 3D model and the built
items. The main difference to previous body of work in this field is
the emphasis on usability and acceptance of the solution. We will
demonstrates some user interaction techniques that ease the navigation
in the augmented CAD documentation and briefly present the different
algorithms developed to registered still images to a CAD coordinates
systems. The talk will also describe a registration approach based on
keyframe. Registration is at the core of every photo-based AR software
such as ours. This alignment of the image to the 3D model coordinate
system is usually achieved with fiducial markers. When a single
keyframe is used, the unknown baseline length has to be estimated in
order to superimpose virtual models onto the image. In this present, I
will present an automatic algorithm to augment the relative pose,
estimated using a single keyframe, into a full pose that will permit
superimposition.

- ''Speaker:'' Pierre Georgel (Technical University of Munich), http://campar.in.tum.de/Main/PierreGeorgel

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (12/11)

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 13, 2009 ==
- '''Ensemble-Vis: A Framework for the Statistical Visualization of Ensemble Data'''

Scientists are increasingly using "ensemble data sets"
to explore relationships present in dynamic systems. Ensemble data
sets combine spatio-temporal simulation results generated using
multiple numerical models, sampled input conditions and perturbed
parameters. While ensemble data sets are a powerful tool for
mitigating uncertainty, they pose significant visualization and
analysis challenges due to their complexity. We present
"Ensemble-Vis", a framework consisting of a collection of overview
and statistical displays linked through a high level of interactivity
for gaining key scientific insight into the distribution of the
simulation results as well as the uncertainty associated with the
data. In contrast to methods that present large amounts of diverse
information in a single display, we argue that combining multiple
linked statistical displays yields a clearer presentation of the data
and facilitates a greater level of visual data analysis. We
demonstrate this approach using driving problems from climate modeling
and meteorology and discuss generalizations to other fields.

- ''Speaker:'' Kristi Potter (SCI), http://www.sci.utah.edu/~kpotter/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/13)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-12T15:20:26Z

Jtierny: /* November 13, 2009 */

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 13, 2009 ==
- '''Ensemble-Vis: A Framework for the Statistical Visualization of Ensemble Data'''

Scientists are increasingly using "ensemble data sets"
to explore relationships present in dynamic systems. Ensemble data
sets combine spatio-temporal simulation results generated using
multiple numerical models, sampled input conditions and perturbed
parameters. While ensemble data sets are a powerful tool for
mitigating uncertainty, they pose significant visualization and
analysis challenges due to their complexity. We present
"Ensemble-Vis", a framework consisting of a collection of overview
and statistical displays linked through a high level of interactivity
for gaining key scientific insight into the distribution of the
simulation results as well as the uncertainty associated with the
data. In contrast to methods that present large amounts of diverse
information in a single display, we argue that combining multiple
linked statistical displays yields a clearer presentation of the data
and facilitates a greater level of visual data analysis. We
demonstrate this approach using driving problems from climate modeling
and meteorology and discuss generalizations to other fields.

- ''Speaker:'' Kristi Potter (SCI), http://www.sci.utah.edu/~kpotter/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/13)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-12T15:20:06Z

Jtierny: /* November 6, 2009 */

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 13, 2009 ==
- '''DEnsemble-Vis: A Framework for the Statistical Visualization of Ensemble Data'''

- ''Speaker:'' Kristi Potter (SCI), http://www.sci.utah.edu/~kpotter/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/13)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-05T15:36:58Z

Jtierny: /* November 6, 2009 */

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-05T15:36:45Z

Jtierny: /* November 6, 2009 */

== November 20, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/20)

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-05T15:36:15Z

Jtierny: /* October 30, 2009 */

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-11-05T15:36:03Z

Jtierny: /* November 6, 2009 */

== November 6, 2009 ==
- '''Depth Dependent Halos''' (VIS paper discussion)

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-29T14:47:09Z

Jtierny: /* November 6, 2009 */

== November 6, 2009 ==
- '''Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations''' (VIS paper discussion)

- ''Speaker:'' Dave Koop (SCI), http://www.sci.utah.edu/people/dakoop.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-29T14:43:59Z

Jtierny: /* November 6, 2009 */

== November 6, 2009 ==
- '''A User Study to Compare Four Uncertainty Visualization Methods for 1D and 2D Datasets''' (VIS paper discussion)

- ''Speaker:'' Blake Nelson (SCI), https://www.sci.utah.edu/people/bnelson.html

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (11/06)

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-29T14:38:15Z

Jtierny: /* October 30, 2009 */

== 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 ==
- '''Exploring the Millennium Run - Scalable Rendering of Large-Scale Cosmological Datasets''' (VIS paper discussion)

- ''Speaker:'' Linh Ha (SCI), http://www.cs.utah.edu/~lha/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (10/30)

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-25T21:42:53Z

Jtierny: /* November 6, 2009 */

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-25T21:42:42Z

Jtierny: /* October 30, 2009 */

== November 6, 2009 ==
- '''tructuring 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-25T21:40:15Z

Jtierny: /* October 30, 2009 */

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-10-25T21:39:10Z

Jtierny: /* October 9, 2009 */

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-15T17:19:28Z

Jtierny: /* September 18, 2009 */

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-15T17:19:19Z

Jtierny: /* September 18, 2009 */

VisLunch/Fall2009

2009-09-14T16:31:10Z

Jtierny: /* September 11, 2009 */

== 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)

----

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-14T15:44:02Z

Jtierny: /* October 9, 2009 */

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-14T15:43:20Z

Jtierny: /* October 9, 2009 */

== 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),

- ''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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-14T15:39:30Z

Jtierny: /* October 9, 2009 */

== 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 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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-14T15:39:11Z

Jtierny: /* October 2, 2009 */

== 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 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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-13T21:39:48Z

Jtierny: /* October 2, 2009 */

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-13T21:39:35Z

Jtierny: /* September 11, 2009 */

== 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 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-13T21:35:13Z

Jtierny:

== 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)

----

== 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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-03T00:58:35Z

Jtierny: /* Coming up next next friday */

== Coming up next friday ==
- '''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)

----

== Coming up next next friday ==
- '''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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-03T00:58:21Z

Jtierny: /* Coming up next next friday */

== Coming up next next friday ==
- '''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)

----

== Coming up next next friday ==
- '''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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-03T00:57:28Z

Jtierny: /* Coming up next next friday */

== Coming up next next friday ==
- '''Delaunay Methods for Approximating Geometric Domains'''

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

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (09/04)

----

== Coming up next next friday ==
- '''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)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-09-03T00:55:09Z

Jtierny: /* Coming up next friday */

== Coming up next next friday ==
- '''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 (09/04)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-08-30T18:55:21Z

Jtierny: /* Coming up next friday */

== Coming up next friday ==
- '''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 (09/04)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-08-30T18:49:28Z

Jtierny: /* Coming up next friday */

VisLunch/Fall2009

2009-08-30T18:48:03Z

Jtierny: /* Coming up next Friday */

== Coming up next friday ==
- '''Topological Analysis of 2D Steady Vector Fields'''

Topological techniques have become popular for the analysis of scalar 

- ''Speaker:'' Guoning Chen (SCI), http://idav.ucdavis.edu/~jediati/

- ''Where:'' Conference Room 3760

- ''When:'' Friday noon (08/28)

----

== 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)

----

== 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)

----

VisLunch/Fall2009

2009-08-26T15:23:31Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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)

----

VisLunch/Fall2009

2009-08-26T15:22:40Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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)

----

VisLunch/Fall2009

2009-08-26T15:22:19Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

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)

- '''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.

----

VisLunch/Fall2009

2009-08-26T15:22:03Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

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)

- ''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.

----

VisLunch/Fall2009

2009-08-26T15:19:35Z

Jtierny:

== Coming up next Friday ==
- '''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)

----

== 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.

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)

----

VisLunch/Fall2009

2009-08-26T14:50:25Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

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)

VisLunch/Fall2009

2009-08-26T14:50:14Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

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)

VisLunch/Fall2009

2009-08-26T14:50:05Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

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)

VisLunch/Fall2009

2009-08-26T14:45:25Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== 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.

With

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)

VisLunch/Fall2009

2009-08-26T14:42:38Z

Jtierny: /* Open Discussion and Semester Planning */

VisLunch/Fall2009

2009-08-26T14:41:17Z

Jtierny: /* Coming up next Friday */

VisLunch/Fall2009

2009-08-26T14:40:40Z

Jtierny: /* Open Discussion and Semester Planning */

== Coming up next Friday ==
- '''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)

----

== Open Discussion and Semester Planning ==
This semester Julien Tierny and Attila Gyulassy will be responsible for organizing the VisLunch sessions. Here are their contact
informations:

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

VisLunch/Fall2009

2009-08-26T14:39:23Z

Jtierny: /* Coming up next Friday */

== Coming up next Friday ==
- '''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)

----

== Open Discussion and Semester Planning ==
This semester Julien Tierny and Attila Gyulassy will be responsible for organizing the VisLunch sessions. Here are their contact
informations:

Lauro Lins
Room: 4887
Phone: 581-8061
vislunch@sci.utah.edu

VisLunch/Fall2009

2009-08-26T14:37:42Z

Jtierny: /* Coming up next Friday */

VisLunch/Fall2009

2009-08-26T14:37:08Z

Jtierny:

== Coming up next Friday ==
- '''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)

----

VisLunch/Fall2009

2009-08-26T14:25:39Z

Jtierny:

== Coming up next Friday ==
'''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/]

----

VisLunch/Fall2009

2009-08-26T14:23:10Z

Jtierny: /* Headline text */

== Coming up next Friday ==
'''Topology-based systems for data analysis and visualization'''