3D Storytelling of Livia’s Villa

by Anika Radiya-Dixit


Eva Pietroni is in charge of the 3D modeling project, “Livia’s Villa Reloaded”

Have you ever pondered upon how 3D virtual realities are constructed? Or the potential to use them to tell stories about architectural masterpieces built millenniums ago?

The 5th International Conference on Remote Sensing in Archaeology held in the Fitzpatrick Center this weekend explored new technologies such as remote sensing, 3D reconstruction, and 3D printing used by the various facets of archaeology.

In her talk about a virtual archeology project called “Livia’s Villa Reloaded,” Eva Pietroni, art historian and co-director of the Virtual Heritage Lab in Italy, explored ways to integrate 3D modeling techniques into a virtual reality to best describe the history behind the reconstruction of the villa. The project is dedicated to the Villa Ad Gallinas Albas, which Livia Drusilla took as dowry when she married Emperor Augustus in the first century B.C.

The archeological landscape and the actual site have been modeled with 3D scenes in a Virtual Reality application with guides situated around the area to explain to tourists details of the reconstruction. The model combined images from the currently observable landscape and the potential ancient landscape — derived from both hypotheses and historical references. Many parts of the model have been implemented in the Duke Immersive Virtual Environment (DiVE).

Instead of using simple 3D characters to talk to the public, the team decided to try using real actors who talked in front of a small virtual set in front of a green screen. They used a specialized cinematic camera and played around with lighting and filtering effects to obtain the best shots of the actor that would later be put into the virtual environment. Pietroni expressed her excitement at the numerous feats the team was able to accomplish especially since they were not limited by rudimentary technology such as joysticks and push buttons. As a result, the 3D scenes have been implemented by testing the “grammar of gesture” — or in other words, the interactivity of the actor performing mid-air gestures — in a virtual environment. Hearteningly, the public has been “attracted by this possibility,” encouraging the team to work on better enhancing the detailed functionalities that the virtual character is able to perform. In her video demonstration, Pietroni showed the audience the Livia’s villa being reconstructed in real time with cinematographic paradigms and virtual set practices. It was extremely fascinating to watch as the video moved smoothly over the virtual reality, giving a helicopter view of the reconstruction.


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Helicopter view of the villa

One important point that Pietroni emphasized was testing how much freedom of exploration to give to the user. Currently, the exploration mode — indicated by the red dots hovering over the bird in the bottom left corner of the virtual reality — has a predefined camera animation path, since the site is very large, to prevent the user from getting lost. At the same time, the user has the ability to interrupt this automated navigation to look around and rotate the arm to explore the area. As a result, the effect achieved is a combination of a “movie and a free exploration” that keeps the audience engaged for the most optimal length of time.

Another feature provided in the menu options allows the user to navigate to a closer view of a specific part of the villa. Here, the user can walk through different areas of the villa, through kitchens and gardens, with guides located in specific areas that activate once the user has entered the desired region. This virtual storytelling is extremely important in being able to give the user a vicarious thrill in understanding the life and perspective of people living in ancient times. For example, a guide dressed in a toga in a kitchen explained the traditions held during mealtimes, and another guide in the private gardens detailed the family’s sleeping habits. The virtual details of the private garden were spectacular and beautiful, each leaf realistically swaying in the wind, each flower so well created that one could almost feel the texture of the petals as they strolled past.


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Guide talking about a kitchen in the villa

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Strolling through the gardens

The novelty of the “Livia’s Villa Reloaded” project is especially remarkable because the team was able to incorporate new archeological findings about the villa, rather than simply creating a system from old data without ever updating the visual aspects. Sometimes, as the speaker noted, this required the team to entirely reconfigure the lighting of a certain part of the villa when new data came in, so unfortunately, the project is not yet automatic. Of course, to ultimately improve the application, the team often queries the public on specific aspects they liked and disliked, and perhaps in the future, the virtual scenes of the villa may be developed to a perfection that they will be confused with reality itself.


See details about the conference at: http://space2place.classicalstudies.duke.edu/program/dive

Artistic Anatomy: An Exploration of the Spine

By Olivia Zhu

How many times have you acted out the shape of a vertebra with your body? How many times have you even imagined what each of your vertebrae looks like?

On Wednesday, October 1, Kate Trammell and Sharon Babcock held a workshop on the spine as part of the series, Namely Muscles. In the interactive session, they pushed their audience members to gain a greater awareness of their spines.

Participants assemble vertebrae and discs of the spine

Participants assemble vertebrae and discs of the spine

Trammell and Babcock aim to revolutionize the teaching of anatomy by combining art, mainly through dance, and science. They imagine that a more active, participatory learning style will allow students from all backgrounds to learn and retain anatomy information much better. Babcock, who received her Ph.D. in anatomy from Duke, emphasized how her collaboration with Trammell, a dancer and choreographer, allowed her to truly internalize her study of anatomy. The workshop participants, who included dancers and scientists alike, also reflected a fusion of art and science.

Trammell observes the living sculptures of thoracic vertebrae

Trammell observes the living sculptures of thoracic vertebrae

To begin the exploration of the spine, Trammell and Babcock had participants close their eyes and feel models of individual vertebrae to gain tactile perception. Trammell and Babcock then instructed participants to make the shape of the vertebrae they felt with their bodies, creating a living sculpture garden of various interpretations of vertebrae–they pointed out key aspects of vertebrae as they walked through the sculptures.

Finally, Trammell and Babcock taught movement: in small groups, people played the roles of muscles, vertebrae, and spinal discs. They worked on interacting with accurate movements (for example, muscles only pull; they cannot push) to illustrate different movements of the spine.

Interactive illustration of a muscle pulling vertebrae

Interactive illustration of a muscle pulling vertebrae




To complete the series, Trammell performed Namely, Muscles, choreographed by Claire Porter, on October 4th  at the Ark.

Mathematical Restoration of Renaissance Masterpieces

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The Ghissi Masterpiece, missing the ninth panel

By Olivia Zhu

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

Ninth panel of the Ghissi masterpiece, as reconstructed by Charlotte Caspers

What do Renaissance masterpieces and modern medical images have in common?

The same mathematical technique, “oriented elongated filters,” originally developed to detect blood vessels in medical images can actually be used to detect cracks in digital images of antiquated Renaissance paintings.

On September 19, Henry Yan, Rowena Gan, and Ethan Levine, three undergraduate students at Duke, presented their work on oriented elongated filters and many other techniques to the Math Department. Yan, Gan, and Levine performed summer research to detect and correct cracks in the digitized Ghissi masterpiece, an altarpiece done by 14-century Italian painter Francescuccio di Cecco Ghissi. The altarpiece originally consisted of nine panels, but one was lost in the annals of history and has been recently reconstructed by artist and art historian Charlotte Caspers.

The role of the three undergrads was to digitally rejuvenate the panels of the Ghissi masterpiece, which had faded and accumulated cracks in paint layers because of weathering factors like pressure and temperature. Using various mathematical analysis techniques based in Matlab, including oriented elongated filters, linear combinations of 2-D

Henry Yan's K-SVD analysis to detect cracks in the image at left

Henry Yan’s K-SVD analysis to detect cracks in the image at left

Gaussian kernels (which essentially create directional filters), K-SVD (which updates atoms to better fit an image), and multi-scale top-hat (which extracts small elements and details from an image), the research group created a “crack map,” which they overlaid on the original image.

Then they instructed the computer to fill in the cracks with the colors directly adjacent to the cracks, thereby creating a smoother, crack-free image—this method is called inpainting.

In the future, Yan, Gan, and Levine hope to optimize the procedures they have already developed to accomplish color remapping to digitally age or refurbish images so that they look contemporary to their historical period, and to digitally restore gilding, the presence of gold leaf on paintings.

Visibly Thinking about Undergrad Research

By Karl Leif Bates

Undergraduate research is kind of a big deal at Duke.

The grand finale of nearly 200 of this year’s undergrad projects was a giant poster session called “Visible Thinking,” hosted by the Office of Undergraduate Research Support  on April 22.

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

Happy and relieved students sharing posters at Visible Thinking 2014. (Megan Morr, Duke Photo)

This annual showcase just keeps getting bigger, louder and more crowded, which is a great testament to the involvement of undergrads in all areas of Duke’s research enterprise.

The posters and proud students wearing their interview suits filled all the common areas of the first and second levels of the French Family Science Center on Tuesday and spilled into a few out-of-the-way corners as well.

“For many of the students this is the culmination of their four years, in which they’ve made that transition from student to scholar,” said Ron Grunwald, director of the URS office. “They’re no longer simply learning what other people have discovered, they’re discovering things on their own.”

Indeed, Rebecca Leylek wasn’t the least bit discouraged by having to check her experiment every six hours around the clock for days on end to see how the mice’s wounds were healing. The second phase of her project was a protocol she developed and got approval for and it didn’t have the six-hour part. She’s off to grad school at Stanford in immunology.

Ani Saraswathula, who co-chaired the Duke Undergraduate Research Society, apparently missed the deadline for getting his poster into the printed program, but his science on brain tumors was pretty awesome. He’s sticking around after graduation for an MD/PhD at Duke.

The new Bass Connections research teams brought nearly two dozen posters, showing off projects about energy, environmental health, art history, online education, cognitive development,  and decision-making.

And then, there was just an amazing assortment of stinky lemurs and pathogenic yeast and budding investigators talking curious faculty and students through amazing posters like this: Understanding the role of BNP signaling in pak-3 mediated suppression of synaptic bouton defects in spastin null Drosophila.

So, in addition to quizzing the young scientists about their findings, we thought we’d ask a few of them to recite their impressive poster titles from memory:

Sign Up For Datafest 2014 to Work on Mystery Big Data


Heads up Duke undergrads and graduate students — here’s an opportunity to hang out in the beautifully renovated Gross Hall, get creative with your friends using big data and compete for cash prizes and statistics fame.

Datafest, a data analysis competition that started at UCLA, is in its third year in the Triangle. Every year, a mystery client provides a dataset that teams can analyze, tinker with and visualize however they’d like over the course of a weekend. Think hackathon, but for data junkies.

“The datasets are bigger and more complex than what you’ll see in a classroom, but they’re of general interest,” said organizer Mine Çetinkaya-Rundel, an assistant professor of the practice in the Duke statistics department. “We want to encourage students from all levels.”

Last year’s mystery client was online dating website eHarmony (you can read about it here), and teams investigated everything from heightism to Myers-Briggs personality matches in online dating. In 2012, the dataset came from Kiva, the  microlending site.

This year’s dataset provider will be revealed on the first day of Datafest. Sign up ends this Friday, March 7, Monday, March 10, so assemble your team and register here!


Students DiVE into the Body to Learn about Addiction

By: Nonie Arora

Dr. Schwartz-Bloom explains the mechanics of the DiVe. Credit: Nonie Arora

Dr. Schwartz-Bloom explains the mechanics of the DiVE. Credit: Nonie Arora

There are not many six-sided, immersive virtual environments in the world–but one of them is at Duke.

Students had the opportunity to dive into pharmacology visualizations with Dr. Rochelle Schwartz-Bloom last week during a tour of the Duke immersive Virtual Environment (DiVE). She explained that the 3D in the DiVE is different from the 3D of a typical movie theater: the glasses have a refresh rate that’s out of sync between the two eyes.

It’s like being inside of a video game. You use a Nintendo-like wand and press buttons to interact with the environment.

We walked through two simulations modeling different aspects of addiction. In the first, we learned why some people are more likely to become alcoholics than others. In the second, we observed the brain changes that underpin addiction to nicotine.

We dove right into the body of an avatar drinking a beer. Some people metabolize alcohol differently than others, depending on their genetic code, Schwartz-Bloom explained.

The simulation was created by a team of students working with Schwartz-Bloom: she assembled a team of students studying biology, chemistry, computer science, electrical and computer engineering and visual arts. They worked together for a year to build the simulation, which explains how alcohol gets oxidized depending on genetics and whether the changes in metabolism increase or decrease the risk for alcoholism.

Students dragging NAD into the active site of the alcohol metabolizing enzyme in the DiVE. Credit: Nonie Arora

Students dragging NAD into the active site of the alcohol metabolizing enzyme in the DiVE. Credit: Nonie Arora

Dr. Schwartz-Bloom explained the advantages of learning about this reaction with a 3D visualization. “Students made this as a game so that others could go in there to make the changes happen – they’d have to grab and move the atoms. The game gives students a real sense of why you need zinc and NAD for this chemical reaction,” Schwartz-Bloom said.

Through the second visualization, we realized why smokers who are addicted generally increase their consumption of cigarettes over time. We saw how repeated exposure to nicotine changes the brain, causing smokers to need more cigarettes over time to get the same pleasurable feelings. The tool can be used in schools to educate students how smoking actually changes the brain, Schwartz-Bloom said.

In the DiVE, I felt like I was on the Magic School Bus, jumping right into the action to learn about pharmacology principles! Free group tours are available at the DiVE between 4:30 and 5:30 on Thursdays.