Category: News Releases

In a study published recently in the journal Coral Reefs, scientists from Scripps Institution of Oceanography created and analyzed detailed photomosaics of the coral reef at Palmyra Atoll in the Pacific Ocean.  Led by Scripps coral-reef ecology Ph.D. student Clinton Edwards, the team canvassed more than 17,000 square feet of reef and 44,008 coral colonies, taking more than 39,000 images.

Coral reef researchers canvas a reef in Palmyra Atoll,
south of Hawaii. (Photo by Stefani Gordon)

Rather than taking the conventional route of stitching together the collected images into high-resolution 2D image mosaics, Scripps researchers used cloud computing techniques developed by UC San Diego engineers and computer scientists to enable the creation of detailed models in 3D and even in 4D (i.e., adding the dimension of time).  The models can be navigated and studied fully interactively, thanks to a team of technologists from UC San Diego’s Cultural Heritage Engineering Initiative (CHEI), led by UC San Diego structural engineering professor and computer science faculty-affiliate Falko Kuester.

Creating the mosaics and wringing useful information out of them is a time-consuming process. Gathering the data, the scientists generally did three dives a day, and it took more than five full days of diving to collect the images for the 16 plots used in the study. Back in the lab, Edwards used a custom high-performance computing system to stitch together the 2,500-3,500 individual images that make up each mosaic. It takes the software several days to complete the rendering of the composite image, and around 100 hours to label and classify all the corals in each image. Then the final step is to extract the species information and analyze it, which takes another three days or so per image.

GIF of 3D model of coral, achieved using algorithms and techniques developed in QI’s Cultural Heritage Engineering Initiative.

Digitization of the images is clearly the limiting step, said Edwards. But that may change soon, he added: “We have excellent collaborators in the Computer Science and Engineering department at UC San Diego, and are getting close to having a computer-assisted workflow that will dramatically accelerate this process.” The computer scientists and engineers are part of CHEI, based in the Qualcomm Institute.

The data and scans of coral reefs from Palmyra Atoll represent some of the first results from the 100 Island Challenge (100IC), a project to create a global perspective on how coral reefs are changing over time. Scripps professor Stuart Sandin leads the overall project as principal investigator, with technology support from technologists in CHEI. The CHEI team is developing the novel 3D imaging and visual analytics techniques that Scripps scientists are using to create the mosaics that capture every detail of coral reef structure and ecology. So far, Scripps and international partners in 100IC have visited 70 of the 100 islands, and they plan to resurvey each site every two years. The resulting images, 3D models and analysis will also become baseline data to help local agencies study their own reefs.

In addition to Prof. Kuester, the 100 Island Challenge technology team from CHEI includes a handful of researchers affiliated with the CSE department: Ph.D. student Vid Petrovic, who is developing the software that the Scripps scientists use to create, visualize and analyze the coral reefs through 3D models and photomosaics; graduate student Dominique Meyer, who completed his B.S. in Physics at UC San Diego in 2016; software engineer and Computer Science alumnus Chris McFarland (B.S. ’12) and Computer Engineering alumnus  Eric Lo (B.S. ’14), who is a staff robotics engineer in CHEI.

100 Island Challenge tech team includes six researchers affiliated with the Qualcomm Institute (l-r):Calit2 professor of scientific visualization and virtual reality Falko Kuester; CSE Ph.D. student Vid Petrovic; CSE graduate student Dominique Meyer; QI programmer-analyst and CSE alumnus Chris McFarland, QI staff engineer and Computer Engineering alumnus Eric Lo; and QI-CHEI staff Dominique Rissolo, a marine archaeologist.

The CHEI team has also deployed the technology for the Bermuda 100 Challenge , in which CHEI and Bermuda’s Custodian of Historic Wrecks are creating digital replicas of shipwrecks and coral reefs surrounding Bermuda.

CSE’s Petrovic is now working on creating custom algorithms to accelerate the work on the coral-reef effort and other underwater mapping and computer modeling of the environment.

Top photo at Palmyra Atoll contains 5,000 corals;
at bottom, identical photo after being annotated by
hand to label each coral species with different
color. 3D technology can dramatically reduce the
time to capture coral reef data for later analysis
in the lab.
Watch video of Palmyra Atoll coral
reef annotated to label species of coral in color
overlays .

“More and more imagery is being collected across the field of marine sciences, and the pace and scale of the effort will only increase — but more data doesn’t automatically mean more, or better, science,” observed Petrovic. “It’s an honor and a joy to be working so closely with a group of marine ecologists to address this, developing collaboratively the tools and workflows that are needed to make productive use of the imagery, whether for monitoring reef health, or for advancing basic science.”

According to Petrovic’s advisor, Prof. Kuester, the team is demonstrating that extremely detailed models consisting of billions of 3D data points can now be created overnight literally, when using distributed computing strategies. For a recent study, 14,000 images were turned into a comprehensive 3D model in less than a day. A digital surrogate of sorts, the model helped researchers annotate, measure and study the target environment in ways that would be impossible to achieve in-situ. By lifting the image data from 2D to 3D models or even 4D (including time), the technology is adding diagnostic value. Traditional analysis techniques when working on photomosaics can be supported by exporting a mosaic directly from the model, using the equivalent of an ultra-resolution virtual camera with user-definable characteristics.

Petrovic says the team is making it possible for scientists to virtually explore reefs in the lab, allowing them to time-travel from year to year and track the growth and decline of individual colonies, and to study spatial and temporal relationships across the reef.

“We’re speeding up the digitization and annotation, and clearing a path to letting machine-learning techniques carry more of this burden,” Petrovic said. “This is all terribly exciting, and with much more to come. But the most rewarding aspect for me is the interdisciplinary collaboration that makes it possible in the first place, that lets us apply a decade of visualization research in support of vital ecological work.”

Beyond advancing the state of science in order to better safeguard coral reefs, the team’s research is literally giving coral reefs a voice. The 100 Island Challenge’s adoption of 3D digital tools allows the public at large to dive and experience these stunning ecosystems in virtual reality, to see what otherwise cannot be seen, and hopefully become stewards for coral reef preservation. “If a photo is worth a thousand words,” observed CHEI’s Kuester, “just imagine what a fully interactive 3D environment can accomplish for scientific storytelling.”

September 18, 2017. A team of archaeologists from the University of California San Diego and two leading Israeli universities has wrapped up a three-week expedition to document two major sites in Israel using the latest in 3D scientific visualization technologies.

The expedition, led by UC San Diego Department of Anthropology professor Thomas E. Levy, involved a land-and-sea approach to understanding trade and exchange during Biblical times, at sites dating to the Iron Age, circa 1200 to 586 BC. Officially sanctioned by The Explorers Club, the expedition carried Explorers Club Flag #179 to the ancient mining region of Timna in southern Israel as well as to Tel Dor on the Mediterranean coast, the site of a submerged port facility.

“Between the two sites, we captured more than 24,000 high-definition photos for use in creating 3D computer models of these two very historic areas,” said Levy, who directs UC San Diego’s Center for Cyber-Archaeology and Sustainability (CCAS), based in the Qualcomm Institute, and co-directs the Scripps Center for Marine Archaeology (SCMA). “Back in San Diego, we’ll be processing the images to build large-scale virtual models to help archaeologists and students better understand the two historically important regions in Israel and how they were united in antiquity through the copper trade.”

Explorers Club Flag 179 at the submerged Iron Age port adjacent to Tel Dor, Israel.  Thomas Levy (left) and Assaf Yasur-Landau (right) display the flag in rough water. (Photo courtesy T.E. Levy, Scripps Center for Marine Archaeology)

Levy’s co-principal investigators on the expedition included University of Haifa professor Assaf Yasur-Landau in the Department of Maritime Civilizations, and UC San Diego alumnus Erez Ben-Yosef (Ph.D. ’10), who did his doctoral dissertation with Levy and is now a professor of archaeology at Tel Aviv University. Ben-Yosef organized the logistical infrastructure of the Timna imaging projects, while Yasur-Landau organized the 3D Tel Dor imaging project through his Laboratory for Coastal Archaeology and Underwater Survey, with support from former Scripps Institution of Oceanography postdoc Tali Treibitz from the University of Haifa’s Marine Imaging Laboratory. Treibitz facilitated the underwater data collection in the waters of Dor. Also helping to make the expedition a success were CHEI director Falko Kuester for student support and the allocation of processing resources and equipment to the project, as well as researcher Eric Lo for image processing.

Drone view of contact zone between Tel Dor and various Iron Age and Classical period building with the Mediterranean Sea shore (Photo courtesy Griffin Ltd., Scripps Center for Marine Archaeology, and Center for Cyber-Archaeology and Sustainability, UC San Diego)

The UC San Diego team included Christian McDonald, scientific diving safety officer at Scripps Institution of Oceanography, Department of Anthropology graduate student Anthony Tamberino, as well as Dominique Meyer, a Ph.D. student in the Department of Computer Science and Engineering and researcher in the Cultural Heritage Engineering Initiative (CHEI). Meyer and Tamberino were responsible for the provision of equipment and data collection of aerial and ground-based 3D images. Meyer also served as the primary drone operator and flight planner for the expedition, for which he operated Phantom 4 drones with standard 20-mm cameras as well as directing a heavy-lift drone octocopter for video and structure-from-motion (SfM) photography with 36-megapixel cameras operated by the Griffin company. The logistics of the project were greatly supported by the Israel Antiquities Authority whose own drone operator, Yitzhak Marmelstein, worked with the team for the duration of the project.

CSE Ph.D. student Dominique Meyer adjusting Phantom 4 drones before flights over Shiqmim and the Wadi Beersheva. (Photo courtesy T.E. Levy, Scripps Center for Marine Archaeology and Center for Cyber-Archaeology and Sustainability, UC San Diego).

“Previously, copper ingots found in the waters north of Tel Dor were traced via lead isotope analysis to the Faynan region in Jordan, where extensive Iron Age mines and smelting factories have been found and excavated by our UC San Diego team,” said Levy. “It seemed most likely that Tel Dor was the main Iron Age port along the Israeli coast for the trade of copper, from the desert zones of Faynan in the northern Aravah valley and Timna at its southern end.”

Levy (center) with former Scripps postdoc Tali Treiblitz (left) and Scripps’ diving safety officer Christian McDonald.

The aerial drones carried out regional 3D scanning of more than 15 major ancient sites related to copper mining and smelting in the Timna mining region, including at Shiqmim in the northern Negev desert. In Shiqmim, Levy had previously excavated Copper Age ruins, including an ancient 24-acre village dating to the Chalcolithic period (ca. 4500 – 3600 BC), when copper was first smelted and cast in the southern Levant.

To capture the submerged port facility at Tel Dor, the team used scuba and high-precision underwater cameras to image remains of the ca. 9th century BC port.

The Israel 3D Land and Sea Project 2017 was generously funded by Marian Scheuer Sofaer and Abraham Sofaer of Palo Alto, CA..

In addition to the 3D imaging project at Tel Dor and Timna, the expedition laid the groundwork for the first UC San Diego-University of Haifa Marine Archaeology Field School, tentatively planned for July 2018.

San Diego, Calif., Monday, Sept. 11, 2017 — Cultural heritage around the globe is continually subject to a multitude of threats, from malicious acts during wartime to neglect, overexposure and natural disasters. Researchers at the University of California San Diego Qualcomm Institute – along with conservationists and researchers at other universities – increasingly turn to advanced digital tools and techniques to better document, preserve and share the world’s historic places.

Dominique Rissolo and Michael Hess assess the day’s results during a 3D documentation project in Yucatan, Mexico (photo courtesy of Binar Media).

This approach was discussed in detail at the 26th International Comité Internationale de la Photogrammétrie Architecturale (CIPA) Symposium, hosted by Carleton University in Ottawa, Canada. The symposium, titled Digital Workflows for Heritage Conservation, brought together archaeologists, engineers, architects and conservation specialists from universities, government agencies and private foundations around the world. They discussed best practices for digitizing and restoring heritage structures and monuments while exploring advances in virtual and augmented reality to engage more diverse audiences.

In attendance at the conference – along with delegates from more than 25 countries – were Assistant Research Scientist Dominique Rissolo and Structural Engineering Ph.D. student Michael Hess of the QI Cultural Heritage Engineering Initiative (CHEI) at UC San Diego. Rissolo and Hess were part of a research team that included CHEI Director Falko Kuester as well as Vid Petrovic, Dominique Meyer, and Eric Lo, who are students and staff at QI and the Jacobs School of Engineering.

Rissolo presented on digital preservation of ancient Maya cave architecture along the Caribbean coast of Mexico. With the rapid expansion of tourism development on the “Riviera Maya,” many cave sites – and unique altars and shrines that they have long concealed – are exposed to new threats.

Dominique Rissolo acquires dozens of images to create a photogrammetric model of an Maya cave shrine (photo by C. Rojas).

Hess demonstrated new interactive software tools for classifying and analyzing construction materials via 3D point clouds. Novel capabilities adapted by Hess are unique to the point-based visual analytics software developed by Petrovic and are transforming the way specialists analyze data from heritage structures. The paperpresented by Hess was among the top-10 selected to appear in the journal Virtual Archaeology Review.

Other featured projects at the symposium ranged from monitoring rock-fall hazards at Petra in Jordan to digitally preserving war-ravaged mosques in Aleppo, Syria and earthquake-rattled structures in Katmandu, Nepal. Also discussed were novel fabrication techniques used to replace the lost or disappearing architectural elements of Canada’s treasured Parliament buildings.

Says Rissolo: “It was exciting to interface with such a diverse group – there were representatives from UNESCO, Google, the US National Park Service, CyArk, and many other entities that share a common passion for documenting and safeguarding our world cultural heritage. We were also impressed by the extraordinarily talented staff of the Carleton Immersive Media Studio and we look forward to building stronger ties with a broad group of domain experts, innovators and stake holders in pursuit of preserving world heritage.”

Rissolo and Hess were recently invited by the Department of Civil and Environmental Engineering at Princeton University to give a lecture on their work in November. Through CHEI and their CIPA partners, Rissolo and Hess say they hope to contribute to a stronger and more vibrant digital heritage community.

3D mesh model of an at-risk Maya cave shrine.

A team of researchers from across UC San Diego is developing a new approach for detecting damage to buildings during earthquakes and other extreme events.

UC San Diego researchers are using lasers and drones to create a digital record of Geisel Library. Photos by Erik Jepsen/UC San Diego

They came together at the Geisel Library recently to use lasers and drones to create a digital record of the structure that will serve as a baseline health assessment. In the event that a sizeable earthquake hits nearby, the team will reconvene to retake the digital measurements and assess any damage to the building such as tilting or cracks. (View photo gallery.)

The information is intended to provide both researchers and emergency responders with more detailed information on how structures respond during the earthquakes—beyond the simple visual inspection of buildings currently in use—prior to allowing them to reopen.

According to researchers at the Scripps Institution of Oceanography and Jacobs School of Engineering at UC San Diego who are spearheading the project, the iconic library is the perfect location to begin what they hope will become an effort to digitize the entire campus.

“We are using this culturally significant building on campus as a reference model to help detect structural changes over time,” said Falko Kuester, a professor of structural engineering who serves as director of the Qualcomm Institute’s Cultural Heritage Engineering Initiative (CHEI) and DroneLab.

Falko Kuester’s team took thousands of 2D photographs captured by drones and used structure-from-motion techniques to create a 3D computer model of Geisel Library and its surroundings.

For Yehuda Bock, a distinguished researcher and director of the Orbit and Permanent Array Center at Scripps Oceanography, the primary motivation for the recent survey of Geisel Library was to integrate structural monitoring into his early-warning prototype system for earthquakes and tsunamis.

“Our system tracks ground motions at a millimeter level of accuracy,” said Bock. “This allows us to detect large earthquakes within the critical first minute before the shaking begins.”

Six months ago, Bock equipped the Geisel Library with sensors that continuously measure ground motion from the many faults that crisscross Southern California. The technique he helped pioneer, called seismogeodesy, relies on a combination of GPS receivers and accelerators to very rapidly pinpoint the location and magnitude of strong earthquakes—6.0 magnitude or greater—before the hazardous trembling begins.

The late-July project involved nearly two hours of drone flights led by CHEI researcher Eric Lo, capturing more than 1,000 high-resolution images of the Geisel Library that will be turned into a photorealistic model of the structure. Lo’s drone survey was accompanied by a several-hour ground survey by professional land surveyor Richard Maher using lidar (light detection and ranging), an instrument that sends pulsating laser lights at an object to provide a precise 3-D model. By combining these techniques, the team will create a geometrically as well as visually detailed and accurate final model.

Drone flies by Geisel Library while creating the digital model.

Bock’s GPS sensors provide a precise 3-D reference to tie together the high-resolution drone and lidar imagery, allowing for the accurate detection of subtle permanent displacements of the structure’s outer shell as a measure of its integrity after an event.

Kuester currently leads research teams developing drone technology for crisis management and response, as well as applying the work to study and help preserve ancient Mayan structures in Mexico, Neanderthal caves in Italy, and shipwrecks and coral reefs in Bermuda. For him, this project is a first step to create a digital surrogate or as he calls it, a “cyber-twin” of the campus, before new buildings and bridges transform the campus’s physical appearance in the future.

Although Kuester often looks at ancient buildings and ruins, he points out that “it’s important to also document modern buildings before the perils of time or extreme events cause them to deteriorate or create an even less fortunate outcome.”

The digital record on the condition of buildings as they exist today provides a baseline for comparison in the future as a building ages, or in the case of a fire, earthquake or other natural hazard, actionable data, according to the researchers, to swiftly respond and mitigate risks.

QI researcher Eric Lo from the Cultural Heritage Engineering Initiative ran the drone photography project.

Within a few minutes of completing the drone flights, Lo had a quick 360-degree rotating view of the geometrically shaped building from the images collected during the flights for view in 3-D.

Another important motivation for Bock and Kuester is to have students involved in real-world research projects, both on site and as classroom teaching tools.

“As an educator, it’s important that I expose my students to real-world conditions,” said Falko. “The contribution to science needs to be useful and usable.”

Kuester and Lo will also be turning the drone imagery into a virtual reality experience for those interested in flying themselves around the outside of the library.

Bock and Kuester are hoping the project will attract more interest and funding to seismically monitor and digital archive all buildings throughout the UC San Diego campus.

Meanwhile, at Bock’s lab at Scripps Oceanography, the seismic monitoring data is continuously streamed back in real-time. When the next powerful quake strikes, the system will alert him first of the primary signal, called a P-wave, which indicates an earthquake has taken place, and that the destructive S-wave, the one responsible for the strong earth-shaking, is seconds to minutes away. The GPS and seismic sensors on the Geisel Library will quickly indicate whether it has suffered significant shaking and displacement.

For Bock and Kuester, how these buildings and others respond to outside influences is an important component to how we better prepare as a society for extreme events in the future.

San Diego, July 27, 2017 — In a long feature article and companion video, CNN Travel has posted the feature story on “Charted Waters”. In it, writer Alexander Rosen and his co-producer Joseph Coleman follow Dr. Philippe Rouja, Bermuda’s Custodian of Historic Wrecks, offshore and underwater to visit shipwreck sites in Bermuda’s waters. The report notes that “Rouja documents the current state of Bermuda’s wrecks using photography to create 3-D maps and models in a partnership with the University of California San Diego for a project called the Bermuda 100 Challenge.”

The feature article and video are now available on the CNN Travel interactive website at http://cnn.it/2uu28Xi. The article also links to the Bermuda 100 website.

CNN goes on to say that the computer models “provide a snapshot-in-time and comparing them tells a story about the evolution of both Bermuda’s wrecks and the environment.”

The article explains that the Bermuda 100 Challenge also allows anyone on the Internet to take a virtual dive and experience Bermuda’s cultural and environmental heritage through the web portal created by UC San Diego’s Qualcomm Institute. “Aside from its scientific importance, there’s a connectivity importance, that people can connect to a period of history, a shipwreck, the ocean,” Rouja tells CNN. “And that’s what shipwrecks do. They are actually a great segue for people into the marine environment that might otherwise not get there. So, when you’re out looking at a shipwreck, because you care about the history or you think shipwrecks are cool, suddenly you’re also learning about the rock fish that lives on that shipwreck or the particular spawning aggregation that’s next door. Giving shipwrecks that work to do is actually a big part of the work I do.”

San Diego, July 18, 2017 — Technology deployed by the Qualcomm Institute to create a 3D digital database of more than 100 shipwrecks surrounding Bermuda is the focus of a TV report by the BBC in the United Kingdom and broadcast in countries around the world. The report is now also available for viewing on-demand on the BBC Travel Show’s YouTube channel (see below) worldwide.

The widely-watched BBC Travel Show’s latest episode leads with the Bermuda 100 Challenge, a partnership between UC San Diego’s Cultural Heritage Engineering Initiative (CHEI), the island’s Department of Environment and Natural Resources, as well as Look Bermuda and Nonsuch Expeditions.  The project is using photogrammetry to capture shipwrecks in Bermuda waters and turn the data into 3D computer models that can easily be navigated via a web browser. The Bermuda 100 web portal features information on dozens of shipwrecks, including four which are already viewable as 3D models that document each site in crisp detail.

The BBC program follows Bermuda’s lead expert on marine heritage and Custodian of Historic Wrecks,  Dr. Philippe Rouja, on a visit to one of the four shipwrecks already fully documented by the team. The Montana, which was used to run embargoed goods for the Confederacy during the Civil War, sank in 1783. “It was one of the first ships to be digitally recreated using this cutting-edge technology,” Rouja tells Travel Show host Ade Adepitan, before showing what the 70-meter-long vessel looks like on the Bermuda 100 web portal. “I have never really seen this shipwreck from end to end. You can see how big and long it is, so in one snorkel, you can’t visually take it all in.”

BBC Travel Show host Ade Adepitan (left) interviews Bermuda’s Custodian of Historic Wrecks, Philippe Rouja.

Adds Rouja: “The minute that it’s laid out in that 3D fashion, using photogrammetry, suddenly you can see it from the stern all the way to the bow and you just take in the full extent of the ship and it literally brings it back to life.”

According to the TV report, the team in Bermuda is working with the University of California [San Diego] to “record thousands of images and build a 3D digital replica of [each] vessel. It means that it will be preserved for generations.”

Ultimately, reports the BBC’s Adepitan, the Bermuda 100 web portal is bringing the excitement of discovery to people around the world who unlikely to see first-hand Bermuda’s 400 years of shipwrecks (and the coral reef ecosystems that caused most of those wrecks). “Diving is a luxury that is out of reach for many people,” he concludes. “So the plan is now to map at least 100 of the shipwrecks, meaning that anyone from anywhere in the world will be able to take a digital dive and experience centuries of maritime history.”

San Diego, Calif., April 13, 2017 — Together with their colleagues, researchers from the University of California San Diego have announced new findings about a skeleton nicknamed “Naia,” the earliest mostly complete human found so far in the Americas.

Alberto Nava recovers a vertebra from Naia's skeleton. Photo by Roberto Chavez Arce.
Alberto Nava recovers a vertebra from Naia’s skeleton. Photo by Roberto Chavez Arce

Various studies and analyses carried out in laboratories in Mexico, the United States and Canada have revealed that the remains are those of a girl between 15 and 16 years old who lived almost 13,000 years ago in what is now Mexico’s Yucatan peninsula. Multiple lines of evidence, including pubic bone features, suggest that Naia may have given birth months before she died after falling into the 50-meter deep hole known as Hoyo Negro, a site near Tulum, Quintana Roo.

James C. Chatters, a principal investigator and one of the co-directors of the Hoyo Negro Underwater Archaeology Project, announced  the results at the 82nd annual conference of the Society for American Archaeology (SAA), which took place earlier this month in Vancouver, Canada. Chatters’ collaborators include fellow co-director Dominique Rissolo, a UC San Diego archaeologist and Special Projects Coordinator at the UC San Diego Qualcomm Institute Center of Interdisciplinary Science for Art, Architecture and Archaeology (CISA3) and its Cultural Heritage Engineering Initiative (CHEI). The lead director of the project is Pilar Luna Erreguerena of the Sub-Directorate of Underwater Archeology of the National Institute of Anthropology and History (INAH). In addition to INAH support for the Naia study, the project has received funding from the National Geographic Society and the Strauss Family Foundation, and has also partnered with Seattle Children’s Hospital.

“Only five individuals in the Americas have been securely dated to this early period, more than 12,000 years ago,” says Rissolo. “Such studies are important since skeletal evidence of the First Americans is so rare and elusive. What makes Naia unique is that her skeleton is nearly complete and relatively well preserved. This has enabled our international and interdisciplinary team to perform a range of analyses that are revealing more about the life of a young Paleoamerican woman than we ever thought possible.”

Alberto Nava and Alejandro Alvarez recover bones from the lower portion of Naia's skeleton. Photo by Roberto Chavez Arce
Alberto Nava and Alejandro Alvarez recover bones from the lower portion of Naia’s skeleton. Photo by Roberto Chavez Arce

Between 2014 and 2016 and in coordination with Mexican and international experts, a team of underwater cave explorers with training in underwater archaeological site documentation recovered 98 fragments of Naia’s skeleton. From each of these remains, X-rays and CT scans were taken at the Hospital de Especialidades in Mexico’s Campeche City.

Specialists in Campeche perform a CT scan of Naia's cranium. Photo by James C. Chatters.
Specialists in Campeche perform a CT scan of Naia’s cranium. Photo by James C. Chatters

In 2014, Chatters and his colleagues were able to confirm, using Naia’s DNA, that both the earliest American settlers and modern Native Americans are genetically linked to a single group of Asian emigrants. Scientists working on this project, including Chatters of Applied Paleoscience and DirectAMS in Washington State, and Vera Tiesler and Andrea Cucina of the Autonomous University of Yucatan, have revealed that Naia measured 152 centimeters and weighed a maximum of 50.4 kilos when well-fed, as the study of her teeth and long bones proved that she often went through periods of extreme nutritional stress.

According to experts, these findings suggest that the lives of the first settlers of the Americas, or at least some of these groups that came across the Bering Strait region of Siberia on modern day Alaska, were not idyllic. On the contrary, life was extremely challenging.

The Naia skeleton, which also bore evidence that Naia had healed from a previously broken arm, was discovered in 2007 by Alejandro Álvarez, Alberto Nava and Franco Attolini, members of the Tulum Speleological Project (PET), who together with Roberto Chávez Arce and other members of the PET have been key in the discovery not only of human remains but also of a large assemblage of extinct Pleistocene fauna, including gomphotheres (elephant-like creatures), saber-toothed cats, giant ground sloths, canids and bears, and other still extant animals such as tapirs, pumas, and bats, among others.

Andrea Cucina and Julio Chi Keb, of the Autonomous University of Yucatan, x-ray teeth from Naia's mandible. Photo by James C. Chatters.
Andrea Cucina and Julio Chi Keb, of the Autonomous University of Yucatan, x-ray teeth from Naia’s mandible. Photo by James C. Chatters

Much of the work that has led to a better understanding of Naia’s fate was done far from Hoyo Negro in UC San Diego’s Atkinson Hall. Computer science Ph.D. student Vid Petrovic – a member of the Center’s Integrative Graduate Education and Research Traineeship (IGERT) program in cultural heritage diagnostics – used two-dimensional photographs taken by the scientific dive team to ‘stitch together’ and reconstruct digitally 3D structure-from-motion (SfM) models of both the cave site and Naia’s skeleton.

“Our CISA3-CHEI team at UC San Diego, led by Falko Kuester, has extensive experience using photogrammetric techniques to document cultural heritage sites around the world,” noted Rissolo. “Hoyo Negro was especially difficult, given the depth, darkness, and complexity of the site. Alberto (Beto) Nava and Roberto Chavez led an extraordinary effort to image the site in the most challenging of conditions. They were the astronauts collecting imagery from inner-space, while we were the ones back at mission control transforming those data into information for the scientists to evaluate.”

In their Digital Heritage conference presentation published last year, the researchers wrote that “the implementation of different image acquisition methodologies at different scales (site, feature, and object) has resulted in geometrically accurate and complementary models of cave features as well as individual skeletal elements. These 3D digital (and printable) models have proven critical to current and ongoing morphometric and taphonomic analyses [i.e. the quantitative analysis of form and the study of the processes affecting organisms as they become fossilized], as many of the bones have not been removed from the cave.

“These data,” they continued, “will not only serve as documentation of the site, but will enable project researchers from across disciplines to evaluate and annotate the imagery remotely while guiding subsequent sampling and recovery activities.”

San Diego, January 19, 2017 — If the prospect of a mega-earthquake has you quaking — fear not, because UC San Diego engineers are making sure our world will withstand the rumble. And in addition to using the world’s largest outdoor shake table, researchers at the Jacobs School of Engineering also turned to drones to capture the damage from a simulated, large-scale earthquake on a six-story, lightweight steel-frame building on the UC San Diego shake table. The goal: to determine how the structure would fare during a tremor and fires that may follow.

The structure, the tallest cold-formed steel-frame structure to undergo tests on a shake table, was built to represent a multifamily residential condominium or apartment. It was placed through a series of simulated temblors of increasing intensity that mimicked actual earthquakes.

As a better way to determine stress on the materials, the building’s performance was captured by an extensive array of more than 250 analog sensors, as well as digital cameras and aerial drones. Structural engineering professor (and CSE faculty affiliate) Falko Kuester, who leads UC San Diego’s DroneLab, used unmanned aerial vehicles (UAVs) to capture both the seismic and fire testing and create a high-resolution 3D model and video of observed damage. Engineers can use virtual reality (VR) to zoom in to see the tiniest details, such as cracks and changes in shape and color.

CSE Faculty Affiliate Falko Kuester interviewed by
KPBS News. [Click here to watch the report ]

“This is big VR for big data and big science,” says Kuester, who also directs the Qualcomm Institute’s Center of Interdisciplinary Science for Art, Architecture and Archaeology (CISA3) and the Cultural Heritage Engineering Initiative (CHEI).

As for the building? “It could have been easily repaired,” said structural engineering professor Tara Hutchinson. “The occupants would have gotten out safely.” Hutchinson believes the structure fared well because it is lighter than a concrete building and has less mass to generate damaging forces.

Both Kuester and Hutchinson were interviewed after the shake test by Erik Anderson of KPBS-TV, the public-broadcasting station in San Diego. [The KPBS News video can be viewed on YouTube.]

Fire was less kind to the structure, however. Plastic fixtures and hardware melted, as did several video cameras installed to capture the fire’s progression. Simulated quakes occurring after the fire tests further weakened the structure’s floors, bringing it close to collapse.

All the better to learn these effects in a test environment, however. The combination of these technologies—a one-of-a-kind outdoor shake table and powerful data visualization methods—allows structural engineers at the Jacobs School to produce an incredibly detailed digital model of the structures they test. This in turn allows them to make recommendations to improve design methods and building codes around the nation and around the world for when the Big One, or maybe the Mega One, hits.

[This article was adapted from a feature by Ioana Patringenaru in the Winter 2017 issue of TRITON, the UC San Diego Alumni Magazine, Vol. 14, No. 1.]

The Fall 2015 issue of American Archaeology (Vol. 19, No. 3), has a feature story titled “Here Come The Drones,” exploring the possibilities, challenges and overall impact of drones on the field of archaeology. The article is featuring our work and visually highlights results from our 2014 Napa Valley post-earthquake reconnaissance research with focus on historic landmarks.

Professor Kuester presented an invited talk at Cinegrid 2015, titled “From Immersive Frames to 3D Scenes,” covering next generation 2D and 3D imaging and modeling techniques for the rapid creation of 3D scenes for use in immersive environments. The talk explored the potential of ultra-resolution, spherical, stereo image and video acquisition enabled by our CAVEcam, CAVEcam-X, Camlot and SENSEI imaging systems, for the creation of highly realistic and accurate environments. Environments suitable for data exploration and analysis supportung our heritage engineering research, while also creating content and unique opportunities for the coming tidal wave of personal Virtual Reality systems, including head mounted displays (HMDs) such as the Oculus Rift, HTC Vive and Samsung Gear VR, among others.