Live adaptation of organ models in the OR

The non-deformed liver model (red) adapts to the deformed surface profile (blue). Credit: Graphics: Dr. Stefanie Speidel, KIT, in Medical Physics, 41

During minimally invasive operations, a surgeon has to trust the information displayed on the screen: A virtual 3D model of the respective organ shows where a tumor is located and where sensitive vessels can be found. Soft tissue, such as the tissue of the liver, however, deforms during breathing or when the scalpel is applied. Endoscopic cameras record in real time how the surface deforms, but do not show the deformation of deeper structures such as tumors. Young scientists of the Karlsruhe Institute of Technology (KIT) have now developed a real-time capable computation method to adapt the virtual organ to the deformed surface profile.

The principle appears to be simple: Based on computer tomography image data, the scientists construct a virtual 3D model of the respective organ, including the tumor, prior to operation. During the operation, cameras scan the surface of the organ and generate a stiff profile mask. To this virtual mold, the 3D model then is to fit snuggly, like jelly to a given form. The Young Investigator Group of Dr. Stefanie Speidel analyzed this geometrical problem of shape adaptation from the physical perspective. "We model the surface profile as electrically negative and the volume model of the organ as electrically positive charged," Speidel explains. "Now, both attract each other and the elastic volume model slides into the immovable profile mask." The adapted 3D model then reveals to the surgeon how the tumor has moved with the deformation of the organ.

Simulations and experiments using a close-to-reality phantom liver have demonstrated that the electrostatic-elastic method even works when only parts of the deformed surface profile are available. This is the usual situation at the hospital. The human liver is surrounded by other organs and, hence, only partly visible by endoscopic cameras. "Only those structures that are clearly identified as parts of the liver by our system are assigned an electric charge," says Dr. Stefan Suwelack who, as part of Speidel's group, wrote his Ph.D. thesis on this subject. Problems only arise, if far less than half of the deformed surface is visible. To stabilize computation in such cases, the KIT researchers can use clear reference points, such as crossing vessels. Their method, however, in contrary to others does not rely on such references from the outset.

In addition, the model of the KIT researchers is more precise than conventional methods, because it also considers biomechanical factors of the liver, such as the elasticity of the tissue. So for instance, the phantom liver used by the scientists consists of two different silicones: A harder material for the capsule, i.e. the outer shell of the liver, and a softer material for the inner liver tissue.

As a result of their physical approach, the young scientists also succeeded in accelerating the computation process. As shape adaptation was described by electrostatic and elastic energies, they found a single mathematical formula. Using this formula, even conventional computers equipped with a single processing unit only work so quickly that the method is competitive. Contrary to conventional computation methods, however, the new method is also suited for parallel computers. Using such a computer, the Young Investigator Group now plans to model organ deformations stably in real time.

Source: Karlsruhe Institute of Technology

Volunteers can now help scientists seek Ebola cure in their (computer's) spare time

The Scripps Research Institute’s Professor Erica Ollmann Saphire is leading the new effort against Ebola. Credit: Photo courtesy of The Scripps Research Institute.

Although some medical therapies show promise as treatments for Ebola, scientists are still looking urgently for a definitive cure.

For the first time, anyone with access to a computer or Android-based mobile device can help scientists perform this critical research -- no financial contribution, passport or PhD necessary. In fact, volunteers can be asleep, traveling or on a coffee break when they help researchers search for an Ebola cure.

Beginning today, anyone can download a safe and free app that will put their devices to work when the machines would otherwise be idle. With their collective processing power, the computers will form a virtual supercomputer to help The Scripps Research Institute (TSRI) screen millions of chemical compounds to identify new drug leads for treating Ebola. 

Meanwhile, the devices will remain fully available for normal use by their owners.

This citizen science effort is possible through a partnership with IBM's (NYSE: IBM) World Community Grid, which has been making similar data-driven health and sustainability initiatives possible for 10 years as a free, philanthropic service to the science community. 

The "Outsmart Ebola Together" volunteer computing project announced today is being run by the Ollmann Saphire laboratory at TSRI, which has mapped the structures and vulnerabilities of the proteins comprising the Ebola virus.

The best candidate compounds that emerge from this crowdsourced effort will be physically tested in the lab to pinpoint their effectiveness against real virus infection. The most promising compounds will then be modified to perform even better, at lower concentrations, and with fewer side effects. Subsequent drug trials could ultimately lead to an approved medicine.

Crowdsourcing this citizen science effort will dramatically accelerate the process of identifying a cure. The speed and scale of a drug search is essential, as this particularly lethal disease continues to spread and mutate. Once believed to be less of a widespread public health risk than other communicable diseases because of its existence in mainly isolated regions, Ebola now carries a higher risk of spreading farther because people are more mobile than ever before.

"Our molecular images of the Ebola virus are like enemy reconnaissance," said Dr. Erica Ollmann Saphire of TSRI, one of the largest private biomedical research institutes in the United States. "These images show us where the virus is vulnerable and the targets we need to hit. In the Outsmart Ebola Together project, we will be able to harness World Community 

Grid's virtual supercomputing power to find the drugs we need to aim at these targets."

IBM's World Community Grid has successfully run other projects that search for drug candidates for both high- and low-profile diseases -- such as AIDS, cancer, malaria, Dengue fever, and influenza. It has enabled multiple breakthroughs, such as helping the Chiba Cancer Center in Japan discover seven new drug candidates to fight childhood neuroblastoma. The IBM-managed program also hosts projects that have led to important scientific advances in renewable energy and water purification technology.

"It is a privilege to partner with The Scripps Research Institute to advance the process of identifying an Ebola cure," said Stanley S. Litow, IBM's vice president of Corporate Citizenship and president of the IBM International Foundation. "It is only fitting that IBM's World Community Grid 10-year anniversary of accomplishments coincide with the launch of perhaps one of the most critical scientific and humanitarian efforts."

Conceived and managed by IBM, and powered by IBM's reliable and secure SoftLayer cloud technology, World Community Grid provides computing power to scientists by harnessing the unused, surplus cycle time of volunteers' computers and mobile devices. The software receives, completes, and returns small computational assignments to scientists. The combined power contributed by hundreds of thousands of volunteers has created one of the fastest virtual supercomputers on the planet, advancing scientific work by hundreds of years.

Nearly three million computers and mobile devices used by more than 680,000 people and 460 institutions from 80 countries have contributed virtual supercomputing power for vitally important projects on World Community Grid over the last 10 years. Since the program's inception, World Community Grid volunteers have powered more than 20 research projects, donating more than one million years of computing time to scientific research, and enabled important scientific advances in health and sustainability. IBM invites researchers to submit research project proposals to receive this free resource, and invites members of the public to donate their unused computing power to these efforts at worldcommunitygrid.org.

TSRI also invites members of the public to support Dr. Saphire's crowdfunding campaign at www.crowdrise.com/CUREEBOLA to secure resources needed to analyze the enormous volume of data generated by Outsmart Ebola Together.

The software used for screenings in the Outsmart Ebola Together project is called AutoDock and AutoDock VINA, developed by the Olson laboratory at TSRI.

World Community Grid is enabled by software developed in 2002 by Berkeley Open Infrastructure for Network Computing (BOINC) at the University of California, Berkeley and with support from the National Science Foundation. The BOINC project choreographs the technical aspects of volunteer computing.

Source: Scripps Research Institute

Cheaper 3-D virtual reality system: Powerful enough for a gamer, made for an engineer

It's like a scene from a gamer's wildest dreams: 12 high-definition, 55-inch 3D televisions all connected to a computer capable of supporting high-end, graphics-intensive gaming.
Credit: Image courtesy of Brigham Young University

It's like a scene from a gamer's wildest dreams: 12 high-definition, 55-inch 3D televisions all connected to a computer capable of supporting high-end, graphics-intensive gaming.

On the massive screen, images are controlled by a Wii remote that interacts with a Kinnect-like Bluetooth device (called SmartTrack), while 3D glasses worn by the user create dizzying added dimensions.

But this real-life, computer-powered mega TV is not for gaming. It's for engineering.

Welcome to Brigham Young University's VuePod, a 3D immersive visualization environment run by BYU's Department of Civil and Environmental Engineering. Student-built and operated, under the supervision of civil engineering professor Dan Ames, the VuePod is changing the way engineers are viewing environmental engineering challenges.

"This is gold," said fellow BYU civil engineering professor Kevin Franke. "This technology has the ability to revolutionize my job as an earthquake engineer."

That's because the VuePod allows users to virtually fly over, wander through or hover above 3D environments that are otherwise difficult to visit. The images are created by point data from aircraft equipped with LIDAR (think RADAR, but with lasers). The LIDAR scans the landscape and records millions of data points that are then viewed as an image on the VuePod. Point data can also be created from stitched-together photographs taken from low-cost drones, which is Franke's research focus.

One set of data currently available for study in the VuePod captured a canyon area beneath a plateau in southern Idaho. With 3D glasses and the Wii controller, a user can virtually drop down into the canyon from above, and then fly from one end to the other.

As cool as it is to fly through a canyon, the real engineering application comes in when you combine two sets of data for the same canyon, taken five years a part. With the second set of data, changes in the natural landscape that are invisible to the human eye become clear as day. Thanks to the VuePod's massive 108-square-foot screen, all of the image-making data can be presented for viewing.

"Our eyes and our brains are so amazing; we need to take full advantage of them," Ames said. "That's the value of this project: we're presenting more information for the human eyes to detect changes."

In addition to natural change detection, the VuePod has the potential to assist in infrastructure monitoring -- such as tracking how highways hold up (or slough and crack) over time and seeing the affect on buildings after severe weather or earthquakes.

While the VuePod is certainly not the first immersive visualization system in academia, it may just be the most cost efficient built to date. Some systems cost as much as $10 million to build and maintain, while BYU's VuePod just barely topped the $30,000 mark.

Ames details how BYU was able to build such a powerful system for so little in a new paper published by the Journal of Computing in Civil Engineering.

"Our question has been: How can we make this technology accessible?" Ames said. "We're trying to determine the threshold for getting the most function at the most affordable cost. Ultimately, the goal is to take an expensive tool and make it cheaper for an everyday engineering firm to use."

And even though Ames and his students have achieved that, they believe much more can be done.

"We want whoever reads this paper to be able to build a better system than we built," he said.

Source: Brigham Young University

Move over smart cities, the Internet of Things is off to the country

Smart sheep

 Lancaster University is about to take the concept of smart cities out of town. Computer scientists at Lancaster University are investigating how the Internet of Things could work in the countryside.

The Internet of Things - which enables object-to-object communication over the internet and real time data monitoring - has typically been associated with urban environments and until now the countryside has been left out in the cold.

Computer scientist Professor Gordon Blair of Lancaster University has won £171,495 from the Engineering and Physical Sciences Research Council to lead a new project in Conwy, North Wales, which will investigate how the Internet of Things could work in the countryside.

Working with partners at the Centre for Ecology and Hydrology, The British Geological Survey and Bangor University, the project launched on December 1 and will run for 18 months.

Problems from flooding and agricultural pollution to animal movements and drought could all potentially benefit from smart technology in the sticks.

The Internet of Things, which takes everyday objects and hooks them up to the internet, represents a shift in the way we gather and engage with information. Applying this booming technology to the countryside presents challenges – for example how to build a network when there are mountains and trees in the way – but researchers believe the benefits could be huge.

Sheep with digital collars, sensors on riverbanks, rainfall and river flow monitors could all soon form part of the project.

Professor Blair said: “Cities have been the focus of much of the boom in this type of technology – it has been used to keep traffic flowing on our roads, monitor air pollution and even help us find a parking spot on a busy Saturday afternoon. But the countryside faces challenges of its own, from subtle environmental changes to catastrophic events such as flooding. The possibilities of bringing the Internet of Things to the countryside are limitless. The next step will be to identify exactly what will be of most use in the short term and how we will frame the project.”

Source: Lancaster University