A Search Engine for the Human Body

A Search Engine for the Human Body

  2:12:00 AM    Science Lover

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Microsoft software recognizes organs and other structures in medical images.

A new search tool developed by researchers at Microsoft indexes medical images of the human body, rather than the Web. On CT scans, it automatically finds organs and other structures, to help doctors navigate in and work with 3-D medical imagery.

Inside out: A close up of a CT processed by new software from Microsoft.
Credit: Microsoft Research

CT scans use X-rays to capture many slices through the body that can be combined to create a 3-D representation. This is a powerful tool for diagnosis, but it's far from easy to navigate, says Antonio Criminisi, who leads a group at Microsoft Research Cambridge, U.K., that is attempting to change that. "It is very difficult even for someone very trained to get to the place they need to be to examine the source of a problem," he says.

When a scan is loaded into Criminisi's software, the program indexes the data and lists the organs it finds at the side of the screen, creating a table of hyperlinks for the body. A user can click on, say, the word "heart" and be presented with a clear view of the organ without having to navigate through the imagery manually.

Once an organ of interest has been found, a 2-D and an enhanced 3-D view of structures in the area are shown to the user, who can navigate by touching the screen on which the images are shown. A new scan can also be automatically and precisely matched up alongside a past one from the same patient, making it easy to see how a condition has progressed or regressed.

Criminisi's software uses the pattern of light and dark in the scan to identify particular structures; it was developed by training machine-learning algorithms to recognize features in hundreds of scans in which experts had marked the major organs. Indexing a new scan takes only a couple of seconds, says Criminisi. The system was developed in collaboration with doctors at Addenbrookes Hospital in Cambridge, U.K.

The Microsoft research group is exploring the use of gestures and voice to control the system. They can plug in the Kinect controller, ordinarily used by gamers to control an Xbox with body movements, so that surgeons can refer to imagery in mid-surgery without compromising their sterile gloves by touching a keyboard, mouse, or screen.

Body search: This CT image shows organs and other features identified by the Microsoft software. A list of these features appears at left.
Credit: Microsoft Research

Kenji Suzuki an assistant professor at the University of Chicago, whose research group works on similar tools, says the Microsoft software has the potential to improve patient care, providing it really does make scans easier to navigate. "As medical imaging has advanced, so many images are produced that there is a kind of information overload," he explains. "The workload has grown a lot."

Suzuki says Microsoft's approach is a good one, but that medical professionals might be more receptive to the design if it indexed signs of disease, not just organs. His own research group has developed software capable of recognizing potentially cancerous lung nodules; in trials, it made half as many mistakes as a human expert.

Criminisi sticks by the notion of using organs as a kind of navigation system but says that disease-spotting capability is also under development. He says, "We are working to train it to detect differences between different grades of glioma tumor"—a type of brain tumor.

The Microsoft group also intends the tool to be used at large scales. It could automatically index a collection of 3-D scans or other images, making possible new ways of tracking medical records, says Criminisi. Today, records are kept as text that describes scans and other information. A search tool that finds the word "heart", for example, would not know if that meant it appeared in a scan or was mentioned in another context. If a hospital's computer system indexed new scans, the Microsoft software could automatically record what was imaged in a person's records and when.

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Gesturing While Talking Helps Change Your Thoughts

Gesturing While Talking Helps Change Your Thoughts

  9:47:00 AM    Science Lover

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Sometimes it’s almost impossible to talk without using your hands. These gestures seem to be important to how we think. They provide a visual clue to our thoughts and, a new theory suggests, may even change our thoughts by grounding them in action.

Sometimes it's almost impossible to talk without using your hands. These gestures seem to be important to how we think. They provide a visual clue to our thoughts and, a new theory suggests, may even change our thoughts by grounding them in action. (Credit: iStockphoto/Franz Pfluegl)

University of Chicago psychological scientists Sian Beilock and Susan Goldin-Meadow are bringing together two lines of research: Beilock’s work on how action affects thought and Goldin-Meadow’s work on gesture. After a chat at a conference instigated by Ed Diener, the founding editor of Perspectives on Psychological Science, they designed a study together to look at how gesture affects thought.

For the study, published in Psychological Science, a journal of the Association for Psychological Science, Beilock and Goldin-Meadow had volunteers solve a problem known as the Tower of Hanoi. It’s a game in which you have to move stacked disks from one peg to another. After they finished, the volunteers were taken into another room and asked to explain how they did it. (This is virtually impossible to explain without using your hands.) Then the volunteers tried the task again. But there was a trick: For some people, the weight of the disks had secretly changed, such that the smallest disk, which used to be light enough to move with one hand, now needed two hands.

People who had used one hand in their gestures when talking about moving the small disk were in trouble when that disk got heavier. They took longer to complete the task than did people who used two hands in their gestures—and the more one-handed gestures they used, the longer they took. This shows that how you gesture affects how you think; Goldin-Meadow and Beilock suggest that the volunteers had cemented how to solve the puzzle in their heads by gesturing about it (and were thrown off by the invisible change in the game).



In another version of the experiment, published in Perspectives in Psychological Science, the volunteers were not asked to explain their solution; instead, they solved the puzzle a second time before the disk weights were changed. But moving the disks didn’t affect performance in the way that gesturing about the disks did. The people who gestured did worse after the disk weights switched, but the people who moved the disks did not—they did just as well as before. “Gesture is a special case of action. You might think it would have less effect because it does not have a direct impact on the world,” says Goldin-Meadow. But she and Beilock think it may actually be having a stronger effect, “because gesturing about an act requires you to represent that act.” You aren’t just reaching out and handling the thing you’re talking about; you have to abstract from it, indicating it by a movement of your hands.

In the article published in Perspectives in Psychological Science, the two authors review the research on action, gesture, and thought. Gestures make thought concrete, bringing movement to the activity that’s going on in your mind.

This could be useful in education; Goldin-Meadow and Beilock have been working on helping children to understand abstract concepts in mathematics, physics, and chemistry by using gesture. “When you’re talking about angular momentum and torque, you’re talking about concepts that have to do with action,” Beilock says. “I’m really interested in whether getting kids to experience some of these actions or gesture about them might change the brain processes they use to understand these concepts.” But even in math where the concepts have little to do with action, gesturing helps children learn—maybe because the gestures themselves are grounded in action.

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Robot Arm Improves Performance of Brain-Controlled Device

Robot Arm Improves Performance of Brain-Controlled Device

  10:34:00 AM    Science Lover

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The performance of a brain-machine interface designed to help paralyzed subjects move objects with their thoughts is improved with the addition of a robotic arm providing sensory feedback, a new study from the University of Chicago finds.

During the experiment, monkeys used their brain signals to move a computer cursor (red circle) to randomly placed targets (squares). When visual and proprioceptive feedback were included, the monkey's hand was moved by a robotic exoskeleton. The additional sensory information resulted in the cursor hitting the target faster and more directly. (Credit: Courtesy, with permission: Hatsopoulos, et al. The Journal of Neuroscience 2010.)

Devices that translate brain activity into the movement of a computer cursor or an external robotic arm have already proven successful in humans. But in these early systems, vision was the only tool a subject could use to help control the motion.

Adding a robot arm that provided kinesthetic information about movement and position in space improved the performance of monkeys using a brain-machine interface in a study published December 14 in The Journal of Neuroscience. Incorporating this sense may improve the design of "wearable robots" to help patients with spinal cord injuries, researchers said.

"A lot of patients that are motor-disabled might have partial sensory feedback," said Nicholas Hatsopoulos, PhD, Associate Professor and Chair of Computational Neuroscience at the University of Chicago. "That got us thinking that maybe we could use this natural form of feedback with wearable robots to provide that kind of feedback."

In the experiments, monkeys controlled a cursor without actively moving their arm via a device that translated activity in the primary motor cortex of their brain into cursor motion. While wearing a sleeve-like robotic exoskeleton that moved their arm in tandem with the cursor, the monkey's control of the cursor improved, hitting targets faster and via straighter paths than without the exoskeleton.

"We saw a 40 percent improvement in cursor control when the robotic exoskeleton passively moved the monkeys' arm," Hatsopoulos said. "This could be quite significant for daily activities being performed by a paralyzed patient that was equipped with such a system."

When a person moves their arm or hand, they use sensory feedback called proprioception to control that motion. For example, if one reaches out to grab a coffee mug, sensory neurons in the arm and hand send information back to the brain about where one's limbs are positioned and moving. Proprioception tells a person where their arm is positioned, even if their eyes are closed.

But in patients with conditions where sensory neurons die out, executing basic motor tasks such as buttoning a shirt or even walking becomes exceptionally difficult. Paraplegic subjects in the early clinical trials of brain-machine interfaces faced similar difficulty in attempting to move a computer cursor or robot arm using only visual cues. Those troubles helped researchers realize the importance of proprioception feedback, Hatsopoulos said.

"In the early days when we were doing this, we didn't even consider sensory feedback as an important component of the system," Hatsopoulos said. "We really thought it was just one-way: signals were coming from the brain, and then out to control the limb. It's only more recently that the community has really realized that there is this loop with feedback coming back."

Reflecting this loop, the researchers on the new study also observed changes in the brain activity recorded from the monkeys when sensory feedback was added to the set-up. With proprioception feedback, the information in the cell firing patterns of the primary motor cortex contained more information than in trials with only visual feedback, Hatsopoulos said, reflecting an improved signal-to-noise ratio.

The improvement seen from adding proprioception feedback may inform the next generation of brain-machine interface devices, Hatsopoulos said. Already, scientists are developing different types of "wearable robots" to augment a person's natural abilities. Combining a decoder of cortical activity with a robotic exoskeleton for the arm or hand can serve a dual purpose: allowing a paralyzed subject to move the limb, while also providing sensory feedback.

To benefit from this solution, a paralyzed patient must have retained some residual sensory information from the limbs despite the loss of motor function -- a common occurrence, Hatsopoulos said, particularly in patients with ALS, locked-in syndrome, or incomplete spinal cord injury. For patients without both motor and sensory function, direct stimulation of sensory cortex may be able to simulate the sensation of limb movement. Further research in that direction is currently underway, Hatsopoulos said.

"I think all the components are there; there's nothing here that's holding us back conceptually," Hatsopoulos said. "I think using these wearable robots and controlling them with the brain is, in my opinion, probably the most promising approach to take in helping paralyzed individuals regain the ability to move."

Funding for the research was provided by the National Institute of Neurological Disorders and Stroke and the Paralyzed Veterans of America Research Foundation.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect to us.

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Robotic Gripper Runs on Coffee ... and Balloons

Robotic Gripper Runs on Coffee ... and Balloons

  9:03:00 AM    Science Lover

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The human hand is an amazing machine that can pick up, move and place objects easily, but for a robot, this "gripping" mechanism is a vexing challenge. Opting for simple elegance, researchers from Cornell University, University of Chicago and iRobot have bypassed traditional designs based around the human hand and fingers, and created a versatile gripper using everyday ground coffee and a latex party balloon.

Graduate student John Amend, left, and associate professor 
Hod Lipson with the universal robotic gripper. 
(Credit: Robert Barker/University Photography)

They call it a universal gripper, as it conforms to the object it's grabbing rather than being designed for particular objects, said Hod Lipson, Cornell associate professor of mechanical engineering and computer science. The research is a collaboration between the groups of Lipson, Heinrich Jaeger at the University of Chicago, and Chris Jones at iRobot Corp. It is published Oct. 25 online in Proceedings of the National Academy of Sciences.

"This is one of the closest things we've ever done that could be on the market tomorrow," Lipson said. He noted that the universality of the gripper makes future applications seemingly limitless, from the military using it to dismantle explosive devises or to move potentially dangerous objects, robotic arms in factories, on the feet of a robot that could walk on walls, or on prosthetic limbs.

Here's how it works: An everyday party balloon filled with ground coffee -- any variety will do -- is attached to a robotic arm. The coffee-filled balloon presses down and deforms around the desired object, and then a vacuum sucks the air out of the balloon, solidifying its grip. When the vacuum is released, the balloon becomes soft again, and the gripper lets go.

Jaeger said coffee is an example of a particulate material, which is characterized by large aggregates of individually solid particles. Particulate materials have a so-called jamming transition, which turns their behavior from fluid-like to solid-like when the particles can no longer slide past each other.

This phenomenon is familiar to coffee drinkers familiar with vacuum-packed coffee, which is hard as a brick until the package is unsealed.

"The ground coffee grains are like lots of small gears," Lipson said. "When they are not pressed together they can roll over each other and flow. When they are pressed together just a little bit, the teeth interlock, and they become solid."

Jaeger explains that the concept of a "jamming transition" provides a unified framework for understanding and predicting behavior in a wide range of disordered, amorphous materials. All of these materials can be driven into a 'glassy' state where they respond like a solid yet structurally resemble a liquid, and this includes many liquids, colloids, emulsions or foams, as well as particulate matter consisting of macroscopic grains.

"What is particularly neat with the gripper is that here we have a case where a new concept in basic science provided a fresh perspective in a very different area -- robotics -- and then opened the door to applications none of us had originally thought about," Jaeger said.

Eric Brown, a postdoctoral researcher, and Nick Rodenberg, a physics undergraduate, worked with Jaeger on characterizing the basic mechanisms that enable the gripping action. Prototypes of the gripper were built and tested by Lipson and Cornell graduate student John Amend as well as at iRobot.

As for the right particulate material, anything that can jam will do in principle, and early prototypes involved rice, couscous and even ground- up tires. They settled on coffee because it's light but also jams well, Amend said. Sand did better on jamming but was prohibitively heavy. What sets the jamming-based gripper apart is its good performance with almost any object, including a raw egg or a coin -- both notoriously difficult for traditional robotic grippers.

The project was supported by the Defense Advanced Research Projects Agency.

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Dark-Matter Search Plunges Physicists to New Depths

Dark-Matter Search Plunges Physicists to New Depths

  2:06:00 AM    Science Lover

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This month physicist Juan Collar and his associates are taking their attempt to unmask the secret identity of dark matter into a Canadian mine more than a mile underground.

Pictured here is the 1-liter bubble chamber during 
testing at MINOS Hall, 350 feet underneath Fermi 
National Accelerator Laboratory. Physicists installed 
a similar but larger bubble chamber for detecting 
dark matter this summer in a laboratory more than 
a mile underground in Sudbury, Canada. 
(Credit: Reidar Hahn/Fermilab)

The team is deploying a 4-kilogram bubble chamber at SNOLab, which is part of the Sudbury Neutrino Observatory in Ontario, Canada. A second 60-kilogram chamber will follow later this year. Scientists anticipate that dark matter particles will leave bubbles in their tracks when passing through the liquid in one of these chambers.

Dark matter accounts for nearly 90 percent of all matter in the universe. Although invisible to telescopes, scientists can observe the gravitational influence that dark matter exerts over galaxies. "There is a lot more mass than literally meets the eye," said Collar, Associate Professor in Physics at the University of Chicago. "When you look at the matter budget of the universe, we have a big void there that we can't explain."

Likely suspects for what constitutes dark matter include Weakly Interacting Massive Particles (WIMPS) and axions. Theorists originally proposed the existence of both these groups of subatomic particles to address issues unrelated to dark matter. "These seem to be perfect to explain all of these observations that give us this evidence for dark matter, and that makes them very appealing," Collar said.

SNOLab will be the most ambitious in a series of underground locations where Collar and his colleagues have searched for dark matter. In 2004, they established the Chicagoland Observatory for Underground Particle Physics (COUPP) at Fermi National Accelerator Laboratory.

"We started with a detector the size of a test tube and now have increased the mass by a factor of more than a thousand," said Fermilab physicist Andrew Sonnenschein. "It's exciting to see the first bubble chamber being sent off to SNOLab, because the low level of interference we can expect from the cosmic rays there will make our search for dark matter enormously more sensitive."

The COUPP collaboration consists of scientists from UChicago, Fermilab and Indiana University at South Bend. In 2008 the collaboration released its first results that established an old technology of particle physics -- the bubble chamber -- as a potential dark-matter detector.

COUPP extends to the city of Chicago's flood-control infrastructure, called the Tunnel and Reservoir Project. The city has granted COUPP scientists access to the tunnels, 330 feet underground, to test prototypes of their instruments. The collaboration also tested instruments in a chamber 350 feet below Fermilab, and in a sub-basement of the Laboratory for Astrophysics and Space Research on the UChicago campus.

Collar continually seeks underground venues for his research in order to screen out false signals from various natural radiation sources, including cosmic rays from deep space. "It's an interesting lifestyle," Collar said.

The troublesome underground radiation sources consist of charged particles that lose energy as they traverse through a mile or more of rock. But rock has no impact on particles that interact weakly with matter, such as WIMPS, thus the move to Sudbury.

"SNOLab is a very special, spectacular place, because the infrastructure that the Canadians have developed down there is nothing short of amazing," Collar said. Even though SNOLab sits atop a working nickel mine, conditions there are pristinely antiseptic.

"As you walk in, you have to shower to remove any trace of dust," he said. "It's a clean-room atmosphere, meaning that there's essentially no specks of dust anywhere. We have to worry about such things, sources of radiation associated with dust."

Collar also is a member of the Coherent Germanium Neutrino Technology (CoGeNT) collaboration, which operates a detector that sits nearly half a mile deep at the Soudan Underground Mine State Park in northern Minnesota. The 60-kilogram detector that Collar and colleagues will install at SNOLab later this year, meanwhile, undergoes testing in a tunnel 350 feet beneath Fermilab.

Linking the two sites is an invisible beam of neutrinos that stretches 450 miles from Fermi to Soudan. The beam is part of the Main Injector Neutrino Oscillation Search (MINOS), a particle-physics experiment that is unrelated to the search for dark matter.

The two detectors rely on entirely different techniques. CoGeNT uses a new type of germanium detector that targets the detection of light WIMPS.

"Most of us have been concentrating on intermediate-mass WIMPS for decades," Collar said. "In the last few years the theoreticians have been telling us more and more, look, under these other sets of assumptions, it could be a lighter WIMP. This device is actually the first of its kind in the sense that it's targeted specifically for light WIMPS. We're seeing interesting things with it that we don't fully understand yet."

Collar estimates that it'll take a decade or more for physicists to become completely convinced that they've seen dark-matter particles.

"It's going to take a lot of information from very many different points of view and entirely independent techniques," he said. "One day we'll figure it out."

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Color Plays Musical Chairs In The Brain

Color Plays Musical Chairs In The Brain

  2:21:00 PM    Science Lover

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Color is normally thought of as a fundamental attribute of an object: a red Corvette, a blue lake, a pink flamingo. Yet despite this popular notion, new research suggests that our perception of color is malleable, and relies heavily on biological processes of the eye and brain.

The brain's neural mechanisms keep straight which color belongs to what object, so one doesn't mistakenly see a blue flamingo in a pink lake. But what happens when a color loses the object to which it is linked? Research shows for the first time, that instead of disappearing along with the lost object, the color latches onto a region of some other object in view. (Credit: University of Chicago)

The brain's neural mechanisms keep straight which color belongs to what object, so one doesn't mistakenly see a blue flamingo in a pink lake. But what happens when a color loses the object to which it is linked? Research at the University of Chicago has demonstrated, for the first time, that instead of disappearing along with the lost object, the color latches onto a region of some other object in view – a finding that reveals a new basic property of sight.

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