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Friday, February 12th, 2016

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    5:00a
    Imaging with an “optical brush”

    Researchers at the MIT Media Lab have developed a new imaging device that consists of a loose bundle of optical fibers, with no need for lenses or a protective housing.

    The fibers are connected to an array of photosensors at one end; the other ends can be left to wave free, so they could pass individually through micrometer-scale gaps in a porous membrane, to image whatever is on the other side.

    Bundles of the fibers could be fed through pipes and immersed in fluids, to image oil fields, aquifers, or plumbing, without risking damage to watertight housings. And tight bundles of the fibers could yield endoscopes with narrower diameters, since they would require no additional electronics.

    The positions of the fibers’ free ends don’t need to correspond to the positions of the photodetectors in the array. By measuring the differing times at which short bursts of light reach the photodetectors — a technique known as “time of flight” — the device can determine the fibers’ relative locations.

    In a commercial version of the device, the calibrating bursts of light would be delivered by the fibers themselves, but in experiments with their prototype system, the researchers used external lasers.

    “Time of flight, which is a technique that is broadly used in our group, has never been used to do such things,” says Barmak Heshmat, a postdoc in the Camera Culture group at the Media Lab, who led the new work. “Previous works have used time of flight to extract depth information. But in this work, I was proposing to use time of flight to enable a new interface for imaging.”

    The researchers reported their results today in Nature Scientific Reports. Heshmat is first author on the paper, and he’s joined by associate professor of media arts and sciences Ramesh Raskar, who leads the Media Lab’s Camera Culture group, and by Ik Hyun Lee, a fellow postdoc.

    Travel time

    In their experiments, the researchers used a bundle of 1,100 fibers that were waving free at one end and positioned opposite a screen on which symbols were projected. The other end of the bundle was attached to a beam splitter, which was in turn connected to both an ordinary camera and a high-speed camera that can distinguish optical pulses’ times of arrival.

    Perpendicular to the tips of the fibers at the bundle’s loose end, and to each other, were two ultrafast lasers. The lasers fired short bursts of light, and the high-speed camera recorded their time of arrival along each fiber.

    Because the bursts of light came from two different directions, software could use the differences in arrival time to produce a two-dimensional map of the positions of the fibers’ tips. It then used that information to unscramble the jumbled image captured by the conventional camera.

    The resolution of the system is limited by the number of fibers; the 1,100-fiber prototype produces an image that’s roughly 33 by 33 pixels. Because there’s also some ambiguity in the image reconstruction process, the images produced in the researchers’ experiments were fairly blurry.

    But the prototype sensor also used off-the-shelf optical fibers that were 300 micrometers in diameter. Fibers just a few micrometers in diameter have been commercially manufactured, so for industrial applications, the resolution could increase markedly without increasing the bundle size.

    In a commercial application, of course, the system wouldn’t have the luxury of two perpendicular lasers positioned at the fibers’ tips. Instead, bursts of light would be sent along individual fibers, and the system would gauge the time they took to reflect back. Many more pulses would be required to form an accurate picture of the fibers’ positions, but then, the pulses are so short that the calibration would still take just a fraction of a second.

    “Two is the minimum number of pulses you could use,” Heshmat says. “That was just proof of concept.”

    Checking references

    For medical applications, where the diameter of the bundle — and thus the number of fibers — needs to be low, the quality of the image could be improved through the use of so-called interferometric methods.

    With such methods, an outgoing light signal is split in two, and half of it — the reference beam — is kept locally, while the other half — the sample beam — bounces off objects in the scene and returns. The two signals are then recombined, and the way in which they interfere with each other yields very detailed information about the sample beam’s trajectory. The researchers didn’t use this technique in their experiments, but they did perform a theoretical analysis showing that it should enable more accurate scene reconstructions.

    “It is definitely interesting and very innovative to combine the knowledge we now have of time-of-flight measurements and computational imaging,” says Mona Jarrahi, an associate professor of electrical engineering at the University of California at Los Angeles. “And as the authors mention, they’re targeting the right problem, in the sense that a lot of applications for imaging have constraints in terms of environmental conditions or space.”

    Relying on laser light piped down the fibers themselves “is harder than what they have shown in this experiment,” she cautions. “But the physical information is there. With the right arrangement, one can get it.”

    “The primary advantage of this technology is that the end of the optical brush can change its form dynamically and flexibly,” adds Keisuke Goda, a professor of chemistry at the University of Tokyo. “I believe it can be useful for endoscopy of the small intestine, which is highly complex in structure.”

    3:00p
    Targeting cancer from many angles

    Since the discovery of the first cancer-causing genes in the 1960s, scientists have uncovered at least 600 genes that contribute to tumor development. Tyler Jacks, the David H. Koch Professor of Biology and director of MIT’s Koch Institute for Integrative Cancer Research, has spent much of his career trying to unravel the roles of some of these genes, in hopes of designing better cancer treatments.

    “The challenge is to figure out the contribution of all of those different genes. If you can figure out what’s driving a cancer, you can potentially develop a drug that will help to inhibit it,” Jacks said during yesterday’s James R. Killian Jr. Faculty Achievement Award Lecture.

    Jacks received this year’s Killian Award not only for his work in cancer genetics but also for his leadership of MIT’s cancer research community.

    “Professor Jacks is described by colleagues as a bold and visionary leader,” reads the award citation. “His nominators say that it takes a village of passionate and dedicated people to invent solutions for the many cancers that affect our society, and this is exactly what he has created in Building 76.”

    Chosen to direct MIT’s Center for Cancer Research in 2001, Jacks oversaw the evolution of that center into the Koch Institute in 2007, with the vision of bringing together MIT’s scientists and engineers to pursue innovative approaches to diagnosing, treating, and preventing the disease.

    “You don’t find cancer research institutions like this anywhere else,” said Jacks, who thanked others whom he described as critical to the formation of the new institute, including associate directors Jacqueline Lees and Dane Wittrup, former President Susan Hockfield, President L. Rafael Reif, executive director Anne Deconinck, assistant director Cindy Quense, and David H. Koch.

    Under Jacks’ leadership, the Koch Institute has also launched new collaborations with local hospitals to help translate new cancer biology knowledge into patient treatments, and 42 companies have been created by Koch Institute faculty members or with intellectual property developed at the institute.

    “We want to deliver technologies that can benefit patients,” said Jacks, who pointed out that cancer kills more people each year than HIV, malaria, and tuberculosis combined.

    Modeling cancer

    Jacks’ roots at MIT run deep. His father was a professor at the MIT Sloan School of Management from 1959 to 1980, and he often accompanied his father to campus.

    “Kendall Square in the 1960s was a very different place,” Jacks recalled. “There was literally one place to eat, the F&T Diner. I still remember the taste of the pastrami sandwiches.”

    As an undergraduate at Harvard University, Jacks heard a lecture from Robert Weinberg, an MIT biology professor who had discovered the first oncogene (a gene that drives cancer progression), known as H-ras, and the first tumor suppressor gene, known as Rb. Jacks decided that he wanted to study cancer, and after earning his PhD at the University of California at San Francisco he joined Weinberg’s lab as a postdoc at MIT’s Whitehead Institute for Biomedical Research.

    There, he began work that he would continue in his own lab at MIT — genetically engineering mice to develop tumors, which allowed researchers to track the progression of the disease and to test new ways to detect and treat it. The strains of mice his lab has developed are now used in labs around the world to study cancer.

    Much of Jacks’ research has focused on lung cancer, which in 2012 accounted for 160,000 deaths in the United States. He developed a mouse model for the most common form of lung cancer, adenocarcinoma, by manipulating the oncogene Kras, which is present in 30 percent of such tumors, and the tumor suppressor gene p53, which is missing in 50 percent of adenocarcinomas.

    Tracking the progression of this type of cancer has led to the discovery of other genes involved in the process, which Jacks hopes may lead to new targeted drugs, just as the discovery of the HER2 breast cancer oncogene led to the drug Herceptin, which is very effective for the patients who have an overactive form of HER2.

    New directions

    Several years ago, as cancer genome sequencing studies turned up more and more genes involved in tumor progression, Jacks says he and his students began to feel a bit overwhelmed at the sheer number of genes they were facing: The typical lung tumor has about 175 mutated genes, and using traditional genetic engineering techniques, it takes two to three years to develop a strain of mice that express a particular cancerous mutation.

    “How could we look at all of those genes and their potential contributions to cancer?” Jacks said. “We didn’t know quite what to do.”

    Just in time, scientists reported the development of a new genome-editing technique known as CRISPR. This system, originally discovered in bacteria, allows researchers to create gene-editing complexes that can precisely target genes and delete or replace them.

    Jacks and colleagues immediately began using the new technology and showed that it could be used to create cancerous mutations in mice much faster than previously possible. In just seven months, they created hundreds of different tumors bearing multiple distinct mutations — a feat that previously would have taken years and cost hundreds of thousands of dollars.

    That project illustrates one of the key philosophies that Jacks has tried to instill at the Koch Institute — to embrace alternative approaches to solving problems. Asked after his talk what advice he would give students and postdocs just beginning their scientific careers, Jacks reinforced that message.

    “If you just focus on what you know, you’re blinding yourself to new opportunities,” he said.

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