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New Ways to Analyze Ocean Imagery

New Ways to Analyze Ocean Imagery

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Moore Foundation grant sparks ocean informatics initiative

Over the past decade, ocean scientists have built underwater systems that have greatly expanded their capacity to collect images from under the sea. But the value of such instruments remains limited by the lack of efficient tools to extract information from millions of images gathered each day—and then make this potential treasure trove of scientific data readily accessible to many users.

In a significant step toward designing innovative solutions to organize and analyze the incoming flood of scientific data from new ocean sensors, Woods Hole Oceanographic Institution has received a $2.17 million grant from the Gordon and Betty Moore Foundation to develop ocean imaging informatics tools.

“Informatics has been described as the art and science of organizing knowledge and making it useful for problem solving,” said WHOI information systems specialist Andrew Maffei, who will co-lead the project with WHOI biologist Heidi Sosik. “I’m most excited about learning how to build ocean scientist / computer scientist partnerships.” The work will be done in collaboration with the Tetherless World Research Constellation group at Rensselaer Polytechnic Institute.

The project will focus on three innovative underwater imaging systems WHOI has developed in recent years to study fisheries, corals, and harmful algal blooms. The Imaging FlowCytobot, an automated underwater microscope system developed by Sosik and colleagues, has been recording high-resolution images of hundreds of millions of phytoplankton at the WHOI Martha’s Vineyard Coastal Observatory (MVCO) for more than four years. HabCam, a vehicle-mounted camera system, is towed over the ocean bottom, taking high-resolution images and each day creating continuous 100-nautical-mile-long ribbons of images like the one above. SeaBED, developed by WHOI engineer Hanumant Singh, is an autonomous underwater vehicle that can swim slowly or hover over the seafloor to depths of 6,561 feet (2,000 meters); it collects highly detailed sonar and optical images of the seafloor, which can be made into photomosaics.

“HabCam provides an expansive view of the seafloor, but we are swamped in images—we collect a half million every day,” said WHOI biologist Scott Gallager, who co-developed HabCam, along with WHOI engineers Johathan Howland and Lane Abrams, Commercial Fishermen Richard Taylor and Norman Vine, and other members of the HabCam Group including Amber York (WHOI), Arnie DeMello and Captain Paul Rosonina (Arnie’s Fisheries), and the crew of the F/V Kathy Marie. “Extracting information from those in an automated and efficient way is essential to addressing long-standing science questions” and could eventually be used to survey sea scallops, ground fish, and other commercially important species for fisheries management.

“It is the beginning of a long-term strategy that involves a close partnership with Rensselaer Polytechnic Institute to help generate image informatics tools that have broad academic and societal impact,” said Susan Avery, president and director of WHOI. “WHOI is known for having a strong connection between scientists and engineers, who together tackle the challenges of working in the marine environment. Informatics is the next essential technological advance that will ensure the rapid production of scientific output.”

Breaking ground on a groundbreaking laboratory

Scientists, politicians, and government officials gathered Aug. 4, 2010, to celebrate the groundbreaking for a new laboratory on the WHOI Quissett Campus that will provide space for major initiatives to create and maintain long-term ocean observatories.

The Laboratory for Ocean Sensors and Observing Systems will house scientists and engineers working on the Ocean Observatories Initiative—a $300-million effort funded by the National Science Foundation to build and operate systems of moored buoys, undersea cabled networks, sensors, and autonomous underwater vehicles—all to measure ocean and atmospheric conditions and provide data to scientists and resource managers. The 27,000-square-foot building will also accommodate other ocean observing programs: the WHOI-operated component of the U.S. National Ocean Bottom Seismograph Instrument Pool; the WHOI cabled underwater Martha’s Vineyard Coastal Observatory; and a lab for a revolutionary marine sensor, the Environmental Sample Processor.

WHOI received an $8.1 million grant for the construction from the U.S. Commerce Department’s National Institute of Standards and Technology (NIST). Funding comes from the American Recovery and Reinvestment Act grants for constructing new scientific research facilities and from Massachusetts’ John Adams Innovation Institute. Occupancy is scheduled for June 2012.

Above, officials break ground on the new building: from left, Susan Avery, president and director of WHOI; Pat Gallagher, director of NIST; Larry Robinson, assistant secretary of commerce for conservation and management, National Oceanic and Atmospheric Administration; Therese Murray, Massachusetts Senate president; Newton Merrill, chairman of the WHOI Board of Trustees; and former U.S. Rep. Bill Delahunt, D-Mass.

Kate Madin


Pioneering program seeks to counteract dearth of diversity in geosciences

For the second consecutive summer, the unique scientific community of Woods Hole banded together to continue its pioneering Partnership in Education Program (PEP) and help rev up the parched pipeline of young, diverse students entering the fields of geosciences and oceanography.

The demographics are stark: Of the more than 21,000 people who earned Ph.D.s in geosciences between 1973 and 2003, only 415 were Hispanic-, African- or Native Americans, according to the American Geophysical Union. In 2010, whites held 92 percent of the geosciences jobs, according to the Bureau of Labor Statistics. By 2018, the bureau projects 18 percent employment growth in geosciences occupations. With minorities expected to comprise about 50 percent of the national population by 2050, the National Research Council warned that unless more minorities enter the field, a dire shortage of a skilled, knowledgeable workforce, which will undermine the United States’ competitive edge in geosciences.

Seeking to change this course, six Woods Hole institutions joined to launch the PEP program in 2009, bringing 16 undergraduates from underrepresented groups for a four-week course on environmental and ocean science taught by scientists from all the institutions. Then the students conducted research internships with mentors from the Woods Hole institutions: the National Oceanographic and Atmospheric Administration’s Northeast Fisheries Science Center, Woods Hole Oceanographic Institution, the U.S. Geological Survey, Marine Biological Laboratory, Woods Hole Research Center, and Sea Education Association. NOAA supplied the majority of funding for PEP, while the other institutions contributed a wealth of in-kind services, including housing, seminars, teachers, and mentors. The University of Maryland Eastern Shore, a historically black college, and the NOAA Living Marine Resources Cooperative Science Center helped design the course and arrange college credit for students.

Sixteen more undergraduates attended the program in 2010, and eight of the students pursued research with WHOI scientists Ken Foote, Scott Gallager, Porter Hoagland, Gareth Lawson, and Lauren Mullineaux, on topics ranging from biology to engineering and marine policy. Anna-Mai Christmas (above), a 2010 graduate of the University of the Virgin Islands, worked on coastal ocean invertebrates in biologist Gallager’s lab. Christmas, now in graduate school at the University of Washington, studied changes in lobster development.

Lonny Lippsett


Oceanographers—the next generation

Nineteen graduates of the MIT/WHOI Joint Program in Oceanography and Applied Ocean Sciences and Engineering marched to receive their degrees June 5, 2010, during ceremonies at WHOI. Casey Saenger (left) holds the traditional ship’s belaying pin, the program’s nautical equivalent for the academic mace used in commencement processions.

WHOI hosts commencement every five years, and this year’s ceremonies also recognized 18 students who graduated since 2005. Since its inception in 1968, the Joint Program has awarded 865 graduate degrees.

Rita R. Colwell, Distinguished University Professor at the University of Maryland and the Johns Hopkins University and former director of the National Science Foundation gave the commencement address. Degrees were conferred by Susan K. Avery, president and director of WHOI; Newton P.S. Merrill, chairman of the WHOI Board of Trustees; John F. O’Brien, chairman of the WHOI Corporation; and Edward A. Boyle, Joint Program Director at MIT. Speakers included Avery, Merrill, Jim Yoder, WHOI vice president for Academic Programs and Dean, and Paul Snelgrove, president of the Joint Program Alumni Association.


A sub out of water

Alvin, the deep-diving, three-person research submarine, is generally on the job, which means it’s at sea. But every few years, it returns to Woods Hole Oceanographic Institution for routine maintenance and upgrades. In October 2010, WHOI took advantage of one of these rare chances to invite the public to see Alvin up close and personal, and WHOI scientists gave presentations on the iconic sub’s past, present, and future. In December, the sub will be completely rebuilt, receiving a new personnel sphere with an interior redesign.


WHOI goes to Times Square

Did the image at left catch your eye? Good, we hoped for the same impact when WHOI launched a video campaign on the world’s biggest stage to highlight the importance of the planet’s largest life-sustaining feature—the ocean.

The three-month ocean awareness campaign featured a series of three 15-second video spots that aired every hour on the CBS Superscreen above 42nd Street in Times Square, which hosts more than 26 million visitors each year.

The first video, which began in airing in July 2010, called attention to questions regarding the Deepwater Horizon oil spill in the Gulf of Mexico. The second, called “Alien” (left), featured one of the amazing “extraterrestrial” creatures that have been discovered in the sea. The third video highlighted Alvin, the nation’s deepest-diving submersible, and WHOI’s commitment to insure that the ocean bottom remains accessible to the scientific community.

All of the videos from the ocean awareness campaign are available for sharing from the WHOI website or the Institution’s YouTube channel.