WHOI Receives Gordon and Betty Moore Foundation Grant for Oceanography Imaging Informatics

In a significant step toward a new era in the collection and understanding of ocean science data, the Woods Hole Oceanographic Institution (WHOI) has received a grant of more than $2 million from the Gordon and Betty Moore Foundation for work in imaging informatics in oceanography.

The WHOI study—to be done in collaboration with the Tetherless World Constellation group at Rensselaer Polytechnic Institute (RPI)—is an interdisciplinary project that will develop new tools for ocean scientists who work with underwater imagery, said Heidi M. Sosik, a senior scientist in Biology and a principal investigator along with WHOI Information Systems Specialist Andrew Maffei. “This project will address some of the challenges we face in converting our huge underwater imagery data sets into a better understanding about the ocean and its ecosystems,” Sosik said.

The Gordon and Betty Moore Foundation’s Chief Program Officer, Science, Dr. Vicki Chandler, cited WHOI’s research as critical in generating “new knowledge about marine ecosystems through designing innovative informatics solutions to organize and analyze ocean sensor data.”

A New Scientific Partnership
A team of oceanographers and computer scientists will work together closely to adapt emerging informatics approaches to solve data analysis and interpretation problems related to underwater imaging. “Informatics has been described as the art and science of organizing knowledge and making it useful for problem solving—this capability is of growing importance for scientists dealing with complex systems such as climate change and ecosystems. I’m most excited about learning how to build ocean-scientist / computer-scientist partnerships,” said Maffei. “If we are successful, there will be important benefits to a wide range of science.”

As with most scientific investigations, any such success will rest on the project’s ability to enhance scientific knowledge. For Sosik, this involves understanding how and why phytoplankton blooms occur at different times and places in the ocean. “We are very interested in the basic question of what regulates phytoplankton communities,” she said. “For example, the timing and occurrence of the winter plankton blooms are very important for other species that rely on them as a food source—fish and invertebrates. If the bloom fails one winter, then you may get low survival of fish. We’re all hopeful that, down the road, the kind of basic information we are collecting will allow us to do a better job of managing fisheries and other coastal resources.”

Imaging the Ocean
WHOI has developed a number of innovative underwater imaging systems for research and emerging applications to address issues such as harmful algal bloom mitigation and ecosystem-based fisheries management. Sosik is co-developer of the Imaging FlowCytobot, an automated underwater microscope system that has been recording high-resolution images of hundreds of millions of phytoplankton at the Martha’s Vineyard Coastal Observatory (MVCO) for more than four years.

The value of such instrument systems is limited, however, by the lack of efficient and easy to use tools to extract information from huge numbers of images and then make that information readily available to many users. The partnership between WHOI and RPI is expected to go a long way toward bridging that gap and will also set the stage for extending informatics solutions into other areas of the ocean and Earth sciences.

“This data set has the potential to provide us with phenomenal information about blooms in New England waters,” Sosik said of the Martha’s Vineyard observations. “And this project will help us develop the tools we need to efficiently extract that information and quickly learn from it.”

“The informatics solutions will also make it really easy to help other users do the same with their data sets, which is very important since a commercial version of Imaging FlowCytobot is being developed right now,” said Sosik, who is currently funded under the Gordon and Betty Moore Foundation’s Marine Microbiology Initiative.

The Foundation grant will focus on two other projects as well: SeaBED, developed by WHOI scientist Hanumant Singh and colleagues, and HabCam, a camera system that provides a unique glimpse of the seafloor through optical imaging. SeaBED, an autonomous underwater vehicle (AUV) that can fly slowly or hover over the seafloor to depths of 6,000 feet (2,000 meters), is particularly suited to collect highly detailed sonar and optical images of the seafloor, which can be made into mosaics.

“Over the last decade we have built up the capabilities in our underwater imaging platforms to gather large quantities of data,” said Singh, an associate scientist in the Applied Ocean Physics and Engineering department. “This grant will help us leap forward, taking that data and digesting it into useable information.”

The HabCam vehicle flies over the ocean bottom, taking high-resolution images and creating a continuous image ribbon 100 nautical miles (185 kilometers) in length each day. “HabCam provides an expansive view of the seafloor, but we are swamped in images—we collect a half million every day,” said Scott Gallager, lead scientist for the vehicle. “Extracting information from those in an automated and efficient way is essential to addressing long-standing science questions in benthic ecology. It may also enable us to move this technology into operational fisheries oceanography for the survey of sea scallops, ground fish, and other commercially important species. The Gordon and Betty Moore Foundation project will provide new tools to process and understand an ever-increasing amount of image data.”

Maffei said the collaboration with RPI’s Tetherless World Constellation, headed by Peter Fox, was “crucial to our success” in securing the grant. “RPI is a group with strong interest and skills in the area of data science.”

Added Fox: “This award to WHOI will greatly enhance the RPI-WHOI informatics collaboration, as it highlights the key investments that need to be made to unlock the full potential of the rich scientific data—in this case underwater imagery—and greater scientific understanding. It is only the beginning….”

A Revolution in Understanding
Susan K. Avery, president and director of WHOI, added that the project is a high priority for WHOI. “It is the beginning of a long-term strategy that involves a close partnership with Rensselaer Polytechnic Institute, to help advance our informatics capabilities,” she said. “Lessons learned through this project will be widely distributed to domain scientists in oceanography and other scientific disciplines.

“To revolutionize understanding of complex marine ecological systems, the proposed project will generate image informatics tools that have broad academic and societal impact,” Avery said.

“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.”

Christopher Mentzel, program officer, Science at the Foundation, remarked that efforts such as the imaging informatics project at WHOI are critically important in tackling the data-intensive challenges emerging across all science disciplines.

“Oceanography is a rich area of study from the data perspective due to the high volume of heterogeneous information coming from a variety of automated and manual techniques,” he said.  “Imaging data in particular provides a focused area with myriad challenges that, when addressed in efforts such as this, should have a broad impact.”

Larry Madin, WHOI director of research, said the project “will allow new ideas and concepts to emerge, with WHOI in the forefront. We hope this will benefit everybody at the Institution and in the field of informatics.” 

The exact grant amount is $2,170,431.