Mapping Seafloor Habitats
NOAA Uses Sonar, Lidar, and Optical
NOAA used ENVI to produce a PCA surface – the foundation for their mapping methodology – from four different acoustic and multispectral datasets spanning the monument’s 20,000-acre extent. Image courtesy of NOAA.
NOAA used the feature extraction tool in ENVI to “pull out” unique habitats from the sea floor around Buck Island (above) and assign attributes to the features (below). Image courtesy of NOAA.
The feature extraction process identifies unique objects and habitat types on the ocean floor from a depth-derived PCA surface. Image courtesy of NOAA.
NOAA COLLECTS AND ANALYZES DETAILED SONAR, LIDAR AND OPTICAL IMAGERY DATA TO DETERMINE the best regulations and practices to preserve vital habitats. They are using ENVI image analysis software to process, analyze, and fuse different types of geospatial imagery and to integrate information with Esri’s ArcGIS.
The National Oceanic and Atmospheric Administration (NOAA) uses GIS and imagery for a variety of environmental management and conservation efforts including conserving and managing coastal and marine ecosystems and resources. NOAA provides these services to academic, state, federal and private sector partners. NOAA recently assisted one of these partners to map and extract detailed information about seafloor habitats within a marine protected area. In order to do so efficiently, NOAA needed to develop a new semi-automated approach that would allow them to process, analyze and fuse different types of imagery and provide their partner with the fundamental data needed to make informed decisions.
The National Park Service (NPS) asked NOAA to map and extract detailed information about seafloor habitats in Buck Island Reef National Monument off the U.S. Virgin Island of St. Croix, which has been dubbed "one of the finest marine gardens in the Caribbean Sea." The monument is one of only a few fully marine protected areas in the U.S. National Park System and is home to a coral reef ecosystem that supports a large variety of native flora and fauna, including several endangered and threatened species, such as hawksbill turtles and brown pelicans.
The NPS called upon NOAA's Biogeo-graphy Branch to assist by providing products to inform ecosystem-based management in the monument. To do this, NOAA needed an efficient and effective method to map and assess the distribution and ecology of living marine resources.
The resources in Buck Island Reef National Monument are impacted by its visitors, boaters, snorkelers and scuba divers as well as pollution, climate change and extreme weather events like hurricanes. The habitat map with which NOAA provided monument resource managers will be used to understand the current state of the area and how things are changing so that they can determine the best rules, regulations and practices to preserve and conserve its habitats well into the future.
When One Sensor Isn’t Enough
After evaluating the area, NOAA determined that traditional marine mapping methods that rely on the manual interpretation of optical imagery couldn’t produce a comprehensive habitat map of the monument given its depths, which extend from the coastline of Buck Island to 1,800 meters at its deepest extent. "We had a very unique problem," said Tim Battista, an Oceanographer at NOAA. "There is no one technology or sensor that allowed us to collect the data we needed in the range of depths present at the monument. We had to devise an innovative method that would allow us to both measure sea floor depths as well as characterize its habitats across the entire seascape."
NOAA ultimately devised a new method that fuses the strengths of four different sonar, lidar and optical imagery sensors to gather the information they needed. NOAA chose ENVI image analysis software as a key part of their solution because it combines the latest spectral image processing and image analysis capabilities with automated workflows, allowing users to obtain scientifically proven, accurate results quickly and efficiently. Because ENVI gives users the capability to fuse multiple data modalities such as radar, lidar, optical, hyperspectral, stereo, thermal, acoustic and more, the strengths of different sensors can be exploited together, which creates a rich context that aids decision making.
NOAA recorded depth and other characteristics of shallow areas in the monument using multispectral and lidar imagery. This imagery was acquired from planes that flew over areas up to about 30 meters in depth, the point at which light is unable to penetrate to the seafloor. At depths of more than five meters, NOAA used sonar technology located onboard vessels and ships, such as the Nancy Foster, to scan the sea bed. The Nancy Foster emits more than 3,500 pings per second and receivers on the ship record the time and angle of the echoes returning from the sea floor. Days spent sailing and employing sonar technology yielded bathymetry or depth information. The intensity of the echo also provided information about the sea floor, such as how hard, soft, rough or smooth it is, which often indicates discrete habitats such as coral, sand and sea grasses.
ENVI Helps Distinguish the Sea Floor
The lidar and acoustically collected bathymetry was also used to calculate a suite of complexity metrics in Esri’s ArcGIS, such as slope, rugosity and curvature, which emphasize the differences between habitats on the sea floor. As part of their preprocessing work, NOAA used Principle Component Analysis (PCA) to reduce redundancy in the data and better understand the complexity on the sea floor. This information, along with ancillary information including intensity information, was loaded into ENVI, allowing the researchers to draw distinctions between softer and harder sediments in flatter areas of the sea floor.
Using an automated workflow, NOAA staff performed segmentation in ENVI using the software’s extraction tool. Following image segmentation, the workflow in ENVI provides users with several options for classifying or assigning attributes to the features in their imagery. NOAA classified features by selecting locations with unique acoustic or optical signatures, and performed ground validation using still and video cameras operated by divers and Remotely Operated Vehicles (ROVs). NOAA’s classification scheme used to describe these sites takes into consideration what the sea floor is made of, what is growing on top of it and the quantity of cover.
NOAA then took the segments and classified ground validation points and applied a free ENVI add-on called RuleGen developed by an ENVI user. RuleGen includes a classification and regression tree which was well-suited for NOAA’s acoustic datasets. Then, NOAA staff returned to the field and verified the accuracy of the output – a draft classified habitat map.
"Acoustic data is often very noisy and heterogeneous, which makes classification difficult using traditional pixel-based approaches," said Sam Tormey, Marine Spatial Analyst contracted with NOAA through C S S-Dynamac. "ENVI has allowed us to overcome these challenges, so we are no longer classifying a pixel, but rather, an object. We are now able to more objectively and efficiently deal with heterogeneity and make products that meet our partners’ needs."
Integrating GIS and Imagery
Finally, NOAA took the habitat maps and other information derived from imagery and moved them into ArcGIS for additional analysis and the creation of applications. This information includes the structure, biological cover and percent cover – key pieces of information that resource managers need to make effective ecosystem management decisions. Information extracted from imagery and added to a GIS provides a complete picture of a geographic area of interest that includes pertinent, current information. ENVI makes it seamless to update ArcGIS with information from geospatial imagery by delivering image analysis tools directly from the ArcGIS desktop and server environments.
One application that NOAA develops for some partners is a Web-based mapping portal so that partners have the option of displaying each habitat class separately, overlaying ground-truth points, viewing the videos and images that were captured and creating custom maps. These portals are especially useful for partners who may not be familiar with traditional GIS software. "The seamless integration of ENVI and ArcGIS allows us to leverage the image analysis capabilities of ENVI with the geospatial tools and statistics in ArcGIS, which gives us tremendous analytical power," said Costa. "It also allows us to put our habitat maps on the Web for anyone to see and use."
NOAA will be delivering the final habitat maps, information derived from imagery, still images and videos and related applications that are developed to monument managers in July 2012. Previously, NOAA staff could only monitor limited areas because the process was very time-intensive and depended on the experiences and interpretation skills of the analyst, which isn’t highly replicable.
"Our past mapping efforts were conducted by manually digitizing and interpreting optical imagery," said Tormey. "The new methods that were developed coupled with the power of ENVI allow us to integrate the strengths of multiple acoustic sensors, multispectral and lidar imagery and produce a seamless product across the entire extent of our study areas." NOAA is now able to also produce products at a much finer spatial scale, so maps are more reflective of the true features on the ground.