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Advanced Remote Sensing Methods for Coastal Science and Management

Completed
By St. Petersburg Coastal and Marine Science Center March 5, 2018

This project focused on developing algorithms for quantifying benthic habitat complexity from images, modeling the structural complexity of the seafloor, and using fluorescence signatures to classify coral reef habitats. 

 

Along-Track Reef Imaging System specifications
Sources/Usage: Public Domain. View Media Details
Shallow, Deep, and Drift ATRIS (Along-Track Reef Imaging System) and system specifications. (Public domain.)

Project Specifications

The project included ship-based, multibeam sonar, and diver-based fluorescence imaging systems. Algorithms were developing to characterize and classify features on the seafloor using data collected by both airborne and underwater instrumentation.

Principles of fractal geometry were applied to model the structural complexity of the seafloor. The fluorescent properties of corals were used to improve automated image classification and investigate linkages to coral diseases.

In addition to their scientific merit, these tools benefited a number of research projects, including several tasks within the Coral Reef Ecosystem Studies (CREST) project.

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.

Applications of Coral Fluorescence

Fluorescence is an often-overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.

Fractal dimensions of 500-m x 500-m tiles
Sources/Usage: Public Domain. View Media Details
Fractal dimensions of 500-m x 500-m tiles within the study site. For reference, the 7-m contour is plotted on top of the fractal map. (Public domain.)
Fuorescent images of two coral colonies
Sources/Usage: Public Domain. View Media Details
Fuorescent images of two coral colonies, Diploria clivosa (left) and Orbicella faveolata (right) growing on the seawall at Ft. Jefferson, Dry Tortugas National Park. The two colonies are separated by an area of dead coral that has been colonized by algae. In the fluorescent image, red corresponds to chlorophyll and green to GFP. Note that the GFP is concentrated in the center of each coral polyp. (Credit: David Zawada, USGS. Public domain.)

Below are other science projects associated with this project.

link
Location and submerged topographic map of the study site

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.
By
St. Petersburg Coastal and Marine Science Center
link

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.
Learn More
link
Fuorescent image of a Montastrea cavernosa 

Applications of Coral Fluorescence

Fluorescence is an often overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.
By
St. Petersburg Coastal and Marine Science Center
link

Applications of Coral Fluorescence

Fluorescence is an often overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.
Learn More
link
Along-Track Reef Imaging System

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.
By
St. Petersburg Coastal and Marine Science Center
link

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.
Learn More

Below are publications associated with this project.

Filter Total Items: 13

A comparison between boat-based and diver-based methods for quantifying coral bleaching

Recent increases in both the frequency and severity of coral bleaching events have spurred numerous surveys to quantify the immediate impacts and monitor the subsequent community response. Most of these efforts utilize conventional diver-based methods, which are inherently time-consuming, expensive, and limited in spatial scope unless they deploy large teams of scientifically-trained divers. In th
Authors
David G. Zawada, Rob Ruzicka, Michael A. Colella
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Fluorescence-based classification of Caribbean coral reef organisms and substrates

A diverse group of coral reef organisms, representing several phyla, possess fluorescent pigments. We investigated the potential of using the characteristic fluorescence emission spectra of these pigments to enable unsupervised, optical classification of coral reef habitats. We compiled a library of characteristic fluorescence spectra through in situ and laboratory measurements from a variety of s
Authors
David G. Zawada, Charles H. Mazel
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Possible return of Acropora cervicornis at Pulaski Shoal, Dry Tortugas National Park, Florida

Seabed classification is essential to assessing environmental associations and physical status in coral reef ecosystems. At Pulaski Shoal in Dry Tortugas National Park, Florida, nearly continuous underwater-image coverage was acquired in 15.5 hours in 2009 along 70.2 km of transect lines spanning ~0.2 km2. The Along-Track Reef-Imaging System (ATRIS), a boat-based, high-speed, digital imaging syste
Authors
Barbara H. Lidz, David G. Zawada
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Habitat use of breeding green turtles Chelonia mydas tagged in Dry Tortugas National Park: Making use of local and regional MPAs

Use of existing marine protected areas (MPAs) by far-ranging marine turtles can be determined using satellite telemetry. Because of a lack of information on MPA use by marine turtles in the Gulf of Mexico, we used satellite transmitters in 2010 and 2011 to track movements of 11 adult female breeding green turtles (Chelonia mydas) tagged in Dry Tortugas National Park (DRTO), in the Gulf of Mexico,
Authors
Kristen Hart, David G. Zawada, Ikuko Fujisaki, Barbara H. Lidz
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Fractal analysis of the Navassa Island seascape

This release provides the numerical results of the fractal analyses discussed in Zawada and others (2010) for the Navassa Island reefscape. The project represents the continuation of a U.S. Geological Survey (USGS) research effort begun in 2006 (Zawada and others, 2006) to understand the patterns and scalability of roughness and topographic complexity from individual corals to complete reefscapes.
Authors
David G. Zawada
By
Contaminant Biology, St. Petersburg Coastal and Marine Science Center

Benthic habitat classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey Along-Track Reef Imaging System (ATRIS)

The Comprehensive Everglades Restoration Plan (CERP) funded in partnership between the U.S. Army Corps of Engineers, South Florida Water Management District, and other Federal, local and Tribal members has in its mandate a guideline to protect and restore freshwater flows to coastal environments to pre-1940s conditions (CERP, 1999). Historic salinity data are sparse for Florida Bay, so it is diffi
Authors
C. D. Reich, D.G. Zawada, P.R. Thompson, C.E. Reynolds, A.H. Spear, D.K. Umberger, R.Z. Poore
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Inter-nesting habitat-use patterns of loggerhead sea turtles: Enhancing satellite tracking with benthic mapping

The loggerhead sea turtle Caretta caretta faces declining nest numbers and bycatches from commercial longline fishing in the southeastern USA. Understanding spatial and temporal habitat-use patterns of these turtles, especially reproductive females in the neritic zone, is critical for guiding management decisions. To assess marine turtle habitat use within the Dry Tortugas National Park (DRTO), we
Authors
Kristen M. Hart, David G. Zawada, Ikuko Fujisaki, Barbara H. Lidz
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Detailed seafloor habitat mapping to enhance marine-resource management

Pictures of the seafloor capture important information about the sediments, exposed geologic features, submerged aquatic vegetation, and animals found in a given habitat. With the emergence of marine protected areas (MPAs) as a favored tactic for preserving coral reef resources, knowledge of essential habitat components is paramount to designing effective management strategies. Surprisingly, detai
Authors
David G. Zawada, Kristen M. Hart
By
Ecosystems Mission Area, Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center, Wetland and Aquatic Research Center

A multiscale analysis of coral reef topographic complexity using lidar-derived bathymetry

Coral reefs represent one of the most irregular substrates in the marine environment. This roughness or topographic complexity is an important structural characteristic of reef habitats that affects a number of ecological and environmental attributes, including species diversity and water circulation. Little is known about the range of topographic complexity exhibited within a reef or between diff
Authors
D.G. Zawada, J. C. Brock
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Applying New Methods to Diagnose Coral Diseases

Coral disease, one of the major causes of reef degradation and coral death, has been increasing worldwide since the 1970s, particularly in the Caribbean. Despite increased scientific study, simple questions about the extent of disease outbreaks and the causative agents remain unanswered. A component of the U.S. Geological Survey Coral Reef Ecosystem STudies (USGS CREST) project is focused on devel
Authors
Christina A. Kellogg, David G. Zawada
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

A new towed platform for the unobtrusive surveying of benthic habitats and organisms

Maps of coral ecosystems are needed to support many conservation and management objectives, as well as research activities. Examples include ground-truthing aerial and satellite imagery, characterizing essential habitat, assessing changes, and monitoring the progress of restoration efforts. To address some of these needs, the U.S. Geological Survey developed the Along-Track Reef-Imaging System (AT
Authors
David G. Zawada, P.R. Thompson, J. Butcher
By
St. Petersburg Coastal and Marine Science Center

Along-Track Reef Imaging System (ATRIS)

"Along-Track Reef Imaging System (ATRIS)" describes the U.S. Geological Survey's Along-Track Reef Imaging System, a boat-based sensor package for rapidly mapping shallow water benthic environments. ATRIS acquires high resolution, color digital images that are accurately geo-located in real-time.
Authors
John Brock, Dave Zawada
By
St. Petersburg Coastal and Marine Science Center

This project focused on developing algorithms for quantifying benthic habitat complexity from images, modeling the structural complexity of the seafloor, and using fluorescence signatures to classify coral reef habitats. 

 

Along-Track Reef Imaging System specifications
Sources/Usage: Public Domain. View Media Details
Shallow, Deep, and Drift ATRIS (Along-Track Reef Imaging System) and system specifications. (Public domain.)

Project Specifications

The project included ship-based, multibeam sonar, and diver-based fluorescence imaging systems. Algorithms were developing to characterize and classify features on the seafloor using data collected by both airborne and underwater instrumentation.

Principles of fractal geometry were applied to model the structural complexity of the seafloor. The fluorescent properties of corals were used to improve automated image classification and investigate linkages to coral diseases.

In addition to their scientific merit, these tools benefited a number of research projects, including several tasks within the Coral Reef Ecosystem Studies (CREST) project.

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.

Applications of Coral Fluorescence

Fluorescence is an often-overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.

Fractal dimensions of 500-m x 500-m tiles
Sources/Usage: Public Domain. View Media Details
Fractal dimensions of 500-m x 500-m tiles within the study site. For reference, the 7-m contour is plotted on top of the fractal map. (Public domain.)
Fuorescent images of two coral colonies
Sources/Usage: Public Domain. View Media Details
Fuorescent images of two coral colonies, Diploria clivosa (left) and Orbicella faveolata (right) growing on the seawall at Ft. Jefferson, Dry Tortugas National Park. The two colonies are separated by an area of dead coral that has been colonized by algae. In the fluorescent image, red corresponds to chlorophyll and green to GFP. Note that the GFP is concentrated in the center of each coral polyp. (Credit: David Zawada, USGS. Public domain.)

Below are other science projects associated with this project.

link
Location and submerged topographic map of the study site

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.
By
St. Petersburg Coastal and Marine Science Center
link

Modeling Seafloor Structural Complexity

This effort focused on understanding the patterns and scalability of roughness and topographic complexity of marine habitats, such as coral reefs.
Learn More
link
Fuorescent image of a Montastrea cavernosa 

Applications of Coral Fluorescence

Fluorescence is an often overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.
By
St. Petersburg Coastal and Marine Science Center
link

Applications of Coral Fluorescence

Fluorescence is an often overlooked property of reef-building corals that can improve the classification of reef habitats from imagery and provide diagnostic information on corals.
Learn More
link
Along-Track Reef Imaging System

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.
By
St. Petersburg Coastal and Marine Science Center
link

Along-Track Reef Imaging System (ATRIS)

ATRIS is a benthic-survey tool that simultaneously acquires geo-located, color, digital images with corresponding water depths.
Learn More

Below are publications associated with this project.

Filter Total Items: 13

A comparison between boat-based and diver-based methods for quantifying coral bleaching

Recent increases in both the frequency and severity of coral bleaching events have spurred numerous surveys to quantify the immediate impacts and monitor the subsequent community response. Most of these efforts utilize conventional diver-based methods, which are inherently time-consuming, expensive, and limited in spatial scope unless they deploy large teams of scientifically-trained divers. In th
Authors
David G. Zawada, Rob Ruzicka, Michael A. Colella
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Fluorescence-based classification of Caribbean coral reef organisms and substrates

A diverse group of coral reef organisms, representing several phyla, possess fluorescent pigments. We investigated the potential of using the characteristic fluorescence emission spectra of these pigments to enable unsupervised, optical classification of coral reef habitats. We compiled a library of characteristic fluorescence spectra through in situ and laboratory measurements from a variety of s
Authors
David G. Zawada, Charles H. Mazel
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Possible return of Acropora cervicornis at Pulaski Shoal, Dry Tortugas National Park, Florida

Seabed classification is essential to assessing environmental associations and physical status in coral reef ecosystems. At Pulaski Shoal in Dry Tortugas National Park, Florida, nearly continuous underwater-image coverage was acquired in 15.5 hours in 2009 along 70.2 km of transect lines spanning ~0.2 km2. The Along-Track Reef-Imaging System (ATRIS), a boat-based, high-speed, digital imaging syste
Authors
Barbara H. Lidz, David G. Zawada
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Habitat use of breeding green turtles Chelonia mydas tagged in Dry Tortugas National Park: Making use of local and regional MPAs

Use of existing marine protected areas (MPAs) by far-ranging marine turtles can be determined using satellite telemetry. Because of a lack of information on MPA use by marine turtles in the Gulf of Mexico, we used satellite transmitters in 2010 and 2011 to track movements of 11 adult female breeding green turtles (Chelonia mydas) tagged in Dry Tortugas National Park (DRTO), in the Gulf of Mexico,
Authors
Kristen Hart, David G. Zawada, Ikuko Fujisaki, Barbara H. Lidz
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Fractal analysis of the Navassa Island seascape

This release provides the numerical results of the fractal analyses discussed in Zawada and others (2010) for the Navassa Island reefscape. The project represents the continuation of a U.S. Geological Survey (USGS) research effort begun in 2006 (Zawada and others, 2006) to understand the patterns and scalability of roughness and topographic complexity from individual corals to complete reefscapes.
Authors
David G. Zawada
By
Contaminant Biology, St. Petersburg Coastal and Marine Science Center

Benthic habitat classification in Lignumvitae Key Basin, Florida Bay, using the U.S. Geological Survey Along-Track Reef Imaging System (ATRIS)

The Comprehensive Everglades Restoration Plan (CERP) funded in partnership between the U.S. Army Corps of Engineers, South Florida Water Management District, and other Federal, local and Tribal members has in its mandate a guideline to protect and restore freshwater flows to coastal environments to pre-1940s conditions (CERP, 1999). Historic salinity data are sparse for Florida Bay, so it is diffi
Authors
C. D. Reich, D.G. Zawada, P.R. Thompson, C.E. Reynolds, A.H. Spear, D.K. Umberger, R.Z. Poore
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Inter-nesting habitat-use patterns of loggerhead sea turtles: Enhancing satellite tracking with benthic mapping

The loggerhead sea turtle Caretta caretta faces declining nest numbers and bycatches from commercial longline fishing in the southeastern USA. Understanding spatial and temporal habitat-use patterns of these turtles, especially reproductive females in the neritic zone, is critical for guiding management decisions. To assess marine turtle habitat use within the Dry Tortugas National Park (DRTO), we
Authors
Kristen M. Hart, David G. Zawada, Ikuko Fujisaki, Barbara H. Lidz
By
Ecosystems Mission Area, Wetland and Aquatic Research Center

Detailed seafloor habitat mapping to enhance marine-resource management

Pictures of the seafloor capture important information about the sediments, exposed geologic features, submerged aquatic vegetation, and animals found in a given habitat. With the emergence of marine protected areas (MPAs) as a favored tactic for preserving coral reef resources, knowledge of essential habitat components is paramount to designing effective management strategies. Surprisingly, detai
Authors
David G. Zawada, Kristen M. Hart
By
Ecosystems Mission Area, Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center, Wetland and Aquatic Research Center

A multiscale analysis of coral reef topographic complexity using lidar-derived bathymetry

Coral reefs represent one of the most irregular substrates in the marine environment. This roughness or topographic complexity is an important structural characteristic of reef habitats that affects a number of ecological and environmental attributes, including species diversity and water circulation. Little is known about the range of topographic complexity exhibited within a reef or between diff
Authors
D.G. Zawada, J. C. Brock
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

Applying New Methods to Diagnose Coral Diseases

Coral disease, one of the major causes of reef degradation and coral death, has been increasing worldwide since the 1970s, particularly in the Caribbean. Despite increased scientific study, simple questions about the extent of disease outbreaks and the causative agents remain unanswered. A component of the U.S. Geological Survey Coral Reef Ecosystem STudies (USGS CREST) project is focused on devel
Authors
Christina A. Kellogg, David G. Zawada
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center

A new towed platform for the unobtrusive surveying of benthic habitats and organisms

Maps of coral ecosystems are needed to support many conservation and management objectives, as well as research activities. Examples include ground-truthing aerial and satellite imagery, characterizing essential habitat, assessing changes, and monitoring the progress of restoration efforts. To address some of these needs, the U.S. Geological Survey developed the Along-Track Reef-Imaging System (AT
Authors
David G. Zawada, P.R. Thompson, J. Butcher
By
St. Petersburg Coastal and Marine Science Center

Along-Track Reef Imaging System (ATRIS)

"Along-Track Reef Imaging System (ATRIS)" describes the U.S. Geological Survey's Along-Track Reef Imaging System, a boat-based sensor package for rapidly mapping shallow water benthic environments. ATRIS acquires high resolution, color digital images that are accurately geo-located in real-time.
Authors
John Brock, Dave Zawada
By
St. Petersburg Coastal and Marine Science Center
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