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Along-Track Reef Imaging System (ATRIS) Completed

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

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

Mapping the Seafloor with ATRIS

ATRIS (Along-Track Reef Imaging System) is an effective tool for rapidly mapping the seafloor over large areas. For example, during a 2011 study in Dry Tortugas National Park, over 258,000 color digital images were acquired along 79 km of transect lines in just 26 hours of operation. The system has 3 possible configurations: "Shallow," "Deep," and "Drift." Shallow and Deep ATRIS are typically deployed from a 25-foot boat.

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

Past uses of ATRIS include habitat mapping in support of sea turtle research within Dry Tortugas National Park and surveying the patch reefs off of Marathon, Florida, after a 2011 coral-bleaching event.

 

Shallow ATRIS

Shallow ATRIS is a boat-mounted system with the camera, transducer, laser pointers, and GPS antenna all mounted to a movable pole. Maximum pole length is ~4 m, making this configuration suitable for water depths up to 10 m under ideal conditions. be suspended in the water column as the boat drifts over a region of interest. Both Deep & Drift ATRIS can accommodate additional sensors, depending on size and power requirements.

ATRIS photo of coral rubble
Sources/Usage: Public Domain. Visit Media to see details.
ATRIS photo of coral rubble.
ATRIS photo of sand
Sources/Usage: Public Domain. Visit Media to see details.
ATRIS photo of sand.
ATRIS photo of senile reef
Sources/Usage: Public Domain. Visit Media to see details.
ATRIS photo of senile reef.
ATRIS photo of seagrass
Sources/Usage: Public Domain.
ATRIS photo of seagrass.

 

Deep ATRIS

Along-Track Reef Imaging System
Sources/Usage: Public Domain.
 ATRIS (Along-Track Reef Imaging System) equipped for deep water survey. (Public domain.)

Deep ATRIS is based on a light-weight, computer-controlled, towed vehicle that is capable of following a programmed diving profile. The vehicle is 1.3 m long with a 63-cm wing span and can carry a wide variety of research instruments, including CTDs, fluorometers, transmissometers, and cameras. Deep ATRIS is currently equipped with a high-speed (20 frames per sec.) digital camera, light-emitting-diode (LED) lights, a compass, a 3-axis orientation sensor, and both a downward- and forward-looking altimeters. The latter is part of an obstacle-avoidance system. The vehicle dynamically adjusts its altitude to maintain a fixed height above the seafloor. The camera has a 29° x 22° field-of-view and captures color images that are 1360 x 1024 pixels in size. GPS coordinates are recorded for each image. A gigabit ethernet connection enables the images to be displayed and archived in real time on the surface computer. Deep ATRIS has a maximum tow speed of 2.6 m/sec and a theoretical operating tow-depth limit of 27 m. The operating depth could be extended to 90 m by replacing the data-transmission wires with fiber optics. Mosaicked images illustrate the high-quality imagery that can be obtained with this system. The images also reveal the potential for unobtrusive animal observations; fish and sea turtles are unperturbed by the presence of Deep ATRIS.

 

octocorals, sponges, and the zoanthid Palythoa caribaeorum
Sources/Usage: Public Domain.
A 6-image mosaic of an area dominated by various octocorals, sponges, and the zoanthid Palythoa caribaeorum. A midnight parrotfish (Scarus coelestinus) is visible in the central portion of the mosaic. The areal coverage is approximately 5 meters by 13 meters. Water depth at the base of the ledge was 10.4 m and Deep ATRIS was 9.7 m above the bottom. 

 

Grey Angelfish
Sources/Usage: Public Domain. Visit Media to see details.
 Grey Angelfish (Ponacanthus arcualus). Water depth was 8.8 m, and Deep ATRIS was 2.4 m above the bottom. Image resolution is 0.9 mm/pixel. 

 

Spadefish
Sources/Usage: Public Domain. Visit Media to see details.
Spadefish (Chaetodipterus faber) are in the foreground with several grunts (Haemulon sp.) hovering above a brain coral head (Diploria sp.) in the background. Water depth was 9.2 m, and Deep ATRIS was 2.35 m above the bottom. Image resolution is 0.9 mm/pixel.

 

Hawksbill turtle
Sources/Usage: Public Domain.
 A Hawksbill turtle (Eretmochelys imbricata) resting on the sea-floor. Water depth was 9.2 m, and Deep ATRIS was 2.93 m above the bottom. Image resolution is 1.1 mm/pixel.

 

Drift ATRIS

For Drift ATRIS, all of the instrumentation is mounted to a frame that can be lowered to 95 m. As the name implies, it is designed to be suspended in the water column as the boat drifts over a region of interest. Both Deep & Drift ATRIS can accommodate additional sensors, depending on size and power requirements.

Along-Track Reef Imaging System
Sources/Usage: Public Domain.
Drift ATRIS (Along-Track Reef Imaging System).

 

 

Below are other science projects associated with this research.

link
bathymetry plotted in 3D

Advanced Remote Sensing Methods for Coastal Science and Management

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.
By
St. Petersburg Coastal and Marine Science Center
link

Advanced Remote Sensing Methods for Coastal Science and Management

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.
Learn More
link
Along-Track Reef Imaging System

Fine-scale Benthic Habitat Mapping

Both ATRIS configurations were deployed in Dry Tortugas National Park (DRTO) to fill information gaps in the spatial coverage of existing habitat maps.
By
Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center
link

Fine-scale Benthic Habitat Mapping

Both ATRIS configurations were deployed in Dry Tortugas National Park (DRTO) to fill information gaps in the spatial coverage of existing habitat maps.
Learn More
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

Below are publications associated with this project.

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
By
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,
By
Ecosystems, Wetland and Aquatic Research 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
By
Ecosystems, 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
By
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
By
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
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.
By
St. Petersburg Coastal and Marine Science Center
  • Overview

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

    Mapping the Seafloor with ATRIS

    ATRIS (Along-Track Reef Imaging System) is an effective tool for rapidly mapping the seafloor over large areas. For example, during a 2011 study in Dry Tortugas National Park, over 258,000 color digital images were acquired along 79 km of transect lines in just 26 hours of operation. The system has 3 possible configurations: "Shallow," "Deep," and "Drift." Shallow and Deep ATRIS are typically deployed from a 25-foot boat.

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

    Past uses of ATRIS include habitat mapping in support of sea turtle research within Dry Tortugas National Park and surveying the patch reefs off of Marathon, Florida, after a 2011 coral-bleaching event.

     

    Shallow ATRIS

    Shallow ATRIS is a boat-mounted system with the camera, transducer, laser pointers, and GPS antenna all mounted to a movable pole. Maximum pole length is ~4 m, making this configuration suitable for water depths up to 10 m under ideal conditions. be suspended in the water column as the boat drifts over a region of interest. Both Deep & Drift ATRIS can accommodate additional sensors, depending on size and power requirements.

    ATRIS photo of coral rubble
    Sources/Usage: Public Domain. Visit Media to see details.
    ATRIS photo of coral rubble.
    ATRIS photo of sand
    Sources/Usage: Public Domain. Visit Media to see details.
    ATRIS photo of sand.
    ATRIS photo of senile reef
    Sources/Usage: Public Domain. Visit Media to see details.
    ATRIS photo of senile reef.
    ATRIS photo of seagrass
    Sources/Usage: Public Domain.
    ATRIS photo of seagrass.

     

    Deep ATRIS

    Along-Track Reef Imaging System
    Sources/Usage: Public Domain.
     ATRIS (Along-Track Reef Imaging System) equipped for deep water survey. (Public domain.)

    Deep ATRIS is based on a light-weight, computer-controlled, towed vehicle that is capable of following a programmed diving profile. The vehicle is 1.3 m long with a 63-cm wing span and can carry a wide variety of research instruments, including CTDs, fluorometers, transmissometers, and cameras. Deep ATRIS is currently equipped with a high-speed (20 frames per sec.) digital camera, light-emitting-diode (LED) lights, a compass, a 3-axis orientation sensor, and both a downward- and forward-looking altimeters. The latter is part of an obstacle-avoidance system. The vehicle dynamically adjusts its altitude to maintain a fixed height above the seafloor. The camera has a 29° x 22° field-of-view and captures color images that are 1360 x 1024 pixels in size. GPS coordinates are recorded for each image. A gigabit ethernet connection enables the images to be displayed and archived in real time on the surface computer. Deep ATRIS has a maximum tow speed of 2.6 m/sec and a theoretical operating tow-depth limit of 27 m. The operating depth could be extended to 90 m by replacing the data-transmission wires with fiber optics. Mosaicked images illustrate the high-quality imagery that can be obtained with this system. The images also reveal the potential for unobtrusive animal observations; fish and sea turtles are unperturbed by the presence of Deep ATRIS.

     

    octocorals, sponges, and the zoanthid Palythoa caribaeorum
    Sources/Usage: Public Domain.
    A 6-image mosaic of an area dominated by various octocorals, sponges, and the zoanthid Palythoa caribaeorum. A midnight parrotfish (Scarus coelestinus) is visible in the central portion of the mosaic. The areal coverage is approximately 5 meters by 13 meters. Water depth at the base of the ledge was 10.4 m and Deep ATRIS was 9.7 m above the bottom. 

     

    Grey Angelfish
    Sources/Usage: Public Domain. Visit Media to see details.
     Grey Angelfish (Ponacanthus arcualus). Water depth was 8.8 m, and Deep ATRIS was 2.4 m above the bottom. Image resolution is 0.9 mm/pixel. 

     

    Spadefish
    Sources/Usage: Public Domain. Visit Media to see details.
    Spadefish (Chaetodipterus faber) are in the foreground with several grunts (Haemulon sp.) hovering above a brain coral head (Diploria sp.) in the background. Water depth was 9.2 m, and Deep ATRIS was 2.35 m above the bottom. Image resolution is 0.9 mm/pixel.

     

    Hawksbill turtle
    Sources/Usage: Public Domain.
     A Hawksbill turtle (Eretmochelys imbricata) resting on the sea-floor. Water depth was 9.2 m, and Deep ATRIS was 2.93 m above the bottom. Image resolution is 1.1 mm/pixel.

     

    Drift ATRIS

    For Drift ATRIS, all of the instrumentation is mounted to a frame that can be lowered to 95 m. As the name implies, it is designed to be suspended in the water column as the boat drifts over a region of interest. Both Deep & Drift ATRIS can accommodate additional sensors, depending on size and power requirements.

    Along-Track Reef Imaging System
    Sources/Usage: Public Domain.
    Drift ATRIS (Along-Track Reef Imaging System).

     

     

  • Science

    Below are other science projects associated with this research.

    link
    bathymetry plotted in 3D

    Advanced Remote Sensing Methods for Coastal Science and Management

    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.
    By
    St. Petersburg Coastal and Marine Science Center
    link

    Advanced Remote Sensing Methods for Coastal Science and Management

    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.
    Learn More
    link
    Along-Track Reef Imaging System

    Fine-scale Benthic Habitat Mapping

    Both ATRIS configurations were deployed in Dry Tortugas National Park (DRTO) to fill information gaps in the spatial coverage of existing habitat maps.
    By
    Coastal and Marine Hazards and Resources Program, St. Petersburg Coastal and Marine Science Center
    link

    Fine-scale Benthic Habitat Mapping

    Both ATRIS configurations were deployed in Dry Tortugas National Park (DRTO) to fill information gaps in the spatial coverage of existing habitat maps.
    Learn More
    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
  • Publications

    Below are publications associated with this project.

    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
    By
    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,
    By
    Ecosystems, Wetland and Aquatic Research 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
    By
    Ecosystems, 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
    By
    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
    By
    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
    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.
    By
    St. Petersburg Coastal and Marine Science Center