Gerald A. Hatcher
Christine J. Kranenburg
Jonathan A. Warrick
20220611
Overlapping seabed images collected at Eastern Dry Rocks coral reef, Florida, 2021
TIFF
data release
DOI:10.5066/P93RIIG9
Santa Cruz, California
U.S. Geological Survey - Pacific Coastal and Marine Science Center
https://doi.org/10.5066/P93RIIG9
Gerald A. Hatcher
Christine J. Kranenburg
Jonathan A. Warrick
Stephen T. Bosse
David G. Zawada
Kimberly K. Yates
Selena A. Johnson
2022
Overlapping seabed images and location data acquired using the SQUID-5 system at Eastern Dry Rocks coral reef, Florida, in May 2021, with derived point cloud, digital elevation model and orthomosaic of submerged topography
data release
DOI:10.5066/P93RIIG9
Santa Cruz, California
U.S. Geological Survey - Pacific Coastal and Marine Science Center
https://doi.org/10.5066/P93RIIG9
Underwater images totaling 138,733 in number were collected at Eastern Dry Rocks coral reef, near Key West, Florida, in May 2021, using the SQUID5 Structure-from-Motion (SfM) system, a towed-surface vehicle with five downward-looking underwater cameras developed by the U.S. Geological Survey. The images are organized in zipped files grouped by survey line. The SQUID-5 records images as TIFF (.tif) format to maintain the highest resolution and bit depth. Each image includes EXIF metadata, containing GNSS date, time, latitude, longitude, and altitude of the GNSS antenna mounted on the towed surface vehicle, copyright, keywords, and other fields.
The underwater images and associated location data were collected to provide high-resolution elevation data and precisely co-registered, full-color orthomosaic base maps for use in environmental assessment and monitoring of the coral reef and surrounding seafloor habitat. Additionally, the data were collected to evaluate their potential to improve USGS scientific efforts including seafloor elevation and stability modeling, and small-scale hydrodynamic flow modeling.
Additional information about the field activity from which these data were derived is available online at:
https://cmgds.marine.usgs.gov/fan_info.php?fan=2021-620-FA and https://cmgds.marine.usgs.gov/fan_info.php?fan=2021-313-FA
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
20210507
20210513
ground condition
None planned
-81.84582229
-81.83788892
24.46363355
24.45790608
USGS Metadata Identifier
USGS:8c977484-38e7-4273-9adb-185ef3ac6c67
Marine Realms Information Bank (MRIB) keywords
seabed
coral reefs
Data Categories for Marine Planning
Physical Habitats and Geomorphology
ISO 19115 Topic Category
oceans
elevation
USGS Thesaurus
reef ecosystems
geospatial datasets
remote sensing
visible light imaging
structure from motion
None
U.S. Geological Survey
USGS
Coastal and Marine Hazards and Resources Program
CMHRP
Pacific Coastal and Marine Science Center
PCMSC
St. Petersburg Coastal and Marine Science Center
SPCMSC
Geographic Names Information System (GNIS)
Eastern Dry Rocks
State of Florida
None
USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator of the dataset and in products derived from these data. This information is not intended for navigation purposes.
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-4747
pcmsc_data@usgs.gov
CAM13-20210508191029_000-216-fullrez.jpg
Example of underwater image from one of the cameras.
JPG
Data collection was funded by the U.S. Geological Survey Pacific Coastal Marine Science Center and the U.S. Geological Survey Saint Petersburg Coastal and Marine Science Center. The authors would like to thank Captain Chad Stolka, Operations Specialist for the NOAA Florida Keys National Marine Sanctuary, for his local knowledge and maritime expertise during data acquisition; Dr. Jason Spadaro, Assistant Professor, Marine Science and Technology, College of the Florida Keys for installing calibration targets on the reef; Lisa Symons, Regional Response Coordinator, and staff of the Eastern Region, Office of National Marine Sanctuaries, NOAA Florida Keys National Marine Sanctuary, for coordination efforts.
Microsoft Windows 10
Gerald A. Hatcher
Jonathan A. Warrick
Andrew C. Ritchie
Evan T. Dailey
David G. Zawada
Christine Kranenburg
Kimberly K. Yates
2020
Accurate bathymetric maps from underwater digital imagery without ground control
Hatcher, G.A., Warrick, J.A., Ritchie, A.C., Dailey, E.T., Zawada, D.G., Kranenburg, C., and Yates, K.K., 2020, Accurate bathymetric maps from underwater digital imagery without ground control: Frontiers in Marine Science, v. 7, art. 525, doi:10.3389/fmars.2020.00525
https://doi.org/10.3389/fmars.2020.00525
The accuracy of the position data used for SfM data processing is based on the accuracy of the post-processed GNSS navigation data, which produced a 10-Hz vehicle trajectory with an estimated 2-sigma accuracy of 10 cm horizontal and 15 cm vertical.
Note that the accuracy of the positions in the image EXIF headers are GNSS antenna positions and are limited to six decimal places, whereas the positions in the accompanying navigation file (SQUID5_EDR_2021_Image_Locations.txt) are accurate to ten decimal places and are therefore highly recommended for use in SfM processing to produce the highest quality derived products.
All data fall within expected ranges.
Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
Positions provided in the accompanying navigation file (SQUID5_EDR_2021_Image_Locations.txt) have an estimated 2-sigma horizontal accuracy of 10 cm. The accuracy of the positions in the image EXIF headers are reduced due to field size limitations for storing latitude/longitude.
Positions provided in the accompanying navigation file (SQUID5_EDR_2021_Image_Locations.txt) have an estimated 2-sigma vertical accuracy of 15 cm.
IMAGE ACQUISITION
Images were collected in tiff (.tif) format in synchronized quintets by the SQUID-5 system while towed at a speed of approximately 3 knots behind the NOAA vessel R/V Rachael Carson during USGS field activity 2021-620-FA also known as 2021-313-FA. The image-collection frequency was 1 Hz, and GNSS positions were recorded at 10 Hz. Image-gain settings were adjusted as needed depending on water depth and lighting conditions. Aperture and shutter speed were consistent for each group of images at a study site. Image files were named programmatically with the last two digits of the camera's serial number, a 14-digit UTC datetime value formatted as yyyymmddhhmmss, thousandths of seconds, and the sequential image number for that camera. For example, 'CAM13-20210512185837_001-1.tif' indicates camera 13, May 12, 2021, 18:58:37.001 (UTC), collection event number 1 of the survey line.
20210513
raw images
U.S. Geological Survey
Gerald Hatcher
Ocean Engineer
Mailing and Physical
2831 Mission Street
Santa Cruz
CA
95060
831-460-7524
831-421-9209
ghatcher@usgs.gov
SQUID-5 NAVIGATION PROCESSING
Raw GNSS data received by the antenna mounted atop the SQUID-5 were recorded at 10 Hz by a dual-frequency survey-grade GNSS receiver, which was post-processed and differentially corrected against the Key West, Florida, (FLKW) continuously operating reference station (CORS) in Novatel's GrafNav software (v. 8.80.2720; https://novatel.com/products/waypoint-post-processing-software/grafnav) to produce 10-Hz SQUID-5 trajectories.
The SQUID-5 trajectories, in combination with precisely recorded image capture event times, are used to generate SQUID-5 GNSS antenna positions at the moment of each image capture in the accompanying navigation file (SQUID5_EDR_2021_Image_Locations.txt). The positions in the SQUID-5 navigation file represent the position of the SQUID-5 GNSS antenna reference point (ARP), not the position of the cameras or features imaged. To determine actual image positions, photogrammetric software such as Agisoft Metashape can be used to apply the lever arm offsets (in the camera frame of reference) from the GNSS antenna reference point to the camera lens. Using this method the following values for each camera were calculated for x,y,z in units of meters. Camera 13, 0.03291 m(x), 0.01029 m(y), 0.82907 m(z); Camera 30, -0.30997 m(x), -0.03118 m(y), 0.90784 m(z); Camera 39, 0.27389 m(x), -0.11370 m(y), 0.91150 m(z); Camera 75, 0.13191 m(x), 0.55707 m(y), 0.74864 m(z); Camera 82, -0.011540 m(x), -0.59631 m(y), 0.75578 m(z).
20210610
Christine J. Kranenburg
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Cartographer
Physical and Mailing
600 4th Street South
St. Petersburg
FL
33701
USA
727-502-8000
ckranenburg@usgs.gov
IMAGE EXIF SORTING
Georeferencing, copyright, and other relevant information were added to the EXIF header of each image using Phil Harvey's ExifTool (v. 11.88; https://exiftool.org/). To extract the information from the image headers using ExifTool, the following command can be used (tested with ExifTool version 11.88):
exiftool -csv -f -filename -GPSDateStamp -GPSTimeStamp -GPSLongitude -GPSLatitude -GPSAltitude -n -Artist -Credit -comment -keywords -Caption -Copyright -CopyrightNotice -Caption-Abstract -ImageDescription directoryname/*.tif > out.csv
The -csv flag writes the information out in a comma-delimited format. The -n option formats the latitude, longitude, and altitude as signed decimal values. Note that the altitude is referenced to the NAD83 (2011) ellipsoid and are all negative for this dataset. CAUTION: Without the -n option, the command may return the absolute value of the altitude.
Images are sorted by survey line number and stored within zip files to limit the file sizes.
20220316
Christine J. Kranenburg
U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center
Cartographer
Physical and Mailing
600 4th Street South
St. Petersburg
FL
33701
USA
727-502-8000
ckranenburg@usgs.gov
Raster
Pixel
0.000001
0.000001
Decimal degrees
North American Datum of 1983 (2011)
GRS 1980
6378137.000000
298.257222101
North American Datum 1983 (2011)
0.001
meters
Attribute values
SQUID-5 Imagery (Line_##.zip) - Individual images are available in TIFF format and contained within zip files organized by survey lines (##). See Process_Step/IMAGE ACQUISITION for naming convention of individual images.
U.S. Geological Survey
U.S. Geological Survey - CMGDS
Mailing and Physical
2885 Mission Street
Santa Cruz
CA
95060
1-831-427-4747
pcmsc_data@usgs.gov
These data are available in TIFF format contained in zip files organized and named by survey line as Line_##.zip, where ## represents a number in the range 1-73. The image files are named with the following convention: camera serial number, 14-digit UTC datetime value, thousandths of seconds, and sequential image number for specified camera. The TIFF image files contain EXIF metadata, including GNSS time and position data, and are included as an open-source format for preservation purposes.
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
TIFF
The .zip files contains images in tagged image file format (.tif)
PKZIP
1074881
https://doi.org/10.5066/P93RIIG9
Image data can be downloaded per survey line using the Network_Resource_Name link. File names correspond to the tracklines shown in the Overview Map on the landing page of the data release and are named according to the following convention: Line_##.zip, where ## is a sequential trackline number indicating the order in which lines were collected. ## is a number in the range 1-73.
none
20220611
U.S. Geological Survey, Pacific Coastal and Marine Science Center
PCMSC Science Data Coordinator
mailing and physical
2885 Mission Street
Santa Cruz
CA
95060
831-460-4747
pcmsc_data@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998