Geotagged sea-floor images and locations of bottom images collected in Cape Cod Bay, Massachusetts, in September 2019 by the U.S. Geological Survey during field activity 2019-034-FA (JPEG images, point shapefile, and CSV file; GCS WGS 84)

Step 1: Collected data.
A marine geological survey (field activity 2019-034-FA) was conducted in Cape Cod Bay, Massachusetts, in September 2019. The R/V Tioga occupied one of the target sites, and the MiniSEABOSS was deployed off the vessel's A-frame on the stern of the ship. The MiniSEABOSS was equipped with a modified Van Veen grab sampler, a GoPro HERO4 Black digital camera, an oblique downward-looking SeaViewer 6000 HD Sea-Drop video camera with a topside feed, a Paralenz DiveCamera+ recording backup video, and a dive light to illuminate the sea floor for video and photograph collection. The elements of this particular MiniSEABOSS were held within a stainless-steel frame that measured ~1 x 1 meter. The frame had a stabilizer fin that oriented the system as it drifted over the seabed. Two red lasers were set 20 centimeters apart (both as they were mounted on the MiniSEABOSS frame and as seen in photographs and video on the seabed) for scale measurements. The red laser dots can usually be seen in the sea-floor photos and videos depending on the bottom type and distance to the sea floor. The winch operator lowered the MiniSEABOSS until the sea floor was observed in the topside live video feed. Generally, the vessel and MiniSEABOSS drifted with wind and current for up to a few minutes to ensure a decent photo with a clear view of the sea floor was acquired. The GoPro camera was set to take photos every 2 seconds during a MiniSEABOSS deployment. The photographed area is most often within 0.5 to 1.25 meters from left to right. Bottom video was also recorded during the drift from the oblique downward-looking SeaViewer 6000 HD Sea-Drop video camera directly to a solid-state drive using an Odyssey7 video recorder. Fifteen sites did not have any usable GoPro photographs, so still-image frame grabs were captured from the SeaViewer bottom videos for these sites in a subsequent process step. Then, the winch operator lowered the Van Veen grab sampler until it rested on the sea floor. When the system was raised, the Van Veen grab sampler closed and collected a sample as it was lifted off the sea floor. The sampler was recovered to the deck of the survey vessel where a subsample was taken for grain-size analysis at the sediment laboratory at the USGS Woods Hole Coastal and Marine Science Center. During the survey, DGPS navigation from a Hemisphere R131 DGPS receiver was logged through a DataBridge data logger and QGIS (version 3.0.0) GPS Tools. The DGPS was set to receive fixes at a 1-second interval in geographic coordinates (WGS 84). Dates and times were recorded in UTC. Log files were saved for each Julian day in NMEA text format. The GPS data were also overlaid onto the SeaViewer video using a Proteus-V Pro video overlay device. A total of 49 sites were occupied aboard the R/V Tioga with the MiniSEABOSS during field activity 2019-034-FA, and bottom imagery was collected at all 49 sites.

Step 2: Processed navigation.
To process the NMEA navigation data, GPSBabel (version 1.7.0) was used to read the GPRMC navigation sentences from the NMEA log files, translate them to waypoints, and write the waypoints to a GPX XML file (nmea_nav_jd260_jd262.gpx). The GPX file was then converted to a shapefile in QGIS (version 3.10.9). New fields for the latitude and longitude were added to the shapefile and calculated to six decimal places. The shapefile was exported as a Comma Separated Values (CSV) text file, which was then formatted in Microsoft Excel for Mac (version 16.16), creating a processed NMEA navigation CSV file for the survey (nmea_nav_jd260_jd262.csv).
Due to an issue with the data logger, the raw navigation data were recorded to NMEA files for only 22 of the 50 sampler deployments. For the remaining 28 deployments, the latitude and longitude recorded on the video overlay were used for the navigation data. To obtain the navigation data from the overlay, first, a command was run to extract a still-image frame grab every 1 second from the videos using FFmpeg (version 4.3.1). Next, a command was run to crop the latitude from each frame grab. The cropped image of the latitude was then converted to text using the optical character recognition engine Tesseract (version 4.1.1) and saved as a text file. These commands were repeated to crop the longitude from each frame grab and convert it to text, and then again to crop and convert the time to text. All the latitude, longitude, and time text files were concatenated and merged into a single text file. This text file was then imported and formatted in Microsoft Excel for Mac, creating a processed video overlay navigation CSV file for the survey (videocrop_coords_and_times.csv). The video overlay navigation data were checked to see if any times were missing. Occasionally, frame grabs were not extracted for the first or last second of the video. These missing frame grabs were identified, and the navigation data from the missing frame grabs were added to the video overlay navigation CSV file.
Shapefiles of the NMEA and video overlay navigation CSV files were created in ArcGIS (version 10.7.1). The sites with no NMEA navigation were identified, and the video overlay navigation data for those sites were exported as a table. The exported table was added to the NMEA navigation in Microsoft Excel for Mac and saved as a CSV file, creating a final navigation file for the survey (nmea_and_videocrop_nav.csv). Finally, the CSV text file was converted to a GPX file (nmea_and_videocrop_nav.gpx), which is a GPS track log file format used by ExifTool for geotagging, using GPS Visualizer (http://www.gpsvisualizer.com/convert_input?convert_format=gpx, accessed February 14, 2021). This process step and the subsequent process steps were performed by the same person, Emily Huntley.

Step 3: Identified camera time offsets for the GoPro photos.
The original GoPro JPEG images do not represent spatial data; however, they were geotagged in a subsequent process step by linking the time the image was taken, which was recorded in the metadata embedded in the header of each JPEG image, to the corresponding time in the navigation file. Before geotagging the images, the GoPro camera time, which was set to UTC, was compared to the GPS time using calibration photos to see if a time offset should be applied to the camera time of the photos. Camera time drift and the precision with which the camera time can be set often result in a time offset. During the first day of surveying (Julian day 260), photos of an accurate UTC time were taken with the GoPro camera so that the camera time could be calibrated to the GPS time during image processing. These calibration photographs indicated that the GoPro camera time was up to 1 second behind the GPS time. GoPro calibration photos were not available for the second day of surveying (Julian day 262), so four images from that day were visually compared to the bottom videos (which were recorded with an overlay of the GPS time) and found to have a camera time 12 to 13 seconds ahead of the GPS time. The time offset for Julian day 260 was negligible and was not corrected, while the time offset for Julian day 262 was corrected in a later process step.

Step 4: Geotagged the GoPro photos.
To geotag the images, the following commands were used with ExifTool (version 11.86) to populate the GPS tags (GPSLatitudeRef, GPSLatitude, GPSLongitudeRef, GPSLongitude, GPSTimeStamp, and GPSDateStamp) in the metadata embedded in the header of each JPEG image. Since various time offsets were applied to the GoPro photos, different commands were run for each day's images.
GoPro photos from Julian day 260: exiftool -api GeoMaxIntSecs=0 -api GeoMaxExtSecs=0 -P -m -geotag ./nmea_and_videocrop_nav.gpx '-geotime<${DateTimeOriginal}+00:00' ./JD260
GoPro photos from Julian day 262: exiftool -api GeoMaxIntSecs=0 -api GeoMaxExtSecs=0 -P -m -geotag ./nmea_and_videocrop_nav.gpx -geosync=-12 '-geotime<${DateTimeOriginal}+00:00' ./JD262
In the above commands, the "-api GeoMaxIntSecs" option sets the maximum interpolation time to 0 seconds for geotagging. The "-api GeoMaxExtSecs" option sets the maximum extrapolation time to 0 seconds for geotagging. The "-P" option preserves the FileModifyDate. The "-m" option ignores a warning given by ExifTool when reading or writing a file containing unknown MakerNotes. If this option is not used, the following warnings are issued since ExifTool does not recognize the MakerNotes in the GoPro images: "Warning: [minor] Unrecognized MakerNotes; Warning: [minor] Maker notes could not be parsed." The "-geosync" option is used when the image timestamps are not properly synchronized with the GPS time and is equal to the time offset identified in a previous process step; it is the time difference in seconds that is added to the camera time before determining the image's GPS time and location with a leading "+" or "-" added for positive or negative differences (negative if the camera clock was ahead of the GPS time). Finally, the "-geotime<${DateTimeOriginal}+00:00" argument is added to geotag images for which the camera clock was set to UTC. For more information about the ExifTool commands, see https://exiftool.org/geotag.html and https://exiftool.org/faq.html.

Step 5: Culled the GoPro photos.
Fifty-three of the GoPro photos had no corresponding navigation data and were removed from the dataset. These photos were taken on deck or in the water column. Since the GoPro camera was set to take photos every 2 seconds during a MiniSEABOSS deployment, the remaining bottom photographs were culled to select a few representative images for each site for publication. To do this, photos that intersected a bottom video trackline were selected to remove geotagged photos collected within the water column or on deck. The selected photos were then reviewed to choose representative photos with a clear view of the sea floor. If a site had many photos with a clear view of the sea floor, then a photo generally every 15 to 20 seconds was selected for publication.

Step 6: Incorporated survey information into the GoPro photos' metadata.
Additional survey information was incorporated into the metadata embedded in the header of each JPEG image. Images may have different metadata formats embedded in their headers, and the commands below incorporated survey information into the following three image metadata formats: Exchangeable image file format (Exif), International Press Telecommunications Council (IPTC), and Extensible Metadata Platform (XMP). The second command below duplicates values from Exif and IPTC metadata tags to XMP tags because various software packages read different tags. Please note that only a subset of these tags may be accessed depending on the software used to view the image metadata.
Command to incorporate survey information into the metadata embedded in the header of each JPEG image using ExifTool (version 11.86):
exiftool -P -m "-XMP:PreservedFileName<Filename" -IPTC:Credit="U.S. Geological Survey" -IPTC:Contact="WHSC_data_contact@usgs.gov" -EXIF:Copyright="Public Domain" -XMP:UsageTerms="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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty." -EXIF:ImageDescription="https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-034-FA; Photograph of the sea floor in Cape Cod Bay, Massachusetts, from USGS field activity 2019-034-FA" -XMP:AttributionURL="https://doi.org/10.5066/P99DR4PN" -EXIF:GPSAreaInformation="position post-processed from nearby GPS" -EXIF:GPSMapDatum="EPSG:4326 (WGS 84)" -EXIF:Artist="Woods Hole Coastal and Marine Science Center (WHCMSC) Sea Floor Mapping Group (SFMG)" -overwrite_original *.JPG
Command to duplicate metadata from the Exif and IPTC formats to XMP using ExifTool:
exiftool -P -m "-XMP-photoshop:Credit<IPTC:Credit" "-XMP-iptcCore:CreatorWorkEmail<IPTC:Contact" "-XMP-dc:Rights<EXIF:Copyright" "-XMP-dc:Description<EXIF:ImageDescription" "-XMP-exif:all<GPS:all" "-XMP-exif:GPSLatitude<Composite:GPSLatitude" "-XMP-exif:GPSLongitude<Composite:GPSLongitude" "-XMP-exif:GPSDateTime<Composite:GPSDateTime" "-XMP-photoshop:DateCreated<EXIF:DateTimeOriginal" "-XMP-xmp:ModifyDate<EXIF:ModifyDate" "-XMP-dc:Creator<EXIF:Artist" "-XMP-tiff:Make<EXIF:Make" "-XMP-tiff:Model<EXIF:Model" -overwrite_original *.JPG
The following metadata tags were populated in the JPEG image header using the above ExifTool commands:
Exif tags and the information used to populate these tags:
Artist: Woods Hole Coastal and Marine Science Center (WHCMSC) Sea Floor Mapping Group (SFMG) Copyright: Public Domain GPSAreaInformation: position post-processed from nearby GPS GPSMapDatum: EPSG:4326 (WGS 84) ImageDescription: https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-034-FA; Photograph of the sea floor in Cape Cod Bay, Massachusetts, from USGS field activity 2019-034-FA
IPTC tags and the information used to populate these tags:
Contact: WHSC_data_contact@usgs.gov Credit: U.S. Geological Survey
XMP tags and the information used to populate these tags:
AttributionURL: https://doi.org/10.5066/P99DR4PN Creator: duplicated from Exif Artist CreatorWorkEmail: duplicated from IPTC Contact Credit: duplicated from IPTC Credit DateCreated: duplicated from Exif DateTimeOriginal Description: duplicated from Exif ImageDescription GPSAreaInformation: duplicated from Exif GPSAreaInformation by copying all the Exif GPS tags to the same-named tags in XMP (-XMP-exif:all<GPS:all) GPSDateTime: duplicated using the composite of Exif GPSDateStamp and Exif GPSTimeStamp GPSLatitude: duplicated using the composite of Exif GPSLatitude and Exif GPSLatitudeRef GPSLongitude: duplicated using the composite of Exif GPSLongitude and Exif GPSLongitudeRef GPSMapDatum: duplicated from Exif GPSMapDatum by copying all the Exif GPS tags to the same-named tags in XMP (-XMP-exif:all<GPS:all) Make: duplicated from Exif Make Model: duplicated from Exif Model ModifyDate: duplicated from Exif ModifyDate PreservedFileName: original image file name, which is unique for each image Rights: duplicated from Exif Copyright UsageTerms: 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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty.
To extract the geotagging and survey information (except for the duplicated tags) from the image metadata using ExifTool, the following command can be used (tested with ExifTool version 11.86):
exiftool -csv -filename -EXIF:GPSTimeStamp -EXIF:GPSDateStamp -GPSLatitude -GPSLongitude -n -IPTC:Credit -IPTC:Contact -EXIF:Copyright -XMP:UsageTerms -EXIF:ImageDescription -XMP:AttributionURL -EXIF:GPSAreaInformation -EXIF:GPSMapDatum -EXIF:Artist *.JPG > out.csv
The "-csv" option writes the information to a CSV file. The "-n" option formats the latitude and longitude as signed decimal degrees. Please note that the above command was tested on macOS; Windows users may need to use "exiftool.exe" instead of "exiftool."

Step 7: Selected bottom video frame grabs for publication.
Fifteen sites with no usable GoPro photographs were identified (sites 2019-034-FA-022, 2019-034-FA-035, and 2019-034-FA-037 through 2019-034-FA-049). For these sites, one to three images per site were selected from the bottom video frame grabs that were created when processing the navigation. The frame grabs from a video drift were reviewed to choose representative images with a clear view of the sea floor. If a site had many frame grabs with a clear view of the sea floor, then a frame grab generally every 15 to 20 seconds was selected for publication. Finally, the selected frame grabs were converted from PNG images to JPEG images using Preview (version 10.1).

Step 8: Geotagged the bottom video frame grabs and incorporated survey information into the frame grabs' metadata.
To geolocate the bottom video frame grabs, a CSV file was created with fields for the filename, GPS date, and GPS time. The videos were recorded with an overlay of the GPS date and time, so this information was entered using the date and time shown on each frame grab. The latitude and longitude of each video frame grab were added to the CSV file by matching the frame grab time with a CSV file of the final processed navigation in Microsoft Excel 2016 for Mac. The CSV file was formatted to have the following fields: SourceFile, GPSDateStamp, GPSTimeStamp, GPSLatitude, GPSLatitudeRef, GPSLongitude, and GPSLongitudeRef. To geotag the images, the following command was used with ExifTool (version 11.86) to populate the GPS tags (GPSLatitudeRef, GPSLatitude, GPSLongitudeRef, GPSLongitude, GPSTimeStamp, and GPSDateStamp) in the Exif metadata of each JPEG image:
exiftool -P -csv="video_frame_grabs_geotag.csv" -overwrite_original *.JPG
Additional survey information was then incorporated into the Exif, IPTC, and XMP metadata embedded in the header of each JPEG image using the following ExifTool command:
exiftool -P -m "-XMP:PreservedFileName<Filename" -IPTC:Credit="U.S. Geological Survey" -IPTC:Contact="WHSC_data_contact@usgs.gov" -EXIF:Copyright="Public Domain" -XMP:UsageTerms="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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty." -EXIF:ImageDescription="https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-034-FA; Video frame grab of the sea floor in Cape Cod Bay, Massachusetts, from USGS field activity 2019-034-FA" -XMP:AttributionURL="https://doi.org/10.5066/P99DR4PN" -EXIF:GPSAreaInformation="position post-processed from nearby GPS" -EXIF:GPSMapDatum="EPSG:4326 (WGS 84)" -EXIF:DateTimeOriginal="0000:00:00 00:00:00" -EXIF:ModifyDate="0000:00:00 00:00:00" -EXIF:Artist="Woods Hole Coastal and Marine Science Center (WHCMSC) Sea Floor Mapping Group (SFMG)" -EXIF:Make="SeaViewer" -EXIF:Model="6000 HD Sea-Drop" -overwrite_original *.JPG
Finally, the following command was run to duplicate metadata from the Exif and IPTC formats to XMP using ExifTool:
exiftool -P -m "-XMP-photoshop:Credit<IPTC:Credit" "-XMP-iptcCore:CreatorWorkEmail<IPTC:Contact" "-XMP-dc:Rights<EXIF:Copyright" "-XMP-dc:Description<EXIF:ImageDescription" "-XMP-exif:all<GPS:all" "-XMP-exif:GPSLatitude<Composite:GPSLatitude" "-XMP-exif:GPSLongitude<Composite:GPSLongitude" "-XMP-exif:GPSDateTime<Composite:GPSDateTime" "-XMP-photoshop:DateCreated<EXIF:DateTimeOriginal" "-XMP-xmp:ModifyDate<EXIF:ModifyDate" "-XMP-dc:Creator<EXIF:Artist" "-XMP-tiff:Make<EXIF:Make" "-XMP-tiff:Model<EXIF:Model" -overwrite_original *.JPG
The same information that was incorporated into the GoPro photos' metadata was populated in the headers of the video frame grabs with the following exceptions for the Exif tags:
DateTimeOriginal: 0000:00:00 00:00:00 [No data] ImageDescription: https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-034-FA; Video frame grab of the sea floor in Cape Cod Bay, Massachusetts, from USGS field activity 2019-034-FA Make: SeaViewer Model: 6000 HD Sea-Drop ModifyDate: 0000:00:00 00:00:00 [No data]
To extract the geotagging and survey information (except for DateTimeOriginal, ModifyDate, and the duplicated tags) from the image metadata using ExifTool, the following command can be used (tested with ExifTool version 11.86):
exiftool -csv -filename -EXIF:GPSTimeStamp -EXIF:GPSDateStamp -GPSLatitude -GPSLongitude -n -IPTC:Credit -IPTC:Contact -EXIF:Copyright -XMP:UsageTerms -EXIF:ImageDescription -XMP:AttributionURL -EXIF:GPSAreaInformation -EXIF:GPSMapDatum -EXIF:Artist -EXIF:Make -EXIF:Model *.JPG > out.csv
The "-csv" option writes the information to a CSV file. The "-n" option formats the latitude and longitude as signed decimal degrees. Please note that the above command was tested on macOS; Windows users may need to use "exiftool.exe" instead of "exiftool."

Step 9: Renamed the images.
The images were renamed to include the field activity identifier, camera, and GPS date and time in the ISO 8601 standard (YYYYMMDD T [time separator] HHMMSS Z [Zulu/UTC time]) in the filename. Renaming the images was done by creating a shell script with the original image name and the new filename with the GPS date and time information parsed from the image's Exif metadata tags.

Step 10: Created a CSV file of the bottom image locations.
The information from the image metadata tags was extracted using the following ExifTool (version 11.86) command:
exiftool -csv -f -GPSTimeStamp -DateTimeOriginal -GPSDateStamp -GPSLatitude -GPSLongitude -n *.JPG > out.csv
Microsoft Excel 2016 for Mac was used to rename the field names for the filename (PICNAME), GPS time (GPSTIME), original camera time (CAMR_TIME), GPS date (DATE), latitude (LAT), and longitude (LONG); add new fields for the camera (CAMERA), time offset applied to the camera time (TIMEOFFSET), Julian day of collection (JD), year of collection (YEAR), survey ID (FA_ID), sampling device used to collect the image (DEVICE_ID), and survey vessel (VEHICLE_ID); and remove additional fields extracted from the ExifTool command.

Step 11: Created a final shapefile and CSV file of the bottom image locations.
A shapefile was created from the bottom image locations CSV file using the XY Table To Point tool in Esri ArcGIS Pro (version 2.4.1). The Spatial Join tool was then run to calculate the site number (FIELD_NO) and video trackline (LINENAME) for each bottom image by joining the attributes of the bottom video tracklines shapefile (see "2019-034-FA_videos.shp" in the larger work citation) using the intersect match option with a search radius of 0.01 meters. Unnecessary fields created when running the Spatial Join tool were deleted (i.e., Join_Count and TARGET_FID). The shapefile was reordered using the Sort tool to sort the images in chronological order (JD and GPSTIME sort fields in ascending order). Finally, the shapefile's attribute table was exported in Esri ArcGIS Pro and saved as a CSV file. The FID field was deleted in the CSV file.