Metadata: Identification_Information: Citation: Citation_Information: Originator: Christine J. Kranenburg Originator: Gerald A. Hatcher Originator: Jonathan A. Warrick Originator: Andrew C. Ritchie Originator: David G. Zawada Originator: Kimberly K. Yates Publication_Date: 20231130 Title: SfM Quantitative Underwater Imaging Device with 5 cameras (SQUID-5) – Field data from periodic surveys of the Florida Keys and other select shallow water environments Geospatial_Data_Presentation_Form: application/service Series_Information: Series_Name: data service Issue_Identification: DOI:10.5066/P9M3NYWI Publication_Information: Publication_Place: St. Petersburg, Florida Publisher: U.S. Geological Survey – St. Petersburg Coastal and Marine Science Center Other_Citation_Details: Suggested Citation: Kranenburg, C.J., Hatcher, G.A., Warrick, J.A., Zawada, D.G., and Yates, K.K., 2023, SfM Quantitative Underwater Imaging Device with 5 cameras (SQUID-5) – Field data from periodic surveys of the Florida Keys and other select shallow water environments, in Remote Sensing Coastal Change Simple Data Distribution Service: U.S. Geological Survey data service, accessed [MMMM d, YYYY], at https://doi.org/10.5066/P9M3NYWI. [Data directly accessible at https://cmgds.marine.usgs.gov/data-services/rscc/SQUID/] Online_Linkage: https://doi.org/10.5066/P9M3NYWI Larger_Work_Citation: Citation_Information: Originator: Andrew C. Ritchie Originator: Peter J. Triezenberg Originator: Jonathan A. Warrick Originator: Gerald A. Hatcher Originator: Daniel D. Buscombe Publication_Date: 20230221 Title: RSCC Simple Data Distribution Service Edition: 1.0 Geospatial_Data_Presentation_Form: application/service Series_Information: Series_Name: data service Issue_Identification: DOI:10.5066/P9M3NYWI Publication_Information: Publication_Place: Santa Cruz, California Publisher: U.S. Geological Survey - Pacific Coastal and Marine Science Center Online_Linkage: https://doi.org/10.5066/P9M3NYWI Description: Abstract: The U.S. Geological Survey (USGS) Remote Sensing Coastal Change (RSCC) and Processes Impacting Seafloor Change and Ecosystem Services (PISCES) projects collect underwater imagery of coral reefs and other scientifically interesting, submerged environments using the novel SfM (Structure-from-Motion) Quantitative Underwater Imaging Device with 5 cameras (SQUID-5) system. This sensor collects imagery with optimized endlap/sidelap and precise position information to create high-resolution orthomosaics, three-dimensional (3D) point clouds, and digital elevation/surface models (DEMs/DSMs) using SfM photogrammetry methods. These products are valuable for measuring submerged topographic and ecological change, and for understanding reef vulnerability and response to disturbance events. This is an ongoing collection of underwater imagery surveys of coral reefs and other clear water environments. Shallow water (approximately 2-10 meters [m] depth) digital imagery is acquired using the "SfM Quantitative Underwater Imaging Device with 5 cameras" (SQUID-5) towed surface sensor system. The system consists of five synchronized rigidly connected downward-looking digital cameras with overlapping views of the seafloor, along with a custom integrated survey-grade Global Navigation Satellite System (GNSS) receiver. Purpose: The underwater images and associated location data were collected to provide high-resolution elevation data and precisely co-registered, full-color orthomosaic basemaps for use in environmental assessment and monitoring of coral reefs and other underwater environments. 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. Supplemental_Information: The USGS RSCC simple data distribution service is designed to release data using a standardized workflow in support of timely best science while maintaining USGS Fundamental Science Practices (FSP) and meeting the high-quality data standards of the USGS. The data service includes big data (up to hundreds of thousands of digital images) and related derivative data products, and serves as a digital data repository for manual, semi-automated, and fully automated retrieval of published data. The data service is structured in a folder (directory) hierarchy with subfolders corresponding to individual data collection platforms (DCPs) or groups of DCPs, which in turn contain folders with products grouped by collection effort. For more information on the RSCC simple data distribution service, refer to Ritchie and others (2023), https://doi.org/10.5066/P9M3NYWI. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20190709 Ending_Date: Present Currentness_Reference: ground condition Status: Progress: In work Maintenance_and_Update_Frequency: As needed Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -180 East_Bounding_Coordinate: 180 North_Bounding_Coordinate: 90 South_Bounding_Coordinate: -90 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:269bf285-a1bc-428f-ae87-5d7d5bf58b89 Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: geoscientificInformation Theme_Keyword: imageryBaseMapsEarthCover Theme_Keyword: environment Theme_Keyword: oceans Theme_Keyword: elevation Theme: Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords Theme_Keyword: seabed Theme_Keyword: coral reefs Theme: Theme_Keyword_Thesaurus: Data Categories for Marine Planning Theme_Keyword: Physical Habitats and Geomorphology Theme_Keyword: Bathymetry and Elevation Theme_Keyword: Habitat Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: structure from motion Theme_Keyword: remote sensing Theme_Keyword: image collections Theme_Keyword: image analysis Theme_Keyword: visible light imaging Theme_Keyword: time series datasets Theme_Keyword: geospatial datasets Theme_Keyword: earth sciences Theme_Keyword: geomorphology Theme_Keyword: reef ecosystems Theme_Keyword: geography Theme_Keyword: geology Theme_Keyword: ecology Theme_Keyword: coastal processes Theme_Keyword: geologic processes Theme_Keyword: coastal ecosystems Theme: Theme_Keyword_Thesaurus: None Theme_Keyword: U.S. Geological Survey Theme_Keyword: USGS Theme_Keyword: Coastal and Marine Hazards and Resources Program Theme_Keyword: CMHRP Theme_Keyword: St. Petersburg Coastal and Marine Science Center Theme_Keyword: SPCMSC Place: Place_Keyword_Thesaurus: None Place_Keyword: United States Place_Keyword: United States and Territories Access_Constraints: None Use_Constraints: 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(s) of the dataset and in products derived from these data. Point_of_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center Contact_Position: SPCMSC Data Management Group Contact_Address: Address_Type: mailing and physical Address: 600 4th St South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: gs-spcmsc_data_inquiries@usgs.gov Native_Data_Set_Environment: NovAtel’s GrafNav software; Phil Harvey’s ExifTool; Global Mapper. Cross_Reference: Citation_Information: Originator: Gerald A. Hatcher Originator: Jonathan A. Warrick Originator: Christine J. Kranenburg Originator: Andrew C. Ritchie Publication_Date: 20230726 Title: Accurate Maps of Reef-scale Bathymetry with Synchronized Underwater Cameras and GNSS Series_Information: Series_Name: Remote Sensing Issue_Identification: 15(15), 3727 Online_Linkage: https://doi.org/10.3390/rs15153727 Cross_Reference: Citation_Information: Originator: Gerald A. Hatcher Originator: Jonathan A. Warrick Originator: Andrew C. Ritchie Originator: Evan T. Dailey Originator: David G. Zawada Originator: Christine Kranenburg Originator: Kimberly K. Yates Publication_Date: 20200626 Title: Accurate Bathymetric Maps From Underwater Digital Imagery Without Ground Control Series_Information: Series_Name: Frontiers in Marine Science Issue_Identification: Volume 7, Article 525 Online_Linkage: https://doi.org/10.3389/fmars.2020.00525 Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: The accuracy of the position data is based on the accuracy and precision of the GNSS equipment, camera timing, number and length of baselines, and environmental conditions at the time of collection. Note that the positions in the imagery headers are GNSS antenna positions and are limited to six decimal places. Whereas the positions in the external navigation file are accurate to ten decimal places and are therefore highly recommended for use in SfM photogrammetric processing to produce the highest quality derived products. These data represent raw imagery, as collected, and subsequently used in SfM photogrammetric processing workflows. The user may find it useful and/or necessary to color correct these raw data, as appropriate for their application. Logical_Consistency_Report: RGB (red, green, blue) values are 8-bits per band, generally not saturated or underexposed. Occasionally, usually at the start of a new survey day, some imagery may be over or underexposed due to inappropriate initial operator-set gain settings. Appropriate gain settings are usually achieved by the 2nd or 3rd survey line. GNSS values are checked for consistency and outliers. Bad data are discarded, and missing data are interpolated. Completeness_Report: This is an ongoing collection of underwater imagery surveys of shallow water environments. Some images may lack position information in their imagery header metadata resulting from a momentary disruption in GNSS signals, but in most cases interpolated positions were applied to these images. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: Horizontal positions are provided in the image locations files (.txt) and generally have an estimated 2-sigma horizontal accuracy of 10 centimeters (cm). The accuracy of the positions in the imagery headers are reduced due to field size limitations for storing latitude/longitude. Any variations in positional accuracy are described in the collection-level metadata record. Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: Vertical positions are provided in the image locations files and generally have an estimated 2-sigma vertical accuracy of 15 cm. Any variations in positional accuracy are described in the collection-level metadata record. Lineage: Process_Step: Process_Description: IMAGE AND POSITION ACQUISITION The USGS operates the SQUID-5 system to conduct underwater imagery surveys over shallow water environments with optimized endlap/overlap to facilitate SfM processing (Hatcher and others, 2020 and 2023). The SQUID-5 system is comprised of five synced 5-megapixel (MP) machine vision cameras attached to a rigid frame, along with a custom integrated survey-grade Global Navigation Satellite System (GNSS) receiver, which is towed behind a motorized support vessel. The cameras are triggered by an acquisition computer which is time synchronized using a local GNSS regulated Network Time Protocol (NTP) server. An event mark is subsequently recorded and timestamped by the GNSS for each camera trigger signal. The raw dataset is comprised of the raw imagery, raw dual-frequency carrier phase GNSS data and photo capture event time data. Individual image names conform to the following naming convention: CAM##-YYYYMMDDhhmmss_fff-n[nnn].tif, where ## comprise the last 2 digits of the serial number of the camera that captured the image, YYYYMMDD represents the year (YYYY), month (MM) and day (DD) of capture; hhmmss_fff is the time of capture as hours (hh), minutes (mm), seconds(ss) and fractional seconds (fff) in Universal Coordinated Time (UTC) and n[nnn] is a sequence number (image counter) which is reset at the beginning of each survey line. For example, CAM82-20210508215908_001-115.tif was collected by the camera whose serial number ends in 82 on 2021-05-08 at 21:59:08.001 UTC, and it was the 115th shot of that survey line. Images from the camera whose serial number ends in 01 come off the system named CAM1- YYYYMMDDhhmmss_fff-n[nnn].tif. Images from this camera and any future one that ends in 0#, where # is in the range [1-9]), is renamed using the script below by inserting the missing ‘0’ such that it conforms to the naming convention and becomes CAM01-*. #!/usr/bin/bash for i in CAM1-*.tif; do echo "$i" mv "$i" "`echo $i | sed "s/CAM1/CAM01/"`"; done GNSS positions record the location of the phase center of the GNSS antenna at the moment an image capture is initiated (see Positional_Accuracy metadata element for uncertainty discussion). Lever arm distances are used to translate the position from the GNSS antenna reference point to the nodal point of the camera lenses; these are provided relative to the coordinate systems of each camera, where the camera is 0,0, and the axes run as follows: X axis runs from left (negative) to right (positive) Y axis runs from bottom (negative) to top (positive) Z axis runs from front of lens (negative) to back of camera (positive) The SQUID system hardware is oftentimes disassembled for transportation and reassembled at the survey site. It is also updated as new technological advances become available, which may include new cameras and/or new GNSS system components. Although every effort is made to reassemble the system in exactly the same positions, both these events cause changes to the lever arm distances. The methodology by which the original lever arm measurements were determined is described in Hatcher and others (2020). Starting lever arm measurements of the SQUID system are listed below; these distances are then refined during the SfM process. Lever Arm Distances: Center camera: 0.034 m, 0.011 m, and 0.84 m (x, y, z) Forward camera: -0.010 m, -0.594 m, 0.762 m Rear camera: 0.131 m, 0.559 m, 0.754 m Left camera: 0.273 m, -0.109 m, 0.916 m Right camera: -0.311 m, -0.029 m, 0.911 m Estimated uncertainties in the lever arm distances are 5 cm in each direction for the outboard cameras and 2.5 cm in each direction for the nadir (center) camera. Equipment specifications of the different SQUID versions and the dates they were in use are listed below. VERSION 1.1 Survey Dates Valid: 2019-07 to 2019-12 Camera Model: Teledyne FLIR BlackFly BFS-PGE-50S5C-C Lens focal length: 6 mm GNSS Receiver: Trimble R7 GNSS Antenna: Trimble Zephyr 2 VERSION 1.2 Survey Dates Valid: 2020-01 to 2022-06 Camera Model: Teledyne FLIR BlackFly BFS-PGE-50S5C-C Lens focal lengths: Center cam 8 mm, outboard cams 6 mm GNSS Receiver: Trimble R7 GNSS Antenna: Trimble Zephyr 2 VERSION 2 Survey Dates Valid: 2022-07 to Present Camera Model: Teledyne FLIR BlackFly BFS-PGE-50S5C-C Lens focal lengths: Center cam 8 mm, outboard cams 6 mm GNSS Receiver: Spectra Geospatial SP90M GNSS Antenna: Spectra Geospatial SPP 135000.00 Process_Date: Not complete Source_Produced_Citation_Abbreviation: raw imagery Source_Produced_Citation_Abbreviation: raw GNSS Source_Produced_Citation_Abbreviation: event marks Process_Step: Process_Description: IMAGE AND GNSS QA/QC Quality control of the raw imagery and raw GNSS data occurs in the field where the entire processing workflow is performed on the day of collection. A preliminary processing of the GNSS data is done against either the closest continuously operating reference station (CORS) or a locally-established base station, at 1 hertz (Hz), using either broadcast or ultra-rapid ephemerides and assessed by reviewing plots and quality metrics from NovAtel’s GrafNav software. The resulting image positions are then ingested into Agisoft Metashape along with the raw imagery where a medium quality point cloud and medium resolution DEM are produced. If any issues that preclude successful model building are detected during this field processing, the batch is discarded, and the data is re-collected. If an issue is found by the data processor that affects two or fewer cameras, a re-collect is not performed, but the images from those cameras will be discarded during final processing. Hatcher and others (2023) determined that the SQUID-5 has enough redundancy to build high quality high-resolution models with as few as 3 cameras operating. Data from the local base station is converted to Receiver Independent Exchange Format (RINEX) using a proprietary utility provided by the manufacturer of the GNSS receiver, down-sampled to a 10 or 30-second interval using TEQC (https://www.unavco.org/software/data-processing/teqc/teqc.html) if necessary to comply with file size limits, and submitted to the National Oceanic and Atmospheric Administration (NOAA) Online Positioning User Service (OPUS) website (https://geodesy.noaa.gov/OPUS/) for validation. This website computes the position of the uploaded data and ties it to the high-accuracy National Spatial Reference System (NSRS) coordinate system. Source_Used_Citation_Abbreviation: raw imagery Source_Used_Citation_Abbreviation: raw GNSS Source_Used_Citation_Abbreviation: event marks Process_Date: Not complete Source_Produced_Citation_Abbreviation: validated imagery Source_Produced_Citation_Abbreviation: validated GNSS Source_Produced_Citation_Abbreviation: preliminary picture positions Process_Step: Process_Description: KMZ CREATION In order to provide a visual map of the survey extent, image capture locations, to aid a user in determining which images they might want to download, and to aid in completing the geospatial information in the collection-level metadata, a Keyhole Markup Language Zipped file (.kmz) is created for each collection using Global Mapper to convert the image positions file to a kmz. Source_Used_Citation_Abbreviation: preliminary picture positions Process_Date: Not complete Source_Produced_Citation_Abbreviation: kmz Process_Step: Process_Description: GNSS FINAL DATA PROCESSING Raw GNSS data received by the antenna mounted atop the SQUID-5 are recorded at 10 Hz by a dual-frequency survey-grade GNSS receiver. This reprocessing of the GNSS data uses precise ephemerides (obtained through the GrafNav software from external sources), multiple base stations if possible, and is run at 10 Hz, to achieve higher accuracy image positions than was obtained during the field processing described in the ‘IMAGE AND GNSS QA/QC’ step above. If the collection-level metadata describes the dataset as PROVISIONAL, it means the image positions were computed using a lower accuracy ephemeris. This is sometimes necessary if the imagery is collected to rapidly assess damage from natural or unnatural (e.g. boat groundings) disasters. The trajectories, in combination with precisely recorded image capture event times, are used to generate GNSS antenna positions at the moment each image capture is initiated and is provided for each collection. Images with missing positions are reconciled through direct interpolation based on the image and GNSS time stamps. The positions in the image positions file represent the position of the SQUID-5 GNSS antenna, not the position of the camera or features photographed. To determine actual camera 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 lenses. Source_Used_Citation_Abbreviation: validated imagery Source_Used_Citation_Abbreviation: raw GNSS Source_Used_Citation_Abbreviation: event marks Process_Date: Not complete Source_Produced_Citation_Abbreviation: final picture positions Process_Step: Process_Description: IMAGERY HEADERS Georeferencing, copyright, and other relevant information is added to the imagery headers of each image using Phil Harvey’s ExifTool. To extract the information from the image headers using ExifTool, the following command can be used: exiftool -n -csv *.tif > allheaders.csv The -csv flag writes the information out in a comma-delimited format. The -n option formats the latitude and longitude as signed decimal degrees. Source_Used_Citation_Abbreviation: validated imagery Source_Used_Citation_Abbreviation: final picture positions Process_Date: Not complete Source_Produced_Citation_Abbreviation: populated imagery Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: This metadata record describes characteristics of the SQUID-5 system data collection platform (DCP) and the organization and processing steps for data collected from that platform. The images are downloadable in Tag Image File Format (TIFF, .tif) and corresponds to a single 3-band, 24-bits per pixel, RGB image containing imagery header metadata locating the image in space and time and describing basic documentation (including but not limited to: camera model, resolution, and copyright information). Datasets are organized by directory with each directory (folder) corresponding to a single collection effort. Product types (raw imagery, derivatives, and any ancillary products) for each collection effort are organized in subfolders with associated metadata and are populated as data are processed. In some cases, multiple versions or formats of a product may be released, including emergency and provisional data subject to change. Process steps in the collection-level metadata for each product describe naming conventions, methods, and disclaimers. Directory structure for each survey uses the following naming convention: {State[-State]}_{YYYY[MM][DD]}_{AOIName}_{[Event]}, where {State[-State]} is the two-letter abbreviation for the state where the survey occurred, {YYYY[MM][DD]} is the year and, if necessary, the month and day of collection, {AOIName} is a unique name or acronym for the specific survey location (for example, EasternDryRocks or LooeKey, for FL Keys surveys), and {[Event]} denotes a named event for which the data was collected (for example, a named hurricane). Items in square brackets [] are optional. Entity_and_Attribute_Detail_Citation: U.S. Geological Survey Distribution_Information: Distributor: Contact_Information: Contact_Person_Primary: Contact_Person: SPCMSC Data Management Group Contact_Organization: U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center Contact_Address: Address_Type: mailing and physical Address: 600 4th St. South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@usgs.gov Resource_Description: CAM##-YYYYMMDDhhmmss_fff-n[nnn].tif Distribution_Liability: This publication was prepared by an agency of the United States Government. Although these data were processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data on any other system, nor shall the act of distribution imply any such warranty. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and (or) contained herein. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: TIFF Format_Information_Content: TIFF images can be opened directly with any TIFF-compatible image viewer. Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://cmgds.marine.usgs.gov/data-services/rscc/SQUID/ Access_Instructions: Images and supplementary files can be downloaded by going to the Network_Resource_Name link above and navigating to the subfolder for a particular study area/collection of interest. Digital_Form: Digital_Transfer_Information: Format_Name: columnar text Format_Information_Content: TXT files can be opened directly with any text-editing software, such as Notepad. Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://cmgds.marine.usgs.gov/data-services/rscc/SQUID/ Access_Instructions: Images and supplementary files can be downloaded by going to the Network_Resource_Name link above and navigating to the subfolder for a particular study area/collection of interest. Digital_Form: Digital_Transfer_Information: Format_Name: KMZ Format_Information_Content: KMZ files can be opened with software capable of viewing geographic information system (GIS) data, such as Global Mapper, or the Google Earth web viewer (https://earth.google.com/web/). Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://cmgds.marine.usgs.gov/data-services/rscc/SQUID/ Access_Instructions: Images and supplementary files can be downloaded by going to the Network_Resource_Name link above and navigating to the subfolder for a particular study area/collection of interest. Fees: None Metadata_Reference_Information: Metadata_Date: 20231129 Metadata_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: SPCMSC Data Management Group Contact_Address: Address_Type: mailing and physical Address: 600 4th St. South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998