Amy C. Foxgrover Bruce E. Jaffe Theresa A. Fregoso 20220701 raster digital data set data release DOI:10.5066/P9BIB67S Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P9BIB67S Amy C. Foxgrover Bruce E. Jaffe Theresa A. Fregoso 2022 data release DOI:10.5066/P9BIB67S Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey https://doi.org/10.5066/P9BIB67S Bathymetric survey data were collected in February 2009 just south of Dumbarton Bridge in south San Francisco Bay, California. Portions of the main channel and western shallows/intertidal mudflats were surveyed using an interferometric sidescan sonar system following procedures detailed in Foxgrover and others, 2011 . The bathymetry is provided as a 1-m resolution raster in geoTIFF format, referenced to the vertical datum of mean lower low water (MLLW). To convert to the North American Vertical Datum of 1988 (NAVD88), subtract a static offset of 0.37 m (datum conversions provided in Foxgrover and others, 2007). In 2008 the USGS began mapping the main channel and shallow intertidal mudflats between the Dumbarton Bridge and a railroad bridge located 1 km to the south in south San Francisco Bay. This information was collected to document bathymetric change before and after restoration to inform the South Bay Salt Pond Restoration Project (https://www.southbayrestoration.org), which initiated the restoration of a former salt pond (SF2) on the western shore in 2010. In 2011, following the collection of eight bathymetric surveys, funding for this site-specific project came to an end, yet the location remained an instrumentation calibration site for ongoing research in Alviso Slough (Foxgrover and others, 2011). The calibration surveys collected near the Dumbarton Bridge resulted in an additional eight surveys, collected primarily in the main channel, from 2013 to 2019. 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=S109SF Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this Federal Geographic Data Committee-compliant metadata file is intended to document the data set in nonproprietary form, as well as in Esri format, this metadata file may include some Esri-specific terminology. 20090209 20090211 ground condition at time data were collected Complete None planned -122.126574 -122.111816 37.504676 37.491590 USGS Metadata Identifier USGS:f623ba20-21b4-442c-9a1f-f25e94648a62 ISO 19115 Topic Category elevation inlandWaters Data Categories for Marine Planning Bathymetry and Elevation USGS Thesaurus bathymetry bathymetry measurement digital elevation models interferometric sonar sidescan sonar GPS measurement Marine Realms Information Bank (MRIB) keywords geographic information systems (GIS) wetland restoration None U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CMHRP Pacific Coastal and Marine Science Center PCMSC Geographic Names Information System (GNIS) State of California San Francisco Bay Alameda County San Mateo County Dumbarton Bridge 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(s) 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

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Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov DB_Feb2009_bathy.png A shaded relief image of the February 2009 bathymetric survey with 10X vertical exaggeration to accentuate the tidal flat and channel morphology. PNG Funding was provided by the U.S. Geological Survey, California Coastal Conservancy, U.S. Environmental Protection Agency, the Resources Legacy Fund, and Santa Clara Valley Water District. SEA Swath Processor (ver. 3.12.7), Caris HIPS and SIPS (ver. 9.1) and ArcMap (ver. 10.7.1) on a Windows 10 computer. Amy C. Foxgrover David P. Finlayson Bruce E. Jaffe Theresa A. Fregoso 2011 Open-File Report 2011-1315 Reston, VA U.S. Geological Survey https://doi.org/10.3133/ofr20111315 Amy C. Foxgrover Bruce E. Jaffe Gerald T. Hovis Craig A. Martin James R. Hubbard Manoj R. Samant Steve M. Sullivan 2007 Open-File Report 2007-1169 Reston, VA U.S. Geological Survey https://doi.org/10.3133/ofr20071169 Applied Microsystems Ltd. 2005 Applied Microsystems Ltd., 2005, SVplus sound velocity, temperature, and depth profiler user's manual, ver. 1.23, https://amloceanographic.com/. T. Soler R.A. Snay 2004 Soler, T., and Snay, R.A., 2004, Transforming positions and velocities between the International Terrestrial Reference Frame of 2000 and North American Datum of 1983: Journal of Surveying Engineering, v. 130, no. 2, https://doi.org/10.1061/(ASCE)0733-9453(2004)130:2(49) These bathymetric data have not been independently verified for accuracy. All bathymetric values are derived from the same instruments and processing workflow. No formal logical accuracy tests were conducted. 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. Uncertainty in the horizontal position of each sounding is a function of the total uncertainty propagated through each of the following component instruments: 1) base station GPS, 2) vessel GPS, 3) inertial motion unit (IMU), 4) water sound velocity model, and 5) beam spreading in the water column. Assuming no systematic errors in the measurement instruments themselves, beam spreading is the dominate source of positional uncertainty. The 1-degree sonar beam of the SWATHplus-M results in horizontal uncertainty ranging from 0.10 m at 10 m slant range, to about 0.45 m at 50 m slant range. For relatively flat regions, the standard deviation of sounding elevations within each 1 m by 1 m cell is a good representation of survey precision. After filtering the data to remove obvious outliers, the standard deviation of the remaining sounding elevations was calculated for each cell (each containing tens of soundings) in CARIS. The mean standard deviation on the intertidal flats is 4 cm and below MLLW where actual variability in slope influences the values, the average standard deviation is 10 cm. When possible, an additional assessment of survey accuracy was conducted by analyzing sounding values at the intersection of perpendicular trackline crossings. The mean difference of trackline crossing on the intertidal flats 2 cm (SD = 4) matched that of the channel and channel margin (depths below MLLW) but with increased spread in the data, 2 cm (SD = 10). Sonar Data Collection. Bathymetry data were collected using a 234.5 kHz SEA (Systems Engineering and Assessment Ltd.) SWATHplus-M phase-differencing sidescan sonar. The sonar was pole-mounted on the 34-foot USGS mapping vessel R/V Parke Snavely and affixed to a hull brace. Real-time kinematic (RTK) GPS position data were passed through a CodaOctopus F180 inertial measurement unit (IMU) to the sonar hardware and data collection software. Sonar heads, GPS antennae, and the IMU were surveyed in place to a common reference frame with a Geodimeter 640 Total Station. The R/V Parke Snavely was outfitted with three networked workstations and a navigation computer for use by the captain and survey crew for data collection and initial processing. 2009 Geodetic Control. Geodetic control for the survey was established using a shore based Global Positioning System (GPS) base station broadcasting Real Time Kinematic (RTK) corrections to the survey vessel via UHF radio link. The base station was located near the historic Dumbarton fishing pier, on a benchmark identified as RAV3. Reference Frame: NAD83 (NSRS2007) Epoch Date: 2007.00, Latitude: N 37 degrees 29' 55.62946", Longitude: W 122 degrees 07' 42.47332", Orthometric Height: 2.438 m (NAVD88 height modernization project elevation) 2009 Vessel Position and Attitude. The R/V Parke Snavely was equipped with a CodaOctopus F180 attitude and positioning system for the duration of the survey. The F180 was running F190 firmware and received real-time kinematic (RTK) corrections directly. The RTK GPS data (2 cm error ellipse) were combined with the inertial motion measurements directly within the F190 hardware so that high-precision position and attitude corrections are fed in real-time to the sonar acquisition equipment. The NAD83 (NSRS2007) Epoch 20007.00 3-dimensional reference frame was used for all data acquisition. 2009 Sound Velocity Measurements. Sound velocity measurements were collected continuously with an Applied Micro Systems Micro SV deployed on the transducer frame for real-time sound velocity adjustments at the transducer-water interface. The Micro SV is accurate to +/- 0.03 m/s. In addition, sound velocity profiles (SVP) were collected with an Applied MicroSystems, SvPlus 3472. This instrument provides time-of-flight sound-velocity measurements by using invar rods with a sound-velocity accuracy of +/- 0.06 m/s, pressure measured by a semiconductor bridge strain gauge to an accuracy of 0.15 percent (Full scale) and temperature measured by thermistor to an accuracy of 0.05 degrees Celsius (Applied Microsystems Ltd., 2005). 2009 Sonar Sounding Processing. GPS data and measurements of vessel motion were combined in the F180 hardware to produce a high-precision vessel attitude packet. This packet was transmitted to the Swath Processor acquisition software in real-time and combined with instantaneous sound velocity measurements at the transducer head before each ping. Up to 20 pings per second were transmitted with each ping consisting of 2048 samples per side (port and starboard). The returned samples were projected to the seafloor using a ray-tracing algorithm working with the previously measured sound velocity profiles in SEA Swath Processor (version 3.05.18.04). A series of statistical filters were applied to the raw samples to isolate the seafloor returns from other uninteresting targets in the water column. Finally, the processed data were stored line-by-line in both raw (.sxr) and processed (.sxp) trackline files. 2009 Digital Elevation Model Production. The raw bathymetry data were filtered in SEA Swath Processor (version 3.12.7) and imported into CARIS HIPS and SIPS (version 9.1) for post-processing. Within CARIS a swath angle BASE (Bathymetric with Associated Statistical Error) surface was created at 1-m resolution and the subset editor used to manually eliminate any remaining outliers or artifacts. The average depth within each 1 by 1 m cell was exported as an ASCII text file and imported into Surfer (version 10) for interpolation using a linear kriging algorithm with a 1-simga nugget of 0.07 m and a 5 by 5 m search radius. The resultant grid was exported to ESRI ArcMap (version 10.7.1) for display and further analyses. The surveys collected from December 2008 through January 2011 using the F180 IMU were deepened by 13 cm to account for the measured F180/POS MV bias (detailed in Foxgrover and others, 2011). 2009 Datum Conversions. To convert the bathymetry from the geodetic vertical datum of NAVD88 to the tidal datum of MLLW (1983–2001 tidal epoch), 0.37 m was added, as specified in datum conversions provided by the CO-OPS division of NOAA for a 2005 bathymetric survey of south San Francisco Bay (Foxgrover and others, 2007). 20210601 Raster grid cell 1439 1291 Universal Transverse Mercator 10 0.9996 -123 0.0 500000 0.0 row and column 1.0 1.0 meters North American Datum of 1983 (NSRS2007) Geodetic Reference System 80 6378137 298.257 Mean Lower Low Water (MLLW) 0.01 meters Explicit elevation coordinate included with horizontal coordinates Altitude Elevation relative to MLLW in meters. Values are positive up. Producer defined U.S. Geological Survey - CMGDS mailing and physical

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Santa Cruz CA 95060 1-831-427-4747 pcmsc_data@usgs.gov These data are available in GeoTIFF format, including a tif world file (.tfw) and CSDGM FGDC-compliant metadata. 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. GeoTIFF ArcGIS 10.7.1 Downloadable zip file contains the TIFF (.tif), and the tif world file (.tfw). WinZip 2.2 https://doi.org/10.5066/P9BIB67S Data can be downloaded using the Network_Resource_Name links and scrolling down to the survey data of interest. None. The downloadable data file has been compressed with the "zip" command and can be unzipped with Winzip (or other tool) on Windows systems. To utilize these data, the user must have software capable of uncompressing the WinZip file and importing and viewing a GeoTIFF file. 20220701 U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998