October 2015 bathymetry (NAVD88) of Coyote Creek and Alviso Slough, South San Francisco Bay, California

Bathymetric surveys were conducted 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. GPS position data were passed through an Applanix Position and Motion Compensation System for Marine Vessels POS/MV 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 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.

An Applanix Position and Motion Compensation System for Marine Vessels (POS/MV) was used to accurately determine the survey vessel's position. The POS/MV utilizes Global Navigation Satellite System (GNSS) data in combination with angular rate and acceleration data from the IMU and heading data from the GPS Azimuth Measurement Systems (GAMS) to produce accurate position and orientation information through a virtual network of base stations. As opposed to receiving high-accuracy Real-Time Kinematic (RTK) corrections, the POS records raw inertial and GNSS data while surveying, which is later refined through post processing to incorporate publicly available GPS data from nearby base stations. During post processing the POS/MV data is run through POSPac software to produce a Smoothed Best Estimate of Trajectory (SBET) file, which is then imported back into Swath Processor to produce high-accuracy positions relative to the WGS84 ellipsoid. The RMS results from our POS/MV surveys show positional errors of less than 5 cm in X, Y, and Z.

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 Micro Systems, 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).

GPS data and measurements of vessel motion (heave, pitch, and roll) are combined in the POS/MV hardware to produce a high-precision vessel attitude packet. This packet is transmitted to the Swath Processor acquisition software in post-processing and combined with instantaneous sound velocity measurements at the transducer head before each ping. Up to 20 pings per second are transmitted with each ping consisting of 2048 samples per side (port and starboard). The returned samples are projected to the seafloor using a ray-tracing algorithm working with the previously measured sound velocity profiles in SEA Swath Processor (version 3.10.6). A series of statistical filters are applied to the raw samples that isolate the seafloor returns from other uninteresting targets in the water column. Finally, the processed data are stored line-by-line in both raw (.sxr) and processed (.sxp) trackline files.

The raw bathymetry data were filtered in SEA Swath Processor (version 3.10.6) and imported into CARIS HIPS and SIPS (version 8.1) 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 0.05 m and a 2 by 2 m search radius. The resultant grid was exported to ESRI ArcMap (version 10.2.2) for display and further analyses. The entire survey was shoaled by 4 cm to account for a combination of biases resulting from changes in the boat instrumentation and configurations that occurred since the initial survey was collected in 2010.

To convert the bathymetry from WGS84 ellipsoid heights to the tidal datum of MLLW the data were first transformed from WGS84(ITRF2000) to the NAD83(CORS96) ellipsoid using a 14-point Helmert transformation described by Soler and Snay (2004) using the command line tool CS2CS in the Proj4 library (http://trac.osgeo.org/proj/). A fixed Geoid09 offset of -32.62 m was then applied to convert the NAD83 ellipsoid heights to orthometric heights NAD83(CORS96)/NAVD88. The orthometric NAVD88 elevations were converted to MLLW using the conversions provided by the CO-OPS division of NOAA for a 2005 bathymetric survey of South San Francisco Bay (Foxgrover and others, 2007).

Edited metadata to add keywords section with USGS persistent identifier as theme keyword. No data were changed.