2010 Bathymetric Survey and Digital Elevation Model of 

Corte Madera Bay, California

By Amy C. Foxgrover, David P. Finlayson, Bruce E. Jaffe, John Y. Takekawa, Karen M. Thorne, and 

Kyle A. Spragens

Open-File Report 2011–1217

U.S. Department of the Interior 

U.S. Geological Survey 
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011 

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Suggested citation:

Foxgrover, A.C., Finlayson, D.P., Jaffe, B.E., Takekawa, J.Y., Thorne, K.M., and Spragens, K.A., 2011, 2010 

bathymetric survey and digital elevation model of Corte Madera Bay, California: U.S. Geological Survey Open-File 

Report 2011-1217, 20 p., available at http://pubs.usgs.gov/of/2011/1217/. 

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 report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.

Cover: Seamless bathymetric/topographic DEM of Corte Madera, California; from figure 12
iii

Contents

Abstract....................................................................................................................................................................................................1

Introduction .............................................................................................................................................................................................1

Data Collection .......................................................................................................................................................................................1

Geodetic Control................................................................................................................................................................................4

Sound Velocity Measurements.......................................................................................................................................................4

Processing Procedures ........................................................................................................................................................................5

Real-time Sonar Sounding Processing.........................................................................................................................................6

Swath Cleaning and Filtering ..........................................................................................................................................................6

Water-Column Artifacts in S-3-10-SF........................................................................................................................................6

Horizontal and Vertical Datum Conversions ................................................................................................................................9

Estimates of Bathymetric Uncertainty .........................................................................................................................................10

Digital Elevation Model Production ..................................................................................................................................................13

Bathymetric Grids............................................................................................................................................................................13

Lidar Data .........................................................................................................................................................................................14

Bathymetric / Topographic DEM ..................................................................................................................................................14

Evaluation of Lidar Bare Earth Elevations in Marsh Vegetation ........................................................................................16

Data Tables...........................................................................................................................................................................................18

A Note on Coordinate Systems and Datums.............................................................................................................................18

Bathymetry........................................................................................................................................................................................18

Bathymetric / Topographic DEM ..................................................................................................................................................18

Acknowledgments ...............................................................................................................................................................................19

References Cited .................................................................................................................................................................................19

Appendix................................................................................................................................................................................................20

Figures 

1. Map of study area, Corte Madera Bay, California............................................................................................................2

2. U.S. Geological Survey, Coastal and Marine Geology Research Vessel Parke Snavely. ......................................2

3. Fore and aft views of the SWAT Hplus sonar pole mount on the R/V Snavely. .........................................................3

4. Processing workflow diagram for converting soundings to a digital elevation model (DEM).................................. 5

5. Sample cross-sectional views of sounding swaths within CARIS demonstrating typical sounding distributions 

upon a flat surface and curvatures resulting from refraction artifacts ..........................................................................7

6. 1-m resolution bathymetry grid generated by merging surveys S-3-10-SF and S-9-10-SF....................................8

7. 1-m resolution bathymetry grid with interpolation performed to fill the gaps between tracklines. ..........................9

8. Histogram of sounding elevation standard deviations within each 1 by 1 m cell. ...................................................11

9. Plan-view map of bathymetric soundings standard deviation within each 1 by 1 m cell. ......................................11

10. Uncertainty in sounding elevation compared to IHO standards as a function of water depth ..............................13

11. Difference between tidal flat elevations calculated from aerial lidar versus bathymetry. .......................................15

12. Seamless bathymetric/ topographic DEM of Corte Madera. .......................................................................................16

13. Comparison between RTK GPS ground-truth measurements and bare earth lidar elevations............................17

Tables 

1. SWATHplus-M Sonar Specifications (SEA Ltd., 2004). ................................................................................................. 4

2. National Geodetic Survey OPUS solutions for Corte Madera GPS base station CM01..........................................4

3. Parameters adopted for transformation between WGS84 (G1150) and NAD83 (CORS96). ...............................10

4. Minimum IHO survey order requirements. ......................................................................................................................12

5. Difference statistics between RTK measurements and bare earth lidar elevations in the marsh ........................17

6. Bathymetric data files provided. ........................................................................................................................................18

7. Bathymetric/topographic DEM files provided..................................................................................................................19
iv

Conversion Factors

 

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

mile, nautical (nmi) 1.852 kilometer (km)

yard (yd) 0.9144 meter (m)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2) 

acre 0.004047 square kilometer (km2)

square foot (ft2) 929.0 square centimeter (cm2)

square foot (ft2) 0.09290 square meter (m2)

square inch (in2) 6.452 square centimeter (cm2)

section (640 acres or 1 square mile) 259.0 square hectometer (hm2) 

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 
2010 Bathymetric Survey and Digital Elevation Model of 

Corte Madera Bay, California

By Amy C. Foxgrover1, David P. Finlayson1, Bruce E. Jaffe1, John Y. Takekawa2, Karen M. Thorne2, and 

Kyle A. Spragens2 

1USGS Pacific Science Center, Santa Cruz, Calif. 

2USGS Western Ecological Research Center, Vallejo, Calif. 

Abstract

A high-resolution bathymetric survey of Corte Madera Bay, California, was collected in early 2010 

in support of a collaborative research project initiated by the San Francisco Bay Conservation and 

Development Commission and funded by the U.S. Environmental Protection Agency. The primary 

objective of the Innovative Wetland Adaptation in the Lower Corte Madera Creek Watershed Project is 

to develop shoreline adaptation strategies to future sea-level rise based upon sound science. 

Fundamental to this research was the development of an of an up-to-date, high-resolution digital 

elevation model (DEM) extending from the subtidal environment through the surrounding intertidal 

marsh. We provide bathymetric data collected by the U.S. Geological Survey and have merged the 

bathymetry with a 1-m resolution aerial lidar data set that was collected by the National Oceanic and 

Atmospheric Administration during the same time period to create a seamless, high-resolution DEM of 

Corte Madera Bay and the surrounding topography. The bathymetric and DEM surfaces are provided at 

both 1 m and 10 m resolutions formatted as both X, Y, Z text files and ESRI Arc ASCII files, which are 

accompanied by Federal Geographic Data Committee compliant metadata. 

Introduction

Data Collection

Corte Madera Bay is located in the northwestern portion of Central San Francisco Bay, 

California, just south of the Richmond-San Rafael Bridge (fig. 1). Two separate bathymetric surveys of 

Corte Madera Bay were completed: the first (USGS Field Activity ID: S-3-10-SF) from January 26-29, 

2010 and the second (USGS Field Activity ID: S-9-10-SF) on March 29-30, 2010. The combined 

bathymetric surveys consist of 215 survey lines covering an area of approximately 6.5 km2 extending 

north to the dredged ferry channel leading to Corte Madera Creek and to the south, just beyond Paradise 

Cay Yacht Harbor. Both surveys were done aboard the research vessel R/V Parke Snavely, a state-ofthe-art research vessel outfitted with a pole-mounted 234.5 kHz SEA (Systems Engineering & 

Assessment Ltd.) SWATHplus-M phase-differencing sidescan sonar (figs. 2 and 3). 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 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. See table 1 for the sonar system 

specifications. 
2

Figure 1. Location map of study area, Corte Madera Bay, California, with bathymetric survey tracklines colored by 

cruise ID. 

Figure 2. U.S. Geological Survey, Coastal and Marine Geology Research Vessel Parke Snavely. Photo courtesy 

of Thomas E. Reiss. 
3

Figure 3. Fore and aft views of the SWATHplus sonar pole mount on the R/V Snavely. 
4

Table 1. SWATHplus-M Sonar Specifications (SEA Ltd., 2004). 

Sonar frequency 234.5 kHz

Maximum water depth 120 m

Maximum swath width 300 m (typically 7 to 12 times water depth)

Resolution across track (best case) 5 cm

Transmit pulse length 34 ms to 500 ms

Ping repetition rate

 150 m swath width 10 pings per second

 300 m swath width 5 pings per second

Vertical accuracy (range dependent)

 57 m 0.1 m

 114 m 0.2 m

 171 m 0.3 m

Geodetic Control 

Geodetic control for the survey was established using a shore-based GPS base station 

broadcasting RTK corrections to the survey vessel by UHF radio link. The GPS base station (CM01) 

was established in the nearby hills along Taylor Drive (see figure 1). The average National Geodetic 

Survey (NGS) Online Positioning User Server (OPUS) solutions for CM01 are provided in table 2. 

Table 2. National Geodetic Survey OPUS solutions for Corte Madera GPS base station CM01. 

Reference frame

WGS84 (G1150)

(same as ITRF00) NAD83, UTM zone 10

Epoch 2010.1532 2002.0000

Latitude / Northing N 37° 54 ́ 51.37819 ̋ 4196426.825 m

Longitude / Easting W 122° 29 ́ 13.21786 ̋ 545093.607 m

Ellipsoid height 88.780 m 89.310 m

Orthometric height N/A 121.651 m (based on GEOID09)

The R/V Snavely was equipped with a CodaOctopus F180 attitude and positioning system for 

the duration of the survey. The F180 is running F190 firmware and receives RTK corrections directly. 

The RTK GPS data (2 cm error ellipse) are 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 WGS84 (G1150)/ITRF 2000 reference frame was used for both 

horizontal and vertical positioning. In post-processing, the data was converted to orthometric heights 

NAD83 (CORS96)/NAVD88 (see processing procedures section below). All data is projected in UTM 

coordinate space in meters, zone 10 north. 

Sound Velocity Measurements 

Sound-velocity measurements were collected continuously with an Applied Micro Systems 

Micro SV (accurate to ± 0.03 m/s) deployed on the transducer frame for real-time sound-velocity 
5

adjustments at the transducer/water interface. Additionally, sound-velocity profile measurements of the 

water column were collected at the beginning and ending of each survey day and when there were large 

changes in water depth (that is, when transitioning from collecting data in the channels to the tidal flats 

or vice versa). Sound-velocity profile measurements were collected using an Applied Micro Systems 

SvPlus 3472, which provides time-of-flight sound-velocity measurements using invar rods with a 

sound-velocity accuracy of ± 0.06 m/s. Pressure was measured by a semiconductor bridge strain gauge 

to an accuracy to 0.15 percent (full scale), and temperature measured by thermistor to an accuracy of 

0.05 C (Applied Microsystems Ltd., 2005).

Processing Procedures

The general processing work-flow procedures for converting raw bathymetric soundings to a 

DEM are shown in figure 4. Critical aspects of the processing procedure are discussed in more detail 

below. 

Figure 4. Processing workflow diagram for converting soundings to a digital elevation model (DEM). 
6

Real-time Sonar Sounding Processing 

GPS data and measurements of vessel motion are combined in the F180 hardware to produce a 

high-precision vessel attitude packet. This packet is 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 are transmitted with each ping consisting of 2,048 

samples per side (port and starboard). The returned samples are projected to the seafloor using a raytracing algorithm working with the previously measured sound-velocity profiles in SEA Swath 

Processor (version 3.05.18.04). 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 is 

stored line-by-line in both raw (.sxr) and processed (.sxp) trackline files. For these surveys, processed 

files were filtered across-track with a mean filter at 0.2 m resolution. 

Swath Cleaning and Filtering 

The processed .sxp files were imported to CARIS HIPS and SIPS (version 7.0.1.0 Service Pack 

1) for additional cleaning and filtering. Swath filters were applied to clean the data based upon 

characteristics such as depth, across-track angle, and across-track distance. A CARIS Swath Angle 

BASE (Bathymetric with Associated Statistical Error) surface was created at 1 m resolution, and the 

subset editor was used to manually eliminate remaining outliers or artifacts. The average depth within 

each 1 by 1 m cell was exported as an ASCII text file along with calculations of the bin standard 

deviation (of all soundings within the 1 m by 1 m cell spacing) and the sounding density. 

Water-Column Artifacts in S-3-10-SF

It became apparent during the January bathymetric cruise (S-3-10-SF) that the sound ray-tracing 

algorithm used by the SWATHplus software was calculating some sounding ranges and/or angles 

improperly. This situation usually is the result of a bad sound-velocity model for the water column and 

results in (sound) refraction artifacts which manifest themselves as curvatures (either upwards or 

downwards) in the across-profile depth solutions. Curvature becomes more pronounced with increased 

distance from nadir. The usual remedy to this problem is to re-measure the sound-velocity profile and to 

recalculate the ray-tracing model; however, despite the collection of numerous sound-velocity profiles, 

we were not able to eliminate the refraction errors. We suspect that a strong storm system that moved 

through the region the week prior to the survey affected the water-column properties of the bay in a 

complex way. Properties such as salinity, temperature, and sediment concentration, which all affect 

sound velocity, could have been influenced by increased freshwater input to the bay through surface 

runoff, accidental sewage overflow, or through ground-water efflux. The sound-velocity profile 

measurements taken aboard the vessel were insufficient to characterize the spatial variability of sound 

velocity throughout the study area, which in turn compromised the ability of the sonar to properly raytrace the soundings to the seafloor. Fortunately, refraction artifacts are a function of slant-range and 

angle of incidence, so that soundings directly beneath the vessel are less affected than the off-nadir 

soundings. 

At the time of collection, six sidescan surveys had been completed in similar settings within San 

Francisco Bay using the identical system configuration, and this was the first time that refraction 

artifacts were a problem. Furthermore, the identical setup was used for the second cruise just two 

months later, and the refraction artifacts did not appear, which leads us to believe that the artifacts were 

a function of water-column properties at the time of the survey. As a result, during the post-processing 

of S-3-10-SF within CARIS, the bathymetric swath was trimmed to retain only those soundings within 
7

close proximity to nadir so as to minimize any refraction artifacts (fig. 5). The accuracy of the retained 

soundings from S-3-10-SF was verified by differencing the north/south oriented tracklines from the 

intersecting east/west oriented tracklines collecting during S-9-10-SF. The intersecting tracklines had a 

mean offset of 5 cm (SD=6) and a maximum difference of up to 61 cm. These differences fall within 

the accuracy of the system (discussed further in the section ―estimates of bathymetric uncertainty‖) and 

within the anticipated scale of geomorphic change that could occur within the two months between 

surveys. Owing to the aggressive trimming of data to eliminate refraction artifacts, there is not 100 

percent overlap with adjacent tracklines for S-3-10-SF, resulting in narrow data gaps (~15 m wide) 

between some survey lines when the data is exported at 1 m cell size (fig. 6). Fortunately, the majority 

of tracklines displaying the refraction artifact were within the intertidal flats, and although the acrossswath trimming of data left gaps between adjacent tracklines, the gently sloping terrain is highly 

conducive to interpolating across these gaps (fig. 7).

Figure 5. A cross-sectional view looking along-swath at soundings edited by individual trackline in CARIS. The 

yellow triangle represents the location of the transducer with soundings on the left (port side) and right 

(starboard) side of the boat. Gray dots represent all of the potential solutions for depth soundings, and the 

colored dots (red for port and green for starboard) represent soundings retained after filtering and manually 

cleaning the data in CARIS. A, A typical shallow-water profile collected in the intertidal flats, with scatter 

increasing uniformly with distance from nadir. B, A sample taken from S-3-10-SF where refraction artifacts 

result in an underestimate of surface elevation increasing with distance from nadir. C, A sample taken from S3-10-SF where refraction artifacts result in an overestimate of surface elevation increasing with distance from 

nadir. 
8

Figure 6. 1-m resolution bathymetry grid generated by merging surveys S-3-10-SF and S-9-10-SF, Corte Madera 

Bay, California. Narrow gaps between tracklines exist as a result of trimming across-swath widths to eliminate 

refraction artifacts. 
9

Figure 7. 1-m resolution bathymetry grid generated using a weighted moving average gridding algorithm , with a 

search diameter of 100 m, to interpolate across gaps between tracklines, Corte Madera Bay, California. 

Horizontal and Vertical Datum Conversions 

To convert the data from the WGS84 (G1150) ellipsoid to NAD83 (CORS96), the 1-m grid 

resolution data was exported from CARIS to an X, Y, Z point file. Next, a 14-point Helmert 

transformation was applied with time-dependent transformation parameters figured for January 23, 

2010, according to methods outlined in Soler and Snay (2004). Table 3 shows the specific parameters 

in the format required by the cs2cs program found in the Proj4 library used to transform the points. The 

NAD83 (CORS96) ellipsoid elevations were then converted to orthometric heights based on NAVD88 

and the National Geodetic Survey (NGS) Geoid09 Model (National Geodetic Survey, 2009) in VDatum 

v 2.3.0 (http://vdatum.noaa.gov/). 
10

Table 3. Parameters adopted for transformation between WGS84 (G1150) and NAD83 (CORS96). 

Parameter Definition Units Value at t0=1997.0 Value at tF=2010.0630

Tx x-shift meters 0.9956 1.0047

Ty y-shift meters -1.9013 -1.9104

Tz z-shift meters -0.5215 -0.5150

ωx x-rotation1arc seconds 0.025915 -0.026790

ωy y-rotation1arc seconds 0.009426 .000461

ωz z-rotation1arc seconds 0.011599 -0.010933

S scale parts-per-million 0.00062 -0.00173

1Note that the Proj4 program cs2cs reverses the sign of the rotation parameters from the Soler and Snay (2004) algorithm. 

Estimates of Bathymetric Uncertainty 

For relatively flat portions of the seafloor, the standard deviation of sounding elevations within a 

small area is a good measure of the precision of the sonar instrumentation; this is not true in areas where 

the seafloor is naturally variable or steep. In these areas, the standard deviation reflects the combination 

of natural variation of the surface, and sonar measurement uncertainty. After post-processing the data in 

CARIS to remove obvious outliers, the standard deviation of the soundings within each 1 by 1 m cell 

(containing more than 400 soundings on average) was calculated. The mean of the standard deviation 

for all of the cells in the survey is 0.06 m, and 98 percent of the cells have a standard deviation less than 

0.15 m (fig. 8). These absolute numbers are a good indication of the distribution of uncertainty in 

bathymetric soundings, however, measurement errors naturally increase with range from the system 

(that is, with increasing depth). A plan-view map of spatial variability in standard deviations throughout 

the study area is shown in figure 9. Although slightly higher standard deviations exist in the tidal flats 

along the west/easterly oriented tracklines, this can likely be attributed to actual changes in bed 

elevation during the two month timespan between surveying the overlapping tracklines. The overall 

spatial pattern of standard deviation reveals low standard deviation in the low-relief intertidal flats and 

increases with increasing depth and slope of the bay floor. This highlights the need for a measure of 

survey reliability that accounts for water depth as a factor. The International Hydrographic 

Organization (IHO) standards described next provide such a metric. 
11

Figure 8. Histogram of sounding elevation standard deviations within each 1 by 1 m cell. 

Figure 9. Plan-view map of the bathymetric soundings standard deviation within each 1 by 1 m cell, Corte Madera 

Bay, California. 
12

The IHO defines several survey orders based on a combination of coverage, depth, and accuracy 

(IHO, 2008). The IHO defines maximum allowable total vertical uncertainty (TVU) using a depthdependent formula with two additional variables as defined below (from IHO Standards for 

Hydrographic Surveys 5th Edition): 

 

(1) 

where a represents the portion of the uncertainty that does not vary with depth, b is a coefficient which 

represents that portion of the uncertainty that varies with depth, and d equals depth. 

IHO standards require a 95 percent confidence level, defined as 1.96 times the standard 

deviation in sounding uncertainty. IHO survey orders use the values found in table 4 as minimums for 

their survey orders (note that descriptions are generalized, and Order 1 and 1a are combined because 

they have the same values for minimum TVU). If we assume that the elevation uncertainty in 

bathymetric soundings is normally distributed, we can estimate the total vertical uncertainty (TVU) in 

an elevation cell at the 95 percent level using: 

(2) 

where αis the standard deviation of all soundings in a cell located at coordinate (x, y). By 

comparing the calculated values from equation 2 against the standardized TVU thresholds represented 

by equation 1, we have an objective measure of the quality of the bathymetric surface. 

Table 4. Minimum IHO survey order requirements. 

Survey Order Special Combined 1 and 1a 2

Description Areas where underkeel clearance is 

critical

Areas shallower than 100 

meters

Areas generally 

deeper than 100 

meters

Maximum allowable 

TVU 95% confidence 

level

a = 0.25 meter

b = 0.0075

a = 0.5 meter

b = 0.013

a = 1.0 meter

b = 0.023

Figure 10 shows a plot of the calculated TVU values (equation 2) for a representative subset of 

the survey as a function of water depth. For reference, lines indicating the IHO thresholds for Special 

Order, First Order, and Second Order surveys derived from equation 1 also are displayed. The vast 

majority of elevation uncertainty in the data set satisfies the IHO standard for First Order surveys, the 

same standard that the National Oceanic and Atmospheric Administration’s (NOAA) National Ocean 

Service follows, and serves as a testament to the quality of the survey. 
13

Figure 10. Uncertainty in sounding elevation compared to IHO standards as a function of water depth 

(approximated to mean high water), Corte Madera Bay, California. For clarity, only 0.1 percent of the data set 

(randomly selected) is shown out of a total 5.2 million cells in the DEM. The maximum vertical uncertainty 

allowed for each International Hydrographic Organization survey order is plotted as red lines along with the 

running average vertical uncertainty of the data set shown in cyan. 

Digital Elevation Model Production

Bathymetric Grids 

The cleaned and filtered BASE surface was exported from CARIS at 1-m resolution and 

converted to elevations relative to NAVD88 using the procedures outlined above. Three derivations of 

the bathymetric grid are provided to fit the varying needs of the end users. 

1) A 1-m resolution BASE surface created in CARIS using a swath angle weighting scheme 

where higher weight is given to soundings from the inner part of a swath than to outer beams 

from adjacent tracklines. This data set is the original bathymetry with datum conversions 

applied. No additional smoothing or interpolation has been applied so some small-scale 

ripple features are distinguishable on the bed floor, but gaps exist near nadir and between 

tracklines. 

2) A 1- m resolution grid which has been interpolated to fill gaps between tracklines. The 1-m 

resolution BASE surface was exported from CARIS to an ASCII text file, datum conversions 

were applied, and the data then imported into Fledermaus for interpolation using a weighted 

moving average gridding algorithm with a weight diameter of 100 m. 

3) A 10-m resolution grid. The 1-m resolution BASE surface was exported from CARIS to an 

ASCII text file, datum conversions were applied, and the data was then imported into 

Fledermaus for interpolation at 10 m cell size using a weighted moving average gridding 

algorithm with a weight diameter of 80 m (8 cells). 
14

Lidar Data 

The National Oceanic and Atmospheric Administration’s Coastal Services Center contracted the 

acquisition of aerial topographic lidar by Fugro EarthData, Inc., which happened to cover our study 

area, in the spring of 2010. NOAA’s Northern San Francisco Bay aerial lidar was collected from 

February 25 to April 16, 2010, using a Piper Navajo twin engine aircraft equipped with a Lecia ALS60 

lidar system. Acquisition was designed to support a nominal point spacing of 1 meter and was collected 

at low tide to optimize coverage of the intertidal flats. Lidar data was processed by Fugro to achieve a 

bare-earth ground surface and was provided as 1-m resolution hydro-flattened grids. The stated 

horizontal accuracy of the lidar is 1 meter RMSE or better. When Fugro compared the lidar to survey 

grade-GPS points in generally flat, nonvegetated areas the vertical accuracy of 95 percent of the 

positions had errors less than or equal to 18 cm (equivalent to a 9 cm RMSE, if evenly distributed). The 

lidar is projected in UTM coordinate space, zone 10. The vertical datum is NAVD88, and the horizontal 

datum is NAD83 (NSRS2007). Within our study area, NAD83 (NSR2007) closely approximates the 

horizontal datum of the bathymetric data, NAD83 (CORS96), and is within the accuracy of the data. 

For our purposes the two versions of NAD83 are considered equivalent. For additional information on 

NOAA’s Northern San Franscisco Bay lidar data set or to download the data directly visit NOAA’s 

CSC Web site: http://www.csc.noaa.gov/ldart. 

Bathymetric / Topographic DEM 

Prior to merging the bathymetry with the topographic lidar a comparison was made between 

elevations of the two independent data sets where they overlap in the intertidal flats. There is 

approximately 470,000 m2 of overlap between lidar and bathymetry within Corte Madera Bay. The 

bathymetry is a maximum of 27 cm higher than, or 24 cm lower than, the lidar in the region of overlap. 

The average difference is 0 cm (SD=4), which suggests that there is not a consistent offset or bias 

between the two data sets (fig. 11). The 1-m resolution bathymetric grid (interpolated to fill gaps 

between tracklines) was merged with the topographic lidar using the blend algorithm in the ―Mosaic to 

New Raster‖ tool in Arc Toolbox (fig. 12). The resultant DEM is provided at 1 m resolution and also 

was also resampled to 10 m resolution using a bilinear interpolation. 
15

Figure 11. Difference between tidal flat elevations calculated from aerial lidar versus bathymetry, Corte Madera 

Bay, California. 
16

Figure 12. Seamless bathymetric/topographic DEM of Corte Madera, California.

Evaluation of Lidar Bare Earth Elevations in Marsh Vegetation 

The ability of aerial lidar to capture bare earth in vegetated areas is largely dependent upon the 

density of vegetation at a given site. In a separate study, scientists at the USGS Western Ecological 

Research Center collected measurements of ground elevation throughout the marsh within our study 

area using a Lecia RTK GPS unit with a published vertical and horizontal accuracy of ± 3 cm. More 

than 700 elevation measurements were collected in March of 2010; points were taken approximately 

every 25 meters along shore-parallel transects with a nominal spacing of approximately 50 meters 

between transects. The RTK ground measurements were differenced from the bare earth lidar 

elevations to evaluate lidar penetration into the vegetation at this site and thus how well the bare earth 

model performs in the vegetated marsh regions. There was a mean positive offset of 23 cm between the 

two measurements, indicating that the bare earth lidar in this marsh is, on average, 23 cm (SD=10) 

higher than the elevations obtained by RTK measurements. Depending upon the particular needs of the 

end-user, this bias in bare earth elevations in the marsh may or may not be significant. We have divided 

the marsh into three regions to quantify spatial variations between lidar and RTK measurements in the 

northern, central, and southern reaches of the marsh (fig. 13). The statistics from this analysis are 

provided in table 5 so that the end-user may apply adjustments as needed. 
17

Table 5. Difference statistics between real time kinematic (RTK) measurements and bare earth lidar elevations in 

the marsh. Positive differences indicate that the lidar elevation is higher than the RTK measurement. 

Northern Central Southern Total

Number of Measurements 264 156 324 744

Difference Statistics

Minimum (cm) -20 -6 -41 -41

Maximum (cm) 41 45 44 45

Mean (cm) 18 27 26 23

Standard Deviation (cm) 9 7 9 10

Estimated RMSE (cm) 20 28 27 25

 

Figure 13. Real time kinematic (RTK) measurements colored by difference between ground elevations as 

determined by RTK survey versus bare earth lidar DEM, Corte Madera Bay, California. 
18

Data Tables

A Note on Coordinate Systems and Datums 

WGS84 and NAD83 have been revised several times resulting in coordinate shifts of up to 

several meters in X, Y, and Z. The revision is indicated by the designator following the name (G1150 

following WGS84, for example). Software that does not distinguish between the different versions of 

these datums likely does not support 3D datum properly. Users should pay particular attention to the 

accompanying metadata files to ensure that the data are properly georeferenced. In particular, note that 

most current GIS software (including ArcGIS 10) cannot properly transform high-resolution elevation 

data from one 3D datum to another (such as WGS84 G1150 to NAD83 CORS96) without introducing 

errors on the order of 1 to 2 m in X, Y, and Z. For this reason, data are provided in both WGS84 G1150 

(equivalent to ITRF2000) and NAD83 CORS96 (equivalent to NSRS2007). The geodetic vertical 

datum of NAVD88 closely approximates the tidal datum of mean lower low water (MLLW) in Corte 

Madera Bay. VDatum conversions within our study area show that the datum of MLLW is, on average, 

3 cm below the datum of NAVD88, however, estimates vary spatially from 12 cm below to 7 cm above 

the datum of NAVD88. 

Bathymetry 

Bathymetry data are provided as elevation in meters relative to both the ellipsoid 

WGS84(G1150) and as orthometric heights NAD83(CORS96)/NAVD88 (table 6). All data are 

projected in UTM zone 10 North, and all values (eastings, northings, and elevation) are in meters. Each 

zip file contains the data formatted as both ASCII X, Y, Z text files (*.txt) and ESRI ASCII GRID files 

(*.asc; see appendix), as well as Federal Geographic Data Committee (FGDC) compliant metadata in 

both text and .xml format. 

Table 6. Bathymetric data files provided. 

File name Horizontal resolution, 

in meters

Reference frame Vertical datum

Corte_Madera_bathy_raw_1m_NAVD88.zip 1 NAD83 (CORS96) NAVD88

Corte_Madera_bathy_raw_1m_WGS84.zip 1 WGS84(G1150) WGS84(G1150)

Corte_Madera_bathy_interp_1m_NAVD88.zip 1 NAD83 (CORS96) NAVD88

Corte_Madera_bathy_interp_1m_WGS84.zip 1 WGS84(G1150) WGS84(G1150)

Corte_Madera_bathy_10m_NAVD88.zip 10 NAD83 (CORS96) NAVD88

Corte_Madera_bathy_10m_WGS84.zip 10 WGS84(G1150) WGS84(G1150)

Bathymetric / Topographic DEM 

Seamless bathymetric/topographic DEMs are provided as elevations in meters relative to both the 

ellipsoid WGS84(G1150) and as orthometric heights NAD83(CORS96)/NAVD88 (table 7). All data 

are projected in UTM, zone 10 North, and all values (eastings, northings, and elevation) are in meters. 

Each zip file contains the data formatted as both ASCII X, Y, Z text files (*.txt) and ESRI ASCII GRID 

files (*.asc; see appendix), as well as FGDC-compliant metadata in both text and .xml format. The 

DEMs are provided as both 1 m and 10 m resolution grids. 
19

Table 7. Bathymetric/topographic DEM files provided. 

File name Horizontal resolution, 

in meters

Reference frame Vertical datum

Corte_Madera_topobathy_DEM_NAVD88_1m.zip 1 NAD83 (CORS96) NAVD88

Corte_Madera_topobathy_DEM_NAVD88_10m.zip 10 NAD83 (CORS96) NAVD88

Acknowledgments

Thanks to the survey crew of the RV Snavely: Mike Boyle, Greg Gabel, and Pete Dal Ferro (all 

of the USGS) who assisted with the bathymetry collection and to Tom Reiss who established GPS base 

stations for the bathymetric surveys. Paul Elsen, Tony Henner, and Kevin Buffington (all of USGS 

Western Ecological Research Center) assisted with collection and processing of RTK measurements in 

the marsh. The bathymetry was collected in support of the Innovative Wetland Adaption in the Lower 

Corte Madera Creek Watershed Project initiated by the San Francisco Bay Conservation and 

Development Commission and funded by the U.S. Environmental Protection Agency with additional 

support provided by the USGS Coastal and Marine Geology Program. 

References Cited

Applied Microsystems Ltd., 2005, SVplus sound velocity, temperature, and depth profiler—User’s 

manual, revision 1.23: 2071 Malaview Ave. Sidney, B.C., Canada, V8L5X6. 

International Hydrographic Organization (IHO), 2008, IHO standards for hydrographic surveys (5th 

ed.): Special publication 44, International Hydrographic Bureau, Monaco. 

Gann, J.T., 1992, YoNav—your own integrated navigation system for DOS platforms: U.S. Geological 

Survey, Open File Report 92–565, 48 p., available at 

http://pubs.usgs.gov/of/1992/0565/report.pdf. 

National Geodetic Survey, NOAA, 2009, GEOID09 geoid model, 1315 East-West Highway, Silver 

Spring, MD 20910–3282, available at http://www.ngs.noaa.gov/GEOID/GEOID09/.

Systems Engineering & Assessment (SEA) Ltd., 2004, SWATHplus training pack: Beckington Castle, 

P.O. Box 800, Frome, England, BA11 6TB. 

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, May 2004 (49). 
20

Appendix

Description of the ESRI ASCII Grid raster format: 

To import ASCII Grids into common GIS packages: 

ArcGIS: Use ArcTools's Import ASCII to GRID function 

ArcView: Use the import ASCII Grid function (May need Spatial Analyst) 

GRASS: Use the 'r.in.arc' function. 

The ASCII file consists of header information containing a set of keywords, followed by cell values in row-major order. The 

file format is: 

<NCOLS xxx> 

<NROWS xxx> 

<XLLCENTER xxx | XLLCORNER xxx> 

<YLLCENTER xxx | YLLCORNER xxx> 

<CELLSIZE xxx> 

{NODATA_VALUE xxx} 

row 1 

row 2 

. 

. 

. 

row n 

where xxx is a number, and the keyword nodata_value is optional and defaults to -9999. Row 1 of the data is at the top of the 

grid, row 2 is just under row 1 and so on. The nodata_value is the value in the ASCII file to be assigned to those cells whose 

true value is unknown. In the grid they will be assigned the keyword NODATA. Cell values are be delimited by spaces. No 

carriage returns are necessary at the end of each row in the grid (although they are included in this case). The number of 

columns in the header is used to determine when a new row begins. The number of cell values is equal to the number of rows 

times the number of columns.