Marine Sanctuaries Conservation Series ONMS-06-07

U.S. Department of Commerce 

National Oceanic and Atmospheric Administration

National Ocean Service 

Office of Ocean and Coastal Resource Management 

Olympic Coast National Marine Sanctuary 

Habitat Mapping: Survey report and classification 

of side scan sonar data from surveys 

HMPR-114-2004-02 and HMPR-116-2005-01 

National Marine Sanctuary Program September 2006 
About the Marine Sanctuaries Conservation Series 

The National Oceanic and Atmospheric Administration’s National Ocean Service (NOS) administers the

National Marine Sanctuary Program (NMSP). Its mission is to identify, designate, protect and manage the 

ecological, recreational, research, educational, historical, and aesthetic resources and qualities of nationally

significant coastal and marine areas. The existing marine sanctuaries differ widely in their natural and 

historical resources and include nearshore and open ocean areas ranging in size from less than one to over 

5,000 square miles. Protected habitats include rocky coasts, kelp forests, coral reefs, sea grass beds, estuarine 

habitats, hard and soft bottom habitats, segments of whale migration routes, and shipwrecks. 

Because of considerable differences in settings, resources, and threats, each marine sanctuary has a tailored

management plan. Conservation, education, research, monitoring and enforcement programs vary accordingly. 

The integration of these programs is fundamental to marine protected area management. The Marine 

Sanctuaries Conservation Series reflects and supports this integration by providing a forum for publication 

and discussion of the complex issues currently facing the National Marine Sanctuary Program. Topics of

published reports vary substantially and may include descriptions of educational programs, discussions on 

resource management issues, and results of scientific research and monitoring projects. The series facilitates 

integration of natural sciences, socioeconomic and cultural sciences, education, and policy development to 

accomplish the diverse needs of NOAA’s resource protection mandate. 
Olympic Coast National Marine Sanctuary Habitat Mapping: 

Survey report and classification of side scan sonar data from 

surveys HMPR-114-2004-02 and HMPR-116-2005-01 

Steven S. Intelmann1

, and Guy R. Cochrane2

1

Olympic Coast National Marine Sanctuary, NOAA 

2

Coastal and Marine Geology Program, USGS 

Silver Spring, Maryland

September 2006

U.S. Department of Commerce 

Carlos M. Gutierrez, Secretary 

National Oceanic and Atmospheric Administration 

VADM Conrad C. Lautenbacher, Jr. (USN-ret.) 

Under Secretary of Commerce for Oceans and Atmosphere

National Ocean Service 

John H. Dunnigan, Assistant Administrator 

National Marine Sanctuary Program

Daniel J. Basta, Director 
DISCLAIMER 

Report content does not necessarily reflect the views and policies of the National Marine 

Sanctuary Program or the National Oceanic and Atmospheric Administration, nor does 

the mention of trade names or commercial products constitute endorsement or 

recommendation for use. 

REPORT AVAILABILITY 

Electronic copies of this report are available from the National Marine Sanctuary

Program web site at www.sanctuaries.nos.noaa.gov. Hard copies are available from the 

following address: 

National Oceanic and Atmospheric Administration

 National Marine Sanctuary Program

 SSMC4, N/ORM62 

 1305 East-West Highway 

Silver Spring, MD 20910 

COVER

The cover features a sonar waterfall display showing an area where the towfish

unfortunately slammed into a rock wall during the HMPR-114-2004-02 survey. The red 

line represents the towfish altitude up to the point of impact when sonar packets ceased to 

be recorded. This image represents an excellent example of what sonar operators hope

never to see. 

SUGGESTED CITATION

Intelmann, S.S. and G.R. Cochrane. 2006. Olympic Coast National Marine Sanctuary 

Habitat Mapping: Survey report and classification of side scan sonar data from surveys 

HMPR-114-2004-02 and HMPR-116-2005-01. Marine Sanctuaries Conservation Series 

MSD-06-07. U.S. Department of Commerce, National Oceanic and Atmospheric 

Administration, National Marine Sanctuary Program, Silver Spring, MD. 35 pp. 

CONTACT

Steven S. Intelmann 

Habitat Mapping Specialist 

NOAA/National Marine Sanctuary Program

N/ORM 6X26 

115 E. Railroad Avenue, Suite 301 

Port Angeles, WA 98362 

(360) 457-6622 X22 

steve.intelmann@noaa.gov 
ABSTRACT 

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant 

resources into seafloor mapping activities along Washington’s outer coast (Intelmann and 

Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual 

mapping efforts offer a snapshot of current ground conditions, help to guide research and 

management activities, and provide a baseline for assessing the impacts of various threats 

to important habitat. During the months of August 2004 and May and July 2005, we used 

side scan sonar to image several regions of the sea floor in the northern OCNMS, and the

data were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, 

bathymetry data, sedimentary samples and side scan sonar mapping were integrated to 

describe geological and biological aspects of habitat. Polygon features were created and 

attributed with a hierarchical deep-water marine benthic classification scheme (Greene et

al. 1999). For three small areas that were mapped with both side scan sonar and 

multibeam echosounder, we made a comparison of output from the classified images 

indicating little difference in results between the two methods. With these 

considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (<30 meters) rocky waters of 

OCNMS. The image quality is sufficient for classification purposes, the associated 

depths provide further descriptive value and risks to gear are minimized. In shallow 

waters (<30 meters) which do not have a high incidence of dangerous rock pinnacles, a 

towed multi-beam side scan sonar could provide a better option for obtaining seafloor 

imagery due to the high rate of acquisition speed and high image quality, however the 

high probability of losing or damaging such a costly system when deployed as a towed 

configuration in the extremely rugose nearshore zones within OCNMS is a financially 

risky proposition. The development of newer technologies such as intereferometric 

multibeam systems and bathymetric side scan systems could also provide great potential 

for mapping these nearshore rocky areas as they allow for high speed data acquisition, 

produce precisely geo-referenced side scan imagery to bathymetry, and do not experience 

the angular depth dependency associated with multibeam echosounders allowing larger 

range scales to be used in shallower water. As such, further investigation of these 

systems is needed to assess their efficiency and utility in these environments compared to

traditional side scan sonar and multibeam bathymetry.

KEY WORDS 

Benthic, habitat mapping, sediment classification, side scan sonar, multibeam 

echosounder, textural analysis, Olympic Coast National Marine Sanctuary, essential fish 

habitat, groundtruthing 

i 
TABLE OF CONTENTS 

Topic Page

Abstract and Key Words......................................................................................... i 

Table of Contents.................................................................................................... ii 

List of Figures and Tables....................................................................................... iii 

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

Survey Area ............................................................................................................ 1 

Sonar Acquisition and Data Logging...................................................................... 3 

Sonar Data Processing and Image Classification.................................................... 4 

Groundtruthing........................................................................................................ 4 

Survey Results and Interpretation........................................................................... 6 

Discussion of Classification Based on Different Sonar Types............................... 10 

Acknowledgments................................................................................................... 16 

References............................................................................................................... 16 

Appendix 1. Isis Processing Parameters................................................................. 18 

Appendix 2. Side Scan Sonar Imagery ................................................................... 19 

Appendix 3. Habitat Classification Polygons......................................................... 25 

Appendix 4. Habitat Classification Tables ............................................................. 31 

Appendix 5. Groundtruthing images representative of associated habitat classes. 33 

ii 
LIST OF FIGURES AND TABLES

Figure/Table Number and Title Page

Figure 1. Sonar survey footprint and track lines for HMPR-114-2004-02 (green) and 

HMPR-116-2005-01 (orange) shown with selected isobaths. ................................ 2 

Figure 2. Survey platform R/V TATOOSH............................................................. 3 

Figure 3. EG&G Model 272 towfish. .................................................................... 3 

Figure 4. Towed camera sled for groundtruthing ................................................... 5 

Figure 5. Location of video transects (black circles) and usSeabed sediment samples 

(blue cross hair) shown with HMPR-114-2004-02 (green) and HMPR-116-2005-01 

(orange) survey footprints and selected isobaths.................................................... 5 

Table 1. Survey effort statistics for HMPR-114-2004-02 (green) and HMPR116-2005-01 ........................................................................................................... 6 

Figure 6. Example of hard complex rocky bottom providing habitat for basket 

star, white-plumed anemone, and rockfish ............................................................ 7 

Table 2. Distribution of bottom hardness for survey HMPR-114-2004-02 (green) and 

HMPR-116-2005-01 .............................................................................................. 7 

Figure 7. Digital terrain model showing bathymetry of survey block 

114_0402b .............................................................................................................. 8 

Figure 8. Bottom induration codes produced from textural classification of side scan 

sonar mosaics of survey blocks 114_0402b and 116_0501n. ................................ 9 

Figure 9. Footprint of survey block 114_0402b showing overlapping areas 

mapped with both types of sonar. ........................................................................... 10 

Table 3. Comparison of classification results of bottom hardness for the overlapping area within survey block 114_0402b mapped with both side scan sonar 

imagery and multibeam bathymetry.. ..................................................................... 11 

Figure 10. Footprint of survey block 116_0501d showing overlapping areas 

mapped with both types of sonar. ........................................................................... 11 

iii 
Table 4. Comparison of classification results of bottom hardness for the overlapping area within survey block 116_0501d mapped with both side scan sonar 

imagery and multibeam bathymetry.. ..................................................................... 12 

Table 5. Comparison of classification results of bottom hardness for the overlapping area within survey block 114_0402c mapped with both side scan sonar 

and multibeam bathymetry.. ................................................................................... 12 

Figure 11. Results of texture classification for survey block 114_0402c based 

on side scan sonar imagery and multibeam backscatter imagery. .......................... 13 

Figure 12. Multibeam backscatter imagery compared with side scan sonar imagery 

for the same area within survey block 114_0402c.................................................. 14 

iv 
INTRODUCTION

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant 

resources into seafloor mapping activities along Washington’s outer coast (Intelmann and 

Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual 

mapping efforts offer a snapshot of current ground conditions, help to guide research and 

management activities, and provide a baseline for assessing the impacts of various threats 

to important habitat. 

During the months of August 2004 and May/July 2005, we used side scan sonar to image

several regions of the sea floor in the northern OCNMS, and we mosaicked the data at 1-

meter pixel resolution. We integrated video from a towed camera sled, bathymetry data, 

sedimentary samples and side scan sonar mapping to describe geological and biological 

aspects of habitat. With a hierarchical deep-water marine benthic classification scheme, 

we created and attributed polygon features (Greene et al. 1999). This report provides a 

description of the mapping efforts and the results of the image classification procedure 

for each of the areas surveyed in 2004 and 2005. 

Additionally, portions of these side scan sonar surveys partially overlapped a region of 

the sanctuary previously mapped with multibeam bathymetry from a survey which 

utilized a combination of Reson 8101 and 8125 echosounders as described in Intelmann 

et al. 2006. In that survey, radiometric and geometric corrections were applied to the 

multibeam backscatter (Beaudoin et al. 2002), and the side scan, ri theta and snippet 

packets were all processed applying across-track signal normalization to minimize the

variations due to the angular response of the seafloor. 

When considering the operational logistics of data acquisition in open coast environments 

that experience significant swell and chop, one can successfully acquire multibeam 

bathymetry at vessel speeds near 8 knots, in comparison to the typical 3.0 to 3.5 knots as 

normally targeted for acquiring traditional single beam side scan sonar imagery, such as

with the model EG&G 272 or Klein 3000 which are both presently used for seabed 

mapping activities at OCNMS. Currently, with only an approximate 20 percent of the 

8,200 nm2

 of the sanctuary adequately characterized, this difference in acquisition 

efficiency becomes an important consideration for meeting the ultimate goal of 100 

percent sea floor characterization in a timely manner. Thus having a small sample of 

seafloor mapped with various methods provided an opportunity to assess classification 

results based on the two different types of acoustic imagery. With this, we hope to gain a 

better understanding of classification performance between the two types of imagery, 

helping to guide future mapping strategies at the OCNMS. 

SURVEY AREA 

OCNMS conducted approximately 21 km2

 and 34 km2 of seafloor mapping surveys

aboard the R/V TATOOSH during the field seasons of 2004 and 2005, respectively. All 

survey areas were in the general vicinity of Cape Flattery, with exception of one southern 

block, located approximately 12 km offshore of Point of the Arches (Figure 1). We

1 
acquired survey lines from August 5 through 18 in 2004 and on May 16 and 17 and July 

12 through 14 in 2005. Water depths ranged between 20 and 110 meters throughout the 

survey grounds. 

Figure 1. Sonar survey footprint and track lines for HMPR-114-2004-02 (green) and HMPR-116-

2005-01 (orange) shown with selected isobaths. 

2 
SONAR ACQUISITION AND DATA LOGGING

The NOAA research vessel 

TATOOSH, measuring 11.5 

meters in length, served as the

survey platform. We acquired 

ship positioning with a Trimble 

DSM 212L differential GPS 

(DGPS) and controlled line 

planning through Hypack Max 

software. We estimated 

towfish position through use of 

a digital cable counter, 

manufactured by Hydrographic 

Surveys, which logged line out. 

We used an EG&G Model 272 

analog side scan sonar to

acquire the acoustic imagery (Figure 3). The sonar system has a horizontal beam width 

of 1.2 o at 100 kHz with a vertical beam width measuring 50 o. We maintained vessel 

speed at between 3 and 3.5 knots throughout operations. We logged sonar imagery as 16 

bit data with 1,024 samples per channel using Triton Imaging, Inc. (TII) Isis Sonar and 

recorded as eXtended Triton Format (XTF). 

Figure 2. Survey platform R/V TATOOSH. 

We used an analog control interface (ACI) 

kit to convert the analog sonar signal to 

digital format plus provide individualchannel analog gain control of the towfish 

signal. 

The 2004 survey was designed around a 

150-meter line spacing plan, but in 2005 

was increased to 175-meter spacing to 

reduce overlap and allow more ground to be 

covered over a given span of time. In both 

field seasons a 100-meter range scale was 

set on the sonar. 

Figure 3. EG&G Model 272 towfish. Note 

magnetic cable counter attached to upper block 

housing.

3 
SONAR DATA PROCESSING AND IMAGE CLASSIFICATION

The algorithm used to calculate towfish layback (horizontal distance behind the tow 

point) requires the input of an estimate of towfish depth (distance below water surface), 

towfish altitude (height above the sea floor) and the amount of cable out at any given 

time. Since this particular towfish was not equipped with a depth sensor, we did not 

precisely know the distance below the surface. As such, we had to estimate this value in

some other way. To address this minor issue, we recorded water depth under keel as 

towfish depth in the XTF. After insuring proper bottom tracking, we used the Isis ASCII 

Report Utility to export a time stamp, depth (water depth) and towfish altitude from the

XTF into a separate text file for each line of data. In an external spreadsheet, we simply 

subtracted towfish altitude from water depth to provide an estimate of continuous towfish 

depth. Although this method will not provide an absolutely accurate measurement for 

towfish depth, especially in areas of higher relief, the value will be relatively close

because we designed the line planning to parallel the bathymetric contours to minimize 

differences in along track relief. Using the NavInXTF Utility, we imported the estimated 

towfish depth values back into the XTF files, thus replacing the previously logged water 

depth values. With final entry of the DGPS antennae offsets, we used a normal catenary 

layback calculation to provide an estimate of towfish position in the mosaics. 

The navigation data was smoothed in Isis Sonar using a combination of a Kalman filter 

and a 7-point moving average filter. We accomplished slant range correction and bottom 

tracking in Isis Sonar, in addition to the application of time-varied gain and beam angle

compensation curves. 

We imported individual line mosaics into TII’s DelphMap, merged them into separate

mosaics for each survey block and then exported them as geotiff images. Image 

homogeneity and entropy were calculated for each mosaic using custom designed 

software (Cochrane and Lafferty 2002). Mosaics from the side scan packets, entropy and 

homogeneity images were all layer stacked in Erdas Imagine to create multi-spectral

images. A supervised classification was performed using a maximum likelihood 

decision rule to produce a final classified image (Intelmann et al. (2006). Adobe 

Photoshop was then used to edit misclassified data such as that occurring nadir or in other 

various areas such as misclassified side lobes. Raster images were then smoothed with a 

low pass filter and converted to Features in ArcGIS. 

GROUNDTRUTHING

In August 2005, we used a custom designed camera sled (Figure 4) to acquire underwater 

videography for validating the sonar imagery (Intelmann et. al 2006). Although not 

available in every survey block, the usSeabed project (Reid et al. 2001) provided 34 

samples as further weight of evidence for the video and sonar interpretation. Video 

transects and usSeabed sample locations are shown in Figure 5. 

4 
Figure 4. Towed camera sled used for groundtruthing efforts. 

Figure 5. Location of video transects (black circles) and usSeabed 

sediment samples (blue cross-hair) shown with HMPR-114-2004-02 

(green) and HMPR-116-2005-01 survey footprints and selected

isobaths.

5 
SURVEY RESULTS AND INTERPRETATION

We acquired over 156 linear km of survey lines aboard the R/V TATOOSH in 2004 

(Table 1), although we lost several potential days of survey time due to poor weather 

and/or various equipment challenges. We collected nearly 165 km of sonar survey lines 

in 2005, even though during the month of August, we spent the majority of the limited 

time available for habitat mapping related work aboard this same vessel conducting 

groundtruthing video surveys. 

Table 1. Below are the survey effort statistics for HMPR-114-2004-02 and HMPR-116-2005-01. We

acquired data aboard the R/V TATOOSH using an EG&G Model 272 side scan sonar. We surveyed two

areas in 2004 and four areas in 2005. Area is presented in square kilometres, length of linear track lines in

kilometers, and hours of actual logged sonar packets in hours, minutes, and seconds. 

Year Block Date Area (km2) Tracks (km) Hours (h:m:s) 

2004 114_0402b August 5-18 19.72 140.9 21:47:26

114_0402c August 18 1.28 15.3 1:13:37

Total 21.00 156.2 23:01:03

2005 116_0501c May 16-17 3.24 17.2 3:08:25

116_0501d May 17 2.70 19.3 3:08:52

116_0501n July 12-14 20.18 87.0 14:12:50

116_0501s July 14 7.50 41.1 6:33:15

Total 33.62 164.6 27:03:22

We defined megahabitat categorization for all of the survey blocks as continental shelf 

(Greene et al. 1999). Survey block 116_0501s consisted entirely of soft (s), silty 

substrates (Table 2). Textural classification of the imagery suggested that mixed 

sediment (m) including cobbles, pebbles, gravel and boulders (mixed with soft substrate)

characterized 80 percent of blocks 114_0402c and 116_0501c (both located offshore of

Chibahdehl Rocks in the Strait of Juan de Fuca), while the remaining 20 percent of each 

of these two areas consisted of hard (h) complex rocky bottom (see Appendix for 

imagery). We classified block 116_0501d, which surrounded Duncan and Duntze Rocks 

and followed the western edge of Tatoosh Island, as 90 percent mixed substrate (see 

Appendix for imagery). Video imagery further revealed the surface to be mostly a 

combination of gravel, pebble, cobble and shell hash. The submerged basalt rock flanks 

of both Duncan and Duntze Rocks (Snavely et al. 1993) represent the remaining 10 

percent of the habitat in this particular region. 

Of the six areas surveyed, block 114_0402b contained the highest diversity of substrates. 

We classified six distinct outcrops, covering 18 percent of block 114_0402b, as hard 

complex rocky bottom. These hard areas are easily distinguishable in the multibeam 

bathymetry data as well as the side scan sonar imagery. Video observations confirmed 

these areas as being highly utilized by various species of rockfish and numerous other 

organisms (Figure 6). The imagery further reveals heavily tilted, and differentially 

eroded bedrock strands (Figure 7) resultant of anticlinal folding and thrust faulting

occurring in the area (McCrory et al. 2004). Scattered areas of mixed substrate 

interspersed among bedrock strands define more than 37 percent of seafloor in this area. 

6 
In general, soft substrates occur in the southern portion of the survey block, and continue 

to the west throughout the majority of block 116_0501n (Figure 8). We easily delineated 

several areas of sediment waves, indicating active sediment movement occurring in 

specific areas. 

Table 2. Distribution of bottom hardness for each sonar mosaic classified from survey HMPR-114-2004-

02 and HMPR-116-2005-01. See Figure 1 for area locations. Bottom hardness codes are hard (h), mixed 

(m) and soft (s) – see previous section for description of classes. Area is presented in square meters (top 

value) and area as percentage of each individual mapped area (bottom bold value in the matrix). 

Year Survey Block h m s

2004 114_0402b 3,553,093.3

18.0 

7,371,749.0 

37.3 

8,817,661.4 

44.7 

114_0402c 266,065.6

21.0 

1,001,958.9 

79.0 

0.0 

0.0 

2005 116_0501c 738,181.5

22.8 

2,503,968.7 

77.2 

0.0 

0.0 

116_0501d 280,836.0

10.4 

2,420,793.9 

89.6 

0.0 

0.0 

116_0501n 10,240.0

0.0 

341,667.0 

1.7 

19,842,000.0 

98.3 

116_0501s 0.0

0.0 

0.0 

0.0 

7,585,526.0 

100.0 

Figure 6. Example of hard, complex rocky bottom, providing a 

habitat for basket star, white-plumed anemone and rockfish. 

7 
Figure 7. Digital terrain model showing multibeam bathymetry of survey block 114_0402b. Six

distinct areas of high rugosity are easily distinguishable in the sun-illuminated bathymetry data. Note, 

however, that differences between soft and mixed substrates are not recognizable in this data. As such,

side scan sonar imagery becomes the preferred data set for remotely delineating differences in these 

substrate classes.

8 
Figure 8. Bottom induration codes produced from textural classification of side scan sonar

mosaics of survey blocks 114_0402b (green outline) and 116_0501n (orange outline). Note the 

ability to distinguish between mixed and soft substrates which was not possible through

examination of the multibeam bathymetry data previously shown in Figure 7. h= hard substrate, 

m= mixed, and s= soft substrate. 

The Appendices presents all side scan sonar mosaics, other attributed polygon layers 

showing bottom hardness (as in Figure 8) and matrix tables describing habitat 

classification for each of the six blocks surveyed in 2004 and 2005. 

9 
DISCUSSION OF CLASSIFICATION BASED ON DIFFERENT SONAR TYPES 

For all intents and purposes, side scan sonar and multibeam backscatter are essentially the 

same and are often spoken of interchangeably. Multibeam backscatter offers an 

advantage over traditional single beam side scan imagery in that the imagery is precisely 

geo-referenced, the systems are usually better calibrated and the data can be successfully 

acquired at much higher speeds when surveying in rough water. Multibeam 

echosounders, however, produce data based on much higher aspect ratios, and as such 

generally yield poorer resolution imagery than is possible through traditional single beam

side scan sonar methods. Therefore, important image textural properties (including 

shadows) are often lost with hull-mounted multibeam echosounder systems, making for

increased challenges during the classification procedure. This is especially noteworthy

because textural homogeneity and entropy are two key components used by OCNMS in 

the classification process (Cochrane and Lafferty 2002; Intelmann and Cochrane 2006). 

Of the 19.74 km2

 of seafloor characterized in survey block 114_0402b, 4.5 km2 were also 

previously imaged with multibeam echosounder (Figure 9). In comparing results of 

textural classification for this overlapping area, which occurred in depths to 50 meters, 

overall results were nearly identical (Table 3). Only small areas of mixed sediment 

within the rock outcrops were lost in the backscatter method of classification but general 

features were still adequately delineated. 

Multibeam Backscatter Side Scan Sonar

Figure 9. This figure is a footprint of survey block 114_0402b (black outline) showing

overlapping areas mapped with both types of sonar (shaded polygons). Results of texture

classification are based on side scan sonar (right) and multibeam backscatter (left). Note the 

overall similar results with only small areas of mixed sediment recognizable in the side scan

imagery being lost in the backscatter classification. Tan=soft (s), green = mixed (m), and red =

hard (h). 

10 
Table 3. This table is a comparison of classification results of bottom hardness for the overlapping area 

within survey block 114_0402b mapped with both side scan sonar and multibeam echosounder. Bottom

hardness codes are hard (h) and mixed (m), and soft (s). Area is presented in square meters (top value) and 

area as percentage of each individual mapped area (bottom bold value in the matrix). 

Substrate Class Side Scan Sonar Multibeam Backscatter

h 

257,717.99

16.23

269,652.06 

16.99 

m 

1,330,012.99

83.77

1317856.23 

83.01 

m 

1,330,012.99

83.77

1317856.23 

83.01 

As with the area of 114_0402b, the classification results for two methods of data 

acquisition that overlapped in survey block 116_0501d compared well (Figure 10). Of 

the 2.7 km2

 of seafloor characterized by side scan sonar in survey block 116_0501d, 1.58 

km2 were also previously imaged with multibeam echosounder (Table 4). Results of this 

small dataset are comparable to 100-meters depth in this region. 

Side Scan Sonar Multibeam Backscatter

Figure 10. Footprint of survey block 116_0501d (black outline) showing overlapping areas mapped

with both types of sonar (shaded polygons). Results of texture classification are based on side scan

sonar imagery (left) and multibeam backscatter (right). Note the overall similar results with only

one small area of hard bottom recognizable in the side scan imagery being lost in the backscatter 

classification. green = mixed (m), and red = hard (h). 

11 
Table 4. This table is a comparison of classification results of bottom hardness for the overlapping area 

within survey block 116_0501d mapped with both side scan sonar and multibeam echosounder. Bottom

hardness codes are hard (h) and mixed (m). Area is presented in square meters (top value) and area as

percentage of each individual mapped area (bottom bold value in the matrix).

Substrate Class Side Scan Sonar Multibeam Backscatter

h 

257,717.99

16.23

269,652.06 

16.99 

m 

1,330,012.99

86.77

1,317,856.23 

83.01 

More noticeable differences became apparent when examining the classification results

between the two methods within survey block 114_0402c (Table 5). Of the 1.26 km2

 of 

seafloor characterized by side scan sonar in survey block 114_0402c, 100 percent of this 

same area was previously surveyed with multibeam echosounder. Although the general 

shape of the major rock feature in this area remained similar (Figure 11), when compared

to classification results based on backscatter from multibeam echosounder data, side scan 

sonar classification produced an increase in hard bottom substrate of nearly 7 percent. 

Table 5. This table is a comparison of classification results of bottom hardness for the overlapping area 

within survey block 114_0402c mapped with both side scan sonar and multibeam bathymetry. Bottom

hardness codes are hard (h) and mixed (m). Area is presented in square meters (top value) and area as

percentage of each individual mapped area (bottom bold value in the matrix).

Substrate Class Side Scan Sonar Multibeam Backscatter

h 

266,065.56

20.98

179,146.10 

13.99 

m 

1,001,58.88

79.02

1,101,063.00 

86.01 

Beyond the 30-meter isobath, the textural properties of the mutlibeam backscatter 

imagery were far inferior to the imagery produced by the side scan sonar (Figure 12). A 

combination of the seafloor slope, a thin superficial layer of fine sediment on the rock

surface as evident from video imagery and the high aspect ratio associated with the 

multibeam bathymetry (in comparison to towed side scan sonar which placed the sonar 

closer to the seafloor), are all likely causes for this reduction of image textural

enhancement. Although the image classification performance of the two different sonar 

methods were comparable in various regions of survey blocks 114_0402b and 

116_0501d, the loss of image resolution in the multibeam backscatter data of block

114_0402c is the main drawback to using this type of data to create habitat maps in 

OCNMS. 

12 
Side Scan Sonar

Multibeam Backscatter 

Figure 11. Results of texture classification for survey block 114_0402c based on side scan

sonar imagery (top) and multibeam backscatter (bottom). Note the slight increase in area of

the predominant rock feature produced through the classification of side scan sonar imagery 

as compared to multibeam backscatter. green = mixed (m), and red = hard (h).

13 
Multibeam Backscatter Side Scan Sonar 

Figure 12. Multibeam backscatter imagery (left) compared with side scan sonar imagery (right) for 

the same area within survey block 114_0402c. The enhanced textural properties associated with the 

side scan sonar imagery are easily identifiable. The images are geospatially linked with the red 

cross hair which represents the same geographic position in each image. 

Unlike side scan sonar, when using multibeam echosounder systems swath width will

decrease with decreasing water depths (Kashomita et al. 2005). This reduced area of 

coverage, however, can be offset by the increased speed of acquisition when comparing

to use of a traditional single beam side scan sonar. Moreover, the ubiquitous unexposed 

rock pinnacles and outcrops occurring within the 30-meter isobath in OCNMS create 

dangers to towed side scan sonar gear that are not realized with multibeam echosounder 

systems. In depths shallower than 30-meters, the high aspect ratio associated with 

multibeam bathymetry systems appears to not degrade results of the texture classification 

procedure being used at OCNMS. But, the degrading effects of this high aspect ratio 

associated with multibeam echosounders would become even more pronounced with 

increasing water depths since the distance from the sonar to the seafloor would be greatly 

increased in a hull-mounted technique as compared to a towed side scan sonar scenario. 

Due to the swath width/depth dependency associated with multibeam bathymetry

systems, it makes even more sense to use multibeam backscatter for surveying in deeper

water, only to return with more labor intensive deep-towed side scan sonar in areas where 

the poorer resolution hull-mounted multibeam bathymetry systems suggest features of 

interest exist. In deep water (> 200 meters), traditional single beam side scan sonar 

imagery would be best considered as a complement to multibeam bathymetry (and 

backscatter) to further interrogate areas of extreme interest that require increased 

resolution. 

It is important to note that more recent technology has led to the production of multibeam side scan sonar (such as the Klein 5000 series) which function through use of 

electronic phase delay to accomplish beam steering and allows for successful data 

14 
acquisition to speeds approaching 10 knots. NOAA’s Hydrographic Survey Division has

even successfully hull-mounted these newer generation sonar models on survey launches

and presently has several of these specific configurations in operation throughout the 

fleet. Use of this newer generation multi-beam side scan sonar could provide the best of 

both worlds in shallow water due to the high resolution and existing potential for high 

speed acquisition. But there are also several drawbacks to using multi-beam side scan 

sonar that warrant consideration, namely cost (a Klein 5000, for example, is nearly four 

times as costly as a Klein 3000) and size. Unlike deployment of a traditional single beam 

side scan sonar, the multi-beam side scan sonar systems are much larger in size and 

generally require multiple individuals to handle which make them far more unwieldy to 

deploy and retrieve in a towable configuration off a small vessel. 

As previously mentioned, these newer generation systems can be hull-mounted but they 

then lose utility in water depths much greater than 30 meters since they are only currently 

available to the commercial market as 455 kHz systems, and as such suffer from signal 

attenuation when used in deeper waters as a hull-mount. Furthermore, unlike towed side 

scan sonar a hull-mounted side scan sonar would also be subject to greater geometric 

distortions created by excessive vessel movement which would otherwise be 

compensated through attitude corrections in multibeam bathymetry. Since the open 

coastal environment within OCNMS is often plagued with annoying wind chop and 

confused seas, it is almost certain that vessel movement would propagate into the 

imagery when used in a hull-mounted configuration in this area. As a towed setup much 

of this distortion would be removed since the tow cable would absorb much of the vessel 

pitch and roll. 

With these considerations, backscatter derived from multibeam bathymetry is currently a

cost-efficient and safe method for seabed imaging in the shallow (<30 meters) rocky 

waters of OCNMS. The image quality is sufficient for classification purposes, the 

associated depths provide further descriptive value and risks to gear are minimized. In 

shallow waters (<30 meters) which do not have a high incidence of dangerous rock 

pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining

seafloor imagery due to the high rate of acquisition speed and high image quality. A 

hull-mounted multi-beam side scan sonar would likely suffer from image degradation due 

to vessel movement in this environment and is not an option in deeper water as the range 

scale is limited to 150 meters. Additionally, the high probability of losing or damaging 

such a costly system when deployed as a towed configuration in the extremely rugose 

nearshore zones within OCNMS is a financially risky proposition. 

The development of newer technologies such as intereferometric multibeam systems and 

bathymetric side scan systems could also provide great potential for mapping these 

nearshore rocky areas as they allow for high speed data acquisition, produce precisely

geo-referenced side scan imagery to bathymetry, and do not experience the angular depth 

dependency associated with multibeam echosounders allowing larger range scales to be 

used in shallower water. As such, further investigation of these systems is needed to

assess their efficiency and utility in these environments compared to traditional side scan

sonar and multibeam bathymetry. 

15 
ACKNOWLEDGMENTS

The authors wish to thank Dave Kirner, Mike Levine, and Andy Palmer for assisting with 

survey mobilization, deployment and retrieval of the towfish and camera sled during 

survey operations, and for operating the R/V TATOOSH. 

REFERENCES

Beaudoin, J., Hughes Clarke, J.E., Van den Ameele, E. and Gardner, J., 2002, Geometric 

and radiometric correction of multibeam backscatter derived from Reson 8101 

systems: Canadian Hydrographic Conference 2002 Proceedings (CDROM), 

Toronto, Canada. 

Cochrane, G.R., and K.D. Lafferty. 2002. Use of acoustic classification of sidescan sonar 

data for mapping benthic habitat in the Northern Channel Islands, California. 

Continental Shelf Research 22: 683-690. 

Greene, H.G., M.M. Yoklavich, R.M. Starr, V.M. O’Connell, W.W. Wakefield, D.E. 

Sullivan, J.E. McRea, Jr., G.M. Cailliet. 1999. A classification scheme for deep 

seafloor habitats. Oceanologica Acta. 22(6):663 

Intelmann, S.S. and G.R. Cochrane. 2005. Benthic Habitat Mapping in the Olympic 

Coast National Marine Sanctuary: Classification of side scan sonar data from survey 

HMPR-108-2002-01: Version I. Marine Sanctuaries Conservation Series MSD-05-

07. U.S. Department of Commerce, National Oceanic and Atmospheric 

Administration, Marine Sanctuaries Division, Silver Spring, MD. 13pp. 

Intelmann, S.S., J. Beaudoin, and G.R. Cochrane. 2006. Normalization and 

characterization of multibeam backscatter: Koitlah Point to Point of the Arches, 

Olympic Coast National Marine Sanctuary - Survey HMPR-115-2004-03. Marine 

Sanctuaries Conservation Series MSD-06-03. U.S. Department of Commerce, 

National Oceanic and Atmospheric Administration, Marine Sanctuaries Division, 

Silver Spring, MD. 22pp. 

Intelmann, S.S. 2006. Comments on Hydrographic and Topographic LIDAR Acquisition 

and Merging with Multibeam Sounding Data Acquired in the Olympic Coast National 

Marine Sanctuary. Marine Sanctuaries Conservation Series MSD-06-05. U.S. 

Department of Commerce, National Oceanic and Atmospheric Administration, 

Marine Sanctuaries Division, Silver Spring, MD. 17pp. 

Kamoshita, T., Y. Sato, and T. Komatsu. 2005. Hydro-Acoustic Survey Scheme for SeaBottom Ecology Mapping. Seatechnology 46(6): 39-43. 

McCrory, P.A., S.C. Wolf, S.S. Intelmann, W.W. Danforth, R.J. Weldon, J.L. Blair. 

2004. Quaternary tectonism in a collision zone, Northwest Washington. Eos Trans. 

AGU, 85(47), Fall Meet. Suppl., Abstract T33C-1391. 

16 
Reid, J. A., Jenkins, C., Field, M. E., Gardner, J. V. and Box, C. E. 2001. USSEABED: 

defining the surface geology of the continental shelf through data integration and 

fuzzy set theory. Geological Society of America Annual Meeting, Boston, MA. 

Abstracts with Programs 33:A106. 

Snavely, P.D., Jr., N.S. MacLeod, and A.R. Niem. 1993. Geologic Map of the Cape 

Flattery, Clallam Bay, Ozette Lake, and Lake Pleasant Quadrangles, Northwestern 

Olympic Peninsula, Washington. Map I-1946. U.S. Geological Survey. 

17 
APPENDIX

Appendix 1. Isis Processing Parameters 

HMPR-114-2004-02 

Lateral Offset: 0.0m

Layback Offset: 6.7m

Heading= use CMG 

Mosaic resolution: 0.3m (later reduced to 1m) 

Apply BAC 

TVG: start at first return

 Curve = -4 +0.75 + (-2) 

HMPR-116-2005-01

***area116_0501c 

Lateral Offset: 0.0m

Layback Offset: 6.7m

Heading= use CMG 

Mosaic resolution: 0.3m (later reduced to 1m) 

Apply BAC 

TVG: start at first return

 Curve = -7 + 0.09 + (-1) 

***area116_0501d 

Lateral Offset: 0.0m

Layback Offset: 6.7m

Heading= use CMG 

Mosaic resolution: 0.3m (later reduced to 1m) 

Apply BAC 

TVG: start at first return

 Curve = -5 + 0.08 + (0) 

***area116_0501n and area116_0501s 

Lateral Offset: 0.0m

Layback Offset: 6.7m

Heading= use CMG 

Mosaic resolution: 0.5m (later reduced to 1m) 

Apply BAC 

TVG: start at first return

 Curve = -5 + 0.09 + (1) 

18 
Appendix 2. Side Scan Sonar Imagery 

Appendix 2a. Side scan sonar mosaic of survey block 114_0402b. 

19 
Appendix 2b. Side scan sonar mosaic of survey block 114_0402c. 

20 
Appendix 2c. Side scan sonar mosaic of survey block 116_0501c. 

21 
Appendix 2d. Side scan sonar mosaic of survey block 116_0501d. 

22 
Appendix 2e. Side scan sonar mosaic of survey block 116_0501n. 

23 
Appendix 2f. Side scan sonar mosaic of survey block 116_0501s. 

24 
Appendix 3. Habitat Classification Polygons 

Appendix 3a. Habitat classification polygons of survey block 114_0402b. Refer to table in 

Appendix 4a for description of habitat codes.

25 
Appendix 3b. Habitat classification polygons of survey block 114_0402c. Refer to table in 

Appendix 4b for description of habitat codes.

26 
Appendix 3c. Habitat classification polygons of survey block 116_0501c. Refer to table in 

Appendix 4c for description of habitat codes.

27 
Appendix 3d. Habitat classification polygons of survey block 116_0501d. Refer to table in 

Appendix 4d for description of habitat codes.

28 
Appendix 3e. Habitat classification polygons of survey block 116_0501n. Refer to table in 

Appendix 4e for description of habitat codes.

29 
Appendix 3f. Habitat classification polygons of survey block 116_0501s. Refer to table in

Appendix 4e for description of habitat codes.

30 
Appendix 4. Habitat Classification Tables 

Appendix 4a. Distribution of habitat classified from survey block 114_0402b side scan sonar survey data. 

Habitat codes are provided per Greene et al. (1999) and are presented by area in square meters, and area as

a percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss _u Shelf soft unconsolidated 8,701,399 44.07 

Sm Shelf mixed 6,857,287 34.73

Shd_d Shelf hard deformed, 

differentially eroded 

1,557,155 7.89

She Shelf hard exposed 1,495,263 7.57 

Sh Shelf hard 408,980 2.07

Smw_r Shelf mixed waves ripples 286,531 1.45 

Sm _h Shelf mixed hummocky 227,932 1.15 

Ss Shelf soft 116,263 0.59

Sh _d Shelf hard differentially 

eroded 

91,695 0.46

Appendix 4b. Distribution of habitat classified from survey block 114_0402c side scan sonar survey data.

Habitat codes are provided per Greene et al. (1999) and are presented by area in square meters, and area as

a percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 1,001,959 79.02

She Shelf hard exposed 252,934 19.95 

Sh Shelf hard 13,132 1.03

31 
Appendix 4c. Distribution of habitat classified from survey block 116_0501c side scan sonar survey data. 

Habitat codes are provided per Greene et al. (1999) and are presented by area in square meters, and area as

a percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 2,503,939 77.23

She Shelf hard exposed 738,182 22.77 

Appendix 4d. Distribution of habitat classified from survey block 116_0501d side scan sonar survey data. 

Habitat codes are provided per Greene et al. (1999) and are presented by area in square meters, and area as

a percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss _u Shelf soft unconsolidated 19,829,820 98.20 

Sm Shelf mixed 341,667 1.69

Ss Shelf soft 12,181 0.06

Sh Shelf hard 10,240 0.05 

Appendix 4e. Distribution of habitat classified from survey block 116_0501s side scan sonar survey data.

Habitat codes are provided per Greene et al. (1999) and are presented by area in square meters, and area as

a percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss _u Shelf soft unconsolidated 7,585,526 100 

32 
Appendix 5. Groundtruthing images representative of associated habitat classes.

Soft (s) 

Mixed (m) 

Hard (h)

33 
ONMS CONSERVATION SERIES PUBLICATIONS 

To date, the following reports have been published in the Marine Sanctuaries Conservation Series. All

publications are available on the National Marine Sanctuary Program website

(http://www.sanctuaries.noaa.gov/). 

A Pilot Study of Hogfish (Lachnolaimus maximus Walbaum 1792) Movement in the Conch Reef Research

Only Area (Northern Florida Keys) (NMSP-06-06)

Comments on Hydrographic and Topographic LIDAR Acquisition and Merging with Multibeam Sounding

Data Acquired in the Olympic Coast National Marine Sanctuary (ONMS-06-05)

Conservation Science in NOAA's National Marine Sanctuaries: Description and Recent Accomplishments 

(ONMS-06-04)

Normalization and characterization of multibeam backscatter: Koitlah Point to Point of the Arches, 

Olympic Coast National Marine Sanctuary - Survey HMPR-115-2004-03 (ONMS-06-03)

Developing Alternatives for Optimal Representation of Seafloor Habitats and Associated Communities in

Stellwagen Bank National Marine Sanctuary (ONMS-06-02) 

Benthic Habitat Mapping in the Olympic Coast National Marine Sanctuary (ONMS-06-01) 

Channel Islands Deep Water Monitoring Plan Development Workshop Report (ONMS-05-05) 

Movement of yellowtail snapper (Ocyurus chrysurus Block 1790) and black grouper (Mycteroperca 

bonaci Poey 1860) in the northern Florida Keys National Marine Sanctuary as determined by acoustic

telemetry (MSD-05-4) 

The Impacts of Coastal Protection Structures in California's Monterey Bay National Marine Sanctuary

(MSD-05-3) 

An annotated bibliography of diet studies of fish of the southeast United States and Gray's Reef 

National Marine Sanctuary (MSD-05-2) 

Noise Levels and Sources in the Stellwagen Bank National Marine Sanctuary and the St. Lawrence 

River Estuary (MSD-05-1) 

Biogeographic Analysis of the Tortugas Ecological Reserve (MSD-04-1) 

A Review of the Ecological Effectiveness of Subtidal Marine Reserves in Central California (MSD-04-

2, MSD-04-3) 

Pre-Construction Coral Survey of the M/V Wellwood Grounding Site (MSD-03-1) 

Olympic Coast National Marine Sanctuary: Proceedings of the 1998 Research Workshop, Seattle, 

Washington (MSD-01-04) 

Workshop on Marine Mammal Research & Monitoring in the National Marine Sanctuaries (MSD-01-

03) 

A Review of Marine Zones in the Monterey Bay National Marine Sanctuary (MSD-01-2) 

Distribution and Sighting Frequency of Reef Fishes in the Florida Keys National Marine Sanctuary

(MSD-01-1) 

Flower Garden Banks National Marine Sanctuary: A Rapid Assessment of Coral, Fish, and Algae 

Using the AGRRA Protocol (MSD-00-3) 

34 
The Economic Contribution of Whalewatching to Regional Economies: Perspectives From Two 

National Marine Sanctuaries (MSD-00-2) 

Olympic Coast National Marine Sanctuary Area to be Avoided Education and Monitoring Program

(MSD-00-1) 

Multi-species and Multi-interest Management: an Ecosystem Approach to Market Squid (Loligo

opalescens) Harvest in California (MSD-99-1)

35