Marine Sanctuaries Conservation Series ONMS-07-01

U.S. Department of Commerce 

National Oceanic and Atmospheric Administration

National Ocean Service 

Office of Ocean and Coastal Resource Management 

Survey report of NOAA Ship McArthur II cruises 

AR-04-04, AR-05-05 and AR-06-03: 

Habitat classification of side scan sonar imagery 

in support of deep-sea coral/sponge explorations 

at the Olympic Coast National Marine Sanctuary

National Marine Sanctuary Program May 2007 
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. 
Survey report of NOAA Ship McArthur II cruises AR-04-04, 

AR-05-05 and AR-06-03: Habitat classification of side scan 

sonar imagery in support of deep-sea coral/sponge explorations 

at the Olympic Coast National Marine Sanctuary 

Steven S. Intelmann1

, Guy R. Cochrane2, C. Edward Bowlby1, 

Mary Sue Brancato1

, and Jeffrey Hyland3

1

Olympic Coast National Marine Sanctuary, NOAA 

2

Coastal and Marine Geology Program, USGS 

3

National Centers for Coastal Ocean Science, NOAA 

Silver Spring, Maryland

May 2007

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

Image of the Klein System 3000 side scan sonar used to image the seabed during the 

three separate mapping cruises, shown here with a KwingII depressor. 

. 

SUGGESTED CITATION

Intelmann, S.S., G.R. Cochrane, C. Edward Bowlby, M.S. Brancato, and J. Hyland. 2007. 

Survey report of NOAA Ship McArthurII cruises AR-04-04, AR-05-05 and AR-06-03: 

Habitat classification of side scan sonar imagery in support of deep-sea coral/sponge 

explorations at the Olympic Coast National Marine Sanctuary. Marine Sanctuaries 

Conservation Series MSD-07-01. U.S. Department of Commerce, National Oceanic and 

Atmospheric Administration, National Marine Sanctuary Program, Silver Spring, MD. 50 

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 

Habitat mapping and characterization has been defined as a high-priority management 

issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly 

known deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, 

a team of scientists from OCNMS, National Centers for Coastal Ocean Science 

(NCCOS), and other partnering institutions initiated a series of surveys to assess the

distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for 

evidence of potential anthropogenic impacts in these critical habitats. Initial results 

indicated that remotely delineating areas of hard bottom substrate through acoustic 

sensing could be a useful tool to increase the efficiency and success of subsequent ROVbased surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys 

were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship 

McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping 

coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral/sponge 

habitat, in areas of both high and low commercial-fishing activities, to serve as sites for 

surveying-in more detail using an ROV on subsequent cruises. Several regions of the sea 

floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. 

Imagery from the side scan sonar mapping efforts was integrated with other 

complementary data from a towed camera sled, ROVs, sedimentary samples, and 

bathymetry records to describe geological and biological (where possible) aspects of 

habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et 

al. 1999), we created a preliminary map of various habitat polygon features for use in a 

geographical information system (GIS). This report provides a description of the 

mapping and groundtruthing efforts as well as results of the image classification 

procedure for each of the areas surveyed. 

KEY WORDS 

Benthic, habitat mapping, sediment classification, side scan sonar, textural analysis, 

deep-sea coral, essential fish habitat, Olympic Coast National Marine Sanctuary 

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 ............................................................................................................ 2 

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

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

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

Survey Results and Interpretation........................................................................... 7 

Summary................................................................................................................. 16 

Acknowledgments................................................................................................... 17 

References............................................................................................................... 17 

Appendix 1. Isis Processing Parameters................................................................. 20 

Appendix 2. Side Scan Sonar Imagery ................................................................... 21 

Appendix 3. Habitat Attribute Classification Polygons.......................................... 33 

Appendix 4. Habitat Attribute Classification Tables.............................................. 45 

ii 
LIST OF FIGURES AND TABLES

Figure/Table Number and Title Page

Figure 1. Sonar survey footprints for HMPR-113-2004-01, HMPR-118-2005-03, 

and HMPR-119-2006-01.. ...................................................................................... 2 

Figure 2. Magnetic cable counter shown mounted to the level wind block. ......... 3 

Figure 3. Klein System 3000 side scan sonar shown configured with the shallowwater KwingI depressor and with the heavier KwingII depressor ......................... 3 

Figure 4. Locations of groundtruthing effort in relation to individual survey 

mosaics.................................................................................................................... 5 

Figure 5. Groundtruthing platforms........................................................................ 6 

Table 1. Survey effort statistics for HMPR-113-2004-01 (AR04-04), HMPR-118- 

2005-03 (AR-05-05) and HMPR-116-2005-01 (AR-06-03). ................................. 7 

Figure 6. Example of habitat classification results for a selected region of the side 

scan sonar survey area 113_0401d acquired during the NOAA Ship McArthurII 

cruise AR-04-04. .................................................................................................... 8 

Table 2. Distribution of bottom hardness for each sonar mosaic classified from 

survey HMPR-113-2004-01. ................................................................................. 9 

Figure 7. Habitat classification of mosaic 113_0401p based on slope criteria. 

Slope classes are modified from Greene et al. (1999). ........................................... 10 

Figure 8. Shaded relief model featuring the Quileute “rock pile” offshore from 

LaPush, WA. .......................................................................................................... 11 

Table 3. Distribution of bottom hardness for each sonar mosaic classified from 

survey HMPR-118-2005-03. .................................................................................. 12 

Figure 9. Example of an uncertain feature requiring further video groundtruthing 

for better confirmation.. .......................................................................................... 13 

Figure 10. Area118_0503b footprint shown with sonar track lines and results of 

sediment grabs. ....................................................................................................... 13 

iii 
Figure 11. Selected clip of mosaicked video showing a hard-bottom boulder patch 

with visible Gorgonian, crinoids, sponges, and Lophelia pertusa.......................... 14 

Table 4. Distribution of bottom hardness for each sonar mosaic classified from 

survey HMPR-119-2006-01... ................................................................................ 15 

Figure 12. Example of habitat classified attributed polygon data draped over shaded 

relief bathymetry data in area 119_0601a............................................................... 16 

iv 
INTRODUCTION

The offshore shelf and canyon habitats of the Olympic Coast National Marine Sanctuary 

(OCNMS) are areas of high primary productivity and biodiversity important to 

groundfish fisheries. Additionally, documentation of bioherms discovered off the nearby 

western Canadian continental shelf (Conway et al. 1991; Conway 1999; Conway et al. 

2005; Jamieson et al. 2005) provided evidence that such fauna also likely existed in the 

waters off the Washington coast. These habitats are of tremendous value for their 

inherent biodiversity and as sites of recruitment for commercially important fishes. 

However slow growth rates, ease of disturbance, and long life spans make these 

communities extremely susceptible to destruction from anthropogenic disturbances such 

as bottom trawling and cable trenching, which have been shown to impact benthic 

communities by altering structure (Bergman et al. 1990; Auster et al. 1996; Brancato 

2004; Brancato and Bowlby 2005) and removing benthic fauna (Brown et al. 2000). 

Potential effects of fishing and other commercial operations in such critical habitats, and 

the need to define appropriate strategies for the protection of these resources have been 

identified as a high-priority management issue for the sanctuary (Gittings et al. 2002). As 

a result, a team of OCNMS, NCCOS, and partnering scientists have conducted a series of 

submersible surveys since 2000 to evaluate benthic recovery from cable trenching, study 

the differences in benthic communities in relation to fishing intensity, and to document 

the presence of deep-sea coral/sponge assemblages at the OCNMS (Brancato 2004; 

Bowlby et al. 2005; Hyland et al. 2005). Although sampling coverage has been limited, 

results are significant in demonstrating the presence of deep-sea coral species in these 

waters (Brancato 2004; Bowlby et al. 2005; Hyland et al. 2005). Patches of rare stony 

corals, later confirmed as Lophelia pertusa, were discovered in an area that was defined 

as hard substrate by previous acoustic surveys. 

It appeared that remotely delineating areas of hard bottom substrate through acoustic 

sensing could be a useful tool to increase the efficiency and success of subsequent ROV 

explorations for photographically documenting the presence and condition of deep-sea 

coral and sponge communities. As a result, side scan sonar surveys were conducted in 

May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to obtain

additional side scan sonar imagery of the seafloor for broader habitat mapping coverage 

of sanctuary waters and to help delineate locations of suitable deep-sea coral/sponge

habitat for revisiting and surveying in more detail using an ROV on subsequent cruises. 

Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 

1-meter pixel resolution. We integrated video from a towed camera sled, ROVs, 

sedimentary samples, bathymetry data, and the side scan sonar mapping to describe 

geological and biological (where possible) aspects of habitat. With a hierarchical deepwater marine benthic classification scheme (Greene et al. 1999), we then created and 

attributed polygon features for use in a geographical information system (GIS). This 

report provides a description of the mapping and groundtruthing efforts as well as results 

of the image classification procedure for each of the areas surveyed. 

1 
SURVEY AREA 

OCNMS conducted approximately 137 km2

, 237 km2, and 341 km2 of seafloor mapping 

surveys aboard the NOAA Ship McArthur II during cruises AR-04-04, AR-05-05, and 

AR-06-03, respectively (Figure 1). Survey records were obtained from May 22 - 31 in 

2004, June 19-23 in 2005, and April 7-15 during 2006. Water depths ranged between 50 

and 400 meters throughout the survey area. With the addition of these sonar records, 

approximately 26 percent of the benthic habitat within sanctuary waters has now been 

mapped using contemporary acoustic methods. 

Figure 1. Sonar survey footprints for HMPR-113-2004-01, HMPR-118-2005-03, and

HMPR-119-2006-01. Individual areas classified by mosaic are also noted. 

2 
SONAR ACQUISITION AND DATA LOGGING

For all three cruises, the NOAA 

research vessel McArthur II, 

measuring 68.3 meters in length,

was used 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 Red Lion digital cable 

counter mounted on the winch level 

wind (Figure 2). 

We used a Klein System 3000 digital 

side scan sonar for acquiring the 

acoustic imagery. Only the 100 kHz 

Figure 2. Magnetic cable counter (green box) shown 

mounted to the level wind block. This device logged

cable out data to assist with estimating towfish position.

sonar channels were used for creating mosaics. The sonar system has a horizontal beam

width of 1.0 o at 100 kHz with a vertical beam width measuring 40 o. Depressors were 

used to help drive the towfish to greater depths while deploying the least amount of cable 

in an effort to minimize layback offset and towfish positioning error. However, due to 

the deep water depths typically being surveyed (up to 400 m), a larger wing depressor

was used after the 2004 survey to create a greater hydrodynamic force that would drive 

the towfish more effectively and thus reduce the cable needed to reach a given depth

(Figure 3). 

Figure 3. Klein System 3000 side scan sonar shown configured with the shallow-water KwingI 

depressor (left) and with the heavier KwingII depressor (right). Cruise AR-04-04 was conducted using 

the configuration shown on the left while cruises AR-05-05 and AR-06-03 were operated using the 

setup shown to the right. 

3 
A 300-meter range scale was used in all survey areas except in areas 119_0601c and 

119_0601d, where a 200-meter range was used, and in areas 113_0401r and 119_0601a 

where a 150-meter range scale was used. The areas surveyed with the 300-meter range 

scale were designed around 500-meter line-spacing plans, while the various areas 

surveyed with the 200-meter and 150-meter range scale were designed around 350 and 

200-meter line-spacing plans respectively. We maintained vessel speed at between 3 and 

3.5 knots for all operations. Sonar imagery was logged as 16 bit data with 2,048 samples 

per channel using Triton Imaging, Inc. (TII) Isis Sonar and recorded as eXtended Triton 

Format (XTF). 

SONAR DATA PROCESSING AND IMAGE CLASSIFICATION

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

and an 11-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; Intelmann and Cochrane 2006) consisting of three broad sediment classes

comprised of hard (rock or boulder), soft (sand, silt, clay or mud), and mixed (harder 

sediment such as gravel, pebble, cobble and boulder mixed with soft sediment). Adobe 

Photoshop was then used to edit misclassified data such as those occurring at nadir or in 

other various areas such as misclassified side lobes or shadows. Raster images were then 

smoothed with a low pass filter and converted to Features in ArcGIS where video 

groundtruthing was further used to enhance classification by describing microhabitat in 

more detail and adding roughness components and biological information where 

available (Greene et al. 1999). 

GROUNDTRUTHING

Video data acquired during four separate OCNMS missions and grab samples extracted 

from the usSeabed project (Reid et al. 2006), provided some degree of groundtruthing 

validation for all of the sonar mosaics except 113_0401t (Figure 4). In September 2001, 

the Delta submersible (Figure 5C) was deployed from the R/V Auriga in an effort to

monitor benthic recovery processes after installation of two fiber optic cables that

intersected sanctuary waters. Video from the Delta operations was used to help with 

classification of survey areas 113_0401p and 119_0601c. In June 2004, the US Navy’s 

Phantom DHD2+2 ROV (Figure 5A) was deployed from the NOAA Ship McArthur II to 

conduct the pilot survey of deepwater coral/sponge assemblages at OCNMS (Hyland et 

al. 2005). Although positioning of the ROV was less than desirable due to the Trackpoint 

II and Winfrog acquisition filtering setup, the imagery from this operation was still quite 

4 
Figure 4. Locations of groundtruthing effort in relation to individual survey mosaics. Polygons

represent sonar footprints and are color coded by survey. Black cross-hairs indicate locations of 

sediment grab data available from the USGS usSeabed project. Circles provide the locations of

video groundtruthing and are color coded by specific survey effort. 

useful as a groundtruthing tool and to further classify the sonar imagery according to 

Greene et al. 1999. In August 2005, we used a custom designed camera sled (Figure 5D) 

5 
to acquire underwater videography for validating several shallow-water sonar surveys, 

including data from the “Quileute rock pile”, which was the shallow-water area 

113_0401r. And finally, in May/June 2006, the Canadian Scientific Submersible 

Facility’s (CSSF) ROPOS ROV (Figure 5B), under contract to Canpac, was deployed 

from the NOAA Ship McArthur II as a follow-up effort to the 2004 coral/sponge 

exploration. The IXSEA GAPS system that was used for underwater positioning of the 

ROPOS provided the most reliable positioning information for any of the groundtruthing 

efforts. Video from the ROPOS survey was used to groundtruth mosaics 118_0503c, 

119_0601a and 119_0601b. Additionally, the greater stability of the ROPOS, along with 

higher quality underwater positioning and video equipment, permitted selected clips of 

video to be mosaicked into plan-perspective images by co-registering adjacent video

frames into a single mosaic on a basis of pair-wise transformations (Rzhanov et al. 2006) 

that were ultimately georeferenced to provide more thorough sonar interpretation.

Although not available in every survey block, the usSeabed project (Reid et al. 2006) 

provided many samples as further weight of evidence for the video and sonar 

interpretation. 

 

Figure 5. Groundtruthing platforms. Several operations between 2001 and 2006 provided useful video 

imagery of the seafloor for groundtruthing validation and permitted more descriptive habitat 

characterization in certain areas. Data was acquired from a wide variety of platforms including two

ROVs, the Navy’s Phantom DHD2+2 in June 2004 (inset A) and the CSSF ROPOS (inset B) in June 

2006, the Delta manned-submersible vehicle (inset C) in September 2001, and a custom-designed 

towed-camera sled (inset D) in August 2005. 

6 
SURVEY RESULTS AND INTERPRETATION

We acquired over 335 linear km of survey lines aboard the NOAA Ship McArthur II in 

2004 (Table 1), 523 km of sonar survey lines in 2005, and over 803 km during the 2006 

mapping effort. Between the three cruises nearly 273 hours of actual logged sonar 

records were acquired. 

Table 1. Below are the survey effort statistics for HMPR-113-2004-01 (AR04-04), HMPR-118-2005-03

(AR-05-05) and HMPR-116-2005-01 (AR-06-03). Data were acquired aboard the NOAA Ship McArthur

II using a Klein 3000 side scan sonar. Five areas were surveyed in 2004, three in 2005, four in 2006. Area 

is presented in square kilometres, length of linear track lines in kilometres, and hours of actual logged sonar

packets in hours, minutes, and seconds. 

Year Block Date Area (km2

) Tracks (km) Hours (h:m:s) 

2004 113_0401d May 25-28 69.6 150.4 23:42:49

113_0401p May 28-30 30.8 70.0 10:39:45

113_0401q May 22 8.7 24.9 3:57:35

113_0401r May 24-25 13.3 64.3 10:20:30

113_0401t May 31 15.2 26.0 5:23:13

Total 137.6 335.6 54:03:52

2005 118_0503a June 16-17 57.9 121.1 19:07:43

118_0503b June 18-19 29.1 63.7 9:50:35

118_0503c June 19-23 149.9 338.2 53:31:21

Total 236.9 523.0 82:29:39

2006 119_0601a April 7-8 34.4 139.8 24:45:21

119_0601b April 9-13 253.2 516.5 85:56:27

119_0601c April 13 13.3 37.9 7:19:29

119_0601d April 14-15 37.8 109.7 18:20:23

Total 33.62 803.9 136:21:40

The Appendices present all side scan sonar mosaics, the full-scale attributed polygon 

layers showing the distribution of truncated habitat codes (due to the large number of 

possible categories when displaying the full habitat code) and matrix tables providing the 

descriptions of the habitat classification (with exception of slope, complexity, and 

microhabitat) per Greene et al. (1999) for each of the areas surveyed during cruises AR04-04, AR-05-05 and AR-06-03. 

HMPR-113-2004-01 (Cruise AR-04-04)

Survey block 113_0401d is located along the eastern edge of the Juan de Fuca Canyon 

wall and was characterized as over 90 percent soft (s), silty substrate (Table 2). There 

was one significant area of harder substrate (shown in Figure 6) at the base of the canyon 

slope in the southern portion of the survey area that consisted of mostly gravel, cobbles, 

and mixed boulders along with an exposed bedrock scarp. Several patches of Lophelia 

pertusa coral were later identified in a boulder field along the eastern edge of this rock

7 
ledge through video captured by ROV (Hyland et al. 2005). No contemporary high 

resolution multibeam data existed in the 113_0401d survey area, and as such, slope and 

Figure 6. Example of habitat classification results for a selected region of the side scan sonar 

survey area 113_0401d acquired during the NOAA Ship McArthurII cruise AR-04-04. Location 

of inset region is shown as the black hashed polygon at lower left where the individual sonar 

track lines are shown in green. Contours of large scale map range from –50 meters (blue line) to

–400 meters depth (yellow line). Colored cross hairs (X) define bottom hardness as interpreted

through video, where h=hard, s=soft, and m=mixed sediment. Polygons codes are taken from

Greene et al (1999); where F=flank, S=continental shelf megahabitat, h=hard, m=mixed, s=soft

bottom hardness, e=exposed bedrock, _u=unconsolidated sediment modifier. Letters following

asterisks are determined from video observations and refer to microhabitat classification where 

g=gravel, c=cobble, m=mud, t=tube worms, o=other sessile organisms. 

8 
Table 2. Distribution of bottom hardness for each sonar mosaic classified from survey HMPR-113-2004-

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 percentage 

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

Cruise Survey Block h m s

AR-04-04 113_0401d 482,945.0

0.69 

5,884,356.0 

8.45 

63,250,477.0 

90.85 

113_0401p 92,514.0

0.00 

15,932,845.3 

51.86 

14,693,506.7 

47.83 

113_0401q 1,207,432.0

13.8 

274,922.0 

3.15 

72,411,394.0 

82.97 

113_0401r 3,989,073.0

30.0 

1,739,324.1 

13.08 

7,567,162.9 

56.91 

113_0401t 366,082.0

2.42 

9,835,471.0 

65.10 

4,900,729.0 

32.44 

complexity fields have not been populated at this time. There were only a few areas of 

hard bottom in area 113_0401p, which occurred in the high slope areas shown in Figure 

7. Slightly more than half of the 113_0401p mosaic was classified as mixed sediment 

(Table 2) with the video groundtruthing indicating this as being cobble and gravel mixed 

with sand, although several areas of mixed boulder fields were also noted. Large areas of 

homogeneous seafloor were classified as mud based on a limited amount of video 

coverage. Area 113_0401q, the southern-most area in the sanctuary surveyed during the 

three cruises, covered only a relatively small region (roughly 8 km2

) at the head of 

Quinault Canyon. Textural classification of this imagery suggested that 83 percent of the 

seafloor in this area was soft sediment, although there was a significant band of bedrock 

following the contours of the canyon wall. Video groundtruthing of this rock wall was

attempted during 2004 using the Phantom DHD2+2 ROV, but unfortunately only a mere

glimpse of the wall was captured due to swift currents which made it difficult to keep this

small ROV on station. Located entirely on the continental shelf, the area known as the 

Quileute “rock pile” was also surveyed during AR-04-04 (113_0401r). Side scan 

imagery for this area was classified as 30 percent rock outcrop and 57 percent soft 

sediment (Table 2). Mixed sediment was identified along the periphery of the outcrop 

and interspersed throughout the main rock feature. Figure 8 provides a shaded relief

model of the “rock pile” feature and locations where groundtruthing video was acquired 

using a towed camera sled during August 2005 from the R/V Tatoosh. The multibeam 

bathymetry data available for this area was collected in October 2001 using an Elac 

1050D echosounder onboard the NOAA Ship Rainier. Mosaic 113_0401t was located 

about 12 km directly west of Cape Flattery and consisted of just four lines of side scan 

9 
data to fill a gap between two other previously surveyed areas. This area was also

previously surveyed with multibeam bathymetry in October 2002. Although just 2

percent of this mosaic was classified as hard sediment (Table 2), a prominent exposed 

outcrop greater than one kilometer in length can be found in the southern portion of the 

imagery (see Appendix). 

Figure 7. Habitat classification of mosaic 113_0401p based on slope criteria. Slope 

classes are modified from Greene et al. (1999). High slope areas are shown in orange

and are classified as hard bottom. Purple spheres show the location of video

groundtruthing captured in September 2001 using the Delta submersible mannedvehicle. The inset image shows the survey location in relation to Cape Flattery. 

Bathymetry contours on large scale map range from –50 meters (blue line) to –400

meters (yellow line) depth. Slope data were calculated from multibeam data 

collected in 2002 using an Elac 1050D echosounder onboard the NOAA Ship 

Rainier. 

10 
Figure 8. Shaded relief model featuring the Quileute “rock pile” offshore from LaPush, WA. 

Colorized spheres show the location of video groundtruthing captured in August 2005 using a 

custom-designed camera sled towed from the R/V Tatoosh. The ripple-like features visible in 

the flat areas of the multibeam data are heave artifacts resulting from motion sensor timing

latency issues. 

11 
HMPR-118-2005-03 (Cruise AR-05-05)

Three different areas were surveyed during the month of June 2005. Block 118_0503a

was located just 5 km offshore of Tatoosh Island. Being so near the entrance to the Strait 

of Juan de Fuca, this proved to be an extremely challenging area to conduct side scan 

sonar operations due to the water depth and extreme tide-induced currents that caused 

excessive movement of the towfish, even when using the large KwingII depressor. The 

imagery suffered significant degradation due to both pitch and roll of the towfish. Even 

though previous multibeam bathymetry data was acquired in this area during 2002 and 

2003, sonar interpretation had to be made without any video groundtruth validation. 

Although 12 grab samples were available for this area from the usSeabed database (Reid 

et al. 2006), they provided little assistance with enhancing interpretation. The hummocky 

terrain that occurs throughout a good portion of the mosaic makes it even more difficult

to distinguish shadows from soft sediment. Although results of the textural classification 

suggested that only 5 percent of this area was characterized as hard bottom (Table 3), 

video groundtruthing is needed to refine the habitat classification of this mosaic. Several 

uncertain features need to be examined in more detail to increase confidence in the 

classification, such as the linear features visible in Figure 9 that resemble typical wood 

grain-like sedimentary rock outcrops. Similar to area 118_0503a, no video 

groundtruthing was available for mosaic 118_0503b. However, since this area covered 

the top of a plateau (Figure 10) and the side scan sonar records were typical of mixed 

sediment class, the few grab samples available from the usSeabed database provided 

ample assurance for classification. The mosaic was characterized by minimal hard 

bottom (< 1 percent) with the majority of pixels falling into the mixed sediment class 

(Table 3). Area 118_0503c was another difficult area to survey with towed side scan 

sonar due to the steep canyon walls. Survey lines had to be run in multiple directions to 

safely acquire data without smashing the towfish into the seafloor. Many lines could 

only be accomplished by flying the towfish in a down slope direction. Several rock 

outcrops occurred in this area, however the mosaic was essentially classified as half soft

sediment and half mixed sediment (Table 3). 

Table 3. Distribution of bottom hardness for each sonar mosaic classified from survey HMPR-118-2005-

03. 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 percentage 

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

Cruise Survey Block h m s

AR-05-05 118_0503a 2,889,857.0

5.00 

26,048,737.6 

45.09 

28,836,707.5 

49.91 

118_0503b 165,997.0

0.57 

25,633,750.9 

88.39 

3,200,722.0 

11.04 

118_0503c 3,683,781.4

2.46 

80,263,060.0 

53.53 

65,996,188.6 

44.01 

12 
Figure 9. Example of an uncertain feature 

requiring further video groundtruthing for better 

confirmation. Note the linear striations

paralleling the 340-meter contour (blue line), 

which resemble sedimentary rock layering.

Figure 10. Area118_0503b footprint (black 

outline) shown with sonar track lines (green) 

and results of sediment grabs. Note the large 

percentage of gravel in each grab, and the top 

of plateau evident from the red contour lines. 

In June 2006, over 22 hours of video was acquired in the same area covered by mosaic 

118_0503c using the ROPOS ROV aboard the NOAA Ship McArthur II. These video 

data were of high quality, assisting greatly with validation of the sonar records collected

during AR-05-05. Using software designed at the Center for Coastal Ocean Mapping

(CCOM), University of New Hampshire (UNH), 29 small clips of video acquired at 

selected locations throughout this survey area were mosaicked into seamless images and 

later georeferenced to provide a clearer context of the sediment structure thereby 

facilitating sonar validation and habitat classification to a greater extent than would be 

possible through simple video still frame extractions. The video mosaics, for example, 

were useful in correcting the maximum likelihood classification in several areas where

apparent shadows were actually small pockets of soft sediment. Such small scale pockets 

would not be notable from an individual still-frame extraction, but become immediately 

apparent through the broader perspective provided by a mosaicked video stream. 

Additionally, with use of the 300-meter range scale, less rugose boulder fields are often 

misclassified as mixed sediment due to the associated slower ping rates that produce 

lower resolution imagery. The data in Figure 11 provide a good example of a region 

where the flank of a rock outcrop was initially classified as mixed sediment hardness, but 

through use of the video mosaicking technique, it became apparent that the bottom of this 

13 
gully was actually filled with boulders, providing substrate for gorgonians and Lophelia 

pertusa. 

Figure 11. Selected clip of mosaicked video showing a hard-bottom boulder patch with a 

visible gorgonian (A), crinoids (B), sponges (C), and Lophelia pertusa (D - inside white 

box and shown in expanded inset). The CCOM UNH process takes into account both 

scaling and rotation factors and uses pair-wise transformations to seamlessly stitch

individual video frames. A rock outcrop is clearly visible in the side scan sonar record

shown in the bottom inset. The red box (measuring 35 meters in width) shows the relative 

position of the classified polygon feature, overlain with an 11-meter long strip of

mosaicked video. The green line represents the navigational path of the ROPOS ROV. 

This particular polygon (blue) was classified (see code) as flank, hard exposed wall, with

cobble, gravel, and rockfish being present. 

14 
HMPR-119-2006-01 (Cruise AR-06-03)

Area 119_0601a was located offshore of Cape Flattery. In general, the northern half of 

the mosaic was classified as mixed sediment consisting of gravel, pebble, cobble and 

scattered boulders while the southern portion of the area was soft sand and mud. There 

were two main features of hard bottom evident in the side scan sonar and bathymetry 

data. One band of rock outcropping paralleled Chibahdehl Rocks approximately one 

mile offshore, while the other occurred just off Duncan Rock and continued in a 

northwesterly direction for nearly 3 kilometers (Figure 12). 

No high-resolution multibeam bathymetry data have been acquired at survey area 

119_0601b. The western edge of this survey area was defined as large boulders and 

cobbles, with the video data revealing minimal encrustation but having high densities of 

large ling cod. Several patches of sediment waves were also visible in the side scan sonar 

and video records, indicating swift currents are present in this region of the Juan de Fuca 

canyon. The soft sediment classified in the eastern side of the area is a very fine silt/mud. 

Several gorgonians were found on boulders along the southeastern edge of the mosaic, 

and sediment covered pebble and cobble existed throughout. 

Very little hard bottom was classified in mosaics 119_0601c or 119_0601d (Table 4), 

thus suggesting a low likelihood of habitat suitable for coral or sponge communities. In 

fact, area 119_0601d, located at the very eastern edge of the sanctuary boundary in the 

Strait of Juan de Fuca, was over 90 percent flat bottom (< 5 percent slope) and was 

classified as almost entirely mixed pebble with cobble but having a small area of soft 

sediment and a few scattered areas of hard rock. Several submarine cables were also 

identifiable in the sonar imagery. 

Table 4. Distribution of bottom hardness for each sonar mosaic classified from survey HMPR-119-2006-

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 percentage 

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

Cruise Survey Block h m s

AR-06-03 119_0601a 2,205,347.0

6.41 

17,188,222.2 

50.0 

14,967,752.8 

43.6 

119_0601b 8,614,082.1

3.40 

172,527,478.3 

68.1 

72131056.6 

28.47 

119_0601c 13,059.0

0.09 

6,842,935.9 

51.46 

6,442,094.9 

48.44 

119_0601d 220,125.3

0.58 

36,864,423.6 

97.65 

664,909.0 

1.76 

15 
Figure 12. Example of habitat classified attributed polygon data draped over shaded relief bathymetry 

data in area 119_0601a. The hard exposed rock outcrop visible in the foreground is the northwesterly 

trending rock band off of Duncan Rock. Sun illumination is modeled using a 315 degree azimuth, 17

degree vertical angle, and 2x vertical exaggeration. S=Shelf, F=Flank, m=mixed, s=soft, h=hard. 

SUMMARY 

The side scan sonar imagery acquired during research cruises AR-04-04, AR-05-05, and 

AR-06-03 provided valuable information to broaden our knowledge of seafloor substrate

distribution in OCNMS waters. Another underlying objective of the sonar imagery 

acquisition was to provide supporting data for conducting subsequent video explorations 

with hopes of identifying deep-sea coral/sponge communities. A literature search 

indicated that most prior records of deep-sea coral, especially in neighboring western 

Canadian waters, are at depths of about 100-500 meters (Alfonso and McAllister 2000; 

Jamieson et al. 2005). As such, the present survey work at OCNMS was conducted in 

water depths from 100 to 400-meters. Also, areas within the sanctuary deeper than 400 

meters are located in very steep canyons where it is quite difficult to maintain quality side 

scan sonar records due to both towfish movement and the underwater positioning and

winch limitations. At these water depths, some type of wing-depressor was needed for all 

operations, although it was determined that a larger and heavier wing depressor produced 

the best imagery by creating increased hydrodynamic forces and greater downward 

pressure on the towfish in addition to reducing the amount of cable paid out which 

ultimately increased positional certainty under the layback algorithm.

In general, we chose to use a 300-meter range scale for most of the survey operations. 

This allowed us to cover as much area as possible with a given line while still being able

to delineate hard rocky areas from mixed substrate and soft muddy bottom, even when 

pinging at just 2.5 times per second. This range scale additionally allowed us to fly the 

towfish at altitudes approaching 60-meters which was imperative in the canyon areas to 

avoid damaging the sonar by contact with the seafloor. 

16 
It is important to note that the small coral colonies that were found are not capable of 

being identified from side scan sonar imagery itself when using the frequency and range 

scales as described in this report. Instead, structures on the sea floor were identified that 

fit the requirements of coral growth, such as depth, rugosity and substrate type. Such use 

of acoustic meso-scale sampling proved to be a highly successful means for delineating

hard bottom substrate suitable as habitat for deep-sea coral/sponge assemblages. 

Through examination of three years of deep-towed, side scan sonar mosaics, 48 sites 

were selected to investigate in greater detail using the ROPOS ROV during the 

subsequent June 2006 survey. Of these 48 selected sites, 15 were actually visited and 14 

(93 percent) produced some sighting of coral or sponge. 

Thus it is evident that having a more thorough understanding of the distribution and 

location and benthic substrates can lead to more efficient ROV operations by increasing 

the chances of success at finding a target object dependent upon a specific sediment

association. This becomes increasingly important when considering the cost associated 

with an ROV deployment in deep water. 

 

ACKNOWLEDGMENTS

These surveys would not have been possible without the side scan winch and various 

peripherals made available by the staff of the USGS’s Marine Facility in Redwood City, 

CA, or towfish from the NOAA Ship RAINIER and the Office of Coast Survey. The 

authors would also like to thank NOAA’s National Undersea Research Program for

partially funding the 2006 survey, and Nicholas Perry, Danny Shaylor, Peter Noto, James 

Whitaker, and Tim Jamison for assisting with sonar data acquisition. 

REFERENCES

Alfonso, N., and D.E. McAllister. 2000. The distribution of corals on Canada’s west 

coast. Abstract: First International Symposium on Deep-Sea Corals. July 30 to 

August 2, 2000 Halifax, Nova Scotia, Canada. 

Auster, P.J., R. J. Malatesta, R.W. Langton, L. Watling, P.C. Valentine, C.L. Donaldson, 

E.W. Langston, A.N. Shepard, and I.G. Babb. 1996. The impacts of mobile 

fishing gear on seafloor habitats in the Gulf of Maine (nothwest Atlantic): 

Implications for conservation of fish populations. Reviews in Fisheries Science. 

4(2): 185-202. 

Bergman, M.J.N., M. Fonds, M. Hup, and A. Stam. 1990. Direct effects of beamtrawl 

fishing on benthic fauna in the North Sea. ICES CM 1990/MINI: 11. 

Copenhagen, Denmark. 19 pp. 

Bowlby, E., J. Hyland, M.S. Brancato, C. Cooksey, and S. Intelmann. 2005. Preliminary 

discoveries of Scleractinian coral Lophelia pertusa and other deep-sea coral and 

17 
sponge communities in the Olympic Coast National Marine Sanctuary. Abstract: 

Third International Symposium on Deep Sea Corals, Miami, Nov 28-Dec. 2, 2005 

Brancato, M.S. 2004. Ecological linkages – connections to the benthic community. 

Ecological linkages between nearshore and offshore systems. Proceedings of the 

Western Juan de Fuca Ecosystem Symposium, May 10-11, 2004. Sidney, British 

Columbia. 

Brancato, M.S., and C.E. Bowlby. 2005. Survey of fishing gear and fiber optic cable 

impacts to benthic habitats in the Olympic Coast National Marine Sanctuary. 

Pages 629-630 in P.W. Barnes and J.P. Thomas, eds. Benthic habitats and the 

effects of fishing. American Fisheries Society, Symposium 41, Bethesda, 

Maryland. 

Brown, E., M. Dommisse, S. Hills, and B. Finney. 2000. Immediate and long-term 

effects of commercial bottom trawling to benthic communities and substrates in a 

dynamic soft-bottom environment: Bristol Bay, Alaska. Diving for Science in the 

21st Century, American Academy of Underwater Sciences, 430 Nahant Rd Nahant 

MA 01908 U.S.A. 18pp. 

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. 

Conway, K.W., J.V. Barrie, W.C. Austin, and J.L. Luternauer. 1991. Holocene sponge 

bioherms on the western Canadian continental shelf. Continental Shelf Research. 

11(8-10): 771-790. 

Conway, K.W. 1999. Hexactinellid sponge reefs on the British Columbia continental 

shelf: Geological and biological structure with a perspective on their role in the 

shelf ecosystem. Canadian Stock Assessment Secretariat Research Document 

99/192. 

Conway, K.W., J.V. Barrie, W.C. Austin, P.R. Ruff and M. Krautter. 2005. Deep-water 

sponge and coral habitats in the waters of British Columbia, Canada: multibeam

and ROV survey results. Abstract: Third International Symposium on Deep Sea 

Corals, Miami, Nov 28-Dec. 2, 2005. 

Gittings, S.R., K.E. Benson, P.J. Souik, M.S. Tartt. 2002. Sanctuary science: Evaluation 

of status and information needs. NOAA/ONMS, Silver Spring, MD. 75pp. 

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 

18 
Hyland, J., C. Cooksey, E. Bowlby, M.S. Brancato, and S. Intelmann. 2005. A pilot 

survey of deepwater coral/sponge assemblages and their susceptibility to 

fishing/harvest impacts at the Olympic Coast National Marine Sanctuary 

(OCNMS). Cruise report for NOAA Ship McArthur II Cruise AR-04-04: Leg 2. 

NOAA Technical Memorandum NOS NCCOS 15. NOAA/NOS Center for 

Coastal Environmental Health and Biomolecular Research, Charleston, SC. 13p. 

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. 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. 

Jamieson, G.S., N. Pellegrin, and S. Jessen. 2005. Taxonomy and zoogeography of cold 

water corals in explored areas of coastal British Columbia. Abstract: Third 

International Symposium on Deep Sea Corals, Miami, Nov 28-Dec. 2, 2005. 

Reid, J.A., J.M. Reid, C.J. Jenkins, M. Zimmermann, S.J. Williams, and M.E. Field. 

2006. usSEABED: Pacific Coast (California, Oregon, Washington) offshore 

surficial-sediment data release: U.S. Geological Survey Data Series 182, version 

1.0. Online at http://pubs.usgs.gov/ds/2006/182/

Rzhanov, Y., L. Mayer, S.E. Beaulieu, T. Shank., S.A. Soule, D.F. Fornari. 2006. Deepsea georeferenced video mosaics. Proceedings MTS/IEEE Oceans 2006, Sept. 

2006. 

19 
APPENDIX

Appendix 1. Isis Processing Parameters 

HMPR-113-2004-01 

Lateral Offset: -4.26m

Layback Offset: 13.7m

Heading= use Gyro with offset of 23 degrees 

Mosaic resolution: 1.0m 

Apply BAC 

TVG: start at first return

 Curve = 1.4 +0.022 + (-2) 

HMPR-118-2005-03

Lateral Offset: -3.3m

Layback Offset: 12.5m

Heading= use CMG 

Mosaic resolution: 1.0m 

Apply BAC 

Duration Distance=294m 

TVG: start at first return

 Curve = -2 + 0.09 + 1 

Threshold=5 

HMPR-119-2006-01

Lateral Offset: -3.3m

Layback Offset: 12.5m

Heading= use CMG 

Mosaic resolution: 1.0m 

Apply BAC 

TVG: start at first return

 Curve = -2 + 0.09 + 1 

Threshold=5 

Duration Distance 119_0601a=145m 

 119_0601b=294m

 119_0601c=194m 

 119_0601d=194m

20 
Appendix 2. Side Scan Sonar Imagery 

See Figure 1 for perspective of survey locations in relation to OCNMS boundary. 

Appendix 2a. Side scan sonar mosaic of survey block 113_0401d. 

21 
Appendix 2b. Side scan sonar mosaic of survey block 113_0401p.

22 
Appendix 2c. Side scan sonar mosaic of survey block 113_0401q.

23 
Appendix 2d. Side scan sonar mosaic of survey block 113_0401r.

24 
Appendix 2e. Side scan sonar mosaic of survey block 113_0401t.

25 
Appendix 2f. Side scan sonar mosaic of survey block 118_0503a.

26 
Appendix 2g. Side scan sonar mosaic of survey block 118_0503b.

27 
Appendix 2h. Side scan sonar mosaic of survey block 118_0503c.

28 
Appendix 2i. Side scan sonar mosaic of survey block 119_0601a.

29 
Appendix 2j. Side scan sonar mosaic of survey block 119 0601b.

30 
Appendix 2k. Side scan sonar mosaic of survey block 119_0601c.

31 
Appendix 2l. Side scan sonar mosaic of survey block 119_0601d.

32 
Appendix 3. Attributed Habitat Classification Polygons 

See Figure 1 for perspective of survey locations in relation to OCNMS boundary. 

Appendix 3a. Attributed habitat classification polygons for survey 113_0401d. 

33 
Appendix 3b. Attributed habitat classification polygons for survey 113_0401p. 

34 
Appendix 3c. Attributed habitat classification polygons for survey 113_0401q.

35 
Appendix 3d. Attributed habitat classification polygons for survey 113_0401r. 

36 
Appendix 3e. Attributed habitat classification polygons for survey 113_0401t. 

37 
Appendix 3f. Attributed habitat classification polygons for survey 118_0503a.

38 
Appendix 3g. Attributed habitat classification polygons for survey 118_0503b.

39 
Appendix 3h. Attributed habitat classification polygons for survey 118_0503c.

40 
Appendix 3i. Attributed habitat classification polygons for survey 119_0601a.

41 
Appendix 3j. Attributed habitat classification polygons for survey 119_0601b.

42 
Appendix 3k. Attributed habitat classification polygons for survey 119_0601c.

43 
Appendix 3l. Attributed habitat classification polygons for survey 119_0601d.

44 
Appendix 4. Habitat Attribute Classification Tables 

Habitat codes in the following tables only present information for the megahabitat, bottom induration, 

mesohabitat, and geologic modifier fields. Data for slope, complexity, and microhabitat observations have

been truncated due to the large number of categorical possibilities. 

Appendix 4a. Distribution of habitat classified from survey block 113_0401d side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Fs _u Flank soft unconsolidated 56,539,634.6 81.21 

Ss _u Shelf soft unconsolidated 6,313,940.9 9.07 

Fm Flank mixed 5,744,059.2 8.25 

Fs Flank soft 386,986.3 0.56

Fhe Flank hard bedrock 358,492.0 0.51 

Sm Shelf mixed 140,296.7 0.20

Fh Flank hard 113,040.0 0.16

Sh Shelf hard 11,413.0 0.02

Ss Shelf soft 9,915.0 0.01

Appendix 4b. Distribution of habitat classified from survey block 113_0401p side scan sonar survey data. 

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

percentage of total mapped area.

Habitat Code Descriptor Square m Percentage

Fs Flank soft 12,636,874.6 41.13

Fm Flank mixed 9,132,081.4 29.72

Sm Shelf mixed 6,798,665.6 22.13

Ss Shelf soft 2,024,145.4 6.58

Fh Flank hard 59,440.4 0.19

Sh Soft hard 33,073.6 0.10

Fsg Flank soft gully 32,486.7 0.10 

Fmg Flank mixed gully 2,098.3 0.00 

45 
Appendix 4c. Distribution of habitat classified from survey block 113_0401q side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss _u Shelf soft unconsolidated 5,443,063.8 62.39 

Fs _u Flank soft unconsolidated 1,798,130.1 20.61 

Fhe Flank hard bedrock 644,696.3 7.39 

Sh Shelf hard 327,934.4 3.75 

Fm Flank mixed 191,289.7 2.19

She Shelf hard bedrock 131,235.5 1.50 

Fh Flank hard 103,565.5 1.18

Sm Shelf mixed 83,632.2 0.95

Appendix 4d. Distribution of habitat classified from survey block 113_0401r side scan sonar survey data.

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss Shelf soft 11,236,319.1 65.74

She Shelf hard bedrock 3,961,318.0 23.17 

Sm Shelf mixed 1,723,408.0 10.08

Ssw_r Shelf soft waves ripples 125,594.6 0.73 

Sh Shelf hard 27,754.9 0.16

Smw_r Shelf mixed waves ripples 15,916.0 0.09 

46 
Appendix 4e. Distribution of habitat classified from survey block 113_0401t side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Fm Flank mixed 6,017,690.2 39.84

Fs _u Flank soft unconsolidated 4,834,260.0 32.01 

Sm Shelf mixed 3,817,780.7 25.27

Fh Flank hard 228,727.0 1.51

Sh Shelf hard 97,979.9 0.64

Fs Flank soft 66,105.0 0.43

Fhe Flank hard bedrock 29,030.9 0.19 

She Shelf hard bedrock 10,344.0 0.68 

Ss Shelf soft 364.0 0.00

Appendix 4f. Distribution of habitat classified from survey block 118_0503a side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Fs Flank soft 26,286,693.2 45.49

Fm Flank mixed 22,800,954.4 39.46

Sm Shelf mixed 3,247,783.1 5.62

Fh Flank hard 2,798,650.0 4.84 

Ss Shelf soft 2,550,014.2 4.41

Sh Shelf hard 91,207.0 0.15

47 
Appendix 4g. Distribution of habitat classified from survey block 118_0503b side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 24,351,126.9 83.96

Fs _u Flank soft unconsolidated 2,719,120.2 9.37 

Fm Flank mixed 1,282,623.9 4.42

Ss_u Shelf soft unconsolidated 481,601.7 1.66 

Sh Shelf hard 110,698.3 0.38

Fh Flank hard 55,298.6 0.19

Appendix 4h. Distribution of habitat classified from survey block 118_0503c side scan sonar survey data.

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 62,038,714.8 41.37

Fs Flank soft 42,594,349.8 28.40 

Ss Shelf soft 23,401,838.7 15.60

Fm Flank mixed 17,930,683.9 11.95

Sh Shelf hard 1,559,744.8 1.04

Fh Flank hard 1,379,090.5 0.91

Fhe Flank hard bedrock 696,654.5 0.46 

Smw Shelf mixed waves 287,731.2 0.19

She Shelf hard bedrock 43,225.3 0.02 

Shm_c Shelf hard mixed 

consolidated

5,086.1 0.00

Fmw Flank mixed waves 4,691.7 0.00 

Smm Shelf mixed mound 1,169.9 0.00

Sme Shelf mixed bedrock 68.2 0.00

48 
Appendix 4i. Distribution of habitat classified from survey block 119_0601a side scan sonar survey data.

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Ss Shelf soft 12,632,926.0 36.76

Sm Shelf mixed 11,260,928.0 32.77

Fm Flank mixed 5,927,294.1 17.24

Fs Flank soft 2,334,826.8 6.79

Sh Shelf hard 1,808,231.8 5.26

Fh Flank hard 397,115.1 1.15

Appendix 4j. Distribution of habitat classified from survey block 119_0601b side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 128,789,713.1 50.85

Fs Flank soft 57,412,124.5 22.66

Fm Flank mixed 43,736,995.1 17.26

Ss Shelf soft 14,677,347.2 5.79

Sh Shelf hard 7,873,582.2 3.10

Fh Flank hard 739,851.0 0.29

Ss _r Shelf soft ripples 36,548.4 0.01 

Fs _r Flank soft ripples 5,036.4 0.00 

Fm _l Flank mixed carbonate 770.0 0.00 

Fhs Flank hard scarp 648.7 0.00 

49 
Appendix 4k. Distribution of habitat classified from survey block 119_0601c side scan sonar survey data.

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Sm Shelf mixed 6,872,935.9 51.45

Ss _u Shelf soft unconsolidated 5,382,746.0 40.47 

Fs _u Flank soft unconsolidated 1,051,683.9 7.90 

Sh Shelf hard 13,059.0 0.09

Ss Shelf soft 7,665.0 0.05

Appendix 4l. Distribution of habitat classified from survey block 119_0601d side scan sonar survey data. 

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

percentage of total mapped area. 

Habitat Code Descriptor Square m Percentage

Fm Flank mixed 31,858,451.8 84.39

Sm Shelf mixed 4,796,725.1 12.70

Fs Flank soft 664,909.0 1.76

Fmw Flank mixed waves 209,201.6 0.55 

Fh Flank hard 162,668.7 0.43

She Shelf hard bedrock 25,487.0 0.06 

Fh _a Flank hard anthropogenic 17,654.2 0.04 

Fhe Flank hard bedrock 10,483.3 0.02 

Sh Shelf hard 2,175.9 0.00

Sh _a Shelf hard anthropogenic 1,655.9 0.00 

Fm _a Flank mixed anthropogenic 45.0 0.00 

50 
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/). 

2002 – 03 Florida Keys National Marine Sanctuary Science Report: An Ecosystem

Report Card After Five Years of Marine Zoning (NMSP-06-12) 

Habitat Mapping Effort at the Olympic Coast National Marine Sanctuary – Current Status 

and Future Needs (NMSP- 06-11) 

M/V Connected Coral Reef Restoration Monitoring Report Monitoring Events 2004 –

2005 Florida Keys National Marine Sanctuary, Monroe County, Florida (NMSP-06-10)

M/V Jacquelyn L Coral Reef Restoration Monitoring Report Monitoring Events 2004 – 

2005, Florida Keys National Marine Sanctuary, Monroe County, Florida (NMSP-06-09) 

M/V Wave Walker Coral Reef Restoration Baseline Monitoring Report - 2004 Florida 

Keys National Marine Sanctuary Monroe County, Florida (NMSP-06-08)

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 (NMSP-06-07)

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 (ONMS05-05)

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) 

51 
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) 

360 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) 

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) 

52