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Title: Recreational fisheries habitat assessment project
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Title: Recreational fisheries habitat assessment project
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Language: English
Creator: Vasques, Jason
Publisher: Divison of Fish and Wildlife, Department of Planning and Natural Resources
Place of Publication: St. Croix, USVI
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Table of Contents
    Title Page
        Page i
    Table of Contents
        Page ii
        Page iii
        Page iv
        Page v
    Main
        Page 1
        Page 2
        Page 3
        Page 4
        Page 5
        Page 6
        Page 7
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        Page 11
        Page 12
        Page 13
        Page 14
        Page 15
        Page 16
        Page 17
    Tables
        Page 18
        Page 19
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        Page 24a
        Page 25
        Page 26
        Page 27
        Page 28
        Page 29
        Page 30
        Page 31
    Figures
        Page 32
        Page 33
        Page 34
        Page 35
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    Figures
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Full Text







Final Report







to the
U.S. Fish and Wildlife Service

Recreational Fisheries Habitat Assessment Project








State: United States Virgin Islands

Project Number: F-7

Project Title: Recreational Fisheries Habitat Assessment Project

Study Number: 4

Study Title: Mapping Essential Fish Habitat with Side Scan Sonai

Period Covered: October 1, 2001 to September 30, 2005

Report Written by: Jason Vasques, Fisheries Biologist III
Division of Fish and Wildlife
Department of Planning and Natural Resources
U.S. Virgin Islands

Date of Report: November 28, 2005

Project Staff: Shenell Gordon, Fisheries Biologist I

Report Reviewed By: K. Roger Uwate, Ph.D., Chief of Fisheries
Barbara Kojis, Ph.D., Director






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Study 4: Mapping Essential Fish Habitat with Side Scan Sonar Final Report
Period: FY 2001-FY2005


Table of Contents
List of Tables iii
List of Figures iv-v
1.0 Introduction and Background 1
2.0 Site Description 2
3.0 Side Scan Sonar and Multibeam 2
3.1 Geodetic Parameters and Positioning 3
3.2 Survey Equipment 3
3.2.1 Survey Vessel 3
3.2.2 Sonar System 4
3.3 Survey Operations 4
3.3.1 Post Processing the Data and Creating Mosaics 4
4.0 Ground Truthing the Sonar Images 5
4.0.1 Diver Observations 5
4.0.2 Drop Video Camera 5
4.1 Interpreting the sonar images 5
5.0 Habitat Classification Scheme 7
5.1 Habitat Classification Descriptions 8
6.0 Benthic Habitat Maps 10
6.1 Quantitative Description of Habitats along the Insular Shelf 11
7.0 Discussion 12
7.1 Future Work 13
Acknowledgements 15
References 16






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List of Tables
Table 1 18
Ground truthing coordinates and habitat at each point. The columns
labeled type and descriptor describe the structure and make-up of each site.

Table 2 23
Results of the community composition, 30m photo transects conducted
on the side scan sonar reef (stj9b-stj 10a).

Table 3 24
Results of the community composition, 30m photo transects conducted
for a spur and groove reef in stj2a.

Table 4 25
Structure of NOAA's classification scheme

Table 5 26
Habitat classification scheme as presented in Prada Triana (2003).

Table 6 27
Habitat classification scheme used in this project.

Table 7 28
List of polygons that were either adjusted or drawn using the multibeam
data (NCCOS 2004, 2005).

Table 8 30
Total area for each habitat at the different hierarchical levels of the
broad habitat layer.

Table 9 31
Total area and percent contribution of each habitat in the reef
and hardbottom layer.






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List of Figures

Figure 1 32
Map of St. John depicting approximate boundaries of the Virgin Islands
National Park, Virgin Islands Coral Reef National Monument, and
area surveyed with side scan sonar.

Figure 2 33
Side scan sonar survey area with survey grids.

Figure 3 34
Ground truthing locations.

Figure 4 35
Ground truthing of submerged vegetation.

Figure 5 36






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Figure 14 46
Example of side scan sonar and multibeam to adjust polygons.

Figure 15 47
Differences between the broad habitat layer and reef and hardbottom layer.

Figure 16 48
Total area (km2) of each habitat in the broad habitat layer. The artificial
reef category has been omitted as it contributed less than 0.01km2.

Figure 17 48
The average area (km2) of polygons drawn for each habitat type in the
broad habitat layer. Again artificial reefs have been removed.

Figure 18 49
The total area (km2) of each habitat in the reef and hardbottom layer.

Figure 19 49
The average area (km2) of polygons drawn for each habitat in the reef
and hardbottom layer.






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Period: FY 2001-FY2005


1.0 Introduction and Background
The role of GIS in fisheries and coastal management has increased dramatically in recent years.
Fishery managers must consider such spatial questions as recruitment patterns across marine
ecosystems, the influence of ocean currents or habitat availability on fish populations (Rahel
2004). Advances in the technology used to identify and quantify benthic habitat are providing
information necessary for the spatial management of marine resources (Bax et al. 1999). Critical
to developing models for the spatial management of fisheries and habitat suitability indices is an
accurate description of the abundance and distribution of essential habitats (Battista & Monaco
2004) with knowledge of the association of fishes with those habitats (Bax et al. 1999).

The US Virgin Islands supports a large recreational fishery. Increasing pressures on the reef
resources has led to the need to identify and quantify critical habitats. Data are lacking on the
benthic habitats that support the recreational fisheries of the U.S. Virgin Islands. This is
particularly true of the deeper water shelf habitats of the Virgin Islands. Until recently, benthic
marine habitat maps in the US Virgin Islands have consisted primarily of nearshore, shallow
water environments. NOAA produced maps of nearshore habitats based on aerial photography
(Kendall, et al. 2001). However, use of aerial photography to map and define benthic habitats is
depth limited.

Two methods for collecting information on benthic habitats in deeper or turbid waters are side
scan sonar and multibeam. Recent side scan sonar surveys include McRea et al. 1999, Gingras et
al. 2000, Kendall et al. 2001, Cochrane & Lafferty 2002. Under a contract through the
Caribbean Fishery Management Council Geophysics GPR International (2003) conducted
multibeam and side scan sonar surveys offshore of St. Thomas and St. Croix. Geophysics GPR
International (2003) and Prada Triana (2003) created benthic habitat maps of the Hind Bank
Marine Conservation District, along the shelf edge south of St. Thomas.

In an effort to describe the benthic habitats of the US Virgin Islands the Division of Fish and
Wildlife initiated studies to map and identify benthic marine habitats for incorporation into a GIS
database. Early efforts include the characterization of habitat in the Cas Cay/ Mangrove Lagoon
and St. James Marine Reserves (Chapman 1996, Adams et al. 1998, and Volson 2001). Mapping
efforts include the use of an ROV to record video of subtidal habitats (Chapman et al. 1996).
This project met with substantial difficulties and was subsequently altered to include the use of
side scan sonar.

Since 2001 side scan sonar has been used to map subtidal habitats of the insular shelf south of St.
John as part of a US Fish and Wildlife Service funded grant. The objective of this grant was to
characterize the various shelf habitats that support recreationally important fisheries in the Virgin
Islands and to quantify the extent of each habitat type on the insular shelf platform south of St.
John. It is anticipated that the information gleaned from this study can be combined with the
nearshore habitat maps produced by NOAA/NMFS (Kendall et al. 2001) and the offshore habitat
maps produced by Geophysics GPR International (2003) and Prada Triana (2003). Through the
development of a series of habitat maps that span the entire shelf south of St. Thomas and St.
John fisheries resources can better be assessed and managed.






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2.0 Site Description
The island of St. John, US Virgin Islands is part of a volcanic chain of islands. The island is
dominated by steep mountainous terrain. Much of the island is part of the Virgin Islands
National Park, including some nearshore waters (Figure 1). In 2001 the Virgin Islands Coral
Reef National Monument (Figure 1) was created by presidential proclamation. South of St. John
the national monument covers approximately 4,369.27 ha of submerged land. The insular shelf
south of St. John is managed by several agencies, the National Park Service, the US Virgin
Islands territorial government, and the National Marine Fisheries Service. Therefore, there are
several agencies that potentially benefit from this project.

The shelf platform extends approximately 9 nm to the shelf edge (south drop) where depths
plummet from as little as 30 m to more than 1,000 m. Midway along the shelf platform is the
midshelf ridge, also commonly referred to as the midshelf reef. Depth along the bank shelf
shoreward of the midshelf ridge vary between 1 to 30 m and offshore of the midshelf ridge 30 to
50m.

The survey areas was designed to overlap with a fishery independent reef fish assessment
project, the Southeast Area Monitoring and Assessment Program Caribbean (SEAMAP-C) trap
study. The intent was, in addition to the objectives of this project, to allow for an analysis of reef
fish abundance and habitat associations. Therefore, an area of approximately 64 square nautical
miles was initially divided into sixteen 4 nm2 survey grids, numbered 1 to 16. These were
further broken into 1 nm2 grids, numbered la to Id, 2a to 2d etc.., extending from the south shore
of St. John to the shelf edge (Figure 2). Several of the 1 nm2 grids lie in waters off the shelf edge
and were therefore too deep to be surveyed and included in this project.


3.0 Side Scan Sonar and Multibeam
Side scan sonar and multibeam were collected during this project. Approximately 52.62 km2
(19.17 nm2) of side scan sonar data were collected. Of that, roughly 10 nm2 were collected
directly by the Division of Fish and Wildlife. The remaining area was collected through a
collaborative effort with the US Environmental Protection Agency. In February 2002 onboard
the OSV PWAnderson, the US EPA with DFW staff collected side scan sonar data of survey
areas stj9a to stj 12b (see Figure 2). This data was collected using a dual frequency Klein 595
towfish. Horizontal and vertical positioning was accounted for during the survey, however, that
information is not reported here. The data from this survey effort was provided to DFW and is
included in this report.

In addition to collecting side scan sonar data, DFW collaborated with NOAA's National Ocean
Service, National Centers for Coastal Ocean Science, Biogeography Team to collect multibeam
data south of St. John and St. Thomas. Although the multibeam data were not directly used to
delineate habitats, it was useful in discriminating feature boundaries and correcting the positions
of features.






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regarding this mission is available at the following website:
http://biogeo.nos.noaa.gov/foster mission 2004.

In 2005 another mission to collect multibeam data was conducted. During this mission
approximately 39.9 km2 of data was collected on the Grammanik Bank, St. Thomas, roughly
38.52 km2 in the Virgin Islands Coral Reef National Monument, St. John, and more than 18 km2
off of St. Thomas continuing from the 2004 data set (NOAA NCCOS, 2005). Information
regarding the 2005 survey mission is available at:
http://biogeo.nos.noaa.gov/foster mission 2005.


3.1 Geodetic Parameters and Positioning
The projection used during all survey operations was the Universal Transverse Mercator (UTM)
zone 20N. The datum used in all surveys was WGS-1984. Vertical positioning was not
accounted for during surveys since tidal variation is slight and manually correcting the data for
tidal influence was out of the scope of this project. It is not believed that vertical variation was
great enough to affect the positioning of features for the level of detail included in the final
habitat maps.

Vessel positioning was sent from the GPS unit to a laptop computer running the navigation
software HYPACK MAX by HYPACK, Inc. (formerly Coastal Oceanographics, Inc.). The
survey vessel followed preplanned survey lines from the positioning provided in the navigation
software. Survey lanes were created using the HYPACK MAX software. Twenty-five survey
lanes were created for each -1 nm2 survey grid. Each survey lane spanned 100 m in width, 50 m
on either side of the towfish. Approximately 25 m of overlap was created for each survey lane to
ensure 100% coverage while allowing for minimal vessel wander. Position information was
also routed to the sonar acquisition computer to provide real time positioning in the sonar record.


3.2 Survey Equipment

3.2.1 Survey Vessel
The survey platform for the majority of this study was DFW's 27 ft. diesel trawler R/V Lindsey.
A DC electric winch was used to control the length of cable and subsequently the towfish height
off the seafloor. The height of the tow point was 1.63 m from the surface of the water when the
boat was resting at dock. Positioning during surveys was accomplished using a WAAS enabled
Raytheon RC425 chart plotter GPS. The GPS receiver was positioned approximately midship
above the wheelhouse. The offset from the receiver to the tow point was 6.27 m. The survey
vessel was also fitted with a Furuno FCV-582L depth sounder.

The survey equipment operated off of a 24 volt battery bank charged via two solar panels
mounted to the top of the vessel. A 'true' sinewave 1000 watt power inverter provided 120 VAC
for the computers.






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3.2.2 Sonar System
The side scan sonar system consisted of a single frequency 300 kHz towfish by Marine Sonic
Technology, Ltd. The towfish was fitted with a stainless steel ballast, weighing approximately
45 lbs, mounted to the underside of the towfish. A wing depressor was also fitted on top of the
transducers to assist in the towfish descent. The sonar acquisition software that was used was
Sea Scan PC by Marine Sonic Technology, Ltd. The range of the sonar transducers was set at 50
m on either channel allowing for a 100 m swath width. Numerous towcables of varying length
were used throughout the project.


3.3 Survey Operations
The survey crew generally consisted of three people, the captain, the survey operator, and a deck
hand to assist in deploying and retrieving the towfish. During survey operations the vessel speed
was maintained between 2.5 to 3.5 knots. As mentioned above, the captain followed preplanned
survey lines. The sonar operator monitored the sonar image and adjusted the gain balance for
optimal image clarity. The survey operator also controlled the winch. Adjustments of the cable
altered the height of the towfish off the seafloor. The towfish was towed at an altitude of 3 to 7
m off the seafloor.

The SeaScan PC software by Marine Sonic Technology, Ltd was used during data acquisition.
During data acquisition the sonar operator recorded into an excel spreadsheet the ID number for
the survey line and the survey grid, the filename, date, time, direction of the ship, water depth,
the length of the cable out, and calculated the layback. The towfish did not have a depth
transducer so layback had to be calculated manually using the equation:
Layback = c2 -(d +h-a) 2+o

Where (c) is the length of cable out, (d) is the water depth, (h) is the height of the towpoint, (a) is
the altitude of the towfish (or height off the seafloor), and (o) is the offset. As mentioned above
in section 3.2.1 the height of the towpoint is h = 1.63 m and the offset o = 6.27 m. This layback
value was entered into the excel spreadsheet to facilitate manually adding layback into the raw
sonar image file later. Basic survey procedures and equipment setup are provided in Appendix I.


3.3.1 Post Processing the Data and Creating Mosaics
The side scan sonar image files were post processed to filter out ambient and vessel noise. Basic
post processing procedures are presented in Appendix II. The SeaScan PC software by Marine
Sonic Technology, Ltd. was used to post process the images. Once all the files for a survey day
were filtered they were recorded on a CD as a back-up.

Mosaics of the data were created with a 0.1 m resolution using the software Isis Sonar and
DelphMap by Triton Elics, Intl. The sonar image files were converted from .mst files to .xtffiles.
Each 1 nm2 survey grid was composed of 25 survey lines. Each survey line contained 10 to 12
survey files. All of the files for a single line were 'snipped' together. Layback was added
manually and the files were processed for the final mosaic. Mosaic procedures are presented in
Appendix III. After all 25 lines that compose a single survey area were mosaicked, they were






F-7: Recreational Fisheries Habitat Assessment Project 5
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exported as a single GeoTIFF file. Mosaics of each completed survey area are presented in
Attachment 1 and as on the included CD.


4.0 Ground Truthing the Sonar Images
Several methods were used to validate the side scan sonar images. Representative areas in the
sonar record were selected for examination. Additionally select features were examined. Select
features, such as reefs, were examined to validate the reef composition (i.e. living coral or
gorgonians) and assist in delineating the features edges in the final habitat maps. In all cases
underwater visual confirmation was conducted either by divers or digital drop video camera.


4.0.1 Diver Observations
Divers were used to provide feedback on the habitat and structure for selected areas or features
of interest. The coordinates for features were derived from the geo-referenced side scan sonar
mosaic. To ground truth areas, divers descended at pre-selected coordinates that were
representative of a certain habitat type. The divers swam transects following pre-selected
compass bearings. The direction of the dive was chosen such that different habitat types could
be crossed. Additionally, dive profiles were planned in an effort to locate one feature after
leaving another feature and cross a different habitat enroute. On each dive, one diver towed a
surface float. Once on the bottom the diver tugged on the surface float. The boat operator
navigated the boat directly above the divers and recorded the GPS coordinates. The second diver
took digital video or digital photographs of the habitat and recorded the habitat type. The dive
team then continued along the transect and when the habitat changed the dive team repeated the
above steps recording the new habitat. At the end of the dive the dive team tugged on the surface
float and recorded the habitat as above.


4.0.2 Drop Video Camera
In areas that were too deep to dive safely a drop video camera, by SeaViewer Cameras Inc., with
GPS overlay was used to determine the benthic habitat. As described above in section 4.0.1 GPS
coordinates were determined for selected areas or features. The drop camera was deployed and
drifted just above the bottom. A record of the position, date, time, depth, length of cable
deployed, and habitat was kept. GPS coordinates were overlayed on the video record so points
in the video could be extracted and the track of the drop camera drift could be positioned on the
side scan sonar images. The video was then analyzed and the habitat was described. The video
is provided on the included DVD as .wmv files.


4.1 Interpreting the sonar images
The coordinates recorded during the ground truthing were entered into ArcGIS 9.0 and overlayed
on the side scan sonar mosaic. This allowed the dive transect to be accurately positioned over
the corresponding habitats. Figure 3 illustrates the locations of ground truthing points conducted
by both diver surveys and drop video camera surveys. Each station was given a habitat
classification based on the divers' notes and video or photo documentation. Table 1 is a list of
ground truthing coordinates and the habitat information that was collected for each site.






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Habitat validation proved very useful in interpreting the side scan sonar images. With the 0.1 m
resolution in the side scan sonar mosaics numerous features could be described. At a small scale,
these communities can be delineated. However at the scale the habitat maps were drawn (see
section 6.0), the sonar mosaic becomes 'messy', due to noise in the images or layback not lining
up between survey lines. Thus in the final habitat maps these small scale communities were not
delineated. It should be noted however that if the need to define these communities at a small
scale, the side scan sonar images could allow for this on a line by line basis rather than for an
entire survey grid. In these figures, the photos correlate directly to the side scan sonar image.
Thus interpretation of the sonar image can be made. Figures 4-12 provide examples of habitat
validation and an interpretation of the sonar record.

Submerged vegetation can be distinguished in the side scan sonar mosaics. Seagrass habitats
were found in shallow waters and provided two types of sonar return (Figure 4). Seagrass
appeared as round patches or with a soft grainy appearance. In many instances, particularly in
the rhodoliths/ macroalgae habitat categories, the resolution of the side scan sonar image was
finer than applicable as discussed above. For example, in Figures 5 and 6 various rhodolith and
macroalgae communities are apparent. In shallower waters on the bank shelf (see section 5.1 for
zone description), rhodolith and macroalgae communities provide highly variable sonar returns.
One of the more interesting results is the presence of what ordinarily would look like sand
ripples caused by wave action. However, in most cases south of St. John these ripples are
actually formed by rhodoliths moved by wave action (Figure 5d-f). Additionally, the presence of
infauna can be seen in sand or rhodolith/ macroalgae communities (Figure 5m-o). Offshore of
the midshelf ridge rhodolith communities have very little fleshy macroalgae growth and appear
with a smoother texture in the side scan sonar record (Figure 6a-c). Generally rhodolith
communities 'turn over' from environmental forces at regular to semi regular intervals.
However, along the shelf platform of St. John they appear to be more stable since small hard
coral colonies can be found recruited to them (Figure 6d-f).

Reef and hardbottom habitats can also be distinguished in the sonar record. Spur and groove
habitats provide a strong sonar reflectance and have a striated appearance (Figure 7). Similarly
patch reefs rise steeply from the substrate and provide a strong sonar return (Figure 8). Bank
reefs and linear reefs provide a strong reflectance with numerous oblong structures (Figure 9).
Along the deeper reefs the interface between a reef and the surrounding habitat is often obscured
by the fact that along the edges of the main feature there is usually a mix of living coral and
gorgonians (colonized pavement) or scattered coral and rock (Figure 9a-c). Colonized bedrock
was found only near shore and resulted in a high relief and high reflectance in the sonar return
(Figure 10). Colonized pavement on the other hand was found throughout the survey area and
yielded differing sonar returns (Figure 11). The reflectance of the colonized pavement habitats
was dependant on the relief of the structures. The side scan sonar images from this habitat can
appear as spur and groove returns (Figure 1 la-c and 1 lj-l) except that in general they appear as
lower relief than a spur and groove coral reef habitat. Other side scan sonar images for the
habitat appear flat with a few scattered rocks or barrel sponges (Figure 1 d-f) and in some places
become difficult to discern from other surrounding habitats (Figure 1 lm-o). Finally along the
shelf platform offshore of the midshelf ridge an additional habitat type was found. The sonar
record appeared similar to a linear reef or bank reef except these areas consisted of rock,






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presumably old dead coral heads, which had limited hard coral growth and small sparsely
distributed gorgonians (Figure 12). These areas were classified as scattered coral/rock.

Several collaborations were established to augment ground truthing. Ground truthing was
conducted in collaboration with the University of the Virgin Islands during their efforts to locate
potential grouper and snapper spawning aggregations. These dives followed the protocol
discussed above and are included as sites in Table 1. Additional surveys conducted with
personnel from the University of East Anglia, England resulted in quantitative habitat analysis.
During these surveys five 30 m transect tapes were lain along a reef and which high resolution
digital photographs were taken every Im at a fixed height off the substrate. The photos were
analyzed by placing a set number of random points on each image and identifying the substrate
to species level. This allowed for the community composition to be described. Tables 2 and 3
provide the results of the two surveys conducted on reefs in survey areas stj 10a and stj2a,
respectively. Additionally the results of these two surveys are provided as hyperlinks in the final
ArcGIS project in the ground truthing layer.


5.0 Habitat Classification Scheme
Habitat classification schemes often vary regionally as well as locally. Unfortunately,
inconsistency in coastal habitat classification can hinder the use of habitat maps in coral reef
management and coastal resource management (Mumby & Harborne 1999). Therefore, efforts
were made in this project to maintain some level of consistency with existing local habitat
classification schemes (see Kendall et al. (2001), Geophysics GPR International (2003), and
Prada Triana (2003).

Due to the wide acceptance of the habitat classification scheme developed by Kendall et al.
(2001), where possible, the habitat categories developed by Kendall et al. (2001) were used in
this project. The habitat classification scheme developed by Kendall et al. (2001) was a
hierarchical scheme which was based largely on geomorphological characteristics. At the broad
scale geographic zones were delineated followed by discrete habitat units. Subcategories within
a particular habitat unit were also categorized with widely used structural definitions followed by
a fourth level that described the amount of cover (see Table 4). However, in many circumstances
the geomorphological approach used in Kendall et al. (2001) did not match the geomorphology
and habitat found on the shelf platform south of St. John.

Another habitat classification scheme as presented in Geophysics GPR International (2003) and
Prada Triana (2003) utilizes a more in situ descriptive classification in which the biologic
component drives the habitat classification (Table 5). As in Kendall et al. (2001) this was also a
hierarchical scheme in which the broadest level described the meta-community in a biological
context rather than geomorphologically. The next sublevels also use biological and ecological
descriptions. The fourth level describes the amount of cover of a particular habitat and is more
geomorphological than the first three levels, for example gorgoniann limestone' uses both a
biological and geomorphological description. In many instances the descriptions used by Prada
Triana (2003) match the habitats found along the insular shelf south of St. John more closely
than Kendall et al. (2001). However, this classification scheme is new and is not as widely used






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Therefore, this project attempts to utilize the classification scheme developed in Kendall et al.
(2001) with some modifications similar to Prada Triana (2003) and other modifications used
only to describe this project. The habitat classification scheme developed for this project is also
a hierarchical classification scheme (Table 6). The habitat maps developed by Kendall et al.
(2001) and Prada Triana (2003) utilized an automated habitat digitizer extension created by
NOAA's NOS Biogeography Team for ArcView 3.x. The habitat maps created in this project
were created using ArcGIS 9.0 and at the time the habitat maps were created for this project no
such extension was available. Therefore, the hierarchical scheme in the maps was developed by
entering the values for each polygon in the attribute table manually.

The classification scheme basically contains four levels with two descriptive columns (Table 6).
At the broadest level the zones are defined. The zones are geographic areas on the insular shelf
from the shoreline to the shelf edge. The next level is broad scale habitat. Broad habitats are
general substrate categories. The habitat level provides basic habitat information with general
definitions. The category level provides a more descriptive definition of the habitat. The two
additional columns in the attribute table 'Desc_l' and 'Form' provide descriptions about a
specific habitat category. The 'Desc_l' column identifies patch reefs as either individual patches
or aggregate patch reefs and identified the type of artificial structure. The 'Form' column
provides a description of the growth form of corals to be expected. The two growth forms are
shallow coral, which is the typical columnar and boulder type shallow water form, and plating
coral, which is typical of the deeper habitats. These areas generally have the plating growth
forms ofAgaricia spp. and Montastraea spp.


5.1 Habitat Classification Descriptions
Zone
Bank shelf This zone is similar in description to bank shelf as used in Kendall et al. (2001) in
that this zone is the shelf platform offshore of the shoreline except that this zone does not extend
out to the shelf edge. Instead bank shelf is used to describe the shelf platform between the
shoreline and the mid-shelf ridge, a historic (on geologic time scales) reef structure that follows
the contours of the shelf platform.

Midshelf ridge This zone describes the ridge like feature that run relatively horizontal to the
shelf edge and shoreline. This zone is offshore of the bank shelf. The midshelf ridge appears to
be a relict reef crest that has been flooded with sea level change. Thus it no longer displays the
classic back reef, reef crest, and fore reef zones. For this reason, all three zones are encompassed
in the midshelf ridge. The midshelf ridge is also commonly referred to as the midshelf reef,
however along the areas surveyed in this study the reef appears eroded, has limited live hard
coral and more represents a ridge.

Shelf platform The shelf platform is the zone between the offshore side of the midshelf ridge
and the shelf edge also referred to as the outer shelf platform in this report. This zone is similar
to the bank/ shelf described in Kendall et al. (2001) between the fore reef and the bank/shelf
escarpment. The shelf platform around St. John is generally deeper than the bank shelf.






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Shelf edge The shelf edge is similar to the bank/shelf escarpment in Kendall et al. (2001) and
in many places it forms a ridge like structure. The shelf edge is the zone that drops off
precipitously. Unlike the surveyed portions of the midshelf ridge, along the shelf edge lie
several deep coral reefs.

Habitat descriptions

Unconsolidated Sediment Unconsolidated sediment have little or no vegetation, see (Kendall
et al. 2001) for description.

* Sand Coarse sand has little submerged vegetation and few to no sessile invertebrates.
This is similar in definition to Kendall et al. (2001) and Prada Triana (2003).

Submerged Vegetation Submerged aquatic vegetation that can include seagrass and other
fleshy macroalgae (see Kendall et al., 2001 and Prada Triana, 2003 for descriptions).
Additionally, since rhodoliths are such a large component of the insular shelf in the US Virgin
Islands they were included in this category (see discussion below).

* Seagrass Predominately Thalassia testudinum and Syringodiumfiliforme in this survey
area. This habitat was only found nearshore. See Kendall et al. (2001) for a description.

* Rhodoliths/ macroalgae Any combination of rhodoliths (cf. Lithothamnion ruptile)
and other fleshy macroalgae. Rhodoliths form small calcareous nodules that act much
like rubble. In general rhodoliths move with wave action therefore there is usually little
epiphytic growth and rhodoliths could be categorized as rubble or unconsolidated
sediment. However in the deeper waters along the insular shelf of St. John wave energy
is reduced and rhodoliths exhibit varying degrees of epiphytic macroalgae growth even
including small Scleratinian corals. Rhodoliths are often associated with the fleshy
macroalgae Lobophora variegatta thus are combined into the single habitat category.

Reef and Hardbottom Any rocky or calcium carbonate substrate.

* Coral Reef Substrates composed of Scleratinian coral with varying degrees of live
cover.

o Spur and groove A coral reef with deep to moderately deep channels of
alternating sand and coral cut into the reef structure. Channels generally run
perpendicular to the shoreline or prevailing currents.

o Patch Reef Coral reefs that are separated from other reef structures. Patch
Reefs may vary in size and may be found isolated (individual) or in close
proximity to either other patches (aggregate) or coral reefs. Patch reefs generally
rise sharply off the surrounding substrate.

o Linear Reef A coral reef that follows the contours of the shoreline, midshelf
ridge, or shelf edge, see description in Kendall et al. (2001).






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o Bank Reef A coral reef that does not follow the contours of the shoreline,
midshelf ridge, or shelf edge as above. Bank reefs may have no particular
orientation and may lie either along the bank shelf or outer shelf platform.

* Colonized Hardbottom Substrate composed of limestone or bedrock that is not
primarily composed of living coral. This category may have limited Scleratinian coral
growth (usually small isolated colonies) and may have varying degrees of gorgonian
growth.

o Colonized Bedrock A rocky substrate usually along the shoreline that has
gorgonian growth and limited stony coral growth, see description in Kendall et al.
(2001).

o Colonized Pavement Calcium carbonate substrate that has eroded leaving a
substrate of relatively low relief. The predominate coverage is from gorgonians
and sponges and a limited amount of stony coral growth, see description in
Kendall et al. (2001).

Scattered Coral/ Rock Small coral colonies or rocks that are generally sparse in
unconsolidated sediment and are too small to delineate as patches, see sand and
invertebrate category in Prada Triana (2003) for description. Additionally, this category
includes a unique habitat that was found along the shelf edge and shelf platform which is
similar to colonized pavement and scattered coral/rock. These areas contain a high
density of limestone rocks that appear to be dead coral with some gorgonian growth and
limited stony coral growth (see Figure 12).

Artificial Any structure that is anthropogenetic in nature. These may be small boats or debris
that was either lost at sea or scuttled.


6.0 Benthic Habitat Maps
Habitat delineation was facilitated by side scan sonar imagery. A total of 17 GeoTIFF mosaics
were used to create the final habitat maps. ArcGIS 9.0 developed by ESRI was used to generate
the habitat maps in this project. Habitat features were visually discriminated in each side scan
sonar mosaic. The final habitat maps are presented as Attachment 2. Since the survey area was
such a large area, habitat maps that display the entire survey area may not be very useful.
Therefore, PDF files and a CD containing smaller sections of the habitat maps are also provided
(Attachment 3). These will be posted on the Division of Fish and Wildlife's web page:
http://www.vifishandwildlife.com.

Due to the highly variable quality of the side scan sonar imagery, the habitat maps were drawn at
differing scales. Two habitat maps were created (Attachment 2). The first was a broad scale
habitat map in which features were drawn at a larger scale of 1:2000. This layer of the map is
labeled the broad habitat category. At the scale this layer was drawn, it was often difficult to
discriminate the edges of certain features. Therefore there is likely to be some variation between
the drawn edge in the habitat map and the true feature in the field. NOAA created a habitat






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digitizer extension for ArcView 3.2 which allowed for the setting of a minimum mapping unit
(MMU) whereby an attempt to draw polygons that did not meet the MMU were not allowed.
Therefore maintenance of the MMU was automated. In this project, ArcGIS 9.0 does not have
such a feature therefore adhering to a strict MMU was difficult. Nevertheless, the minimum
mapping unit used in the broad habitat category layer was 50 m2, although some allowances were
made for the artificial category and a few other features that were isolated structures and could
be easily delineated.

Individual features that were larger than the MMU but were obviously a component of a larger
habitat and contained features smaller than the MMU were included in a single polygon for the
larger habitat unit. For example, in several scattered coral/rock habitat polygons some individual
features were larger than the MMU but a polygon was drawn around all of the features in that
habitat unit (see Figure 13). Additionally, at the broad scale, habitat polygons were drawn
around entire patch reef structures rather than individual patches.

The availability of the high resolution multibeam provided by NOAA's NOS Biogeography
Team (section 3.0) allowed for a high precision in positioning of certain features. Since
multibeam provides high resolution bathymetry it was useful in delineating the edges of features
with high relief such as reef and hardbottom habitats. For this reason a second layer was created
in which reef and hardbottom structures were delineated at a smaller scale and a higher level of
positional accuracy. In this layer, side scan sonar was still the primary tool for delineating
habitat. Multibeam was overlain with side scan sonar images where both were available. The
transparency in the properties for the side scan sonar layer were set at 40% transparent to allow
the viewer to see through the side scan sonar yet retain the ability to see the habitat features
(Figure 14). Further, because of the often poor positional accuracy of the side scan sonar, due to
manually inserting layback after data acquisition, some polygons were shifted to line-up with the
multibeam positioning (Figure 14). For the purposes of habitat delineation, polygons were
initially drawn around features in the side scan sonar images those polygons were then manually
shifted to correspond with the same feature in the multibeam. In a few instances, the side scan
sonar coverage ended on a reef and hardbottom feature. In these cases the multibeam was used
to finish constructing the polygon. Table 4 lists the polygons that were either shifted or drawn
using the multibeam data.

Combining the side scan sonar and multibeam technologies allowed for a highly detailed map of
reef and hardbottom features to be drawn. Also because of the strong sonar reflectance of these
structures, features were delineated at a scale of 1:600. Rather than attempting to adhere to a set
MMU in this layer, polygons were created around side scan sonar returns that were visually
distinct from one another. Therefore, the detail in patch reefs is far greater than in the broad
habitat layer. Only two features in this layer were not delineated at the individual structure level.
The scattered coral/rock features described above and in Figure 13 were too complex to delineate
individual features and maintain usefulness to the map user. Likewise due to the poor image
quality and the complex nature of the bank reef in survey areas stj 1 la and stj 1 Ib (Figure 15), a
lower precision can be expected in the boundaries for polygons of that bank reef. Further, within
any polygon in that area (Figure 15), it may be possible to have multiple habitats that were not
A-4- TI_ 41.- A ___-__. .. 41^ ,1 C 4 1 .,1 l-4P 1-.,-4- ,1 ..-, ......... i, A- 4-, ,,






F-7: Recreational Fisheries Habitat Assessment Project 12
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fleshy macroalgae and some small scattered coral that recruited on the rhodoliths. These
rhodoliths plains merged into colonized pavement or scattered coral/rock habitats then onto bank
reefs with plating coral. The boundaries between these habitats were often difficult to discern
visually.



6.1 Quantitative Description of Habitats Along the Insular Shelf

Habitat coverage is presented in Attachment 2 as habitat maps. Since two layers were created
for habitats, there will be some differences in the total area of any given habitat between the
layers. Therefore the total area covered by a habitat was determined for each layer. Figure 16
provides the total area (km2) each habitat covered in the broad habitat layer. At the highest level
in the broad habitat layer, submerged vegetation covered the 77.1% of the total surveyed area
while reef and hardbottom habitats covered 22.3% (Table 8). Interestingly, unconsolidated
sediment only accounted for 0.6% of the total surveyed area. However, if one were to consider
rhodoliths as unconsolidated sediment, this contribution would increase significantly. When
habitats are broken down in this layer, bank reef contributes 13.6% to the total area covered.
Table 8 lists the area and percent of the total area each habitat covered at each of three of the
hierarchical levels. The average polygon area for a particular habitat in this layer is presented in
Figure 17.

The total areas and percent contribution of each habitat in the reef and hardbottom layer are
presented in Table 9. As in the broad habitat layer, bank reefs contribute the most (55.95%) to
the total area covered by reef and hardbottom habitats. The total areas covered by reef and
hardbottom habitats are illustrated in Figure 18. The average polygon areas for each reef and
hardbottom habitat are presented in Figure 19. The average area for bank reefs was just over
0.12 km2. Knowing the average area for a habitat type may reveal some information as to how
large an average feature is in the survey area.



7.0 Discussion
Side scan sonar and multibeam technologies provided a platform to create benthic habitat maps
of the insular shelf south of St. John. Although the areas surveyed in this project are
discontiguous, they do provide critical habitat information for previously undescribed portions of
the insular shelf. One of the major assets gained in this project was the development of
collaborations with other agencies. These collaborations allowed for the collection of data that
otherwise would have been out of the scope of this projects ability. Collaborations with the US
EPA allowed for the collection of side scan sonar data over a large area along the outer shelf
platform (survey areas stj9a to stj12b). Further, through collaborations with NOAA/NOS, high
resolution bathymetric data was collected along large portions of the shelf platform and shelf
edge south of St. Thomas and St. John. This information, when available, can be combined with
the side scan sonar data to provide additional coverage. Maintenance of these collaborations
may provide opportunity to map additional areas in the future.






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Through the efforts to maintain conformity to existing habitat classifications, all existing habitat
maps (Kendall et al. 2001, Geophysics GPR International 2003, Prada Triana 2003) and those
produced in this study may be used in conjunction with each other to provide a broader
description of the habitats in the US Virgin Islands. Some interpretation may be necessary to
accommodate definition differences.

Through the combination of side scan sonar and multibeam technology, high resolution digital
habitat maps were created. However, the images from both the multibeam and side scan sonar






F-7: Recreational Fisheries Habitat Assessment Project 14
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addition to the basic species composition assessments, species health should be monitored,
particularly in light of increasing coastal development and ocean climate change.

In addition to the above, fish and invertebrate assessment should be conducted across a wide
range of the habitats contained in these maps. Coupling the spatial and quantitative habitat
information presented in these habitat maps with an assessment of the fish communities will
allow managers to develop better carrying capacity, stock abundance, and resource distribution
models.






F-7: Recreational Fisheries Habitat Assessment Project 15
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Acknowledgements

Many people were involved in this project at one time or another. Personnel (some no longer
with DFW) involved in this project were Shenell Gordon, Larry Aubain, Joseph Barbel, Ruth
Gomez, Efrain Hatchette, Stacy Albritton, Ron Sjoken, Michael Holt, Jennifer Messineo and
Sheri Casseau. Jos6 Rivera provided critical technical guidance and support. The US
Environmental Protection Agency assisted in conducting side scan sonar surveys. The National
Oceanic and Atmospheric Administration, National Ocean Service, National Center for Coastal
Ocean Science Biogeography Program provided multibeam and backscatter data as well as
technical support. The University of the Virgin Islands assisted in ground truthing efforts. E.A.
Whiteman, U.E.A., assisted in ground truthing efforts, provided habitat survey data, and
technical support.






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REFERENCES CITED

Adams A.J., Brin G.J., Green G. (1998) 1998 Benthic habitat assessment project, Division of
Fish and Wildlife, St. Thomas, U.S. Virgin Islands.

Battista T.A., Monaco M.E. (2004) Geographic information systems applications in coastal
marine fisheries. In: Fisher WL, Rahel FJ (eds.) Geographic information systems in fisheries.
American Fisheries Society, Bethesda, p 189-208

Bax N., Kloser R., Williams A., Gowlett-Holmes K., Ryan T. (1999) Seafloor habitat definition
for spatial management in fisheries: a case study on the continental shelf of southeast Australia.
Oceanologica Acta 22:705-719

Chapman G. (1996) Benthic habitat assessment project F-7-11, Division of Fish and Wildlife, St.
Thomas, U.S. Virgin Islands.

Chapman G., Meyers S., Kojis B., Dalmida-Smith B. (1996) Recreational fishery habitat
assessment project. Report No. F-7-11, Division of Fish and Wildlife, St. Thomas, U.S. Virgin
Islands.

Cochrane G.R., Lafferty K.D. (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

Geophysics GPR International I. (2003) Marine habitat mapping offshore St. Thomas and St.
Croix, U.S. Virgin Islands EEZ. Report No. M-03704, Caribbean Fisheries Management Council

Gingras M., Ven Tresca D., Downing J., Clark S., Fisher J., Donnellan M. (2000) Mapping
shallow subtidal benthic substrate in the Big Creek Ecological Reserve. Report No. Project 5,
Job 1, California Department of Fish and Game, Monterey

Kendall M.S., Kruer C.R., Buja K.R., Christensen J.D., Finkbeiner M., Warner R.A., Monaco
M.E. (2001) Benthic habitats of Puerto Rico and the U.S. Virgin Islands. Report No. 152, U.S.
National Oceanic and Atmospheric Administration. National Ocean Service, National Centers
for Coastal Ocean Science Biogeography Program, Silver Springs, MD

McRea J.E., Greene H.G., O'Connell M., Wakefield W.W. (1999) Mapping marine habitats with
high resolution sidescan sonar. Oceanologica Acta 22:679-686

Mumby P.J., Harborne A.R. (1999) Development of a systematic classification scheme of marine
habitats to facilitate regional management and mapping of Caribbean coral reefs. Biological
Conservation 88:155-163






F-7: Recreational Fisheries Habitat Assessment Project 17
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NOAA National Centers for Coastal Ocean Science (NCCOS). "Benthic Habitat
Characterization of NPS National Coral Reef Ecosystem Monuments in the US Virgin Islands
(USVI): R/V Nancy Foster Mission 2004". Project number NF-04-06. 2004. (Online). Silver
Spring, Maryland. .

NOAA National Centers for Coastal Ocean Science (NCCOS). "Benthic Habitat
Characterization of NPS National Coral Reef Ecosystem Monuments in the US Virgin Islands
(USVI): R/V Nancy Foster Mission 2005". Project number NF-05-06. 2005. (Online). Silver
Spring, Maryland. .

Prada Triana M.C. (2003) Delineation of benthic habitats from side scan sonar mosaics from the
Marine Conservation District, St. Thomas, Lang Bank and Mutton Snapper Closed Area in St.
Croix, U.S. Virgin Islands, Geophysics GPR International, Inc.

Rahel F.J. (2004) Introduction to geographic information systems in fisheries. In: Fisher WL,
Rahel FJ (eds) Geographic information systems in fisheries. American Fisheries Society,
Bethesda, p 1-12

Volson B. (2001) Recreational fisheries habitat assessment for St.Thomas/ St. John. Report No.
F-7, Division of Fish and Wildlife, St. Thomas, U.S. Virgin Islands.







F-7: Recreational Fisheries Habitat Assessment Project
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Period: FY 2001-FY2005


Table 1. Ground truthing coordinates and habitat at each point. The columns labeled type and descriptor describe
the structure and make-up of each site.
DATE X Y HABITAT CATEGORY TYPE DESCRIPTOR


4/30/2003
4/30/2003
4/30/2003
4/30/2003
5/15/2003
5/15/2003
5/15/2003
5/15/2003
6/18/2003
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
1/9/2004
3/25/2004
3/25/2004
3/25/2004
3/25/2004
3/25/2004
3/25/2004


-64.65691
-64.66065
-64.64530
-64.66256
-64.78197
-64.77953
-64.77545
-64.77599
-64.78035
-64.78243
-64.76740
-64.76768
-64.76903
-64.76912
-64.74023
-64.74083
-64.73985
-64.75315
-64.75370
-64.75377
-64.75348
-64.78043
-64.78421
-64.78518
-64.78590
-64.78660
-64.78661


deep water
deep water


18.25017
18.24725
18.26585
18.22458
18.30958
18.31063
18.31497
18.31481
18.30951
18.30483
18.23506
18.23498
18.23493
18.23493
18.23080
18.23068
18.23078
18.24345
18.24347
18.24347
18.24347
18.30470
18.30465
18.30433
18.30325
18.30321
18.30361


coral reef
coral reef
colonized hardbottom
colonized hardbottom
rhodoliths/ macroalgae
colonized hardbottom
seagrass
seagrass
small boat
colonized hardbottom
coral reef
coral reef
scattered coral/ rock
scattered coral/ rock
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
coral reef
coral reef
coral reef
coral reef
rhodoliths/ macroalgae
colonized hardbottom
colonized hardbottom
rhodoliths/ macroalgae
colonized hardbottom
colonized hardbottom


linear reef
linear reef
colonized pavement
colonized pavement
rhodoliths+macroalgae
colonized bedrock
patchy
patchy
boat
colonized pavement
linear reef
linear reef
scattered coral/ rock
scattered coral/ rock
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
linear reef
linear reef
linear reef
linear reef
rhodoliths+macroalgae
colonized pavement
colonized pavement
rhodoliths+macroalgae
colonized pavement
colonized pavement


shelf edge
dense

syringodium
syringodium



<30% live
<30% live



sparse
sparse
sparse
deep water
deep water
deep water
deep water
w/sponges




w/ sand veneer
w/ sand veneer


<30% sponges
<30% coverage




















<30% sponges
>70% coverage
<30% coverage



<30% coverage







F-7: Recreational Fisheries Habitat Assessment Project
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Period: FY 2001-FY2005


Table 1 cont'd. Ground truthing coordinates and habitat at each point. The columns labeled type and descriptor describe
the structure and make-up of each site.
DATE X Y HABITAT CATEGORY TYPE DESCRIPTOR


3/25/2004
3/25/2004
4/2/2004
4/2/2004
4/2/2004
4/2/2004
4/2/2004
4/2/2004
4/2/2004
7/19/2004
7/19/2004
7/19/2004
7/20/2004
7/20/2004
7/21/2004
7/21/2004
7/21/2004
8/18/2004
8/18/2004
8/18/2004
8/18/2004
8/18/2004
8/18/2004
8/18/2004
2/24/2005
2/24/2005
2/24/2005


-64.78670
-64.78713
-64.78413
-64.78560
-64.78573
-64.78580
-64.77466
-64.77583
-64.77496
-64.79280
-64.67720
-64.76790
-64.74860
-64.72550
-64.79780
-64.82357
-64.82240
-64.77564
-64.77602
-64.77650
-64.77616
-64.77648
-64.77712
-64.75716
-64.75228
-64.75170
-64.75093


w/ sand veneer
w/ sand veneer
dense
moderate
w/ sand veneer


18.30376
18.30433
18.30728
18.30736
18.30665
18.30601
18.30663
18.30628
18.30550
18.26760
18.33800
18.27500
18.27500
18.26980
18.26480
18.24958
18.24870
18.30117
18.30093
18.30106
18.30402
18.30413
18.30466
18.24423
18.29810
18.29743
18.29728


<10%
10-30% sc


colonized hardbottom
colonized hardbottom
rhodoliths/ macroalgae
rhodoliths/ macroalgae
colonized hardbottom
colonized hardbottom
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
colonized hardbottom
coral reef
colonized hardbottom
colonized hardbottom
coral reef
colonized hardbottom
coral reef
coral reef
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
rhodoliths/ macroalgae
coral reef
rhodoliths/ macroalgae
sand
scattered coral/ rock


colonized pavement
colonized pavement
rhodoliths+macroalgae
rhodoliths+macroalgae
colonized pavement
colonized pavement
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
colonized pavement
patch reef
colonized pavement
colonized pavement
linear reef
colonized pavement
spur and groove
spur and groove
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
rhodoliths+macroalgae
linear reef
macroalgae
sand
scattered coral/ rock


<10%

<30%
50-70%
30-50%
70%
70%
70% live
70% live
w/ sand c
70% live
50% live
50% live
w/ sand c
w/ sand c
50%
<30% sponges
<30% sponges
<30% sponges
<30% sponges

30-50% ma
<10%
10-30% sc


dense
dense
dense











dense
dense
dense
sparse
sparse
sparse
deep water
sparse






























-64.74809 1
-64.74735 1


18.29938 rhodoliths/ macroalgae
18.29963 coral reef
18.29960 coral reef


N9961 C
30027 c


al reef patch reef
al reef patch reef
al reef Datch reef


-64.73753 18.31112 coral reef spur groove
-64.75946 18.29308 rhodoliths/ macroalgae macroalgae
-64.75915 18.29295 boat decomposed boat
A 1'/Of-1 10 flfflor" 1- -. -1 -1AI







Page 21


is m


ss


ng from


original document







Page 22


is m


ss


ng from


original document










F-7: Recreational Fisheres Habitat Assessment Project
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Period: FY 2001-FY2005







Table 2. Results of the community composition, 30m photo transects conducted on the side scan sonar reef (stj9b-stjl0a).


Side-scan sonar reef
8/18/2004


18014.6538 64045.4296 18.24423 -64.75716
NUMBERS REPRESENT PERCENT OF TRANSECT


Transect Length 30m
CATEGORY 1 2 3 mean (SD) CATEGORY

GORGONIANS 00 03 00 01 02 GORGONIANS
SPONGES 19 1.3 23 1.8 0 SPONGES
ZOANTHIDS 00 00 00 00 00 ZOANTHIDS
MACROALGAB 345 371 358 358 13 MACROALOAB
COALLINE ALGAE 0.0 0.0 0.0 0.0 0.0 COALLINE ALGAE
DEADCORAL AL E 84 77 55 7 DEAD CORAL ALGAE
DISEASED CORALS 0.0 0.0 0.0 0.0 0.0 DISEASED CORALS
AN RUBBLE PAVEMENT 13 0 13 10 06 SAND RUBBLE PAVEMENT
OTHER, LIVE 03 03 03 03 00 OTHER, LIVE
UNKNOWNS 00 00 00 00 00 UNKNOWN
TAPE+ WAND+ SHADOW 00 00 00 000 000 TAPE + WAND + SHADOW
SHANNON WAVERED INDEX 18019 of ll t right)
926 H, including MACX as species in sum of trans.
NUMBERS OF POINTS PER TRANSECT
CATEGORY 1 2 3 sums CATEGORY
CORAL 16 164 170 50 CORAL
GORGONIANS 0 1 0 1 GORGONIANS
SPONGES 6 4 7 17 SPONGES
ZOANTHIDS 0 0 0 0 ZOANTHIDS

COALLINE ALGAE 0 0 0 0 COALLINE ALGAE

DISEASED CORALS 0 0 0 0 DISEASED CORALS
SAND RUBBLE PAVEMENT 4 1 4 9 SAND, RUBBLE PAVEMENT
OTHER, LIVE 1 1 1 3 OTHER, LIVE
UNKNOWNS 0 0 0 0 UNKNOWNS
TAPE + WAND+ SHADOW 0 0 0 0 TAPE+ WAND + SHADOW


t+w+s, noting. in sunms



Corals:
Branching
Lettuce
Finger
Plate/Sheet
Boulder/Mound
Cup/Flower
Bush
Fire corals

Ball sponge
Barrel/Vase sponge
Boring sponge
Encrusting sponge
Rope spone
Tube sponge

Boulder
Sand/Sediment
Rubble
Pavement


53.5483871 52.903226 54.83871 76
0 0 0

0 0.6451613 0.6451613 0
0.96774194 0.9677419 1.2903226 108
52.2580645 50.967742 52.903226 204
0.32258065 0 0
0 0 0 000
0 0.3225806 0 011


Diversity index summary table
*This sums all the points per species ofall transects to calculate the H'.


Categaoes


Acropora cervicomis (AC) coral
Acropora palmata (AP) coral
Acropora prolifera (APR) coral
Agarcia agarcites (AA) coral
Agarcia fragilis (AF) coral
Agarcia grahamae (AG) coral
Agarcia humilis (AH) coral
Agarcia lamarcki (AL) coral
Agarcia tenuifolia (AT) coral
Agarcia undata (AU) coral
Colpophyllianatans (CN) coral
Dendrogyra cylindus (DCY) coral
Diploria clvosa (DC) coral
Diploria labyrinthiformis (DL) coral
Diploria strigosa (DS) coral
Dichocoenia stokesii (DSO) coral
Eusmilia fastigiata (EF) coral
Favia fiagum (FF) coral
Isophyllia sinuosa (IS) coral
Isopyhyllastrea rigida (IR) coral
Leptoseris cucullata (LC) coral
Manicina areolata (MAR) coral
Madracis decactis (MD) coral
Madracis formosa (MAFO) coral
Madracis mirabilis (MM) coral
Meandrinameandrites (MME) coral
Montastraea amularis (MA) coral
Montastraea cavemosa (MC) coral
Montastraea faveolata (MFAV) coral
Montastraea franksi (MFRA) coral
Mussa angulosa (MAN) coral
Mycetophyllia alciae (MAL) coral
Mycetophyllia danaana (MDA) coral
Mycetophylha lamarckiana (ML)- coral
Mycetophyllia ferox (MF) coral
Oculina diffusa (OD) coral

Montastraea amularis complex (MACX)

Including MACX as MA


category sum for each transect
total nts. (ii /N)(l tii /N)


category sum for each transe,
total nts. (i /N)(l tii /N)


Categories


Pontes astreoides (PA) coral
Porites branneri (PB) coral
Porites divaricata (PD) coral
Porites furcata (PF) coral
Porites porites (PP) coral
Scolymia cubensis (SC) coral
Scolymia lacera (SL) coral
Siderastrea radians (SR) coral
Siderastrea siderea (SS) coral
Solenastrea bournmni (SB) coral
Solenastreahyades (SH) coral
Stephanocoenia michehnii (SM) coral
Tubastraea area (TA) coral
Millepora alcicornis (MILA) coral
Millepora complanata (MILC) coral
Millepora squarrosa (MILS) coral



# corals of known species
check of# corals of known species
total number of coral points
(includes un-identifiable species)
percent of coral species un-identifiable

Including MACX in MA Category


H'=
69 2.19
69
500

86.20

H'=


# corals of known species 500 -9.26
total number of coral points 500
percent of coral points identified to spp. 100.00


431 -11.44

431 -11.44


Data and summary provided by Liz Whiteman, U.E.A.


" "


" "`









F-7: Recreational Fishenes Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005












































Data and summary provided by Li iteman U 2


































Data and summary provided by Liz Whiteman, U.E.A. 24











F-7 Recreational Fisheries Habitat Assessment Project
Study 4 Mapping Essential Fish Habitat with Side Scan Sonar
Period FY 2001-FY2005





Table 3. Results of the community composition, 30m transect surveys for a spur and groove reef in survey area stj2a


NUMBERS REPRESENT PERCENT OF TRANSECT
110/1900 NUMBERS REPRESENT PERCENT OF TRANSECT
Transect Length 30
CATEGORY 1 1 5 7 5 3 mean (SD) CATEGORY


CORAL
GORGONIANS
SPONGES
ZOANTHIDS
MACROALGAE
COALLINE ALGAE
DEAD CORAL W/TURF ALGAE
DISEASED CORALS
SAND, RUBBLE PAVEMENT
OTHER, LIVE
UNKNOWNS
TA-PF +Am81ANI3 +AAnnaa


0.0 0.0 0.0 0,0 0.0 0.0 0.0 CORAL
35 2 31 0 33 5 300 41 0 34 1 43 GORGONIANS
1.3 3.5 1.0 0.0 0.0 1.2 1,5 SPONGES
16 1 194 20 6 18 1 21 3 19 1 21 ZOANTHIDS
0.0 0.0 0,0 0,0 0.0 0.0 0,0 MACROALGAE
97 26 29 10 43 41 33 COALLINE ALGAE
0.3 1.6 0,0 0,0 0.0 04 0.7 DEAD CORAL W. TURF ALGAE
00 00 00 00 00 00 00 DISEASED CORALS
0.0 0.0 0.0 0.0 0.0 0.0 0.0 SAND, RUBBLE, PAVEMENT
00 00 00 00 00 00 00 OTHER, LIVE
0.0 0.0 0,0 0,0 0.0 0.0 0,0 UNKNOWNS
nn nn nn nn nn nn no nnn p -mn -annaAI aI


SHANNON WEAVERDIV.INDEX !SENT POINT 0.00 0.00 0.00 0.00 -15,37 H, using sums fall transeds (see right)
-15 37 NH, including MACX as species in sum of trans
NUMBERS OF POINTS PER TRANSECT
CATEGORY 0 96774194 4 83870968 741935484 483870968 3 sums CATEGORY


GORGONIANS 109 96 104 93 123 525 GORGONIANS


ZOANTHIDS 50 60 64 56 64 294 ZOANTHIDS


COALLINE ALGAE 30 8 9 3 13 63 COALLINE ALGAE
,6- ,- s ... ru.;; ,. .: I .. . : T F,: ,. u ... r -6
DISEASED CORALS 0 0 0 0 0 0 DISEASED CORALS


OTHER, LIVE 0 0 0 0 0 0 OTHER, LIVE


TAPE +WAND+SHADOW 0 0 0 0 0 0 TAPE +WAND + SHADOW
t+w+s, not incl. in sums



Data provided by E A Whiteman, UEA


Diversity index summary table
*This sums all the points per species of all transects to calculate the H
category sum for each transect
Categories total pts (n /N)(In ni /N) Categ
Acropora cerv 7 031 Pontes
Acropora pain 0 0 00 Pontes
Acropora proli 0 00 Pontes
Agancia again 0 000 Pontes
Agancia fragile 8 033 Pontes
Agancia grahn 0 000 Scolymi
Agancia humi 0 000 Scolymi
Agancia lama 0 000 Sideras
Agancia tenul 41 -0 08 Sideras
Agancia unda 3 020 Solenas
Colpophyllia n 8 033 Solenas
Dendrogyra c, 1 010 Stephar
Diplona clivos 1 010 Tubastr
Diplona labyn 0 000 Millepor
Diplona stgo 0 0 00 Mllepor
Dichocoena s 0 000 Millepor
Eusmilia fast 0 0 00
Favia fragum 0 000
Isophylla sinu 0 0 00
Isopyhyllastre 0 000 check o
Leptoserns cu 0 0 00 total nu
Manicina areo 0 000 (include
Madracis deci 1 0 10 percent
Madracis form 313 -1737
Madracis mira 0 000 Includir
Meandrina me 32 0 14
Montastraea i 0 0 00 total nur
Montastraeac 0 0 00 percent
Montastraea f 0 000
Montastraea f 0 000
Mussa angulo 0 000
Mycetophyllha 0 000
Mycetophyllia 0 000
Mycetophyllha 0 000
Mycetophyllia 14 0 37
Oculina diffuse 0 000


category sum for each transect
total ots (n /NnIn ni /N)


ones


astreoldes (PA) coral 54 -0 50
brannen (PB)- coral 0 0 00
divancata (PD) coral 0 0 00
urcata (PF) coral 0 0 00
pontes (PP)- coral 0 0 00
a cubensis (SC) coral 0 0 00
a lacera (SL) coral 9 0 34
trea radians (SR) coral 0 0 00
trea siderea (SS) coral 0 0 00
;trea bournonl (SB) coral 0 0 00
trea hyades (SH) coral 5 027
nocoena mlchelin (SM) coral 0 000
aea aurea (TA) coral 0 0 00
a alcicornis (MILA) coral 0 0 00
a complanata (MILC) coral 0 000
a squarrosa (MILS) coral 38 0 00


H'=
# corals of known species 0 -1537
f# corals of known species 535
rber of coral points -15
s un-identifiable species)
of coral species un-identlfiable 357995


ng MACXin MA Category H'=
# corals of known species 535 -1537
mber of coral points -15
of coral points identified to spp -3479 95


Montastraea A


Including MA(


Data and summary provided by E A Whteman, U E A






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Habitat
Third level (structural description)
Fourth level (level of cover)

*Zones:
Land, Shoreline Intertidal, Lagoon, Back Reef, Reef Crest, Fore Reef, Bank/ Shelf,
Shelf Escarpment, Unknown
Habitats:
Unconsolidate Sediments
Sand
Mud
Submerged Vegetation
Seagrass
Continuous
Patchy (4 subcategories)
Macroalgae
Continuous
Patchy (2 subcategories)
Coral Reef and Hardbottom
Coral Reef and Colonized Hardbottom
Linear Reef
Spur and Groove
Individual Patch Reef
Aggregated Patch Reefs
Scattered coral/Rock in Unconsolidated Sediment
Colonized Pavement
Colonized Bedrock
Colonized Pavement with Sand Channels
Uncolonized Hardbottom
Reef Rubble
Uncolonized Pavement
Uncolonized Bedrock
Uncolonized Pavement with Sand Channels
Other
Land
Ar M







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005




Table 5. Habitat classification scheme as presented in Prada Triana (2003).
Habitat
Meta-community Community Sub-community Habitat types Codes

Continuous
coral high relief Corals COCO
coral patch Coral Patch COPA
corals Coral
Coral and gorgonians coral low relief Limestone COLI
on consolidated Gorgonian
sediments gorgonianan patch Patch GOPA
Gorgonian
plains Plains GOPL
gorgonians Eea
Elevated
elevated plains Gorgonians ELGO
Dense Grass DEGR
Sparse Grass SPGR
Grass-
seagrass Seagrass Gr
Invertebrates GRIN
Grass Halo &
Submerged Aquatic Coral Patch HALO
Vegetation (SAV) on D la AL
unconsolidated Dense Algae DEAL
unconsolidated
Sparse Algae SPAL
sediments algae on sand Sparse Algae SPAL
Algae &
macro-
a Invertebrates ALIN
algae
Shallow
algae on silt Algae SHAL
Deep Algae DEEP
Sand
Invertebrates SAIN
S coarse sand Sand no
sand
Ripple SANR
Bare or mixed invertebrates, Ripple SANR
Sand Ripple SARI
on unconsolidated Sand Ripple SARI
sediments fine sand Fine Sand FIMU
sediments -
Mud-
Invertebrates MUIN
silt mud
Mud Bare MUBA
Mud Reef MURE













26







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Table 7. List of polygons that were either adjusted or drawn using the multibeam
data (NCCOS 2004, 2005). The columns refer to columns in the attribute table.
The column Id refers to the polygon Idand the adjmbeam identifies what adjustmetn was made.
Id habitat category desc 1 adi mbeam


coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
colonized hardbottom
colonized hardbottom
coral reef
coral reef
colonized hardbottom
colonized hardbottom
colonized hardbottom
colonized hardbottom
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef
coral reef


patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
colonized pavement
colonized pavement
patch reef
patch reef
colonized pavement
colonized pavement
colonized pavement
colonized pavement
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef
patch reef


individual
individual
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
individual
aggregate
aggregate
aggregate
aggregate



aggregate
aggregate





aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate
aggregate


drawn
drawn
shifted
adjusted edge
adjusted edge
adjusted edge
adjusted edge
shifted
drawn
shifted
shifted
shifted
shifted
drawn
adjusted edge
adjusted edge
adjusted edge
drawn
drawn
drawn
drawn
drawn
drawn
drawn
drawn
drawn
shifted
shifted
shifted
shifted
shifted
drawn
shifted
shifted
shifted
shifted
shifted
shifted
shifted
adjusted edge
shifted
drawn
shifted
shifted
shifted
shifted








Recreational Fisheries Habitat Assessment Project
ly 4: Mapping Essential Fish Habitat with Side Scan Sonar
"I rV onn1 Urvonn;


coral reef
coral reef
ro-l rnPf







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Table 8. Total area for each habitat at the different hierarchical levels of the broad habitat layer.
Area Percent Area Percent Area Percent
Broad Habitat km2 of area Habitat km2 of area Category km2 of area

unconsolidated
sediment 0.32 0.6% sand 0.32 0.6% sand 0.32 0.6%
submerged
vegetation 40.55 77.1% seagrass 0.28 0.5% seagrass 0.28 0.5%
reef and rhodoliths/ rhodoliths/
hardbottom 11.75 22.3% macroalgae 40.27 76.5% macroalgae 40.27 76.5%
colonized spur and
hardbottom 1.58 3.0% groove 0.15 0.3%
coral reef 8.31 15.8% patch reef 1.00 1.9%
scattered
coral/rock 1.86 3.5% linear reef 0.03 0.1%
bank reef 7.14 13.6%
colonized
bedrock 0.01 0.0%
colonized
pavement 1.57 3.0%
scattered
coral/ rock 1.86 3.5%
The category for artificial structures was removed because they constitute such a small area.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005




Table 9. Total area and percent contribution of each
habitat in the reef and hardbottom layer.

Area Percent
Habitat km2 of area

spur and groove 0.15 1.49%
patch reef 0.27 2.75%
linear reef 0.02 0.25%
bank reef 5.49 55.95%







Recreational Fisheries Habitat Assessment Project
y 4: Mapping Essential Fish Habitat with Side Scan Sonar
d: FY 2001-FY2005













St. John






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


St. John


v^r\/\


0 05 1 2 3 4


1A 1B 2A 2B A 4A 4B



1C 1D 2C 2D 3C 3D 4C 4D


5A 5B 6A 6B 7A 7B 8A 8B



5C 5D 6C 6D 7C 7D 8C 8D


9A 9B 10A 10B 11A 11B 12A 12B



9C 9D 10C 10D 11C 11D 12C 12D



13A 13B 14A 14B 15A 15B K 16B



13C 13D 14C 4D 15C 15B 16C 16D
I1I


Figure 2. Side scan sonar survey area with survey grids. Shaded grids indicate survey areas
that were completed in this project.


CJO









w- E
(


<:







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


0 0.5 1 2 3 4


Figure 3. Ground thing locations ical
Figure 3. Ground truthing locations


W+E
Miles
S


~3~3~






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Scale 1:1000







a. -, b. c.










d. -e. f.

Figure 4. Ground truthing of seagrass habitats (a) side scan sonar image of dense
seagrass patches, (b-c) notice the dense patches in the background, sparse patches in the
foreground, and sand channels, (d) side scan sonar image of continuous seagrass
Syringodium sp., and (e-f) sparse seagrass.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Scale 1:1000
,:. .-'-i.%


,&1 C.


M. .n.t _'O N -W 0o.
Figure 5. Ground truthing of rhodoliths/ macroalgae habitats on the insular shelf
platform, (a-c) rhodoliths with little to no fleshy macroalgae, (d-f) swells and wave action
forms ripples in the rhodoliths even at depths greater than 33m, (g-l) rhodoliths with
fleshy macroalgae, usually Lobophora sp., produce bands of light and dark in the side
scan sonar return, with the dark bands usually being rhodoliths with Lobophora sp. and
the lighter areas usually contain sparse macroalgae, (m-o) the appearance of 'holes' in the
side scan sonar record are indicative of areas with a dense population of infauna.


41%~"








ti


a. .


~?I


tt







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005




Scale 1:1000









a. c-



._ .


C Var.Ik I.'r. :._ .. .-







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


KuLt1\t11L111 ILaUUXLt \aU, U, %S, /, UllS II\Jt1 "aUX a ,1 tJ I 1\jt, V-JXU1, tll clIIULa
return (a). Patch reefs also have varying degrees of stony corals and gorgonians (b, c, e,
f). The above images contain examples of shallow water growth forms.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005




Scale 1:1000








a. b. c.
Figure 8. Spur and groove habitats yield distinct banding in the sonar return (a), and have
deep groove features (b, c) that orient perpendicular to the shoreline of prevailing
currents.






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Scale 1:1000


j. k -- 1.
Figure 9. Coral reefs on the outer shelf platform, south of the mid-shelf reef system, (a-i)
and along the shelf edge (j-l) are predominately comprised of plating forms of Agaricia
spp. and Montastraea spp. On these deeper reefs the transition from sand or rhodoliths to
coral reef (a-c) is often difficult to discern as no discrete boundary exists. However, the
arrow in (a) probably indicates the sand to coral interface.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


-e 10.
)relin(
;es (b,


b.
Colonized bedrock ap]
features and can be cc
',






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


a. b.


g. f h. W1.
Figure 11. Colonized pavement has numerous side scan sonar returns that appear to
correspond to position on the shelf platform, substrate topology, and the overlying
invertebrates. Along the bank shelf spur and groove features are apparent (a-c) but have
a smoother appearance than coral reef spur and groove. Across the plateau, also often
referred to as gorgonian plains or hardgrounds, the sonar image appears flatter and has a
grainy texture (d, g). Along this region a sand veneer covers portions of the limestone
substrate which is colonized by large sponges, gorgonians and sparse corals (e, f, h, i).







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005





Scale 1:1000





Z. 16"-b_.- ,-


j - ". k. 1..









m. n. o.
Figure 11 cont'd. Colonized pavement along the mid-shelf ridge appears as linear reef or
again as spur and groove (j-l). Further out along the shelf edge the sonar return appears
flatter with eroded edges. Here it is difficult to discriminate between colonized pavement
habitats and rhodoliths habitats (m). On the colonized pavement gorgonians are often
sparse (n, o).






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005






Scale 1:1000








Figure 12. An additional habitat along the outer shelf platform is similar to both
colonized pavement and scattered rock (a-c). This habitat consists of limestone substrate
that appears to be dead coral and has some gorgonian growth with little stony coral
growth. This habitat has been classified in this project as scattered coral/ rock.






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005






Pi"
--,--. ..- 7:-. .---



be larger than the MMU of 50M2 (yello .

"- "- ... > '% t' '"



a. b. X .' -. --,-., .


Figure 13. Example of (a) scattered coral/ rock (red square) in which the final polygon
was drawn around the entire habitat but (b) individual features within that habitat could
be larger than the MMU of 50m2 (yellow circle).







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


-I I-


"0. 1 IF

71~' ra~~EcF


__~ -* -, -'i~iY~~~5lji
h sII -i' *
k :


r -~ -


V U~


S14.
[to n
, as t


emem"me






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005






















1. b.

Figure 15. Differences between the bank reef in stj 1 la and stj 1 Ib at (a) the broad habitat
scale and (b) the smaller scale of the reef and hardbottom layer. Notice that in some
cases the habitat of certain polygons in the smaller scale layer changed from that of the
broader scale layer. The large yellow polygon in (b) is classified as scattered coral/ rock
in the smaller scale layer and (a) is included in the bank reef in the larger scale layer.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


45.00

40.00

35.00

30.00

25.00

20.00

15.00

10.00

5.00

0.00


sand seagrass rhodoliths/ colonized coral reef scattered
macroalgae hardbottom coral/ rock
Habitat


Figure 16. Total area (km2) of each habitat in the broad habitat layer. The artificial reef
category has been omitted as it contributed less than 0.01km2.


A
C,
d o0
^ ^ 9


Habitat


Figure 17. The average area (km2) of polygons drawn for each habitat type in the broad
habitat layer. Again artificial reefs have been removed.






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


6.00


5.00

4.00

S3.00

2.00

1.00

0.00


Figure 18.


0.14

0.12

0.10

0.08

0.06

0.04

0.02

0.00


I-


spur and patch reef linear reef bank reef colonized colonized scattered
groove bedrock pavement coral/ rock
Habitat


The total area (km2) of each habitat in the reef and hardbottom layer.


spur and patch reef linear reef bank reef colonized colonized scattered
groove bedrock pavement coral/ rock
Habitat

Figure 19. The average area (km2) of polygons drawn for each habitat in the reef and
hardbottom layer.


I






F-7: Recreational Fisheries Habitat Assessment Project Appendix I
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Procedures for side scan sonar acquisition

Equipment Setup
1. install WAAS GPS and primary depth sounder
2. Place the computer tower "acquisition computer" in the mounts under the
Lindsay's cabin
3. place a battery back-ups in the cabin as well and plug it into the power inverter
4. plug the acquisition computer tower into the UPS
5. set the navigation laptop in the platform above the steering for the Lindsay
a. Install the hardlock key into the printer port on the back of the laptop
(Note: the navigation software will not run without this adapter)
b. connect the power cord to the UPS
c. connect one end of the split NMEA connection (serial cord labeled
"NMEA connection") to the laptop and one end to the wires hanging down
from the GPS unit
d. the other end of the NMEA connection goes into serialport 1 on the data
acquisition computer, this end is labeled "to tower"
6. mount the flat screen monitor in the ball and joint mount by the passenger seat on
the port side of the cockpit. The flat screen is powered by 12volts and connects to
the 2pin connector in front of the ledge. The monitor cable runs down to the data
acquisition computer.
7. Data acquisition computer connect the monitor, connect the mouse, connect the
keyboard (Note: there is a new wireless keyboard and mouse in the SSS office for
the new tower) make sure the NMEA connector is connected as described above,
connect the small black wire that runs alongside the power inverter to the
grounding bolt in the back of the tower.
8. Connect the deck cable into the pigtail that runs out of the base of the tower
9. connect the wet end of the towcable to the towfish (it is advised to spray a little
WD40 on and into the towfish connector) also be sure to connect the braided
harness on the cable to the stainless steel safety wire. Run the cable through the
sheave block assembly.
10. Power on the inverter and UPS and all computers


Navigation Laptop
1. start HypackMax
2. click on survey and select survey a new screen starts with several windows open
3. to test the NMEA connection restore the nmea window at the bottom, it should
scroll lat and long data
4. go to line and select selectfile now navigate to select the file that you want to
survey






F-7: Recreational Fisheries Habitat Assessment Project Appendix I
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
6. Once at the site and the towfish is launched line-up for the first survey line use the
Left Right indicator window to aid steering
7. The data display window will show the line to be surveyed, logging status, and
other relevant information.
8. Once you get on the line hit 'ctrl s' to start logging the GPS data at the end of a
line hit 'ctrl e' to end logging, the next line will automatically be the active line.
9. To start a new area go to line unload file and the go to select file







F-7: Recreational Fisheries Habitat Assessment Project Appendix I
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
a. Enter the information under the headings, headings in Blue will update
automatically but you have to enter a new direction change and date
etc...,
b. Enter the filename given in the Data storage status window at the start of
a line, end of line and whenever you winch in or out the cable. Enter the


line or 'eol' for the end of line.







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


I I i Dalta Storace Info


Appendix I







F-7: Recreational Fisheries Habitat Assessment Project Appendix I
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005





















Found under Options -3Settings--Vser
Startup and Shutdown Options
JI Show Multi-Frequeny warning at startup




























% I I I.
I Prompt before save default settings
Automatic Operation
Respond automatically to dialog prompts.
The default response for all dialog boxes
will be selected and all dialog operations
are logged to the SSPCMSG.TXT file.

Runtime Options
VI Prompt and record transducer frequency
Vj Display status box when save data
Vj Set minimum pulse rate (1 pulselsec]
Force 3 pulses/meter at 100m range


Found under Options --Settings~, User








Length Speed
Metric m, km > Metric mIs
English ft, mi Metric kmjh
Nautical -yd, nm English ft/s
English mph
Nautical knots

Location






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


I i InpuI ett x


Navigation Input
> Off
'- NMEA 0183




COG Display
* True
SMagnetic

Time Out Isecondsl


d RMC
I RMA


i GGA
J GLL
I GTD


Communication Port
COM1
4800-8-N-1


d VTG
I HDT
J ZDA


Comm..


Under external navigation-- Settings


Appendix I


Time Since Last Valid Fix: 10O
Maximum Allowed for Interpolation: 10


SiJ







Appendix II


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY2001-FY2005


Post Processing Side Scan Sonar I


iter = Data acquisition computer (LINDSEY computer)




Appendix II


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


II


MI Filter II ^Zoom|^^
L*Lenj1Are1l
-o a 7 1 C 11
----^^B\\;il(

,-II


_.... .






F-7: Recreational Fisheries Habitat Assessment Project Appendix II
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005



Original Filtered











Sobel-Fast
Minimal
Median
Maximal

Spike 2
Spike 1-Fast
IReset Undo 8-bit 6-bit
ir I Data Image





8-bit Data to
6-bit Image I Inv I




Click record button before running filter

Entire Image Filter Button

Figure 2: Filter Dialogue Window






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
Mosaic Procedure Basics


Computer = MOSAIC computer

In Isis Sonar
1. Playback all of the xtf files for a line to check them for targets [to make note of] and
determine if they are usable images.

2. Bottom Track all the files for that survey line before continuing. The files must be
accurately bottom tracked in order to get the towfish altitude. The towfish altitude is
used to determine layback. [Bottom tracking may be done after snipping several files
together but must be done beforefixing time or generating an ASCII report.]

2.1. To Bottom Track Playback a file in Isis. In the Isis Bottom Track dialogue
box be sure Method is set to Amplitude. A thin red line should run vertically in
the Main Waterfall Window this is the bottom track line (Figure 1). If this line
wanders off or cuts into the bottom adjust the Level (a higher % moves the line
deeper towards the bottom or cuts into the image, a lower % moves the line
towards nadir, away from the bottom). Holdoffis the distance the towfish is off
the bottom (altitude) make a guess at what this should be (generally we run at an
altitude of 3-5m so set the holdoffat 2.5m) the track line will not search for the
bottom return until beyond the holdoff level. [Under Options you can put a
check in the Save newly tracked altitude back into the original XTF file box.
This will save the new bottom track (Note: if you have problems uncheck the
box and then just start over and recheck the box when you get the right
adjustments, it will continuously save the new bottom track over previous data).
You can save portions of the new bottom track by checking and unchecking the
box multiple times in one file.]
2.1.1. Replay the line and check the bottom track (to do this be sure to uncheck
the Save newly tracked altidude box and turn off the bottom track in the
Bottom track dialogue box). While you replay the line you can hit the space
bar to pause the playback where the bottom track wanders. See Figure 1 for
the slowdown and speedup playback buttons. If the bottom track wanders
click in the main waterfall window where the track leaves the bottom. Then
go to File- Goto-Ping-OK (this will take the file back to the last point you
clicked in the waterfall window when you replay the line). Adjust the Level
and Holdoff again and replay the segment (by hitting the space bar again),
pause it again and keep going back to the Ping until you get it at the right
level. Then let the line play through being sure to save the new bottom track
segment by placing a check in the Save newly tracked altitude box.

3. Snipping files: If depth or the amount of cable out changes during a survey line you
must process only those files that have the same depth and cable out as one. If two
files have differing amounts of cable out process those separately, they will have






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
different layback. Snip files with the same depth and cable out together to make one
longer file.

3.1. Snipfiles to snip files together in Isis Sonar go to Tools ->Snip File create a
filename for the new file you are creating (example: 101 103.xtf for snipping
files 20nov 10.xtf, 20nov102.xtf, and 20nov 103.xtf together) playback the files
you want to snip in the proper order. When you are done playing back the files
turn off the snipfile function by going back to Tools -> Snip File and clicking it,
this will automatically turn it off. You can also hit the shortcut key on the tool
bar that looks like scissors (Figure 1).

4. FixTime You must fix time in the xtffiles so the navigation and time stamps will
run smoothly. If you do not do this you may have smearing of pixels or gaps in the
final mosaic.
4.1. First copy and paste thefixxtime.exe file to the folder you are working in. The
original can be found in C:\TEI\fixxtime.exe
4.2. To Fixtime replay the snipped file you just created or a single file not snipped.
Write down the time (see Figure 1) at the start of the file and at the end of the
file. Add up the total number of pings in the snipped file (there are 1000 pings
per one file so if you snipped 3 files together you have 3000 pings).
4.3. Open a DOS prompt change the directory to the folder that contains the file
you want to fix time in. Do this by typing in EXACTLY
cd\Documents and Settings\DFW\My Documents\Side Scan Sonar\SSS
Images\stj5a\20 nov 02 (note: stj5a is the folder for the area you
are mosaicking and 20 nov 02 is the folder that contains the file you want to fix
time, these will change to current files you are working in that you copied the
Fixxtime.exe to). See Figure 2 for an example of the Fixxtime dialogue window.
4.3.1. Next type fixxtime (Yes, you must type in two xx's in
fixxtime.)
4.3.2. You will be asked to type in the name of the file. Enter the entire filename
(example: 101 103.xt/)
4.3.3. Then you will be asked to enter the start date and time. This can be found
in the Parameters Window of Isis (see Figure 1).
4.3.4. Then enter the end date and time as above
4.3.5. Then enter the number ofpings in the file
4.3.6. When it is finished fixing the time replay the file in Isis Sonar. The time
and number of pings should scroll sequentially in the Parameters Window.
Note: Sometimes SSPC review (on the Lindsay computer) alters the time stamp
and date (if one file was post processed and saved one day and a second file was
post processed at a later date they will be assigned different dates and times) You
MUST change the date and time for the start date and end date to match.
[Example: if one file was dated 25nov02 and the second file was dated 16nov02
you must enter the same date for the start and end infixxtime.exe. Similarly the
time may be off. If one file time was 17:05:02 and the end file time on the second
was 10:23:26 you must adjust the time to run sequentially. You can do this by
looking at the original files' time stamps for start and finish and changing the time






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
in one file, if file 20nov]O1.xtfhas a start time of 17:05:02 and end time of
17:07:30, and file 20nov]02.xtfhas a start time of 10:23:26 and an end time of
10:26:26 you can change file 102's time to start 1 second after file 101, so it
would start 17:07:31 and end 3 minutes later (because it's total run time was
exactly 3 minutes (10:26:26 minus 10:23:26 = 3 minutes) so the end time for the
file infixxtime.exe will be 17:10:31].

5. Layback-Next generate an ASCII Report. To do this go to Tools->ASCII Report,
put a check in the box for Form 1 and click Setup Form 1. You should get a form
that looks like Figure 3. Put checks in the corresponding boxes. Change the time in
the When to output box to every 1 second. Click the Browse button to create a text
file in a folder you specify. Click OK and then Click OK in the ASCII Report
window. Replay the file (Note: you can just hit the home key on your keyboard to
replay the line from the beginning). After the file plays back turn off the ASCII
Report by going back to Tools ->ASCII Report and removing the check in the Form
1 Box.
5.1. Go to the folder you put the ASCII report into and open the text (.txt) file. Insert
a line at the beginning of the file with identical information as the line below
except make the time 1.000 second before the start of the files' time. Example: if
a file had a start time of 13:54:53.000 make the time for the new line
13:54:52.000. Do the same at the end of the file but make the time 1 second
later. Make the altitude the same as the previous line. Save the file and close the
window.
5.2. Open Microsoft Excel. Open the file you just made as a delimited text file.
When the Import text dialogue box opens click Delimited and Next. Uncheck the
Tabs box and put a check in the comma box and other box then type m in the
other box, then click Next. Highlight the first column and click Date in the
Column data format box. Click Finish. You should get an Excel Spreadsheet
with the first column as dates, the second as time in HH:MM:SS, and the third
column should contain the towfish altitude without the m for meters.
5.2.1. In the 4th column enter the total water depth in meters from the field
sheets (spreadsheet) and in the 5th column enter the cable out in meters.
5.2.2. The 6t column is for the layback calculation. This is a formula based on
the equation Layback = [ cableout2 (depth +1.63 altitude)2 ] + 6.27
Where 1.63 is the height of the tow point and 6.27 is the offset, all
measurements should be in meters. In excel the formula should read:
=(SQRT(E1A2-(D1+1.63-C1)A2)+6.27)

where column E is the cable out, column D is the depth, and column C is the
altitude. Copy this formula and the data for the 4th and 5th columns down the
spreadsheet. Then highlight the three columns and copy and Paste special it
as values. Save the spreadsheet as a comma delimited (.csv) file and close
the file.
5.2.3. Go back to Isis and either close Isis or playback a completely different file
than the one you are working on.






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
5.2.4. Go to Windows explorer and rename the csv file you just made as a txt file.
You will have to give it a different name followed by .txt. I generally name
it the same as the original file but with 2 in front (example: 21ine23.txt).
5.3. Open NavInXtf.exe this is found in C:\TEI\Nav in Xtf
5.3.1. See Figure 4. In the box/ section labeled 1 click Browse and select the txt
file that contains the layback information you just created (the file you just
renamed eg. 21ine23.txt).
5.3.2. In the box/ section labeled 2 click Browse and open the xtffile you want to
put the layback into (eg line23.xt/). Then you will be asked to save a backup
of the file ALWAYS SAVE A BACKUP to a folder labeled Backup.
5.3.3. In section 3 make sure the top box labeled Ship is checked (it shades
lighter color than the others) and the bottom box Sensor&Ship is checked.
Then click Process and Exit when it is done.
5.3.4. Go back to Isis and open View->Layback. Then replay the file you just
added layback to. Layback should scroll in the Layback window. This file
is now ready to be added to others to create a single line file or be mosaicked
if you already snipped all of the files for that one line. Repeat the above
layback and NavinXtf process for all files in that line if they were not
snipped together. When all files have layback and have been time corrected






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
select smooth navigation. This will bring up a window like Figure 9. Leave the
default values and click Smooth now several times, 10-15 times, then close the
window. When the Lock Coverage map dialogue appears select YES to lock the
coverage map. Save the navigation to a txt file into a folder under the area you
are mosaicking called navigation.
7.3. Now put a check in the box next to Build Sidescan Mosaic in the Delph Mosaic
and DM window. Click Start Mosaic and name the line you are mosaicking
after the line it corresponds to (eg. line23). Save this line in a folder for the area
you are working on (eg. stj5a) under the folder MOSAICS (C:\Documents and
Settings\DFW\My Documents\Side Scan Sonar\MOSAICS). The add scrolled
data to mosaic message should highlight and a message successfully started
mosaic should appear. Playback the file you are mosaicking again; when it is
done playing back, click the Done button and close the Delph Mosaic andDTM
window and the Coverage Window.
7.4. If DelphMap was already open the data will automatically scroll into the mosaic.
If it was not open go to step 8.

In DelphMap
8. Open the project you want to work on or start a new project.
8.1. To insert the line/ layer you just created in Isis right click on Image Layers
(Figure 10) and select the line you created. This will insert the line. You may
insert all the lines at the end when you have finished creating them in Isis or as
you go.
8.2. You can move a layer in DelphMap by clicking and dragging a line name up or
down. The line that appears on top in the window on the left will also be on top
in the mosaic. Lines on top will cover-up the line below.
8.3. Once you have finished a mosaic Merge all of the lines into one file to be printed
[if you do not merge the files printing may take several hours].
8.3.1. Under Tools- go to Merge image layers and select the layers you want to
merge (Figure 11). You can merge as few as two layers or the whole
mosaic. You should merge the whole mosaic to print. Unselect the Insert
output layer into project. Select an output file location (use the same folder
as the original mosaic). Click Merge.
8.3.2. Once it is done open a new DelphMap project and insert the layer as
described in 8.1 above. [It is a good idea to also create a GeoTiff of the
mosaic do this by right clicking on the layer name in the left column
and selecting export]

Printing
9. To print a Mosaic using the large plotter first connect the plotter and turn it on -
before opening DelphMap. Then open DelphMap.
9.1. Select Project Print Setup and the plotter. Under the Properties page (Figure
12) check that the paper size is correct.
9.2. IMPORTANT There are hidden settings in the Plotter that must be checked
each time you want to print. If you do not uncheck the Enable SpoolSmart
setting you will not be able to print the mosaic properly. In order to access these



63






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005
settings you must Click on About (Figure 12) and then place the cursor arrow
over the hp invent symbol and hold down F8 while hitting (Figure
13). This will bring up the Special Options window (Figure 14). Uncheck the
box next to 16 enable SpoolSmart and click OK (Figure 14).
9.3. Next select the Scale to Fit box in the properties page (Figure 12). This will
open the ZoomSmart Settings window (Figure 15). Be sure that the paper size is
correct and check the Fit the Document to this paper box and verify the paper
size. Click OK.
9.4. Finally go to Print preview and Map Layout under Project and enter a title and
change the scale if necessary. You should see a preview similar to Figure 16. (I
have found for a mosaic of approximately 1 square mile a scale of 1:2300 works
well). Click OK
9.5. Now go back to the print window and print the file. It may take several minutes
(10-15) to spool and start printing. The print process is slow and may take an
hour or more if you did not merge the files.


If you have any other troubles consult the manuals for Isis and DelphMap or call
Tech support for Triton Elics International at (831) 722-7373.

































64







F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Isis Main Window


Appendix III


Snip File on/off

Slowdown/ speedup playback
I J


winch
noise


M Isis Parameter Disl X1


Navigation G1

Lat: 1 8.2729757
Long:-64.7748942
Ship
Speed: 0.0
Gyro: 277.10


sensor Uata
Pitch: 10.0
Roll: 0.0
H-leading: 277.10
Speed: 3.30kts
JDepth: 0.0
tgAlt: 11i .13m


Change scale
50.0m r
Display units
( meters
C feet
r ms


;ursor
Time: 118:10:48.01 Ping: 1 85
Channel: 2 Stbd Depth: 0.On
S Range: 29.79m Alt: 7.8n
Speed: 4.10kts Hdng: 276.
Lat: 18.2730936
Long:-64.7733645 L


Current -lie
S Path: C:\DOCUMENTS
S Name: 227 228.XTF
--1 Date: 25 NOV 2002
70. Tim 18:11:02 890
P 2000
ogI END PAUSE Switch|


Figure 1. Isis Main Window.


Time at end of file, hit home or end to switch
between start and end. Use space bar to pause
playback


filename





Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


) ogrighmnfy'b200ufMB



NBoumnt nd etins\

,,cdD Buetan eti


UI


U


sw/an isjimY sKeevs> WAAwS
file : 7000 ^^^^


lkimia iirt -iiuiime1334440.000000, End^^ime=1037365395.000000, Tine^^if=955.000000, Tot

inumnll or nH''aviln evrv un nne-Ls-1/15/20 2 13:05 31 Ping Num=N0
Stpe en of file
rI *Es fxiH^f^^^^^^^^^^^^^ ^^^^^^H


m






F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Appendix III


Items to Print


Item
i Dat
F' Time
F File Name
r Disk info
r Ping Number
r Event Number
r Fish Position
rF Fish Heading
r Ship Position"
r Ship Speed
r Ship Gyro
r Kilometer Post
r Dist. Off Track
r Range Scale
r Fish Speed
r Fish Depth
W Primary Altitude
r Aux Altitude
r Water Depth
r Fish Pitch
r Fish Roll
r Heave
r Sound Velocity
r MagX
r MagY
r MagZ


Order



I-


I

I

I

I

I

I

I
F_









F'--
F _---

F_

F_


Item Order
r Aux 1
r Aux 2
r Aux 3
r Aux 4
r Aux 5
r Aux 6
r Layback |
r Cable Out j
r TPDelta X
r TPDelta Y
r TP Err Cod[r
SRaw ASCII [
r XTF Notes F
r Pressure !
r TemperaturF
r Conductivit.
Clear |
Date format
G MM/DDYYTY
r DD/MM/YYTY
C DD MMM YYYY
C Julian
Field separator
F
W Eliminate titles


When to Output

W Time: every 1 seconds
r Distance every [10 meters
F Ping: every 11000 pings
r New Event received


File name change


Jr Output to a Log File


Browse... View...
C:\Documents and Settings\DFW\
Note: Data will be APPENDED to the
output file.

r Output to a Serial Port (record mode only)

F Configure port... I
Use {TELEMOUT} for template.
Re-start record mode to apply changes

r Output to a Window


Change to


-1 1 second


Browse to
create a txt file
'in a folder you
specify


















Click OK
when done


" To change the Lat/Long format, click the little button in the
"Navigation" area of the parameter display.


Figure 3. ASCII Report form. Put checks in the corresponding boxes as shown here.


Rp o I


L t







Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


I 1. 204 nrpt III


Step 1






Step 2





Make sure
/ these buttons
are clicked






Step 3
Click process
when done







F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005





Set Projection and Bounding Box | Use Nav from Coverage Map

Clear Projection and Bounds 1 7 Apply Layback to nav in mosaic

r Build Sidescan Mosaic- Apply Lateral Offset to mosaic

Sar MSetup...

Add s:crolled data to mos: aic
For sensor direction use
r Course made good
r Heading
|- Gyro Bias...
r Gyro
Done
|7 Smooth jumps in time
-Hint fW Fill gaps between pings
Click on "Build Sidescan Mosaic" F Correct for flat-earth assumption
I Correct for Pitch

Merge overlapping lines by
Cover up
<< Less Options r r Shine-through (max value)
( Cloud-over (min value)
r Average


Figure 5. Window to build the mosaic.







Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Map an Prjcto setig


Change to .1 m


- Boundaries
E-W size m

N-S size m


Depth


-< 2000 m


Grid
Resolution .1 m

Datum Height Offset
I0.000 m


r > 2000 m


North-West Origin in Input Projection Coordinate Units


W Set Default Limit


Latitude

Longitude


_ I dd.dddddddd'


NE N

r F


-Input Projection
Projection: Not Projected [LongitudeLatitL A
Datum: WGS Datum (1984)
Semi Major Axis: 6378137 meters
Semi Minor Axis: 6356752.3 meters
Flattening: 298.26
X Translation to WGS 84: 0.00 meters

Output Projection
Projection: Universal Transverse Mercator A
Datum: WGS Datum (1984)
Semi Major Axis: 6378137 meters
Semi Minor Axis: 6356752.3 meters
Flattening: 298.26
X Translation to WG S 84: 0.00 meters V


Test... OK Cancel I

Figure 6. Projection window. Input and output should default correctly. Change the
Grid resolution to 0.1 m.


Change...







Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005








Current C Y: 0.0
"or code: 0
-e vals code les:s : I

(3 Apply Layback

Use logged layback value
rC Enter layback manually
(C Compute layback from Cable Out
Layback Current value
I m I

Accept Close I


Figure 7. Check the Apply Layback to nav in mosaic.
Under setup check the use logged layback value.







F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005



File Nav Show Mosaic/DTM Zoom























Figure 8. Coverage Window. Sonar path is in red. Go to Nav Smooth Navigation 10-
15 times and save the coverage points as a txt file.





-Allowable speeds

Min: 1 knots
Max: 25 knots

Smooth together
19 points
Initial points to skip
rFo

Smooth Now

Un-smooth


Close

Tip: Press the "Smooth Now"
button more than once to get
extra smoothing.
TT~,.,,n__ f 0 *//4L '-, ^r^-i-'-, /^*^ ,,,*^/I/^,T







Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005

Leave defaults. Click Smooth now 10-15 times.


Project Settings Tools Applications GIS Tools Mosaic Tools View Help





to insert 6* Photo Ma, IT j'e X


lines
N: 2018460 gt223



JE: 0322519290 m
drag layers 1814'5352" W
to move up No Data
Distance 92.875 m
or down in Heading: 358 .2 (1 81
the mosaic
window


Figure 10. Delphmap Window with a mosaic.







Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Ill; Ic u IIClllI:
Sidescan I

Layer Band File Name ^
line22 1 line22.DDS_VIF
line23 1 line23.DDSVIF
line24_69 1 line24_69.DDSVI
line24_70 1 line24_70.DDSVI
line24_75 1 line24_75.DDSVI
line24 1 line24.DDS_VIF
line25 1 line25.DDS_VIF v
|C 1 _>_|


Select all


Clear all


upIJIu Is
r Process only the current visible map area.

r Use Shinethrough
Keep ilaimrrium Vfalue:s
SKeep ,' alues ve
"r I, i Value:

r p Fle. r _.p.ut ,u ia ,er into. roieci


O utput File L C D..).- rri'i arI.] S>eli 1.g [


SMerge I


Figure 11. Merge Layer Window. Select layers to merge.






Appendix III


F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Basic Setup CAD D JColor Advanced


Paper


Size: IANSI E- 34 x 44 in.4 j
r Sheet ISheet feed


rT Roll


Quality


142 inch roll


- Optimize


Fast (draft)
C Normal (final]
C Best (enhanced)
Orientation
C Portrait
" Landscape


HP


Scale to Fit...

_______ i l


r for Drawings/Text
r for Images
More...


34 44 in


F Rotate by 90 degrees


-quick Sets

< new configuration > j Save


I ,: l I Cancel Help
Figure 12. Printer/ plotter setup. Select About and go to figure 13.


Make sure
paper size is
correct





-__Click scale
to fit




Click About
---for hidden
settings


HP DesignJet Printer Driver
v5.01
Copyright @ Hewlett-Packard Corp. 1995
Microsoft Corp. 1992



i VK n t

wOK


Place cursor arrow here
press and hold F8 and hit
ENTER


Figure 13. You must change hidden settings to print properly. Place the cursor arrow
over the hp invent symbol and press and hold the F8 key while hitting this
gives you Figure 14.


[4,]t


~_~ ~


About4-"






F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005





r r T r r 2 r3 noBMF
r 4 no' 5 noEMF r 6 noPJLSize r 7 HQ Scale
8 OB 0 r9 L.Paper 10 no
11 TxtGamma: 2 HPA filter level

12 qSeg: 5 Fast: 10 -

13 XtraMarg: 0 mm. Normal: 18 -
r Reserved r Reserved2 Best: 18

r Reserved3

F 16 Enable SpoolSmart F 17
-Warning
Ths.qt. .qettinn





F-7: Recreational Fisheries Habitat Assessment Project Appendix III
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005



ZoomSmart
Page Size HP
Document:
_ANSIE-34x44in.
SPrinted on this paper size:
134 44 in.
If 1i
ZoomSmart Options
No scaling
( Fit the document to this paper: ANSI E 34 x 44 in.
C Apply this scaling factor: 100 %

OK Cancel Help

Figure 15. Click on the Scale to Fit button in the Properties page (see Figure 12). Make
sure the Page size matches the size of paper you have loaded in the plotter. Click on the
Fit the Document to this paper and select the right paper size. Click OK








F-7: Recreational Fisheries Habitat Assessment Project
Study 4: Mapping Essential Fish Habitat with Side Scan Sonar
Period: FY 2001-FY2005


Figure 16. Print preview of the final mosaic


Appendix III


Proha on: Una Tranaere Meatnr
Daum: WGSDaum (19)
Semi Major A 6378137 mer
Se~, MinWoAts; 86752 3 wet
Raten 2W92B
X Tran. la WG84: .mm 0 mete
YTrarn to WGB4: 0.00 meas
Z.e- N-er W


Meters

Scale 1 : 2300


St. John 2003
F-7 Side Scan Sonar
Survey Area stj9a


0I5H A*j



d-,
a" T1





BTEI
.*lkUSN
17TRI


I




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