Benthic Habitats 

of the 

Main Hawaiian Islands

Interim Product 

NOAA National Ocean Service 

National Centers for Coastal Ocean Science 

Center for Coastal Monitoring and Assessment

Biogeography Team
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1

Contents: 

Introduction ................................................................................................................................................. 2 

Chapter 1: Classification Scheme for Benthic Habitats 

Developing the Habitat Classification Scheme........................................................................ 3 

General Description of the Classification Scheme................................................................... 3 

List of Zones and Habitats ....................................................................................................... 4 

Description of Zones................................................................................................................ 6 

Description of Habitats .......................................................................................................... 10 

Chapter 2: On-screen Mapping with ArcView’s Habitat Digitizer ......................................................... 29 

Chapter 3: Creating and Interpreting Digital Orthophotos 

Creating the Digital Mosaic................................................................................................... 37 

Digitizing Benthic Habitats ................................................................................................... 39 

Chapter 4: Assessment of Classification Accuracy ................................................................................. 40 

Evaluating Thematic Accuracy.............................................................................................. 40 

Results of overall accuracy assessment of benthic habitat map products .............................. 42 

Comparison of Thematic Accuracy of Map Products Generated from Color Aerial 

Photography, Hyperspectral Imagery and IKONOS Satellite Imagery ................................. 44 

References ................................................................................................................................................. 47 

Citation: Coyne, M. S.1

, T. A. Battista1, M. Anderson2, J. Waddell1, W. Smith3, P. Jokiel3, M. S. Kendall1, 

and M. E. Monaco1

. 2003. NOAA Technical Memorandum NOS NCCOS CCMA 152 (On-line). Benthic 

Habitats of the Main Hawaiian Islands URL: http://biogeo.nos.noaa.gov/projects/mapping/pacific/. Also 

available on U.S. National Oceanic and Atmospheric Administration. National Ocean Service, National 

Centers for Coastal Ocean Science, Biogeography Program. 2003. (CD-ROM). Benthic Habitats of the 

Main Hawaiian Islands. Silver Spring, MD: National Oceanic and Atmospheric Administration. 

1. NOAA National Ocean Service, Biogeography Team; N/SCI 1, SSMC4; 1305 East West Highway; 

Silver Spring, MD 20910 

2. Analytical Laboratories of Hawaii; 1320 Aalapapa Dr.; Lanikai, Oahu, Hawaii 96734 

3. University of Hawaii at Manoa; Hawaii Institute of Marine Biology; P.O. Box 1346; Kaneohe, HI 

96744
Project Overview ______________________________________________________________________________________ 

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Introduction 

The National Oceanic and Atmospheric Administration (NOAA) National Ocean Service (NOS) initiated a 

coral reef research program in 1999 to map, assess, inventory, and monitor U.S. coral reef ecosystems 

(Monaco et al. 2001). These activities were implemented in response to requirements outlined in the 

Mapping Implementation Plan developed by the Mapping and Information Synthesis Working Group 

(MISWG) of the Coral Reef Task Force (CRTF) (MISWG 1999). As part of the MISWG of the CRTF, 

NOS’ Biogeography Team has been charged with the development and implementation of a plan to 

produce comprehensive digital coral-reef ecosystem maps for all U.S. States, Territories, and 

Commonwealths within five to seven years. Joint activities between Federal agencies are particularly 

important to map, research, monitor, manage, and restore coral reef ecosystems. In response to the 

Executive Order 13089, NOS is conducting research to digitally map biotic resources and coordinate a 

long-term monitoring program that can detect and predict change in U.S. coral reefs, and their associated 

habitats and biological communities. 

Most U.S. coral reef resources have not been digitally mapped at a scale or resolution sufficient for 

assessment, monitoring, and/or research to support resource management. Thus, a large portion of NOS’ 

coral reef research activities have focused on mapping of U.S. coral reef ecosystems. The map products 

will provide the fundamental spatial organizing framework to implement and integrate research programs 

and provide the capability to effectively communicate information and results to coral reef ecosystem 

managers. Although the NOS coral program is relatively young, it has had tremendous success in 

advancing towards the goal to protect, conserve, and enhance the health of U.S. coral reef ecosystems. One 

objective of the program was to create benthic habitat maps to support coral reef research to enable 

development of products that support management needs and questions. An initial step in producing 

benthic habitat maps is the development of a habitat classification scheme. The purpose of this document is 

to outline the benthic habitat classification scheme and protocols used to map the main Hawaiian Islands: 

Hawaii, Maui, Molokai, Lanai, Oahu, Kauai, and Niihau. 

Twenty-seven distinct benthic habitat types within eleven zones were mapped directly into a geographic 

information system (GIS) using visual interpretation of orthorectified aerial photographs and hyperspectral 

imagery. Benthic features were mapped that covered an area of 790 km2

. In all, 204 km2 of unconsolidated 

sediment, 171 km2

 of submerged vegetation, and 415 km2 of coral reef and colonized hardbottom were 

mapped. 

To supplement the maps, digital scans of the original aerial photographs, georeferenced mosaics, a GIS 

mapping tool for use with ArcView, and supporting data sets were also created. To see or download this 

information, visit http://biogeo.nos.noaa.gov/projects/mapping/pacific/. 

This document will show data users how the data was collected and help them replicate the data for 

comparison purposes at a later date. Document contents include: 

• A description of each of the habitat classifications with example aerial and underwater photographs 

• Directions for using the “habitat digitizer” extension to ArcView 3.2 

• A description of the specific methods used to create the habitat maps 

• An assessment of the thematic accuracy of the maps along with a comparison of map accuracy 

utilizing different source imagery 
Chapter 1: Classification Scheme for Benthic Habitats ______________________________________________________________________________________ 

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Developing the Habitat Classification Scheme 

A hierarchical classification scheme was created to define and delineate habitats. The classification scheme 

was influenced by many factors including: requests from the management community, NOS’s coral reef 

mapping experience in the Florida Keys and Caribbean, existing classification schemes for the Pacific and 

Hawaiian Islands (Holthus and Maragos 1995; Gulko 1998; Allee et al. unpublished), other coral reef 

systems (Kruer 1995; Reid and Kruer 1998; Lindeman et al. 1998; Sheppard et al. 1998; Vierros 1997; 

Chauvaud et al. 1998; Florida Fish and Wildlife Conservation Commission, Florida Marine Research 

Institute and NOAA, 1998; Mumby et al. 1998; NOAA et al. 1998; Kendall et al. 2001), quantitative 

habitat data for the Hawaiian Islands, the minimum mapping unit (MMU - 1 acre for visual 

photointerpretation), and analysis of the spatial and spectral limitations of aerial photography and 

hyperspectral imagery. The hierarchical scheme allows users to expand or collapse the thematic detail of 

the resulting map to suit their needs. This is an important aspect of the scheme as it will provide a 

“common language” to compare and contrast digital maps developed from complementary remote sensing 

platforms. Furthermore, it is encouraged that additional hierarchical categories be added in the resulting 

geographic information system by users with more detailed knowledge or data for specific areas. For 

example, habitat polygons smaller than the MMU can be delineated, such as reef holes found in parts of the 

Hawaiian Islands, or habitat polygons delineated as colonized pavement using this scheme could be further 

attributed with health information (i.e., bleached, percent live cover) or species composition (i.e., Porites, 

Montipora). 

The initial classification scheme was developed through a series of workshops with managers, academics 

and other local experts in the Hawaiian Islands. Modifications were made throughout the development 

process based upon feedback provided by workshop participants and other contributors. Additional 

modifications were made during the mapping process to ensure that each category definition reflected the 

intended habitats and zones encountered in the field as accurately as possible. 

General Description of the Classification Scheme 

The classification scheme defines benthic communities on the basis of two attributes: large geographic 

“zones” which are composed of smaller “habitats”. Zone refers only to benthic community location and 

habitat refers only to substrate and/or cover type. Every polygon on the benthic community map will be 

assigned a habitat within a zone (e.g. sand in the lagoon, or sand on the bank). Zone indicates polygon 

location and habitat indicates composition of each benthic community delineated. Combinations of habitat 

and zone that are analogous to traditionally used terminology are noted where appropriate. The description 

of each zone and habitat includes example images. Where available, both underwater and aerial 

photographs are included for habitats. Aerial images are included for zones. The zone/habitat approach to 

the classification scheme was developed by the Caribbean Fishery Management Council; Dr. Ken 

Lindeman, Environmental Defense; and the NOS Biogeography Team to couple habitats to species 

distribution (Christensen et al. 2003). 

Eleven mutually exclusive zones were identified from land to open water corresponding to typical insular 

shelf and coral reef geomorphology (Fig. 1-2). These zones include: land, vertical wall, shoreline 

intertidal, lagoon, reef flat, back reef, reef crest, fore reef, bank/shelf, bank/shelf escarpment, channel, and 

dredged (since this condition eliminates natural geomorphology). Zone refers only to each benthic 

community’s location and does not address substrate or cover types within. For example, the lagoon zone 

may include patch reefs, sand, and seagrass beds; however, these are considered structural elements that 

may or may not occur within the lagoon zone and therefore, are not used to define it. Twenty-seven distinct 

and non-overlapping habitat types were identified that could be mapped by visual interpretation of remotely 

collected imagery. Habitats or features that cover areas smaller than the MMU were not considered. For 

example, sand halos surrounding patch reefs are too small to be mapped independently. Habitat refers only 

to each benthic community’s substrate and/or cover type and does not address location on the shelf. 

Habitats are defined in a collapsible hierarchy ranging from four broad classes (unconsolidated sediment, 

submerged vegetation, coral reef and hardbottom, and other), to more detailed categories (e.g., emergent 

vegetation, seagrass, algae, individual patch reefs, uncolonized volcanic rock), to patchiness of some 

specific features (e.g., 50-90 percent cover of macroalgae). 
 Chapter 1: List of Zones and Habitats 

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Zones: 

Land 

Shoreline Intertidal 

Vertical Wall* 

Lagoon 

Back Reef (w/ Lagoon, see barrier reef - Figure 1) 

Reef Flat (w/o Lagoon, see fringing reef - Figure 2) 

Reef Crest 

Fore Reef 

Bank/Shelf 

Bank/Shelf Escarpment 

Channel* 

Dredged* 

Unknown 

*not depicted in figures

Figure 1. Barrier reef cross-section. Reef separated from the shore by a relatively wide, 

deep lagoon. 

Bank/Shelf

Forereef Escarpment

Bank/Shelf Reef Flat Reef Crest

Shoreline/

Intertidal

Mean High Tide Line

Spring Low Tide Line

Figure 2. Fringing reef cross-section. Reef platform is continuous with the shore. 

Bank/Shelf 

Escarpment

Fore ReefBank/Shelf Reef Crest

Back 

Lagoon Reef

Shoreline/ 

Intertidal 

Mean High Tide Line

Spring Low Tide Line
 Chapter 1: List of Zones and Habitats 

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Habitats: 

Unconsolidated Sediment (0%-<10% submerged vegetation) 

 Mud 

 Sand 

Submerged Vegetation 

 Seagrass 

 Continuous Seagrass (90%-100% Cover) 

 Patchy (Discontinuous) Seagrass (50%-<90% Cover) 

 Patchy (Discontinuous) Seagrass (10%-50% Cover) 

 Macroalgae (fleshy and turf) 

 Continuous Macroalgae (90%-100% Cover) 

 Patchy (Discontinuous) Macroalgae (50%-<90% Cover) 

 Patchy (Discontinuous) Macroalgae (10%-<50% Cover) 

Coral Reef and Hardbottom 

 Coral Reef and Colonized Hardbottom 

 Linear Reef 

 Aggregated Coral 

 Spur and Groove 

 Individual Patch Reef 

 Aggregated Patch Reef 

 Scattered Coral/Rock in Unconsolidated Sediment 

 Colonized Pavement 

 Colonized Volcanic Rock/Boulder 

 Colonized Pavement with Sand Channels 

 Uncolonized Hardbottom 

 Reef Rubble 

 Uncolonized Pavement 

 Uncolonized Volcanic Rock/Boulder 

 Uncolonized Pavement with Sand Channels 

 Encrusting/Coralline Algae 

 Continuous Encrusting/Coralline Algae (90%-100% Cover) 

 Patchy (Discontinuous) Encrusting/Coralline Algae (50%-<90% Cover) 

 Patchy (Discontinuous) Encrusting/Coralline Algae (10%-<50% Cover) 

Other Delineations 

 Land 

 Emergent Vegetation 

 Artificial 

Unknown
 Chapter 1: Description of Zones 

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Description of Zones 

Shoreline Intertidal: Area between the mean high water line (or landward edge of emergent vegetation 

when present) and lowest spring tide level (excluding emergent segments of barrier reefs). Typically, this 

zone is narrow due to the small tidal range in the 

main Hawaiian Islands. 

 

Typical Habitats: Mangrove, hao, sand, 

seagrass, and uncolonized 

volcanic/carbonate rock. 

Vertical Wall: Area with near-vertical slope from shore to shelf or shelf escarpment. This zone is 

typically narrow and may not be distinguishable in 

remotely gathered imagery, but is included because 

it is recognized as a biologically important feature.

Typical Habitats: volcanic rock, algae, 

coral. 

Lagoon: Shallow area (relative to the deeper water of the bank/shelf) between the shoreline intertidal zone 

and the back reef of a reef or a barrier island. This zone is protected from the high-energy waves 

commonly experienced on the bank/shelf and reef 

crest. If no reef crest is present there is no lagoon 

zone.

Typical Habitats: Sand, seagrass, algae, 

pavement, volcanic/carbonate rock, and 

patch reefs. 

 
 Chapter 1: Description of Zones 

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Reef Flat: Shallow (semi-exposed) area between the shoreline intertidal zone and the reef crest of a 

fringing reef. This zone is protected from the high-energy waves commonly experienced on the shelf and 

reef crest. Reef flat is typically not present if there is a lagoon zone.

Typical Habitats: Sand, reef rubble, 

seagrass, algae, and patch reef.

Back Reef: Area between the seaward edge of a lagoon floor and the landward edge of a reef crest. This 

zone is present when a reef crest and lagoon exist. 

Typical Habitats: Sand, reef rubble, 

seagrass, algae, linear reef, and patch reef. 

Reef Crest: The flattened, emergent (especially during low tides) or nearly emergent segment of a reef. 

This zone lies between the back reef and fore reef zones. Breaking waves will often be visible in aerial 

images at the seaward edge of this zone. 

Typical Habitats: Reef rubble, linear reef, 

and aggregated coral. 
 Chapter 1: Description of Zones 

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Fore Reef: Area from the seaward edge of the reef crest that slopes into deeper water to the landward edge 

of the bank/shelf platform. Features not forming an emergent reef crest but still having a seaward-facing 

slope that is significantly greater than the slope of the bank/shelf are also designated as fore reef (Fig. 2).

Typical Habitats: Linear reef and spur and 

groove.

Bank/Shelf: Deep water area (relative to the shallow water in a lagoon) extending offshore from the 

seaward edge of the fore reef to the beginning of the escarpment where the insular shelf drops off into deep, 

oceanic water. The bank/shelf is the flattened platform between the fore reef and deep open ocean waters 

or between the shoreline/intertidal zone and open ocean if no reef crest is present.

Typical Habitats: Sand, patch reefs, algae, 

seagrass, linear reef, colonized and uncolonized 

pavement, colonized and uncolonized pavement 

with sand channels, and other coral reef 

habitats.

Shelf Escarpment: The edge of the bank/shelf where depth increases rapidly into deep, oceanic water. 

This zone begins at approximately 20 to 30 meters depth, near the depth limit of features visible in aerial 

images. This zone extends well into depths exceeding those that can be seen on aerial photographs and is 

intended to capture the transition from the shelf to deep waters of the open ocean.

Typical Habitats: Sand, linear reef, and spur 

and groove.
 Chapter 1: Description of Zones 

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Channel: Naturally occurring channels that often cut across several other zones. 

Typical Habitats: Sand, mud, uncolonized 

pavement. 

Dredged: Area in which natural geomorphology is disrupted or altered by excavation or dredging. 

 Typical Habitats: Sand, mud.

Unknown: Zone uninterpretable due to turbidity, cloud cover, water depth, or other interference. 
 Chapter 1: Description of Habitats 

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Description of Habitats

Unconsolidated Sediment: Unconsolidated sediment with less than 10 percent cover of submerged 

vegetation.

Mud: Fine sediment often associated with river discharge and buildup of organic material in 

areas sheltered from high-energy waves and currents. 
 Chapter 1: Description of Habitats 

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Sand: Coarse sediment typically 

found in areas exposed to currents or 

wave energy.

 
 Chapter 1: Description of Habitats 

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Submerged Vegetation: Greater than 10 percent cover of submerged vegetation in unspecified substrate 

type (usually sand, mud, or hardbottom). 

Seagrass: Habitat with 10 percent or more cover of seagrass (e.g., Halophila sp.). 

Continuous Seagrass: Seagrass covering 90 percent or more of the substrate. May 

include blowouts of less than 10% of the total area that are too small to be mapped 

independently (less than the MMU). This includes continuous beds of any shoot density 

(may be a continuous sparse or dense bed). 

Patchy Seagrass: Discontinuous seagrass with breaks in coverage that are too diffuse or 

irregular, or result in isolated patches of seagrass that are too small (less than the MMU) 

to be mapped as continuous seagrass. 

Patchy Seagrass (50%-90% cover) 

Patchy Seagrass (10%-50% cover) 

Representative Species: 

Halophila sp. 
 Chapter 1: Description of Habitats 

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Macroalgae: An area with 10 percent or 

greater coverage of any combination of 

numerous species of red, green, or brown 

macroalgae. Usually occurs in shallow 

backreef and deeper waters on the bank/shelf 

zone. High relief (hardbottom) habitats take 

precedence over macroalgae cover.

Continuous Macroalgae:

Macroalgae covering 90 percent or 

greater of the substrate. May 

include blowouts of less than 10 

percent of the total area that are too 

small to be mapped independently (less than the MMU). This includes continuous beds 

of any density (may be a continuous, sparse or dense bed). 

Patchy Macroalgae: Discontinuous macroalgae with breaks in coverage that are too 

diffuse or irregular, or result in isolated patches of macroalgae that are too small (smaller 

than the MMU) to be mapped as continuous macroalgae.

Patchy Macroalgae (50%-<90% cover) 

Patchy Macroalgae (10%-<50% cover) 

Representative Species:

Dictyosphaeria spp. 

Halimeda spp. 
 Chapter 1: Description of Habitats 

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Coral Reef and Hardbottom: Hardened substrate of unspecified relief formed by the deposition of 

calcium carbonate by reef building corals and other organisms (relict or ongoing) or existing as exposed 

bedrock or volcanic rock.

Coral Reef and Colonized Hardbottom:

Substrates formed by the deposition of 

calcium carbonate by reef building corals 

and other organisms. Habitats within this 

category have some colonization by live 

coral, unlike the uncolonized hardbottom 

category.

Linear Reef: Linear coral formations that are 

oriented parallel to shore or the shelf edge. These 

features follow the contours of the shore/shelf 

edge. This category is used for such commonly 

used terms as fore reef, fringing reef, and shelf 

edge reef. 
 Chapter 1: Description of Habitats 

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Aggregated Coral: Coral-dominated formations with high relief and structural complexity. 

Often serve the same role as linear reef in fringing reef systems where the reef crest is relatively 

unorganized. 
 Chapter 1: Description of Habitats 

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Spur and Groove: Habitat having alternating sand and coral formations that are oriented 

perpendicular to the shore or bank/shelf escarpment. The coral formations (spurs) of this 

feature typically have a high vertical relief relative to pavement with sand channels (see below) 

and are separated from each other by 1-5 meters of sand or bare hardbottom (grooves), 

although the height and width of these elements may vary considerably. This habitat type 

typically occurs in the fore reef or bank/shelf escarpment zone. 
 Chapter 1: Description of Habitats 

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Patch Reef(s): Coral formations that are isolated from other coral reef formations by sand, 

seagrass, or other habitats and that have no organized structural axis relative to the contours of the 

shore or shelf edge. 

Individual patch reef:

Distinctive single patch reefs 

that are larger than or equal to 

the MMU. 

Aggregate patch reefs:

Clustered patch reefs that 

individually are too small 

(less than the MMU) or are 

too close together to map 

separately. 
 Chapter 1: Description of Habitats 

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Scattered Coral/Rock in 

Unconsolidated Sediment: Primarily 

sand or seagrass bottom with scattered 

rocks or small, isolated coral heads that 

are too small to be delineated 

individually (i.e. smaller than individual 

patch reef). 
 Chapter 1: Description of Habitats 

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Colonized Pavement: Flat, low-relief, solid carbonate rock with coverage of macroalgae, hard 

coral, zoanthids, and other sessile invertebrates that are dense enough to begin to obscure the 

underlying surface.
 Chapter 1: Description of Habitats 

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Colonized Volcanic 

Rock/Boulder: Solid volcanic 

rock that has coverage of 

macroalgae, hard coral, 

zoanthids, and other sessile 

invertebrates that begins to 

obscure the underlying surface.
 Chapter 1: Description of Habitats 

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Colonized Pavement with Sand Channels: Habitat having alternating sand and colonized 

pavement formations that are oriented perpendicular to the shore or bank/shelf escarpment. The 

sand channels of this feature have low vertical relief relative to spur and groove formations. This 

habitat type occurs in areas exposed to moderate wave surge, such as the bank/shelf zone.

Representative 

Species/Live Coral 

Community: 

Porites compressa 

Porites lobata 

Montipora spp. 

Pocillopora meandrina
 Chapter 1: Description of Habitats 

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Uncolonized Hardbottom: Hard substrate 

composed of relict deposits of calcium 

carbonate or exposed volcanic rock.

Reef Rubble: Dead, unstable coral rubble 

often colonized with filamentous or other 

macroalgae. This habitat often occurs 

landward of well developed reef 

formations in the reef crest or back reef 

zone.
 Chapter 1: Description of Habitats 

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Uncolonized Pavement: Flat, low 

relief, solid carbonate rock that is 

often covered by a thin sand 

veneer. The pavement’s surface 

often has sparse coverage of 

macroalgae, hard coral, zoanthids, 

and other sessile invertebrates that 

does not obscure the underlying 

surface. 
 Chapter 1: Description of Habitats 

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Uncolonized Volcanic Rock/Boulder:

Exposed volcanic rock that has sparse coverage 

of macroalgae, hard coral, zoanthids and other 

sessile invertebrates that does not obscure the 

underlying surface.
 Chapter 1: Description of Habitats 

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Uncolonized Pavement with Sand Channels: Habitat having alternating sand and 

uncolonized pavement formations that are oriented perpendicular to the shore or bank/shelf 

escarpment. The sand channels of this feature have low vertical relief relative to spur and 

groove formations. This habitat type occurs in areas exposed to moderate wave surge such as 

the bank/shelf zone. 
 Chapter 1: Description of Habitats 

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Encrusting/Coralline Algae: An area with 10 percent or greater coverage of any combination of 

numerous species of encrusting or coralline algae. May occur in shallow backreef, relatively 

shallow waters on the bank/shelf zone, and at depth. 

Continuous Encrusting/Coralline Algae: Encrusting/coralline algae covering 90 

percent or more of the substrate. 

Patchy Encrusting/Coralline Algae: Discontinuous encrusting/coralline algae with 

breaks in coverage that are too diffuse or irregular, or result in isolated patches of 

coralline algae that are too small (less than the MMU) to be mapped as continuous 

coralline algae.

Patchy Encrusting/Coralline Algae (50%-<90% cover) 

Patchy Encrusting/Coralline Algae (10%-<50% cover) 

Representative Species:

Porolithon gardineri
 Chapter 1: Description of Habitats 

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Other Delineations: 

Emergent Vegetation: Emergent habitat composed 

primarily of Rhizophora mangle (red mangrove) and 

hao trees. Generally found in areas sheltered from 

high-energy waves. This habitat type is usually found 

in the shoreline/intertidal, back reef, or barrier reef 

crest zone.
 Chapter 1: Description of Habitats 

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Artificial: Man-made habitats such as 

submerged wrecks, large piers, submerged 

portions of rip-rap jetties, and the shoreline 

of islands created from dredge spoil. 

Includes active and remnant fish ponds 

walled off from the open ocean along the 

shoreline, often along a reef crest. 

Unknown: Bottom type uninterpretable 

due to turbidity, cloud cover, water depth, 

or other interference. 
Chapter 2: On-Screen Mapping with ArcView’s Habitat Digitizer ______________________________________________________________________________________ 

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Chapter 2: On-Screen Mapping with ArcView’s Habitat Digitizer 

The habitat digitizer extension to ArcView 3.x was developed to facilitate mapping benthic habitats of 

Puerto Rico and the U.S. Virgin Islands (Kendall et al. 2001) and was also used for mapping the main 

Hawaiian Islands. The extension was originally created to map habitats using this scheme by visually 

interpreting orthorectified aerial photos. The extension’s capabilities have been expanded to allow users to 

map from other georeferenced image data such as satellite images and side scan sonar. The extension 

allows users to rapidly delineate and attribute polygons using simple menus. It also allows new 

hierarchical classification schemes to be easily created, modified, and saved for use on future mapping 

projects. 

The extension is available on the “Benthic Habitats of the Main Hawaiian Islands CD-ROM” (Kendall et 

al. 2001). The latest version can be found on the internet at http://biogeo.nos.noaa.gov/products/. The 

extension and accessory files are found in the “Habitat_Digitizer.zip” folder. This folder contains three 

files including: 

habitat.avx the extension 

coral.hcs a habitat classification scheme for tropical marine habitats 

coral.avl an example legend for the coral.hcs classification scheme 

Hardware and Software Requirements 

The habitat digitizer extension is compatible with ArcView 3.x and requires hardware similar to that 

recommended for proper operation of ArcView. Additional memory may enhance performance for 

handling large image files. The appropriate Image Support extension (TIFF, MrSID, etc.) is required 

depending on the format of the image files used. The Image Analyst extension is not necessary, but is 

recommended to facilitate manipulation of image brightness, contrast, and color balance. 

Getting started 

To begin using Habitat Digitizer, save the habitat.avx file in either ArcView’s Ext32 directory or the 

USEREXT directory. The coral.hcs and coral.avl files can be saved anywhere, but they should preferably 

be placed in the ArcView project’s working directory. 

After starting ArcView, load the Habitat Digitizer Extension (and any other desired extensions) by 

selecting “File/Extensions...” and click on the box next to the Habitat Digitizer Extension in the “Available 

Extensions” list. Click “OK” to install the extension. If a project already exists that used the Habitat 

Digitizer Extension, opening the project will automatically load the extension. 

Setting the Projection Parameters for the Image Data: 

The Habitat Digitizer enables users to specify a minimum mapping unit (MMU), digitizing 

scale, and offers several other spatial functions that require the View’s projection and map 

units to be set properly. The projection properties of the View must be set to those of the 

image data from which habitats are being interpreted. Once the View’s projection is set 

properly, shapefiles created using Habitat Digitizer will be unprojected (in decimal degrees). 

To set the projection properties, select View/Properties and set the map and distance units as 

well as the Projection information of the image. If this information is not set, the shapefile 

will be created in the projection coordinates of the image files. 
Chapter 2: On-Screen Mapping with ArcView’s Habitat Digitizer ______________________________________________________________________________________ 

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The Habitat Digitizer Menu 

Once the Habitat Digitizer Extension has been activated the “Habitat 

Digitizer” pull-down menu and digitizing tools which control the 

functions of the extension will appear on the ArcView toolbar. 

Beginning with the process of creating and loading classification 

schemes, a detailed description and instructions for each function in 

the extension are provided below. 

Creating a new classification scheme 

Unless an existing classification scheme such as coral.hcs is used, a new scheme must first be created to 

use the extension. Before creating a new scheme using the dialogs of the extension, it may be useful to 

sketch the scheme out on paper to ensure that all fields and categories in the hierarchy are entered properly. 

There are several advantages to using a scheme with a hierarchical structure including: the detail of habitat 

categories can be expanded or collapsed to suit user needs, the thematic accuracy of each 

category/hierarchical level can be determined, and additional categories can be easily added or deleted at 

any level of the scheme to suit user needs. An example of a scheme framework is provided in Table 2.1 

below. 

Table 2.1: Example Classification Scheme Framework 

Field 1 Field 2 Field 3 Field 4 UniqueID 

Category 1 Subcategory 1 Subcategory 1 (empty) 111 

 Subcategory 2 112 

 Subcategory 2 Subcategory 1 121 

 Subcategory 2 122 

Category 2 Subcategory 1 Subcategory 1 221 

 Subcategory 2 222 

 Subcategory 2 22 

Category 3 Subcategory 1 31 

 Subcategory 2 32 

To create the new scheme using the extension, select 

Habitat Digitizer/Change Classification Scheme

and in the next dialog box, select Create New 

Scheme. Type the name of the new classification 

scheme in the message box and click Okay. The 

other options in this dialog will be unavailable until 

a scheme has been either created or loaded. 
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In the “Add New Field” dialog, selecting Cancel

will end the creation process without creating a 

scheme. Once the first field name has been added, 

this button is replaced with the Finished button, 

which will complete the field naming process and 

go to the next step in creating the scheme. First, 

type in the field name for the most general 

hierarchical level in the new classification scheme 

(Field 1 in Table 2.1). Field names are limited to 

10 characters in length. Select whether the field 

will be character or numeric and click Add Field. 

Add additional field names in the order of the 

classification hierarchy. A fieldname must be 

entered for every level in the hierarchy. Because 

new fields cannot be added after the scheme 

creation process is closed, add a few extra fields 

as placeholders in case any additional unforeseen 

levels in the hierarchy are required at a later time. 

After all the field names have been entered select 

Finished to proceed to the next step. Once 

Finished is selected, no additional fields may be 

added to the classification scheme. Note that a 

field named “UniqueID” is added automatically 

after Finished is selected. 

The extension uses the uniqueID field to identify 

each possible combination of hierarchical categories 

with one unique number (see Table 2.1). ArcView 

uses uniqueIDs to link polygon attributes to the 

legend. The dialog at left sets the method of 

assigning uniqueIDs. When setting up a new 

scheme or altering an existing scheme that has not 

yet been used to create a theme, the Automatic

method should be used. The Automatic method 

creates a logical numbering sequence for each 

uniqueID (see Table 2.1). When modifying a 

scheme that has already been used to create a theme, 

use the Manual method. If Automatic was used, 

new uniqueID’s would be assigned to the scheme, 

creating a mis-match between the ID’s of the new 

scheme and those of the polygons attributed using 

the old scheme. 
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In the “Modify Classification Scheme” 

dialog, categories and subcategories can 

be added to a new or existing 

classification scheme. Begin by adding a 

category to the most general level in the 

classification hierarchy (Category 1 in 

Table 2.1). Click Add Category, then 

type the category name and click Okay. 

Additional categories at this level in the 

hierarchy can be added in this way. 

Adding a category at this level will 

activate the Add Subcategory button. 

Subcategories are added within 

individual categories by selecting the 

category of interest then clicking Add 

Subcategory and completing the dialog 

boxes. If the uniqueIDs are to be 

assigned using the Automatic option 

(previous dialog), the Delete and 

Change buttons are activated and can 

now be used to modify category names. 

In the Automatic method, clicking the 

Finished button will assign a uniqueID 

to each classification combination. If 

Manual was selected, the Delete and 

Change buttons will not be activated 

until the uniqueIDs for each of the 

categories and subcategories have been added (next dialog). To add uniqueIDs manually, click the Commit 

Additions button after all categories and subcategories have been added, then complete the Add Unique 

ID dialogue box as described below. Once the uniqueIDs have been assigned the Delete and Change

buttons will be activated. If the Cancel button is selected, the scheme creation process will end without 

creating a scheme. 

If Manual was selected for assigning 

uniqueIDs, the “Add Unique ID” dialog 

will appear after selecting Commit 

Additions. A unique numeric identifier 

must be entered for each possible 

combination of classifications in the 

hierarchy. The Existing Unique IDs list 

shows which numbers are already used in 

the scheme. Duplicate numbers cannot be 

added. See Table 2.1 or the coral.hcs 

scheme that is included with the extension 

to get suggestions on how to assign 

uniqueIDs. Once uniqueIDs are set 

through either the Manual or Automatic

method and Finished is selected in the 

“Modify Classification Scheme” dialog, 

the new scheme can be saved and used to 

digitize habitats. 
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Saving, Re-Loading, and Creating Scheme Legends 

Once you have finished creating or modifying a 

scheme, save the scheme to a file by selecting Save 

Current Scheme in the “Change Classification” 

dialog box. The file will be saved as a *.hcs (habitat 

classification scheme) file. To access this scheme, 

select Load Existing Scheme in the “Change 

Classification” dialog box. A file selection dialog 

will open showing only the *.hcs files. Additional 

options that can be used at this time include the 

Export Scheme As Text button which will create a 

text file showing the hierarchical structure of the 

scheme, and the Create Legend from Scheme

button which will create a legend that contains each 

uniqueID and its attributes. Legend labels will have 

all of the categories in the classification hierarchy 

concatenated into one string. Colors will be 

randomly selected and an additional Unclassified

category will be added with a uniqueID of zero. 

Editing an existing classification scheme 

To edit an existing scheme, select 

Modify Current Scheme in the “Change 

Classification” dialog box. After 

selecting the method of assigning the 

uniqueID (in this case, using Manual is 

recommended), the “Modify 

Classification Scheme” dialog appears. 

Follow the same instructions in Creating 

a New Scheme to edit this scheme using 

the dialog at left. 
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Digitizing Restrictions 

Minimum Mapping Unit 

Depending on the quality of aerial images used and the specific goals of the project, it is often 

desirable to limit the minimum size of the features that are delineated. For example, poor image 

resolution may preclude the interpretation of features smaller than some minimum size threshold. 

Other features, while interpretable in the imagery, may simply be too small and therefore beyond the 

scope or goals of the desired map 

product. To limit the size of the 

features that can be digitized in the 

habitat map, a minimum mapping 

unit (MMU) can be set in Habitat 

Digitizer. Features must be larger 

than the MMU to be included in 

the habitat map. 

Set the MMU restriction by 

selecting Habitat Digitizer/Set 

Minimum Mapping Unit. If the 

view’s map and distance units are set, a dialog will appear showing the current MMU. Enter the 

desired numerical MMU into the text box and select Apply New MMU. If a satisfactory MMU has 

already been set, Use Current MMU will close the dialog without changing the MMU. Once an 

MMU is set, if the area of a newly digitized polygon is below the value specified, a message box will 

ask whether the polygon should be added to the theme. If no MMU restriction is desired, Habitat 

Digitizer/Set Minimum Mapping Unit/Turn off MMU will allow digitizing polygons with no size 

restriction. 

Scale Restriction 

It is possible to adjust the scale of the image files as they appear on the computer monitor. For 

example, the scale of hard copy photographs used for mapping may be 1:48000, however the actual 

photo interpretation may be conducted on the computer monitor while zoomed in on the scanned 

photographs at a much larger 

scale (e.g.1:6000). It is often 

desirable to conduct all polygon 

delineation at the same scale, so 

that all polygons have the same 

level of detail. Set the scale 

restriction by selecting Habitat 

Digitizer/Set Scale Restriction. 

Enter a number in the text box 

and select Apply New 

Restriction. If digitizing is 

attemped while a scale restriction 

is in place and the view is not at the specified scale, a message box will appear and offer to zoom the 

view to the proper scale. If No is selected, a polygon cannot be digitized. If a scale restriction is not 

desired, use Habitat Digitizer/Set Scale Restriction/Turn off Restriction to allow digitizing at any 

scale. The view’s map and distance units must be set to use this tool. 

Creating a theme and using the digitizing tools 

Once a classification scheme has been loaded, this button creates an empty theme with the 

appropriate fields. If a default legend has not been created using Habitat Digitizer/Set Default 

Legend or the Change Classification dialog, a dialog will appear to select a legend file. A second 
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35

message box will appear asking if this legend should be made the default legend for all new themes 

created using this classification scheme. After creating a new theme, set the snapping tolerance by 

using the menu selection Theme/Properties and in the Editing selection, click the General box and 

set the tolerance to a number smaller than the pixel size of the images used for interpretation (since no 

interpretation will presumably be conducted within pixels). If this is not done, adjacent polygons will 

not always share a common border. 

To start digitizing a new polygon, select this tool and trace the feature of interest by clicking 

around its perimeter with the mouse. A double click closes each new polygon. If a polygon is 

digitized inside or completely around an existing polygon, “donut” and “donut hole” polygons will be 

formed. Once the polygon is complete, a message box will allow the classification to be set as outlined 

below. 

Use this tool to add a polygon adjacent to an existing polygon. To create a polygon using this 

tool, start tracing a line inside of an existing polygon and end the line by clicking twice inside of 

the same or another existing polygon. This tool will not work when attempting to digitize a polygon 

inside of another polygon (use the Split tool below to do that). The scale restriction and MMU also 

apply to this tool. If several polygons are created with a single line and some are below the MMU, a 

warning message will appear. If No is selected on the warning message only the polygons that fall 

below the MMU will be removed. 

Once polygons are completed using the Add and Append tools, a dialog will appear to guide 

assignment of classification attributes. 

 

The Field List displays the hierarchical structure of the fields in the scheme. Current Attribute 

Selection shows the classification type, if any, currently selected. Either select Use Current Selection

or select a new classification type by clicking through the desired classification attributes in the Select 

New Attributes window. As new attributes are selected they will be displayed in the New Attribute 

Selection window. The Use New Selection button will be activated when the attribute in the lowest 

hierarchical level for the new classification is selected. 
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This tool splits one or more polygons into several polygons. All of the attribute information for 

the resulting polygons will be the same as the original(s), but can be changed as explained below 

under “Tools from the Right Mouse Button”. Please note that due to a bug in ArcView, this tool 

sporatically works when attempting to split along the inside border of a donut polygon. The scale 

restriction and MMU also apply to this tool. If several polygons are split and some of the resulting 

polygons fall below the MMU, choosing No will remove the entire line and merge the split polygons 

back together. 

This tool places a MMU sized red box on the view by clicking the button and then clicking 

directly in the View at the desired location. This box enables users to estimate the size of 

features in the imagery relative to the MMU. This box disappears when panning, zooming in or out, or 

after completing a polygon. To use this feature while adding a new polygon see “Tools from the Right 

Mouse Button” below. 

This tool brings up a dialog to display the cursor’s x/y position in the upper right hand corner of 

the ArcView window in either the coordinate system of the view (default) showing from 1-5 

significant digits, or in degrees, minutes, and seconds. This requires that the view’s projection be set 

and the map units specified. 

Tools from the Right Mouse Button 

Click and hold down the right mouse button to view a list of additional tools and options: 

Panning will recenter the display over the spot where the right mouse button was clicked. This is 

useful while digitizing large polygons that do not fit entirely within the view frame. 

Pan to Location will center the display at the coordinates entered in a message box.

Show attributes will display a message box showing the habitat attributes for the currently selected 

polygon. 

Change habitat attribute will allow the user to change the habitat attributes for polygons that are 

selected. 

MMU Box places an MMU box on the View where the right mouse button was clicked (can be added 

while digitizing a polygon). 

Polygon Area shows the area of a selected polygon. 

When a project is saved, the settings (classification scheme, MMU, scale restriction, default legend, cursor 

display precision, and current attribute selection) will be stored along with the project. Upon opening 

the saved project, these settings will be restored and do not need to be re-entered. 
Chapter 3: Creating and Interpreting Digital Orthophotographs ______________________________________________________________________________________ 

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Chapter 3: Creating and Interpreting Digital Orthophotographs 

Habitat maps of the main Hawaiians Islands were created by visual interpretation of aerial photos and 

hyperspectral imagery using the Habitat Digitizer extension (Chapter 2). Aerial photographs are valuable 

tools for natural resource managers and researchers since they provide an excellent record of the location 

and extent of habitats. However, spatial distortions in aerial photos due to such factors as camera angle, 

lens characteristics, and relief displacement must be accounted for during analysis to prevent incorrect 

measurements of area, distance, and other spatial parameters. These distortions of scale within an image 

can be removed through orthorectification. During orthorectification, digital scans of aerial photos are 

subjected to algorithms that eliminate each source of spatial distortion. The result is a georeferenced digital 

mosaic of several photographs with uniform scale throughout the mosaic. After an orthorectified mosaic is 

created, photointerpreters can accurately and reliably delineate the boundaries of features in the imagery as 

they appear on the computer monitor using a software interface such as the Habitat Digitizer. Through this 

process, natural resource managers and researchers are provided with spatially accurate maps of habitats 

and other features visible in the imagery. 

Creating the Digital Mosaic 

Aerial photographs were acquired for the main Hawaiians Islands Benthic Mapping Project in 2000 by 

NOAA Aircraft Operation Centers aircraft and National Geodetic Survey cameras and personnel. 

Approximately 1,449, color, nine by nine inch photos were taken of the coastal waters of the main 

Hawaiian Islands at 1:24,000 scale. Specific sun angle and maximum percent cloud cover restrictions were 

adhered to when possible during photography missions to ensure collection of high quality imagery for the 

purpose of benthic mapping. In addition, consecutive photos were taken at 60 percent overlap on individual 

flightlines and 30 percent overlap on adjacent flightlines to allow for orthorectification and elimination of 

sun glint. 

Prints and diapositives (color transparencies) were created from the original negatives. Diapositives were 

then scanned at a resolution of 500 dots per inch (DPI) using a photogrammetric quality scanner, yielding 

one by one meter pixels for the 1:24,000 scale photography. All scans were saved in tagged image file 

format (TIFF) for the purposes of orthorectification and photointerpretation. Original TIFFs were also 

converted to *.jpg format to reduce file size and facilitate web-based image distribution, and are currently 

available on the NOAA Biogeography Program’s web site at 72, 150, and 500 DPI resolution 

(http://biogeo.nos.noaa.gov/products/data/photos/). 

Georeferencing/mosaicing of the TIFFs was performed using a variety of softcopy photogrammetric 

software including Socet Set Version 4.2.1, Autometric Softplotter, PCI OrthoEngine, and Erdas 

OrthoBase. First, lens correction parameters were applied to each frame to eliminate image distortion. 

Airborne kinematic GPS (location of the aircraft at the time of each exposure) was then used, when 

available, to provide a first order geolocation. When this information was not available, measurements were 

made between flightline strips for input into aerial triangulation software to provide preliminary coregistration. 

Image to image tie-points (distinct features visible in overlap areas of each frame such as street 

intersections, piers, coral heads, reef edges, and bridges) were then used to further co-register the imagery, 

especially for photos taken over open water where ground control points were not available (see below). 

Softcopy photogrammetry software has limited ability to automatically find such features common to 

overlapping photographs but this automated function performs poorly for submerged features. 

Fixed ground features visible in the scanned photos were selected for ground control points (GCPs) which 

were then used to georeference the imagery (i.e. link the image pixels to a real world coordinate system 

such as latitude/longitude). GCPs were measured using DGPS (Differentially-corrected Global Positioning 

System). We obtained points with a wide distribution throughout the imagery, especially on peninsulas and 

outer islands whenever possible since this results in the most accurate registration throughout each image 

(http://biogeo.nos.noaa.gov/projects/mapping/pacific/main8/data/). Only ground control points for 
Chapter 3: Creating and Interpreting Digital Orthophotographs ______________________________________________________________________________________ 

38

terrestrial features were collected due to the difficulty of obtaining precise positions for submerged 

features. 

Pre-existing U.S. Geological Survey (USGS) 10-meter digital elevation models were used to correct for 

relief displacement (http://biogeo.nos.noaa.gov/products/mapping/dems/). Once a draft orthorectified 

mosaic was produced, a set of independent ground control points (i.e. check points) were used to measure 

the quality of each mosaic’s rectification and ensure that it adhered to horizontal and vertical spatial 

accuracy limits. If the spatial accuracy was not acceptable based on this comparison, additional 

modifications were made to the GCPs, tie-points, etc., until a satisfactory mosaic was created for each 

island. In general, mosaics were georeferenced such that pixels are positioned within one pixel width of 

their correct location. 

Average spatial accuracy of the individual mosaics is reported in Table 3.1. Values reported (pixel units) 

are the calculated root mean square error (RMSE) between the geometrically transformed mosaic solution 

and actual check point coordinates. RMSE is an industry standard for reporting the accuracy of 

orthorectified products. RMSE is variable within different areas of each mosaic. Features near land (near 

GCPs) are generally georeferenced with accuracy similar to the values reported in the table while the 

accuracy of features away from land is generally not as good. Where no land is in the original photographic 

frame only kinematic GPS and tie points were used to georeference the images. 

Once all the photos were orthorectified, the best segments of each photo were selected for creation of the 

final mosaic. Segments of each photo were selected to minimize sun glint, cloud interference, turbidity, etc. 

in the final mosaic. Where possible, parts of images obscured by sun glint or clouds were replaced with 

cloud/glint free parts of overlapping images. As a result, most mosaics have few or no clouds or sun glint 

obscuring bottom features. However, in some cases, clouds, sun glint, or turbid areas could not be replaced 

with overlapping imagery. In these areas, such obstructions were minimized but could not be eliminated 

completely. 

Final mosaics were created in “geoTIF” file format (georeferenced image file) with the following 

projection parameters: North American Datum 83, Universal Transverse Mercator (UTM) Zone 4 for 

Niihau, Kauai, Oahu, Molokai, Lanai, and Maui, and UTM Zone 5 for Hawaii. These files are available on 

the “Benthic Habitats of main Hawaiian Islands” CD-ROM and at the NOAA Biogeography Program web 

site in Mr.SID format. No color balancing was attempted since this alters color and textural signatures in 

the original imagery and interferes with the photointerpreter’s ability to delineate habitats. As a result, 

mosaics have visible seams between adjacent photos. This provides the photointerpreter with “true color” 

imagery for maximum ability to identify and delineate benthic features. 

Table 3.1: Mosaic Specifications for each Island. RMSE are in pixels. 

Location UTM 

Zone 

Photo 

Scale 

Pixel 

Width 

(m) 

# of 

Photos 

RMSE X RMSE Y RMSE Z 

Niihau 4 1:24000 1.0 15 0.054 1.120 0.300 

Kauai 4 1:24000 1.0 66 2.582 2.884 1.453 

Oahu 4 1:24000 1.0 25 1.437 1.382 1.139 

Lanai 4 1:24000 1.0 11 1.687 1.873 1.116 

Molokai 4 1:24000 1.0 31 .887 1.024 0.027 

Maui 4 1:24000 1.0 37 1.417 1.223 1.502 

Hawaii 5 1:24000 1.0 21 1.169 1.093 .566 
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39

Digitizing Benthic Habitats 

Coral reef benthic habitat maps were digitized by delineating habitat boundaries from georeferenced 

imagery loaded into ArcView GIS software with Image Analysis and the NOAA digitizing extension 

activated. Mosaiced color aerial photography scanned at one meter resolution, AURORA hyperspectral 

imagery collected at three meter and IKONOS satellite imagery collected at four meter resolution were 

provided for this work. Digitizing was conducted using heads-up computer screen methods with the 

minimum mapping unit (MMU) set to 1 acre and image scale at 1:6,000. This ensures that the level of 

detail produced by the photointerpreter is uniform throughout all products that have been provided on this 

CD-ROM. 

All three types of remotely sensed imagery were processed by NOS prior to map production. Individual 

color aerial photographs were georeferenced and mosaiced. The hyperspectral data composed of 72 ten nm 

wide bands were subsetted to three band composites that enhanced deep and shallow water features. 

IKONOS satellite imagery was corrected for atmospheric and water column effects. During the digitizing 

process, image stretches and manipulating image contrast, brightness and color balance were performed in 

the ArcView Image Analysis Extension to enhance features in the processed imagery. 

Within the extents of the color aerial photography, high quality 1:24,000 scale diapositives were available 

to aid the photointerpreter in the determination of habitat boundaries and type. These were viewed using a 

magnifying loop on a light table. 

The habitat boundaries were visually interpreted based on the signature (color and texture) of visible 

features. Habitat boundaries were delineated on computer screen and attributed in the GIS using the 

NOAA digitizing extension. Initially, a boundary around the entire image was generated and subdivided to 

discrete polygons representing the detailed habitats and zones defined in the Coral Reef Habitat 

Classification Scheme for the main Hawaiian Islands. 

Ground Validation 

A first draft map was completed using the above methods and features in the imagery where uncertainties 

existed, due to confusing or difficult to interpret signatures, were identified for future ground validation 

effort. An ArcView GIS point theme was generated with points positioned on the features of uncertain 

habitat type or along transects through gradients between habitat types. The GIS points were converted to 

GPS waypoints using Trimble Pathfinder Software and were navigated to in the field using a Trimble 

GeoExplorer 3 GPS data logger. 

Color prints of the imagery overlaid by the draft habitat map and waypoints were laminated and taken into 

the field to assist in the identification of signatures in the imagery and actual habitat type at each waypoint. 

A benthic habitat characterization was conducted at each site by snorkeling, free diving or via observations 

from the surface where water depth and clarity permitted. GPS data were collected at each location and site 

ID, depth, habitat type, zone and the method used to make the assessment were recorded on the GPS data 

logger. Longhand notes and descriptive information were hand written in waterproof notebooks. 

All field data were processed at the end of each field day. The data from the GPS data logger were 

downloaded and differentially corrected to the closest Continuously Operating Reference System (CORS). 

These data were converted to a text file that included geographic position and descriptive spatial statistics, 

which were automatically generated from the GPS data logger. A comments field was added to the text file 

and longhand field notes were manually entered. The file was converted to an ArcView shape file and 

overlaid on the original imagery and, where necessary, polygon boundaries were created or revised based 

on field observations using the NOAA digitizing extension. This second draft map was submitted for 

accuracy assessment. 
Chapter 4: Assessment of Classification Accuracy 

40

Figure 1. Distribution of accuracy assessment points (N=231) in red within the Molokai test site boundary displayed in 

yellow. 

Chapter 4: Assessment of Classification Accuracy

It is invalid to assume that habitat maps generated from photointerpretation of remotely sensed imagery are 

100% correct. It is important that the mapmaker know how reliably a given habitat can be classified. This 

parameter is called “producers accuracy”. The users of a map product want to know what percentage of the 

polygons of a particular class are correctly attributed. This parameter is called “users accuracy”. 

Furthermore, remotely sensed imagery that may be suitable for mapping coral reef habitats can be acquired 

from a wide variety of platforms and imaging systems, each having it’s own strengths and limitations. It is 

important to identify the technical merits of each including the thematic accuracy of the map products. 

Benthic habitat maps in ArcView GIS format were prepared by visually interpreting the three types of 

remotely sensed imagery. Conventional methods for assessing the accuracy of living resource maps 

prepared from visual interpretation of remotely sensed imagery were applied to meet two objectives. The 

first was to identify and compare thematic accuracy of maps prepared from the three sources of remotely 

sensed imagery and the second was to generate a scientifically sound statistical estimate of the thematic 

accuracy of the final map products. To meet the first objective, the accuracy of the benthic habitat maps in 

the four test areas was completed for each of the imagery types. These were contrasted to compare the 

accuracy of each. To meet the second objective, the data were then combined and analyzed to establish an 

accuracy of the final mapped products. 

The thematic accuracy of all mapped products was determined at the four most general levels of the 

classification scheme including unconsolidated sediment, submerged vegetation, coral reef/hard bottom and 

other. Four coral reef test areas were selected based on the diversity of the habitat types and to assure that 

all benthic habitats throughout the Hawaiian Islands were represented. The accuracy of all maps is, 

therefore, considered a conservative representation of the thematic accuracy of the habitat maps prepared 

using the same methods for imagery collected throughout the remainder of the main Hawaiian Islands. 

Goals of Accuracy Assessment 

1) Compare the thematic accuracy of benthic habitat maps prepared from three sources of remotely 

sensed imagery 

2) Establish a statistically sound thematic accuracy for routine production of habitat maps for the 

main Hawaiian Islands 

Evaluating Thematic Accuracy: Thematic Accuracy in the Main Hawaiian Islands

Four field test areas comprising over 100 square kilometers of coral reef area were established to determine 

the thematic accuracy of the benthic habitat maps prepared from the color aerial photography, hyperspectral 

airborne and IKONOS satellite imagery. Each area extends from shore to a depth of approximately 30 

meters. The first was located on the Kona Coast in the District of South Kohala on the west side of the 
Chapter 4: Assessment of Classification Accuracy 

41

Test Area Number of Field 

Assessments 

Kaneohe Bay 393 

Kona Coast 304 

Maui 297 

Molokai 231 

Total 1,225 

Table 1. Number of field assessments acquired 

at each of the four test sites 

island of Hawaii. It extends from Kawaihae Harbor to Kiholo Bay. The second study area is located in 

Kaneohe Bay on the island of Oahu. It extends from the Sam Pan Channel on the south end of the bay to 

Chinaman’s Hat on the north end of the bay. The third area is on the Island of Maui from Maalaea Harbor 

to Makena Beach and the fourth is illustrated here and is located on the south shore of the Island of 

Molokai from Palaau to the Kaunakakai Pier (Figure 1). 

A single NOAA contractor conducted all image interpretation and digitizing. The field habitat 

characterization data collection methods for thematic accuracy assessment differed little from the methods 

used to collect data for ground validation. The primary distinction between the two data sets was the 

method of selection of the field points. The assessment sites for ground validation were selected to 

specifically investigate habitat types and gradients of spectral signatures in the imagery and a random 

stratified sampling method was implemented to select field sites to test map accuracy. Subsequent to 

completion of the second draft coral reef habitat maps, polygons representing detailed habitats were 

aggregated into the three major classes and at least 50 random geographically referenced points were 

created in each (Congalton 1991). Waypoint files were generated from these points and all waypoints that 

could be safely accessed were navigated to using a Trimble Geo Explorer 3 GPS data logger. Upon arriving 

at the waypoint, a weighted meter line was dropped, a buoy fastened and site and habitat specific data 

collection was undertaken. 

Three benthic habitat assessments were conducted. A point assessment was conducted by surveying the one 

square meter area around the point where the weight dropped. Two area assessments were conducted in an 

area of a seven meter radius around the weight. The first assessment identified the most common habitat 

type within the area and the second identified the second most common habitat type with in the area. The 

depth of the site was recorded using a hand held depth sounder. Benthic habitat assessments were made 

using a glass bottom look box, diving or observing from the surface. All diving was conducted by breath 

holding or snorkeling on the surface. In areas where waves and sea conditions were prohibitive to safely 

accessing the waypoint by boat, the GPS was placed in a watertight box and swam to the survey point. 

Data including but not limited to site ID, depth, most common habitat, zone and assessment method were 

recorded using the GPS data logger equipped with a custom data dictionary designed to meet the 

specifications of the Coral Reef Habitat Classification Scheme. At the end of each field day, the data were 

downloaded, differentially corrected and seamlessly converted to ArcView GIS format. All hand written 

descriptions were entered in waterproof notebooks and transferred to the GIS by hand. A total of 1,225 

benthic habitat characterizations were completed in all four test areas combined (Table 1). 

To maintain objectivity in the analysis of accuracy, an 

independent team conducted this work. The Coral Reef 

Assessment and Monitoring Program (CRAMP) biologists 

of the Hawaii Institute of Marine Biology from the 

University of Hawaii at Manoa made the official judgments. 

The accuracy assessment point theme and the benthic 

habitat polygon theme were overlaid on the imagery in the 

GIS. The GIS was queried to select all points within the 

polygons that matched the polygon habitat type. These were 

set aside as correct calls. The mismatched pairs were closely 

examined. 

The classification errors that occurred between the MMU and size of accuracy assessment areas were 

accounted for in this analysis. A map classification was not considered incorrect in a case where a seven 

meter radius field assessment fell on a habitat feature in the field that was smaller than the one acre MMU. 

For example, if a field assessment fell on a small patch reef surrounded by sand that was less than the 

MMU and thus was not mapped, the point was excluded from the accuracy assessment report. Points that 

fell close to polygon boundaries were all included as it was assumed that the probability of error 

contributing to false negatives would be equal to that for false positives. Furthermore, the three types of 

imagery were acquired during different days with different weather conditions. The habitat type for the 

portions of the test area that were not interpretable due to cloud cover, glint or water quality were classified 

as “unknown”. The accuracy assessment points that fell within polygons with the habitat type of 

“unknown” were not included in the accuracy analysis. 
Chapter 4: Assessment of Classification Accuracy 

42

 Actual Habitat Type 

Coral Reef/ 

Hardbottom 

Submerged 

Vegetation 

Unconsolidated 

Sediment Other 

Coral Reef/ 

Hardbottom 

136 

96%(U) 

(89%(P) 

5 1 1 

Submerged 

Vegetation 13 

66 

83%(U) 

87%(P) 

1 0 

Unconsolidated 

Sediment 4 5 

88 

90%(U) 

98%(P) 

0 

Mapped Habitat Type 

Other 0 0 0 

9 

100%(U) 

90%(P) 

Overall Accuracy: 91% 

Table 3. Sample error matrix of major classes of classification scheme prepared from visual 

interpretation of hyperspectral imagery at the Kaneohe Bay test site. Numbers in matrix indicate 

class coincidence, (U) indicates users accuracy and (P) indicates producers accuracy based on the 

analysis of 329 field assessments. 

Results of overall accuracy assessment of benthic habitat map products

Thematic accuracy of the benthic habitat maps was determined using the above methods. The mapped 

habitat type was compared with that of the actual habitat type from field observation. The data was 

organized into a matrix with columns representing the field habitat assessment and rows organized into 

mapped habitat type. The correct class for each of the incorrect attributes was recorded and included in a 

comprehensive matrix at the most detailed level of the classification scheme. Twelve of these detailed 

matrices were generated, one for each of the types of imagery at each of the four test areas (Table 2 on 

following page). Error matrices were prepared at the detailed level to identify patterns of confusion in the 

interpretation of the signatures in the imagery. This information has been incorporated into ongoing work 

to improve the accuracy of future mapped products. 

The overall accuracy was calculated by dividing the total correct determinations by the total number of 

assessments. This result only incorporates the major diagonal of the table and excludes the omission and 

commission errors whereas the Kappa analysis (Cohen, 1960) indirectly incorporates the off-diagonal 

elements as a product of the row and column marginals. The Tau analysis generates a similar statistic as 

Kappa but compensates for unequal probabilities of groups or for differences in numbers of groups (Ma 

and Redmond, 1995). This assessment lends itself to statistical analysis wherein the photointerpreter’s 

determination is assigned a probability that it occurred at random. The data was then aggregated to the four 

most general levels of the classification scheme and twelve error matrices were generated, one for each of 

the image types at each of the four test areas (Table 3). 
Chapter 4: Assessment of Class

43

FIELD ASSESSMENT R

AgCr SnG ColPv Artf LCorAl LMacAl SCRUS MMacAl EmgVg Mud RR SAND LinReef UnColPv T

AgCr 27 1 2 3

SnG 0 0 ColPv 2 1 3 Artf 7 7 LCorAl 1 0 1 2 LMacAl 38 4 2 1 4SCRUS 10 1 MMacAl 1 4 5 1 EmgVg 21 2Mud 1 RR 1 SAND 2 1 38 4LinReef 37 3

POLYGON ATTRIBUTE 

UnColPv 1 6 7 

Column Totals 

29 1 3 7 0 45 11 9 21 2 1 43 37 8 2

Producer's Accuracy 93% 0% 33% 100% NA 84% 91% 56% 100% 50% 100% 88% 100% 75% 

Detailed Overall Accuracy 88.5% 

Table 2. Sample error matrix of detailed classes of the classification scheme prepared from visual interpretation of color aerial photo

site. Numbers in matrix indicate class coincidence, (U) indicates users accuracy and (P) indicates producers accuracy based on assessments. Column and row headings have been abbreviated. AgCr: aggregated coral, SnG: spur and groove, ColPv: colonized LCorAl: Coralline algae (10%-<50% cover), LMacAl: macroalgae (10%-<50% cover), MMacAl: Macroalgae (50%-<90% cover), EmRR: reef rubble, LinReef: linear reef and UnColPv: uncolonized pavement. 
Chapter 4: Assessment of Classification Accuracy ______________________________________________________________________________________ 

44

The most common and generally accepted statistic used to represent the accuracy of map products is the 

over all accuracy. The average accuracy for the map products prepared from each of the imagery types was 

estimated by combining the results from the four test areas. This summary was completed for both detailed 

and major habitat accuracy assessment (Table 4). Though the accuracy of maps prepared from IKONOS 

satellite imagery were tested, IKONOS imagery was not used to prepare the final benthic habitat maps for 

the main Hawaiian Islands. Thus, the overall accuracy of the final mapped product prepared from the visual 

interpretation of imagery for the main Hawaiian Islands is estimated to be 90% (Kappa and Tau 0.86) for 

the major class level and 80% at the most detailed level of the classification scheme. Kappa and Tau were 

calculated and reported for the major habitat levels but not calculated for the detailed level. 

Comparison of Thematic Accuracy of Map Products Generated from Color Aerial Photography, 

Hyperspectral Imagery and IKONOS Satellite Imagery 

The cost effectiveness of acquisition and processing of remotely sensed imagery varies significantly 

between types of platforms deployed and imaging systems used to acquire the data. Logistics constrain the 

area accessible by fixed wing platforms while satellite imagery is relatively inexpensive for large scale 

acquisitions. The enhanced spectral resolution of hyperspectral and control of bandwidth of multispectral 

data yield an advantage over color aerial photography particularly when coral health and time series 

analysis of coral reef community structure are of interest. NOAA is transitioning away from aerial 

photography in very large and remote areas that are difficult to access by airplane. As a result, it is 

important to identify the strengths and weaknesses of the map products prepared from each of the types of 

digital imagery. Of particular interest is the thematic accuracy of the mapped products. 

The Z test or Z score, which reveals the probability that there is no difference between the accuracy of the 

maps in a contrast, was applied to these data. A contrast result of an absolute value of 1.96 or less indicates 

a 95% confidence that there is no significant difference between the accuracy of the maps being compared. 

Three of the four contrasts between the accuracy of maps prepared from one meter color aerial photography 

and three meter hyperspectral imagery resulted in a insignificant difference (Table 5). The contrasts 

conducted between maps prepared from three meter hyperspectral and four meter IKONOS satellite 

imagery all showed insignificant differences. Two of the four contrasts conducted between maps prepared 

from one meter color aerial photography and 4 meter IKONOS satellite imagery resulted in significant 

difference at 95% confidence interval. When all four sites were combined, there was no significant 

difference between the map accuracy when contrasting color aerial photography and hyperspectral imagery 

or when contrasting hyperspectral imagery with IKONOS satellite imagery. The contrast between color 

aerial photography and IKONOS satellite imagery yielded an absolute Z value of 3.07 indicating that there 

is a significant difference between the accuracy of habitat maps produced from these image sources. 

The work conducted here was not designed to analyze the difference in map accuracy based on pixel size 

independent of color of an image or vise versa. While the two are statistically inseparable in this work, 

Accuracy Statistics 

Imagery Type 

(All test areas 

Combined) 

Overall Accuracy 

at Detailed 

Habitat Level 

Over all Accuracy 

at Major Habitat 

Level 

Kappa for 

Major habitat 

Level 

Tau for Major 

Habitat Level 

Color Aerial 

Photography 80.8% 90.7% 0.87 0.87 

Hyperspectral 

Imagery 78.1% 89.0% 0.85 0.86 

IKONOS Satellite 

Imagery 74.1% 86.5% 0.82 0.83 

Table 4. Accuracy of final map products summarized for each of the three types of imagery. An 

overall accuracy was estimated to be 90% at major level and 80% at detailed level (Kappa and Tau 

0.86) as color aerial photography was predominantly used for map preparation. 
Chapter 4: Assessment of Classification Accuracy ______________________________________________________________________________________ 

45

Test Area Image Type IKONOS HSI 

Color 0.9990 -0.6166 

MAUI IKONOS -0.0824 

Color 2.6216 -2.3735 

MOLOKAI IKONOS -0.2922 

Color 1.5673 -0.3975 

OAHU IKONOS -1.8923 

Color 2.0126 0.8084 

HAWAII IKONOS -1.1730 

ALL Color -3.0709 1.4236 

COMBINED IKONOS -1.5961 

 

Difference Significant 

P<0.05 

Table 5. Summary of the probability that photointerpretation of coral reef habitat from color aerial 

photography, hyperspectral and IKONOS Satellite imagery are equivalent: P = 0.05 or less with 

significant difference highlighted. 

extensive exposure to these data led the photointerpreter to observations that may be noteworthy. Both 

image color and pixel size has been carefully observed during this work. 

In general, it may be stated that pixel size impacts the ability to interpret features in an image more than 

color when an image is displayed in true color. However, without recognizing that manipulation of the 

large number of bands in a hyperspectral image and optimizing bandwidth in a multispectral image 

introduces some compensation for the lower resolution, very important observations would be overlooked. 

The imagery types used in this work have been optimized to maximize true color and during the map 

preparation the color has been strategically manipulated to extract the most habitat information. Specific 

band combinations were selected that enhanced feature detection in shallow and deep water using 

hyperspectral imagery. The IKONOS satellite imagery was provided to the contractor preprocessed to 

remove atmospheric effects and compensate for water column effects. Furthermore, diapositives of the 

color aerial photography were viewed on a light table allowing for additional color contrast to enhance the 

textural information needed for visual interpretation. Though not scientifically tested here, it is believed 

that if this work had addressed variable pixel size within the same imagery source, the statistical differences 

between the accuracy of these maps would have been much more significant. These enhancements have 

resulted in considerable compensation for the reduced resolution due to pixel size. 

While it may be intuitive that smaller pixel size improves resolution and accuracy of the mapped product 

results, it may be less obvious that the relationship is not a function of the linear dimension of the pixel but 

of the area of the pixel. The one meter color aerial photography may be 16 times more resolved than the 

four meter IKONOS imagery. Although the linear pixel size of the hyperspectral imagery is only slightly 

different than the IKONOS satellite imagery, the area of the pixel differs by nearly 50%. Taken in this 

context the conclusion that accuracy of the maps produced from one meter pixel data were significantly 

more accurate than the maps generated from four meter pixel data when applying a 95% confidence 

interval comes as no surprise. However, the results show that when applying a 90% confidence interval 

there are no significant differences between the accuracy of any of the maps. Thus, it appears that the 

ability to generate coral reef habitat maps with an overall accuracy of 90% at a 95% confidence interval is 

reaching a threshold using imagery with three meter pixel size allowing for spectral enhancement of the 

imagery with reduced resolution. 
Chapter 4: Assessment of Classification Accuracy ______________________________________________________________________________________ 

46

Increasing the intensity of field observation can partially compensate for this decrease in accuracy of the 

maps generated from the larger pixels. Habitat maps prepared from IKONOS satellite imagery should be 

accompanied by field observations wherever possible and if field observations are not feasible, accuracy 

standards should be assigned accordingly.
References ______________________________________________________________________________________ 

47

Allee, R.J., and 11 co-authors. 2000 Draft. Marine and Estuarine Ecosystem Classification. National 

Marine Fisheries Service. Office of Habitat Conservation. Silver Spring, MD. 41 p. 

Chauvaud, S., C.Bouchon, and R. Maniere. 1998. Remote sensing techniques adapted to high resolution 

mapping of tropical coastal marine ecosystems (coral reefs, seagrass beds, and mangrove). 

Int.J.Remote Sens. 19(18):3525-3639. 

Christensen, J.D, C.F.G. Jeffrey, C. Caldow, M.E. Monaco, M.S. Kendall, and R.S. Appeldoorn. 2003. 

Quantifying habitat utilization patterns of reef fishes along a cross-shelf gradient in southwestern 

Puerto Rico. Gulf and Caribbean Research, 14(2):1-15. 

Cohen, J. 1960: A coefficient of Agreement for Nominal Scales. Educ. Psychol. Measurement 20(1): 37-

46 

Congalton, R.G. 1991. A review of assessing the accuracy of classifications of remotely sensed data. 

Remote. Sens. Environ. 37:35-46 

Dobson, J.E., E.A. Bright, R.L. Ferguson, D.W. Field, L.L. Wood, K.H. Haddad, H. Iredale III, J.R. Jensen, 

V.V. Klemas, R.J. Orth, and J.P. Thomas. NOAA Coastal Change Analysis Program (C-CAP): 

Guidance for Regional Implementation. NOAA Technical Report, National Marine Fisheries 

Service 123. Department of Commerce. April 1995. 

Florida Fish and Wildlife Conservation Commission, Florida Marine Research Institute (FMRI) and 

National Oceanic and Atmospheric Administration. 1998. Benthic Habitats of the Florida Keys. 

FMRI Technical Report No. TR-4. 52 pp. 

Gulko, D. 1998. Hawaiian Coral Reef Ecology. Mutual Publishing. Honolulu, HI. 245 p. 

Holthus, P.F., and J.E. Maragos. 1995. Marine ecosystem classification for the tropical island Pacific. In: 

Maragos, J.E., Peterson, M.N.A., Eldredge, L.G., Bardach, J.E., Takeuchi, H.F. Eds.), Marine and 

Coastal Biodiversity in the Tropical Island Pacific Region, East-West Center, Honolulu, pp 239-

278. 

Kendall, M.S., C.R. Kruer, K.R. Buja, J.D. Christensen, M. Finkbeiner, and M.E. Monaco. 2001. Methods 

used to map the benthic habitats of Puerto Rico and the U.S. Virgin Islands. National Ocean 

Service, Center for Coastal Monitoring and Assessment, Biogeography Program, Silver Spring, 

MD. 45pp. 

Kruer, C. 1995. Mapping and characterizing seagrass areas important to manatees in Puerto Rico- Benthic 

Communities Mapping and Assessment. Report prepared for Department of Interior, Nat. Biol. 

Surv., Sirenia Project, Order No. 83023-5-0161. 14 pp. 

Lindeman, K.C., G.A. Diaz, J.E. Serafy, and J.S. Ault. 1998. A spatial framework for assessing cross-shelf 

habitat use among newly settled grunts and snappers. Proc. Gulf Carib. Fish. Inst. 50:385-416. 

Ma, Z., and R.L Redmond, 1995: Tau Coefficients for Accuracy Assessment of Classification of Remote 

Sensing Data. Photogrammetric Engineering and Remote Sensing, Vol. 61, No.4, 435-439 

Mapping and Informations Synthesis Working Group. 1999. Coral Reef Mapping Implementation Plan (2nd

Draft). U.S. Coral Reef Task Force. Washington, DC: NOAA, NASA and USGS (Work Group 

Co-chairs). 17pp. 

Monaco, M.E., J.D. Christensen, and S.O. Rohmann. 2001. Mapping and monitoring of U.S. coral reef 

ecosystems. Earth System Monitor, Vol. 12, No. 1, 1-7. 
References ______________________________________________________________________________________ 

48

Mumby, P.J., A.R. Harborne, and P.S. Raines. 1998. Draft Classification Scheme for Marine Habitats of 

Belize. UNDP/GEF Belize Coastal Zone Management Project. 44 pp. 

NOAA, US Geological Survey, Florida Fish and Wildlife Conservation Commission, and Florida Marine 

Research Institute. 1998. Seagrass and aquatic habitat assessment workshop summary, and 

accompanying participant survey data. July 28-29, 1998 technical workshop at University of 

South Florida, St. Petersburg, FL. 22 pp. 

Reid, J.P., and C.R. Kruer. 1998. Mapping and characterization of nearshore benthic habitats around 

Vieques Island, Puerto Rico. Report to U.S. Navy. U.S. Geological Survey/BRD, Sirenia Project, 

Gainesville, Florida. 11pp. 

Sheppard, C.R., K. Matheson, J.C. Bythel, P. Murphy, C.B. Myers, and B. Blake. 1998. Habitat mapping in 

the Caribbean for management and conservation: Use and Assessment of Aerial Photography. 

Aquat. Cons. 5:277-298. 

Vierros, M. K. 1997. Integrating multisource imagery and GIS analysis for mapping Bermuda’s benthic 

habitats. Presented at the 4th International Conference on Remote Sensing for Marine and Coastal 

Environments. Orlando, FL March 1997, I-649-656