Benthic habitat imagery collected as a part of Towed-diver Surveys (TDS) and Rapid Ecological Assessment (REA) surveys for corals and fish are quantitatively analyzed implementing the Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software, whereby 10 stratified random points are projected on each image and the benthic elements falling directly underneath each point will be identified to three functional groups levels: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.), Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Astreopora sp, Favia sp, Pocillopora, etc.; Macroalgae = Caulerpa sp, Dictyosphaeria sp, Padina sp, etc.).
Power analyses support the methodological approach outlined above, whereby statistically sound sub-jurisdictional (island) level, benthic cover estimates can be successfully derived from REA and TDS photos. Benthic percent cover at the island level can be determined from data derived from towed-diver survey images while benthic percent cover is calculated at the site level for data derived from stratified random sampling images.
Benthic percent cover has been derived from imagery collected during TDS every other year in American Samoa from 2004 to 2010, Guam from 2005 to 2011, and the Main Hawaiian Islands from 2006 to 2010 as well as 2005, and during REA surveys in American Samoa in 2010, Guam and the Commonwealth of the Northern Mariana Islands (CNMI) in 2011, and the Main Hawaiian Islands in 2010 and 2013, survey imagery for Guam and the CNMI collected in 2014 is currently being analyzed (as of the publication date of this record).
2004 Mission: American Samoa Reef RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-04-02; Mission Dates: 03 February-26 February 2004 ; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0402-1.PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila
2005 Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-05-02; Mission Dates: 24 February-06 March 2005; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0502-PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui
Mission: Main Hawaiian Islands MHI RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-05-05; Mission Dates: 14 July-07 August 2005; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0505b-1.PSV.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Maui, Kauai
Mission: Mariana Archipelago RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-05-12; Mission Dates: 03 October-09 October 2005; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0512-1.RES.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam
2006 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-06-02; Mission Dates: 09 February-10 March 2006; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0602-RS.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila
Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-06-10; Mission Dates: 27 July-20 August 2006 ; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0610-REB.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui, Kauai
2007 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-07-02; Mission Dates: 12 May-22 May 2007; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0702-RS.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam
2008 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HI-08-02; Mission Dates: 18 February-19 March 2008; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0802-REB.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, Swains, Tau, Tutuila
Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Oscar Elton Sette, Cruise OES-08-10; Mission Dates: 16 October-14 November 2008 ; Document: MHI RAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0810-BVA.pdf Survey Methods: Towed Diver Images analyzed for the following locations: Hawaii, Maui, Kauai
2009 Mission: Mariana Archipelago RAMP Cruise, Leg 2; Mission ID: Hi'ialakai, Cruise HA-09-02; Mission Dates: 02 April-14 April 2009; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA0902-RES.pdf Survey Methods: Towed Diver Images analyzed for the following location: Guam
2010 Mission: American Samoa RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-10-01, Leg 2; Mission Dates: 17 February-23 March 2010; Document: ASRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1001II-KD.pdf Survey Methods: REA and Towed-diver Images analyzed for the following locations: Ofu and Olosega, Rose Atoll, South Bank, Swains, Tau, Tutuila
Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-10-08; Mission Dates: 07 October-05 November 2010; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1008-KD.pdf Survey Methods: REA and Towed-diver Images analyzed for the following locations: Hawaii, Maui, Kauai, Lanai, Molokai, Ni'ihau, Oahu
Mission: Shore-based Fish Surveys; Mission ID: Small Boat Plan, SB-10-06; Mission Dates: 17 November-08 December 2010; Document: Contact CRED at nmfs.pic.credinfo@noaa.gov for more information. Survey Methods: REA Images analyzed for the following location: Oahu
2011 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-11-01, Legs II and III; Mission Dates: 07 April-09 May 2011; Document: MARAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1101II-KD.pdf Survey Methods: REA (all islands) Towed-diver (Guam only) Images analyzed for the following locations: Guam, Agrihan, Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guguan, Maug, Pagan, Rota, Saipan, Sarigan, Tinian
Mission: Guam Shore-based Surveys; Mission ID: N/A (chartered vessel); Mission Dates: 06 June-17 June 2011; Document: A Report Based on Underwater Visual Surveys in Guam and the Mariana Archipelago, http://www.pifsc.noaa.gov/library/pubs/tech/NOAA_Tech_Memo_PIFSC_33.pdf Survey Methods: REA Images analyzed for the following locations: Guam
2013 Mission: Kauai Shore-based Surveys; Mission ID: Small Boat Plan, SB-13-09; Mission Dates: 29 April-07 May 2013; Document: Small Boat Mission Report: Coral disease surveys in the vicinity of Kauai Island, http://intra.pifsc.gov/sites/default/files/SBR1309-BVA.pdf Survey Methods: REA Images analyzed for the following location: Kauai
Mission: Main Hawaiian Islands RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-13-04, Legs I and II; Mission Dates: 1-23 August 2013; Document: MHIRAMP Cruise Report, http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1304I.pdf Survey Methods: REA Images analyzed for the following locations: Hawaii, Maui, Kauai, Lanai, Molokai, Ni'ihau, Oahu.
Mission: Main Hawaiian Islands RAMP Shore-based Surveys; Mission ID: Small Boat Plan, SB-13-20; Mission Dates: 30 September-23 October 2013; Document: Small Boat Mission Report: 2013 Pacific Reef Assessment and Monitoring Program (continued), Oahu Operations, http://intra.pifsc.gov/sites/default/files/SBR1320-BVA.pdf Survey Methods: REA Images analyzed for the following location: Oahu
2014 Mission: Mariana Archipelago RAMP Cruise; Mission ID: Hi'ialakai, Cruise HA-14-01, Legs I, II and III; Mission Dates: 25 March-07 May 2014; Document: MARAMP Cruise Report, Cruise report not yet published as of the publication date of this record. Contact CRED at nmfs.pic.credinfo@noaa.gov for a draft copy of the report. Survey Methods: REA Images analyzed for the following locations: Guam, Aguijan, Alamagan, Asuncion, Farallon de Pajaros, Guguan, Maug, Pagan, Rota, Saipan, Sarigan, Tinian
Value | Definition |
---|---|
Massive (MASS) | Coral colonies with distinct and boulder-like; small ones have more of a dome or cushion-shape silhouette. It is not unusual for massive colonies to exhibit a bumpy or knobby surface, but for the most part all possess a solid thick shape. |
Tabulate (TAB) | Coral colonies with tabulate growth morphology are those that have the appearance of a table or bench, supported on a short, stout base that is attached to the substrate. The horizontal plate or plates have numerous fused and interlocking branches, forming a roughly circular or oblong plate sometimes several feet in diameter. |
Encrusting (ENC) | Coral colonies with encrusting morphology are those with flattened, thick or thin sheets/plates that adhere to, and follow the contour of the substrate. Colony surfaces often range from smooth to rough, bumpy, knobby, or crinkled, with some specimens exhibiting raised colony edges, giving colonies a platy/foliose appearance. Some corals like Montipora spp. have colonies exhibiting mixed morphologies, such as encrusting bases with vertical, columnar or branching up-growths. If up-growths are low-profile bumps or knob-like protrusions and most of the colony is still encrusting, then the colony should be classified as encrusting. Conversely, if the encrusting base is covered with sizable, vertical, dichotomous branching projections, then the colony should be classified as having a branching morphology. |
Branching (BR) | Corals forming large, arborescent (tree-like) colonies exhibiting elongated branched projections, to smaller, stubby and compact branches with finger-like (digitate) protrusions should be classified as branching morphology. |
Columnar (COL) | Some coral colonies, generally massive- and encrusting-looking, can exhibit club-like or column-like up-growths; these colonies should be classified as having a columnar morphology. Columns can be smooth, knobby, or bumpy, and nearly cylindrical or tapered, but not branched. Columns typically protrude several inches from the base of the colony; this should not include stubby digitate protrusions or incipient branchlets. Corals including Porites rus, P. cyllindrica, P. evermanni, Coscinaraea exesa, Pavona maldivensis, and Favia stelligera, can grow colonies exhibiting columnar morphology. |
Free-living (FREE) | Use the free-living morphology for coral colonies that live unattached from the substrate. This excludes broken-off colony branches or other products of fragmentation. Free-living corals are conspicuous; most develop as flattened, dome-shaped disks, with a central mouth and apparent, radiating ridge-like structures known as septa.. |
Foliose (FOL) | Coral colonies with foliose morphology are those that grow in flattened sheets or plates where a substantial portion of the colony is detached and elevated from the substrate forming shingle-like rows or tiers of overlapping plates, fused or convoluted whorls, vases, or leafy/lettuce-like stands. |
Non-scleractinian hard coral (NS) | This classification category is to be used for other groups of non-scleractinian corals with hard skeletons, including fire corals (Family Milleporidae, e.g., Millepora sp), blue coral (Order Helioporacea, e.g. Heliopora coerulea), and Stylasterid hydrocorals (Family Stylasteridae), regardless of growth form. |
Value | Definition |
---|---|
Octocoral (OCT) | Use this Tier 2 classification for gorgonian corals, sea fans, sea whips, sea pens, and other members of Subclass Alcyonaria (octocorals), except blue coral (Order Helioporacea), which should be classified as Non-scleractinian hard coral. All members of this classification category produce skeletal elements made of protein and calcium carbonate that and give the colony sufficient soft support and the flexibility to sway with the ocean waves and currents. |
Unclassified (USC) | These corals resemble gorgonians forming tree-like colonies. They possess a hard axial protein skeleton and non-retractable polyps, including black coral and wire coral (Order Antipatheria). |
Value | Definition |
---|---|
CCA growing on rubble substrate (CCAR) | CCA commonly grow on rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, in patches. A piece of rubble completely encased in CCA is termed a rhodolith. |
CCA growing on hard[bottom] substrate (CCAH) | CCA commonly grows in patches on hard substrates, forming hard pink crusts. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures. |
Value | Definition |
---|---|
Visible turf on rubble substrate (TURFR) | Turf algae often cover rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, giving the fragments a fuzzy appearance. |
Visible turf on hard[bottom] substrate (TURFH) | Turf algae often appear as fuzzy carpets growing across hard substrates. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures. NOTE that turf algae will tend to trap a fine layer of sediment and this still constitutes a turf covered surface and should NOT be classified as Sand. |
[Invisible turf on] Rubble substrate (RUB) | All hard surfaces are colonized by turf algae within days of being placed in the water. All rubble, which is defined as hard fragments (e.g. rocks, pebbles, pieces of dead coral) typically of gravel (> 5 mm) and cobble (baseball) size with finer and coarser sediments mixed in, are covered by turf algae even though these small organisms might not be visible in a photograph. Sometimes they're even difficult to discern by a diver in the field. |
[Invisible turf on] Hard[bottom] substrate (HARD) | All hard surfaces are colonized by turf algae within days of being placed in the water. All hard substrates are covered by turf algae even though these small organisms might not be visible in a photograph. Hard substrates range from pavement flats to basalt formations to bare carbonate (i.e. coral skeleton) structures. |
Value | Definition |
---|---|
Upright macroalga (UPMA) | Macroalgae that do not form crusts adherent to rubble or the substrate should be termed as upright. |
Encrusting macroalga (EMA) | Encrusting macroalgae may resemble CCA by forming crusts across rubble or hard bottom communities. For the purpose of image analyses, if the encrusting alga is not red or pink, it should be considered an encrusting macroalga rather than CCA. It's important to note that EMA can also be pink and red in addition to all other options. Color can usually NOT be the sole distinguishing factor. Other features used to distinguish EMA include growth pattern, texture, and striations in color pattern. |
Blue-green macroalga (a.k.a. cyanobacteria) (BGMA) | Blue-green algae (more correctly termed cyanobacteria) are rare in the majority of photographs examined. However, when they are recorded, they often form gregarious assemblages that look different from macroalgae or turf algae. When observed, cyanobacteria often form deep purple to black filamentous tufts or mats that may stretch for multiple centimeters in length, and therefore look different from turf algae. They may also form mucilaginous masses that are white or pale yellow in color. |
Halimeda sp. (HAL) | The calcified green algal genus Halimeda is easily discernible by it's plate-like discs that form "chains" of segments. Living plants appear green, although dead segments may be white. |
Seagrass | Seagrasses are flowering plants from one of four plant families (Posidoniaceae, Zosteraceae, Hydrocharitaceae, or Cymodoceaceae), which grow in marine, fully-saline environments. |
Value | Definition |
---|---|
Giant clam (GC) | Classification points that land on giant clams (Family Tridacnidae) should be classified in this Tier 2 category. While their shell may be drab in color and/or colonized by algae or other sessile organisms, the mantle can colorful and they can grow from .25 m to more than 1 m in diameter. The Bivalve category is used for all other bivalves (clams, oysters, and mussels) in Class Bivalvia. |
Bivalve (BI) | Clams, oysters, and mussels are common examples of bivalves (Class Bivalvia). Giant clams (Family Tridacnidae) are a special case, and have their own Tier 2 classification category. |
Sponge (SP) | Sponges (Phylum Porifera) have numerous species and growth morphologies, many of which can be confused with other benthic organisms. Sponges have porous tissue for filter feeding and many have large openings through which expelled water flows (excurrent openings). To help identify sponges, zoom-in with the photograph and examine the surrounding tissue. In general, sponges are more colorful than tunicates. In general, sponges are not as smooth as a tunicate, rather they are "rougher" around the edges due to a lack of a "tunic" and being composed of spicules. In general, most sponges, unlike tunicates, are not able to close their excurrent openings. In general sponges can protrude/extend upwards off the benthos from their encrusting state whereas tunicates tend to grow along the contours of the substrate underneath them. |
Tunicate (TUN) | Tunicates (Class Ascidiacea) have numerous species and growth morphologies, many of which can be confused with other benthic organisms (particularly sponges). They can grow as solitary individuals or in colonies. Their soft body is surrounded by a thick test, or tunic, often transparent or translucent and varying in consistency from gelatinous to leathery. In solitary tunicates, there are two siphons that project from the animal's body; water enters the incurrent siphon at the top of the body and leaves the excurrent siphon at the side. They appear heart shaped. Colonial tunicates share excurrent siphons but zooids (individuals) have their own incurrent siphon. The following is a generalization however, more often than not, if the organism has multiple holes (which represents the individual incurrent siphons of the zooid) with a few larger holes (the shared excurrent siphons) spread out, it is probably a tunicate. Tunicates will be able to close their siphons rather quickly whereas sponges are for the most part unable. Thus if some of the openings of the sessile organism appear to be closed in the photograph, it is likely a tunicate. Another generalization that helps separate tunicates from sponges is that tunicates don't usually have visible "channels," whereas certain sponges do. One final generalization is that tunicates tend to grow with the contours of the substrate whereas sponges can grow upwards from the encrusting state. |
Bryozoan (BRY) | These colonial animals are early colonizers of bare surfaces in coral reefs. Most attach to solid surfaces but some live in sand. Each "member" lives in a zooid, or house, and has lophophores which are "tentacles" that extend out of the house to filter feed. The lophophores are ciliated and very "regular" in appearance. However, unless the image is really clear, it will be hard to detect the lophophores and use them to distinguish between a tunicate or sponge. The individual zoids join to neighboring ones forming bushy, branching, fanlike, or encrusting colonies that may be rigid or flexible. Most bryozoans have a lace-like appearance and can be confused with algae or sponges. However, unlike sponges and tunicates, you will not see incurrent and excurrent openings. This is because the lophophores in bryozoans are used for feeding. In general, bryozoans will not appear smooth like a tunicate and their upright structure will appear to be "flower" and "plant"- like. |
Corallimorph (CMOR) | Corallimorphs (Order Corallimorpharia) are anemone-like animals that are found either solitary or in colonies. Their tentacles are generally much shorter than those of true anemones. They can be invasive and at this stage resemble a fuzzy carpet. |
Anemone (AMNE) | Anemones have many tentacles, the number of which varies by species, surrounding a single mouth opening on top of a tubular body. However, you will probably never see the mouth opening, just the tentacles. Anemones usually attach themselves to the hard substrate with a pedal disc, which is found at the base of the body. Members of Order Actiniaria (anemones) and Order Ceriantheria (tube-dwelling anemones) are classified with this Tier 2 category. |
Zoanthid (ZO) | Zoanthids (Order Zoanthidea) are colonial anemone-like animals having smooth, flat, broad oral disks with tentacles that radiate outward from their margins. Tentacles are found in two nearby rows, and always are in a number that is a multiple of six. The polyp's mouth has a ciliated groove at one or both ends of the mouth. Zoanthids are connected by runners (called stolons) and they lack the hard skeletons of scleractinian corals. |
Unclassified (UI) | This Tier 2 category is used when the classification point falls on a sessile invertebrate that doesn't fall within one of the other Tier 2 categories, or in situations when a sessile invertebrate can't be distinguished, for example, differentiating between an encrusting sponge or tunicate. |
Value | Definition |
---|---|
Mobile fauna (MOBF) | Photographs capture a solitary instant in time. As a result, creatures that are not permanently affixed to a single location on the sea floor (e.g. sea cucumbers, sea stars, sea urchins, fish, marine mammals) sometimes also appear in photographs intended for benthic analysis. While every effort should be made to discern what the benthic classification is underneath the mobile fauna, if that is not possible, this classification category should be used. This is both a Tier 1 and Tier 2 classification category. |
Value | Definition |
---|---|
Sand (SAND) | Sand is defined as sediment with a grain size between 1/16 mm and 5 mm. This can include silica sand, fine calcium carbonate sand, lava sand, and/or Halimeda spp. blade sand. A thin dusting of sand over a turf covered surface is not sufficient to be called Sand habitat. |
Fine sediment (FINE) | Fine sediment is defined as sediment with a grain size of < 1/16 mm. |
Value | Definition |
---|---|
Tape, Wand, or Shadow (TAPE, WAND, SHAD) | This classification is required by the Coral Point Count with Excel Extensions (CPCe) software. It is to be used whenever a classification point lands on a transect line/tape measure, photo quadrat frame/spacing wand, or a shadow cast by natural or anthropogenic features which prevents organism classification. |
Unclassified (UNK) | Unclassified |
These data are part of long-term monitoring or assessment data aimed at providing sound science to enable informed and effective ecosystem-based management of the coral reef ecosystems of the U.S. Pacific at approximately 40 primary islands and atolls in the Hawaiian Archipelago (Main Hawaiian Islands and Northwestern Hawaiian Islands), the Mariana Archipelago (Guam and the Commonwealth of the Northern Mariana Islands), American Samoa, and the Pacific Remote Island Areas, also known as the U.S. Minor Outlying Islands.
2004 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0402-1.PSV.pdf.
2005 "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0502-PSV.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0505b-1.PSV.pdf. "Mariana Archipelago Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0512-1.RES.pdf.
2006 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0602-RS.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0610-REB.pdf.
2007 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0702-RS.pdf.
2008 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHI0802-REB.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Sette/CR0810-BVA.pdf.
2009 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA0902-RES.pdf.
2010 "American Samoa RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1001II-KD.pdf. "Main Hawaiian Islands RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1008-KD.pdf.
2011 "Mariana Archipelago RAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1101II-KD.pdf. "A Report Based on Underwater Visual Surveys in Guam and the Mariana Archipelago", http://www.pifsc.noaa.gov/library/pubs/tech/NOAA_Tech_Memo_PIFSC_33.pdf.
2013 "Small Boat Mission Report: Coral disease surveys in the vicinity of Kauai Island", http://intra.pifsc.gov/sites/default/files/SBR1309-BVA.pdf. "MHIRAMP Cruise Report", http://www.pifsc.noaa.gov/library/pubs/cruise/Hiialakai/CRHA1304I.pdf. "Small Boat Mission Report: 2013 Pacific Reef Assessment and Monitoring Program (continued), Oahu Operations", http://intra.pifsc.gov/sites/default/files/SBR1320-BVA.pdf. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: main Hawaiian Islands 2013", http://www.pifsc.noaa.gov/library/pubs/DR-13-016.pdf.
2014 "Mariana Archipelago RAMP Cruise Report", Cruise report not yet published as of the publication date of this record. Contact CRED at nmfs.pic.credinfo@noaa.gov for a draft copy of the report. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: southern Mariana Archipelago 2014.", http://www.pifsc.noaa.gov/library/pubs/DR-14-009.pdf. "Pacific Reef Assessment and Monitoring Program. Fish monitoring brief: northern Mariana Archipelago 2014.", http://www.pifsc.noaa.gov/library/pubs/DR-14-010.pdf.
"Coral Reef Ecosystem Division standard operating procedures: data collection for Rapid Ecological Assessment fish surveys", http://www.pifsc.noaa.gov/library/pubs/admin/PIFSC_Admin_Rep_11-08.pdf.
It is assumed that images have already undergone appropriate post-collection processing in the field to catalog and rename the images using standard naming conventions prior to the beginning of the benthic image analysis.
If images need to be corrected for photo analysis run series or calibration exercises, a copy of the original image is preserved. Generally, for stratified random coral and fish site survey photos, if the cameras were properly white-balanced in the field, no color-correction is required. TDS all photos analyzed have undergone color correction implementing Picasa. Corrections may include brightness/contrast adjustments, color adjustments, sharpening, etc. In general, the software's auto-adjustment capabilities are sufficient for the majority of images. Some additional manual adjustments may still be required. If color-correction doesn't improve the image, this image may be excluded from the analysis for that location or transect.
Images are quantitatively analyzed implementing the Coral Point Count with Excel extensions (CPCe; Kohler and Gill, 2006) software. Images are opened up in the CPCe program and the area for image analysis is set. Due to how the images are collected the area for image analysis may vary. Due to image distortion that occurs along the edges of the majority of images, all towed-diver survey imagery and REA survey imagery from 2014 and beyond are analyzed with a pixel buffer around the entire perimeter of the image; pixel offset (228,192) and (60,42) for TDS and REA respectively. Prior to that the entire image was used for stratified random fish and benthic REA site survey photos.
Ten stratified random points are calculated and projected on each image by the CPCe software. The benthic elements falling directly underneath each point are identified to two (TSD) or three (REA surveys) functional groups levels: Tier 1 (e.g., hard coral, soft coral, macroalgae, turf algae, etc.) and Tier 2 (e.g., Hard Coral = massive, branching, foliose, encrusting, etc.; Macroalgae = upright macroalgae, encrusting macroalgae, bluegreen macroalgae, and Halimeda, etc.), and Tier 3 (e.g., Hard Coral = Acropora, Montipora, Pocillopora, etc.; Macroalgae = Padina, Dictyota, Dictosphaeria, etc.). In cases where a coral colony exhibits more than one growth form, it is the morphology directly under the point that is classified, rather than the morphology of the colony overall. If a point falls precisely between two coral growth morphologies, or on the border between two benthic categories (e.g., coral-algae), the benthic category occupying the greatest area within symbol (circle wrapping the cross-hairs) is classified. Additionally, if the two benthic categories occupy equal space within the symbol, the benthos falling on the top left quadrant within the point symbol is classified. The category Shadow is used when the point falls on an area that is dark and the nature of the benthos cannot be assessed due to diminished light. The category Unclassified is used when the nature of the benthos cannot be determined due to image quality or unfamiliarity with the type of benthos. The category Wand is used when the point falls on a transect line/tape measure, or photo quadrat frame/spacing wand.
If any photo has more than 5 combined points classified as Shadow or Unclassified, or if a stratified random site photo has more than 1 point classified as Wand these data are not saved. Instead a new set of points to analyze is generated by using the Point Overlay menu and selecting Recalculate point coordinates. This step of regenerating points for analysis will be repeated up to three times before the image is removed from the production series. For tows with several photographs whose quality is insufficient for use, ~35% (40 images) of the total number of images to be analyzed is the minimum acceptable number that need to be analyzed to grant retention of those data in the production series.
Power analyses support the methodological approach outlined above, whereby statistically sound sub-jurisdictional (island) level, benthic cover estimates can be successfully derived from REA and TDS photos processed at: 300 points/survey (i.e., 10 points/photo x 30 photos) and 600-700 points/survey (i.e., 10 points/image x 60-70 photos), respectively. Percent cover at the island level can be determined from data derived from towed-diver survey images while percent cover is calculated at the site level for data derived from stratified random sampling images.
The complete Benthic Image Analysis Standard Operating Procedure (SOP) is available on the NOAA Wiki at https://www.st.nmfs.noaa.gov/confluence/display/CRED/Benthic+Image+Analysis. Non-NOAA users can contact CRED at nmfs.pic.credinfo@noaa.gov to request a copy of the SOP.
For REA survey imagery analyzed or collected since 2013, classification is completed to the functional group/genus level (Tier 3); prior to 2013 classification is done to the functional group level (Tier 2). All TDS survey imagery is analyzed to the functional group level (Tier 2).
Benthic percent cover has been derived from imagery collected during TDS every other year in American Samoa from 2004 to 2010, Guam from 2005 to 2011, and the Main Hawaiian Islands from 2006 to 2010 as well as 2005, and during REA surveys in American Samoa in 2010, Guam and the Commonwealth of the Northern Mariana Islands (CNMI) in 2011, and the Main Hawaiian Islands in 2010 and 2013. Survey imagery for Guam and the CNMI collected in 2014 is currently being analyzed (as of the publication date of this record).
There are several missions in which the benthic images collected by the program are in the process of or have not yet been analyzed. In some cases, the benthic imagery sets are not planned to be analyzed due to funding and resource constraints. Contact CRED at nmfs.pic.credinfo@noaa.gov for more information.
Are there legal restrictions on access or use of the data?Access_Constraints: None
Use_Constraints:Please cite CRED when using data. Coral Reef Ecosystem Division (CRED), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)
While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.
Data are available in csv format upon request