Coral Point Count Research Articles

Quantitative dataset of shallow water reef in Pulau Bidong, Southern of South China sea during pre and post of tropical storm (Pabuk - January 2019).

This article provides raw datasets of the coral reefs status in Pulau Bidong, southern of South China Sea before and after being strike by the tropical storm Pabuk on January 2019. Data were collected using a rapid coral survey method called Coral Video Transect (CVT) technique. The data were collected along a 100 m transect line set up parallel to the shoreline and at a constant depth. In total, eight transects were surveyed during both periods (pre – August 2016, post – March 2019). Back in laboratory, the footage was then extracted into non-overlapping frames or still images prior to image analysis using Coral Point Count with Excel Extension (CPCe) software. The benthic coral reefs relative percentage cover was automatically generated after the image analysis and represented by five major categories; live coral (C), algae (ALG), other invertebrates (OT), dead coral (DC), and sand silt and rock (SR). Live coral cover was identified up to the genus level. This raw dataset was used in this article. The data provided in this article could be of significant use for future studies especially on coral recovery after the natural disturbances. It can provide a baseline assessment especially for coral reefs management as well as to comprehend changes in coral health status in the face of natural and anthropogenic disturbances. The data presented here support the information in the article Safuan et al. (2020).

Preliminary Study of Coral Reef Conditions in Marine Park and Coral Reef Education Centre Plan Area, Seribu Islands National Park, Indonesia

Marine waters surrounding Child-friendly Integrated Public Spaces (RPTRA) at Tanjung Elang still has the potential for highly productive coral reef resources, thus enabling the development of ecological-based tourism, education and conservation. Despite the potential, the coral reefs in the surrounding of RPTRA Tanjung Elang has suffered damage caused by anthropogenic activities and natural factors. The aim of this research is to assess the initial condition of coral reef at the location of marine park areal and coral reef education center plan, RPTRA Tanjung Elang Waters, Pramuka Island, Seribu Islands National Park, DKI Jakarta, Indonesia. This research used Underwater Photo Transect/UPT method were analyzed using CPCe 4.1. software (Coral Point Count with Excel extension). The results of physico-chemical parameters measurements showed that water quality in RPTRA Tanjung Elang Waters Pramuka Island, is still within tolerance limits for coral life. The percentage of live coral cover was in a bad category with a low value (5.35%). The most dominant form of coral growth was submassive (CS) with a percentage value 54.46%. Composition of hard coral genusis consists of 3 family, 5 genus, and 100 species.The most dominant of Porites was with submassive and massive growth form. The index value of diversity shows a low category (0.56). The dominance index value showed a medium category (0.75). Uniformity and mortality index value showed a low category (0.35 and 0.43).

Data On Percentage Coral Reef Cover In Small Islands Bunaken National Park.

This article describes the data on coral reef percent cover small islands (Bunaken Island; Siladen Island; Manado Tua Island; Mantehage Island; Nain Island) in Bunaken National Park, Noth Sulawesi Province, Indonesia. The data of coral percent cover from 20 stations (1000 quadrans), surveys were done by scuba diving along 50 m belt transects established on upper reef slope, mostly with depths ranging from 5 to 10 m. The method Used Underwater Photo Transect (UPT) and Coral Point Count with excel (CPCe) analysis. Percentage of coral cover between 6,27% and 69,20%. Manado Tua Island has a percentage of coral cover 42,02%, Bunaken Island 39,63%, Mantehage Island 29,10%, Siladen Island 27,87%, and Nain Island 25,97%. The average of live coral cover on the five islands is 32.92% with moderate category [2].

Coral conditions and reef fish presence in the coral transplantation area on Kapoposang Island, Pangkep Regency, South Sulawesi

Coral reefs are currently suffering from serious degradation due to human activities. In 2015, the condition of coral reefs in Kapoposang Island has been very poor with the live coral cover only 16%. Therefore, the coral reef ecosystem on this island needs to be rehabilitated. This study aims to assess coral cover based on the age of transplantation and examine abundance of reef fish in relation to age of transplant module at Kapoposang Island which is in the Wallacea region. Coral transplant was carried out from 2014 to 2018. The transplanted corals were corals of the genus Acropora. Transplants were carried out at a depth 3 to 4 m. The determination of the transplant module as the reef fish’s observation was based on the age of the transplant module, i.e. 1, 2, 3 and 4 years old. Data collection was carried out using the UVC (Underwater Visual Census) method. Data collection was done by using the UPT (Underwater Photo Transect) method. Photograph data was processed using CPCe (Coral Point Count with Excel extension) software using 30 random points for each frame. The significant relationship between live coral cover and reef fish shows that the coral transplantation was successful. There was linear relation between coral habitat cover and the reef fish. The difference in abundance in each transplant module shows the linier relation between the increase of reef fishes and live coral cover. The live coral cover was higher at the two and three years old of the transplant module. During the study, it was found 13 families and 56 species of reef fish. Planktivorous group was the most dominant of reef fish.

PENGGUNAAN PROGRAM CPCe (CORAL POINT COUNT WITH EXCEL EXTENSIONS) UNTUK MENGETAHUI KONDISI TERUMBU KARANG DI PERAIRAN SEKITAR PULAU BATAMPENGGUNAAN PROGRAM CPCe (CORAL POINT COUNT WITH EXCEL EXTENSIONS) UNTUK MENGETAHUI KONDISI TERUMBU KARANG DI PERAIRAN SEKITAR PULAU BATAM

A healthy coral reef ecosystem will be used as a place for spawning and foraging for various marine biota. With high primary productivity and diversity, coral reef ecosystems will become ecosystem that has a lot of useful potential. Abang Island and Abang Besar Island, Batam, are two of the locations with a good coral reef ecosystem. Unfortunately, these ecosystems have been disturbed by marine tourism activities. Therefore, observations are needed to determine the condition of coral reefs in Abang and Abang Besar Islands. Coral Point Count with Excel Extensions (CPCe) is a software that helps to identify and know the condition of coral reefs in an area. Data processing in this CPCe program will generate data in the form of Excel files that show the results of identification analysis. Based on data processing using the CPCe program, the results of the percentage of coral cover at the six stations varied (32.67 - 51.33%) from the bad to good categories. At Station 1 or BTMC01, the highest coral cover is 51.33% and the lowest is at Station 2 or BTMC02 at 32.67%. The condition of coral reefs with good categories is only found in BTMC01, the rest has the condition of coral reefs in the medium category. The percentage of coral cover obtained is a combination of Acropora and Non-Acropora coral group species. Good or bad coral cover in an area is strongly influenced by anthropogenic activities.

Estimation of Sand Distribution in Coral Reef Environment using Colour Segmentation and Colour Thresholding Methods

At present, marine scientists employ manual method to estimate the components in coral reef environment, where Coral Point Count with Excel extensions (CPCe) software is used to determine the coral reef components and substrate coverage. This manual process is laborious and time consuming, and needs experts to conduct the survey. In this paper, a prototype for estimating the distribution of sand cover in coral reef environment from still images by using colour extraction methods was introduced. The colour segmentation called delta E was used to calculate the colour difference between two colour samples. Another method used was colour threshold by setting the range of sand colour pixels. The system was developed by using a MATLAB software with image processing toolbox. The developed system was semi-automatic computer-based system that can be used by researchers even with little knowledge and experience to estimate the percentage of sand coverage in coral reef still images.

KONDISI TERUMBU KARANG PULAU MANTEHAGE KABUPATEN MINAHASA UTARA PROVINSI SULAWESI UTARA

Coral reefs are coastal ecosystems with the highest level of diversity. Corals are invertebrates that are included in the Phylum Coelenterata (hollow animal) or Cnidaria. Whereas coral reefs are a collection of millions of polyps. Natural phenomena and various anthropogenic activities threaten the health and presence of Mantehage Island coral reefs and the lack of information about the health conditions of coral reefs on Mantehage Island. The purpose of this study is to determine the condition of coral reefs andto provide baselines data on Mantehage Island. Data collection was done by using UPT method (Underwater Photo Transect). Underwater Photo Transect carried out by underwater shooting using a digital camera that was shielded (housing). Image analysis were done using the CPCe software (Coral Point Count with Excel extensions). The results of coral reef health conditions at four stations on Mantehage Island shows, coral reef cover at each station as follows, station 1 (one) 53.00% were in good condition, station 2 (two) 25.40% were in a moderate condition, station 3 (three) 16.49% were in poor condition, and station 4 (four) 42.07% were in a moderate condition. From the four stations, the condition of Mantehage Island's coral reefs were in the moderate category with a percentage of 34.24%.Keywords:. Mantehage Island, Terumbu Karang, UPT, CPCe

Abiotic effects on the cover and richness of corticolous lichens on Araucaria angustifolia trunks

ABSTRACT Lichens play a key role in natural ecosystems, as they can function as primary producers, recycle minerals and fix nitrogen. Despite their environmental importance, little is known about lichen ecology in Brazil, and especially about how abiotic factors may influence their spatial distribution. In this study, we aimed to verify how the cover and richness of corticolous lichens on Araucaria angustifolia trunks vary between two different habitats (Forest and Grassland). The photoquadrat sampling method was applied to A. angustifolia trunks. The Coral Point Count software with Excel extensions (CPCe) was used to analyze photographs for lichen cover and richness. Additionally, a redundancy analysis was conducted to estimate how five abiotic and two biotic variables affected the spatial distribution of lichens. Twenty-five morphospecies were identified, none of them occurring exclusively in the Grassland habitat. Canopy openness, air humidity and tree trunk rugosity were important parameters influencing lichen distribution; therefore, spatial segregation of growth forms can be explained by environmental selectivity. Foliose lichens require more air humidity, which explains their predominance in the Forest habitat. Canopy openness in Grassland habitat favors fruticose lichens, which depend on factors such as wind for reproduction.

Two-level hierarchical feature learning for image classification

In some image classification tasks, similarities among different categories are different and the samples are usually misclassified as highly similar categories. To distinguish highly similar categories, more specific features are required so that the classifier can improve the classification performance. In this paper, we propose a novel two-level hierarchical feature learning framework based on the deep convolutional neural network (CNN), which is simple and effective. First, the deep feature extractors of different levels are trained using the transfer learning method that fine-tunes the pre-trained deep CNN model toward the new target dataset. Second, the general feature extracted from all the categories and the specific feature extracted from highly similar categories are fused into a feature vector. Then the final feature representation is fed into a linear classifier. Finally, experiments using the Caltech-256, Oxford Flower-102, and Tasmania Coral Point Count (CPC) datasets demonstrate that the expression ability of the deep features resulting from two-level hierarchical feature learning is powerful. Our proposed method effectively increases the classification accuracy in comparison with flat multiple classification methods.

DIVERSITY AND DISTRIBUTION OF EUPHYLLIDAE CORALS IN TIOMAN ISLAND: EMPHASIS ON THE GENETIC VARIATION OF EUPHYLLIA CRISTATA

Euphyllidae corals are among the most beautiful corals that have been exploited for the aquarium trade all over the world. In Malaysia, the information on these coral species particularly on the diversity and genetic variation is not fully documented. Realizing to this matter, the diversity and distribution of Euphylllidae corals were investigated at 13 sampling stations in Tioman Island. The diversity and distribution of Euphyllidae corals were observed and recorded using the Coral Video Transect (CVT) method. The captured images were analyzed using Coral Point Count with Excel extension (CPCe) software. The samples of Euphyllia cristata were collected at three different zones in Tioman Island (East Coast, West Coast and Isolated Island). The samples were extracted and mitochondrial Cytochrome Oxidase 1 gene primer was used to study their genetic variation. A total of six species belong to three genera of Euphyllia, Plerogyra and Physogyra were recorded. Benuang Bay (East Coast) and Bayan Bay (Isolated Island) have shown higher diversity and distribution of Euphyllidae corals among the sampling stations. The Shannon-Weinner index (H’) of Benuang Bay and Bayan Bay were 1.42 and 1.43 respectively. The West Coast zone had the lowest diversity and distribution of Euphyllidae corals due to massive coastal development and loads of human intervention. The genetic sequences from the East Coast and West Coast were closely related. The pairwise distance between these two zones is 0.003. There is a slight difference in the sequence from the Isolated Island. The pairwise distance of West Coast-Isolated and East Coast-Isolated are 0.021 and 0.025 respectively. However, it is relatively low to consider there is evolutionary divergence between the samples. Thus, no genetic variation was observed between all Euphyllia cristata taken at three different zones of Tioman Island. This study has shown that there was a highly significant difference (p<0.01) in the diversity and distribution of Euphyllidae corals with respect to sampling stations.

THE POTENTIAL OF ARTIFICIAL LIVE ROCK AS SUBTRATE FOR CORAL SPAT AND EPIBENTHIC ORGANISMS

Over-exploitation on natural live rock promotes the degradation of ocean ecosystem. This concern has been raised since harvesting may reduce the density of marine ornamentals and degrade marine habitat quality. This study aims to develop artificial live rocks (ALR) that potentially to be used as one of the alternatives to reduce the overharvesting activity toward natural live rocks. The study was conducted at Bidong Island, Terengganu started from April to October 2014. There were 2 types of ALR used in this study; rough and smooth surfaces. A total of 64 pieces of ALR were deployed in April 2014 and retrieved in June, August and October 2014 respectively. Identification in terms of coral spat species and macrobenthic organisms was done after the each retrieval. Coral spat was identified based on the morphology of their columella, septa and corallite wall by using Dinolight Digital Camera. Four species of coral juveniles (Pocillopora damicornis, Stylophora pistillata, Seriatopora hystrix and Acropora millepora) were found attached on ALR surfaces. Whereby, there were 11 phyla of epibenthic organisms were found to attach on ALR which dominated by turf algae and red algae. Percentage coverage of epibenthic calculated using Coral Point Count with Excel extension (CPCe) shown ALR was dominated by turf algae after 2 months (69%) and 4 months (20%) of deployment respectively. Afterward, Red algae (31%) dominated after 6 months of deployment. There was significant difference between coral species and the surfaces (p<0.05). However, no significant difference between types of surfaces with sessile macrobenthic organisms (p>0.05). This finding showed that ALR has a potential to be upgraded as artificial reef towards marine habitat restoration.

Internal bioerosion in dead and live hard corals in intertidal zone of Hormuz Island (Persian Gulf)

Internal macrobioeroders and their erosion rate in three live and dead coral genera (Favia, Platygyra and Porites) from the intertidal zone of the Hormuz Island were studied by collecting five live and five dead colonies from each genus, from which 4mm cross-sections were cut and photographed. Photos were analyzed using the Coral Point Count with Excel extensions. Totally, 9 taxa were identified: four bivalve species, one sponge, three polychaetes, and one barnacle. Bioerosion rate did not significantly differ among the three live corals, but among the dead ones only Porites was significantly more eroded than Favia. Sponge had the highest role in the erosion of the dead Platygyra, while barnacles were the most effective eroding organism in the live Platygyra. Polychaetes, followed by bivalves, were the most destructive bioeroders on the dead and live Porites. Further, none of the bioeroding organisms had selectively chosen either the dead or live Favia.

Reef fish community in presence of the lionfish (Pterois volitans) in Santa Marta, Colombian Caribbean

ABSTRACT Objective. Fish species community structure and benthic organisms coverage were studied in five localities in Santa Marta where the lionfish is present. Materials and methods. Abundance of fish species, including lion fish, was established using 30 m random visual censuses and video transects; trophic guilds were established according to available references. On the other hand benthic coverage was evaluated using the software Coral Point Count (CPCe) 4.0. Results. Families with higher species numbers were Serranidae, Labridae, and Pomacentridae. Lionfish abundances were low (2.6±2.1 ind/120 m2), but in any case Pterois volitans was observed as the eleventh more abundant species, surpassing species of commercial value such as Cephalopholis cruentata. Species that were found in larger numbers (>100, Thalassoma bifasciatum, Haemulon aurolineatum, Canthigaster rostrata, Abudefduf saxatilis, Chromis cyanea, and Stegastes partitus) were mainly invertebrate eaters, planctivores, and territorial herbivores. Coral coverage showed higher coral percentages in Chengue (69.9%) and Cinto (27.4%), larger sponge percentages in Morro (32.7%); Isla Aguja and Remanso showed the larger figures for abiotic substrate (41.6 and 37%, respectively); corals, sponges, and gorgonians were the components best explaining fish community, but not for the lion fish, which inhabit all studied reef formations. Conclusions. Lion fish is ranked between the 20 more abundant species, with none commercially important species larger, hence no species may qualify as a natural control. Lion fish has as well become a relatively abundant species in Santa Marta reefs, independent of benthic coverage.

Field data sets for seagrass biophysical properties for the Eastern Banks, Moreton Bay, Australia, 2004–2014

This paper describes seagrass species and percentage cover point-based field data sets derived from georeferenced photo transects. Annually or biannually over a ten year period (2004–2014) data sets were collected using 30–50 transects, 500–800 m in length distributed across a 142 km2 shallow, clear water seagrass habitat, the Eastern Banks, Moreton Bay, Australia. Each of the eight data sets include seagrass property information derived from approximately 3000 georeferenced, downward looking photographs captured at 2–4 m intervals along the transects. Photographs were manually interpreted to estimate seagrass species composition and percentage cover (Coral Point Count excel; CPCe). Understanding seagrass biology, ecology and dynamics for scientific and management purposes requires point-based data on species composition and cover. This data set, and the methods used to derive it are a globally unique example for seagrass ecological applications. It provides the basis for multiple further studies at this site, regional to global comparative studies, and, for the design of similar monitoring programs elsewhere.

Progression of the Coral-Algal Phase Shift in the Caribbean: A Case Study in Bonaire, Dutch Caribbean

AbstractCoral reefs around the globe are subject to environmental and anthropogenic stressors that are causing habitat degradation and a decline in reef resilience. Past studies of Caribbean reefs document a decrease in coral cover with a simultaneous increase in algal cover after significant stress, disturbance, or coral mortality. The long-term shift from coral-dominated reefs to algae-dominated reefs is known as a coral-algal phase shift. This study assessed the progression of a coral-algal phase shift at a fringing reef around Bonaire, Dutch Caribbean, by comparing current coral and algal benthic cover to historical data, from 1997 to 2008, at a site nearby. Research was conducted over a 5-w period from September to October 2012. Twenty 10-m transects were filmed and analyzed through Coral Point Count with Excel extensions software to determine percent live coral and algal cover. Mean coral cover at the study site was 14.3%, and algal cover was 72.4%. In comparison to historical data, a significant increase in the algae-coral ratio indicated a progression of a coral-algal phase shift in Bonaire. This study contributes to the scientific knowledge of coral-algal phase shifts in the Bonaire reef ecosystem and the broader scientific reef conservation.

Sucesión primaria de una comunidad de coral y algas en el nuevo sustrato vertical en el Cayo de Rackham, Puerto Royal, Jamaica

Jamaica's trans-shipment industry is amongst the largest in the Caribbean with 90% of trans-shipment activities occurring in Kingston Harbour. The eastern ship channel is populated with patch and fringing coral reefs. In 2002, approximately 20% of an originally sloping face of Rackham's Cay, on the southern edge of the channel, was cut vertically to 18m and dredged to widen the channel. The successional changes on the newly created vertical limestone wall was assessed between 2009 and 2012 at 5m, 10m and 15m depths using bi-annual photographs of fixed 1 m 2 quadrats. Photographs were analyzed using Coral Point Count. No colonization of either algal or coralline species was observed at 15m. Initially calcareous and fleshy algae dominated at 5m but showed a gradual decrease over time. Calcareous algae dominated at 10m and increaseed gradually over the 4 years. Stony corals at both 5m and 10m had overall low cover and slow colonization; the shallower depth had more coverage (4.1% maximum in 2011). Siderastrea sidera -which dominated Rackham's Cay before dredging- was consistently present in low coverage. Colonization by species of Acropora and Scolymia indicate slower but better succession at 10m. Ten years following dredging activities, colonization and recruitment have been slow but successful at 5m and 10m; species previously described as abundant lead the colonization. We recommend limiting coral relocation activities to depths not exceeding 10m. Rev. Biol. Trop. 62 (Suppl. 3): 107-114. Epub 2014 September 01.

Status of the coral reefs in Foul and Folly Bays, Morant Wetlands, south-eastern Jamaica, with emphasis on corals and macroalgae

Foul and Folly Bays are located within the Morant Wetlands near the eastern tip of Jamaica. They have never been investigated but were believed to be important for larval productivity because of the extent of benthic habitats, absence of major coastal developments and remote location. The study was aimed at providing baseline data on the spatial distribution and status of corals and associated benthos. We investigated coral reefs and associated areas with phototransects at eight stations analysed with the Coral Point Count software. Most areas were dominated by algae, evidence of a phase shift from coral to algal reefs. Coral cover varied significantly across the bays (ANOVA, p= 0.0342) with a maximum of 27.03% at the deepest station and a mean of 5.6% at all other stations combined. Mean cover of macroalgae was 39% and varied significantly across stations (α= 0.05, F= 7.472, p= 0.005). The deepest station also had the highest percentage of calcareous algae and live coral while dead coral with algae (DCA) was a significant variable across all other stations (ANOVA, p<0.001). Gorgonians (ANOVA, p<0.001), sponges and urchins were also assessed. Diadema antillarum was not observed at any station. Overall the status of the reefs was poor, probably due to overfishing, absence of urchins and the resultant algal proliferation. Rev. Biol. Trop. 62 (Suppl. 3): 39-47. Epub 2014 September 01.

Coral Point Count with Excel extensions (CPCe): A Visual Basic program for the determination of coral and substrate coverage using random point count methodology

Photographic and video methods are frequently used to increase the efficiency of coral reef monitoring efforts. The random point count method is commonly used on still images or frame-grabbed video to estimate the community statistics of benthos. A matrix of randomly distributed points is overlaid on an image, and the species or substrate-type lying beneath each point is visually identified. Coral Point Count with Excel extensions (CPCe) is a standalone Visual Basic program which automates, facilitates, and speeds the random point count analysis process. CPCe includes automatic frame-image sequencing, single-click species/substrate labeling, auto-advancement of data point focus, zoom in/out, zoom hold, and specification of random point number, distribution type, and frame border location. Customization options include user-specified coral/substrate codes and data point shape, size, and color. CPCe can also perform image calibration and planar area and length calculation of benthic features. The ability to automatically generate analysis spreadsheets in Microsoft Excel based upon the supplied species/substrate codes is a significant feature. Data from individual frames can be combined to produce both inter- and intra-site comparisons. Spreadsheet contents include header information, statistical parameters of each species/substrate type (relative abundance, mean, standard deviation, standard error) and the calculation of the Shannon–Weaver diversity index for each species. Additional information can be found at http://www.nova.edu/ocean/cpce/.