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"coral reef monitoring"
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Coral-YOLO: An Intelligent Optical Vision Sensing Framework for High-Fidelity Marine Habitat Monitoring and Forecasting
Coral reefs are facing a catastrophic decline due to climate-induced bleaching, threatening critical marine biodiversity. Automated, large-scale monitoring is essential; however, modern object detectors are hindered by two fundamental limitations in complex underwater scenes: a spatial reasoning deficit in their decoupled heads, which inhibits robust multi-scale feature integration, and a feature robustness deficit, which renders deterministic networks vulnerable to stochastic visual variations. To address these limitations, we propose Coral-YOLO, a novel framework for detection and forecasting. We introduce the Holistic Attention Block Head (HAB-Head), which enables deep cross-scale reasoning through explicit feature interaction, and MCAttention, a randomized training mechanism that enables the network to learn scale-invariant features with inherent robustness. Evaluated on our newly curated, multi-year CR-Mix dataset, Coral-YOLO achieves a state-of-the-art 50.3% AP (average precision at IoU threshold 0.5:0.95, following COCO metrics), representing a +1.8 percentage point improvement over the YOLOv12-m baseline, with particularly pronounced gains on small objects (+2.6 percentage points in APS). Crucially, its integrated temporal forecasting module achieves 82.7% accuracy in predicting future coral health, substantially outperforming conventional methods. Coral-YOLO sets a new performance benchmark and enables proactive reef conservation. It provides a powerful tool to identify at-risk corals long before severe bleaching becomes visually apparent.
Journal Article
A survey on underwater coral image segmentation based on deep learning
Image-based coral reef survey technologies have revolutionized the monitoring of coral reefs by offering a cost-effective and noninvasive method for collecting data across large spatial scales and extended periods. Among these technologies, underwater videography has emerged as a well-established and reliable tool for remote sensing in coral research. Automatic segmentation of coral images represents a forward-looking and fundamental research area in underwater remote sensing. It aims to address a major challenge that limits traditional in situ underwater coral survey research: the difficulty of automatically generating accurate and reproducible high-resolution maps of the underlying coral reef ecosystems. Understanding recent achievements and their relevance to coral ecology monitoring needs is crucial for future planning. This paper presents a literature review on underwater coral image segmentation, focusing on the deep learning implementation pipeline. Furthermore, we introduce a new densely annotated dataset specifically designed for the semantic segmentation of underwater coral images. We systematically evaluate State-of-the-Art (SOTA) methodologies and novel techniques not previously applied to coral image semantic segmentation using the proposed dataset. We then discuss their feasibility in this context. Our goal for this review is to spark innovative ideas and directions for future research in underwater coral image segmentation and to provide readers with an accessible overview of some of the most significant advancements in this field over the past decade. By accomplishing these objectives, we hope to advance research in underwater coral image segmentation and support the development of effective monitoring and conservation strategies for coral reef ecosystems.
Journal Article
Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation
Detecting the impacts of natural and anthropogenic disturbances that cause declines in organisms or changes in community composition has long been a focus of ecology. However, a tradeoff often exists between the spatial extent over which relevant data can be collected, and the resolution of those data. Recent advances in underwater photogrammetry, as well as computer vision and machine learning tools that employ artificial intelligence (AI), offer potential solutions with which to resolve this tradeoff. Here, we coupled a rigorous photogrammetric survey method with novel AI-assisted image segmentation software in order to quantify the impact of a coral bleaching event on a tropical reef, both at an ecologically meaningful spatial scale and with high spatial resolution. In addition to outlining our workflow, we highlight three key results: (1) dramatic changes in the three-dimensional surface areas of live and dead coral, as well as the ratio of live to dead colonies before and after bleaching; (2) a size-dependent pattern of mortality in bleached corals, where the largest corals were disproportionately affected, and (3) a significantly greater decline in the surface area of live coral, as revealed by our approximation of the 3D shape compared to the more standard planar area (2D) approach. The technique of photogrammetry allows us to turn 2D images into approximate 3D models in a flexible and efficient way. Increasing the resolution, accuracy, spatial extent, and efficiency with which we can quantify effects of disturbances will improve our ability to understand the ecological consequences that cascade from small to large scales, as well as allow more informed decisions to be made regarding the mitigation of undesired impacts.
Journal Article
Coral Reef Monitoring by Scuba Divers Using Underwater Photogrammetry and Geodetic Surveying
Underwater photogrammetry is increasingly being used by marine ecologists because of its ability to produce accurate, spatially detailed, non-destructive measurements of benthic communities, coupled with affordability and ease of use. However, independent quality control, rigorous imaging system set-up, optimal geometry design and a strict modeling of the imaging process are essential to achieving a high degree of measurable accuracy and resolution. If a proper photogrammetric approach that enables the formal description of the propagation of measurement error and modeling uncertainties is not undertaken, statements regarding the statistical significance of the results are limited. In this paper, we tackle these critical topics, based on the experience gained in the Moorea Island Digital Ecosystem Avatar (IDEA) project, where we have developed a rigorous underwater photogrammetric pipeline for coral reef monitoring and change detection. Here, we discuss the need for a permanent, underwater geodetic network, which serves to define a temporally stable reference datum and a check for the time series of photogrammetrically derived three-dimensional (3D) models of the reef structure. We present a methodology to evaluate the suitability of several underwater camera systems for photogrammetric and multi-temporal monitoring purposes and stress the importance of camera network geometry to minimize the deformations of photogrammetrically derived 3D reef models. Finally, we incorporate the measurement and modeling uncertainties of the full photogrammetric process into a simple and flexible framework for detecting statistically significant changes among a time series of models.
Journal Article
Marine reef soundscape monitoring with fiber-optic distributed acoustic sensing
Coral reefs are essential marine ecosystems that support a vast array of biodiversity and provide numerous benefits, including fisheries, tourism, and coastal protection. However, these ecosystems are increasingly threatened by various factors, including anthropogenic noise from activities such as shipping and coastal development. Traditional acoustic methods of monitoring reef health, such as hydrophones, are limited by their point-based sensing, reliance on batteries, and need for manual data retrieval, which can be labor-intensive and costly. In this study, we explore the application of fiber-optic distributed acoustic sensing (DAS) for real-time marine reef monitoring, a new application compared to its previous use in deep-sea soundscape monitoring. We deployed a fiber-optic DAS system in a reef area on the coast of the Central Red Sea, alongside a conventional hydrophone for comparison. The experiment was conducted in a degraded inshore reef near the KAUST shoreline, characterized by sand, macroalgae, scattered boulders, and encrusting sponges. This site was selected as a proxy for coral reef monitoring due to its biological activity, including snapping shrimp and the presence of reef-related fish species. Our observations revealed significant acoustic activity within the 1.5 to 5 kHz range, with snapping shrimp sounds increasing after the onshore lights were switched off, consistent with known behavioral patterns of increased acoustic activity during low-light conditions. Additionally, we detected various fish vocalizations, including drums and impulses, within the 100 to 1000 Hz range. The DAS system also successfully tracked the timing and trajectory of scuba diver movements along the reef. These findings demonstrate the potential of fiber-optic DAS technology to provide high-resolution spatial mapping of reef soundscapes, offering a comprehensive and cost-effective solution for continuous reef monitoring, thereby demonstrating the feasibility of DAS for real-time acoustic monitoring in reef environments.
Journal Article
Map the Giants: a new citizen-science portal to map, study and protect the largest coral colonies
Coral reefs are rapidly degrading under escalating local and global pressures and some centennial coral colonies may disappear before they are even documented. These giant colonies embody resistance and resilience in a changing ocean, can archive long-term environmental histories and may hold valuable clues to the traits that have enabled their survival. Yet, coordinated, large-scale information on their distribution, condition and ecology is still lacking. Map the Giants is a global citizen-science initiative launched in 2024 to locate, document and help protect giant coral colonies. This paper has two main aims: first, to synthesise the scientific and practical motivations for focusing on giant corals as both research targets and conservation symbols; and second, to present the design, protocol and operational workflow of Map the Giants. We describe how the project integrates citizen-science principles, user-centred website design, standardised reporting methods and multi-expert validation into a coherent framework, with a public, interactive map and dedicated learning materials to support ocean literacy. Preliminary outcomes from the first 18 months: 195 submissions from 22 countries, of which 133 entries have been validated and added to the public database, demonstrate the feasibility and scientific value of this approach. Contributors routinely exceeded minimum data requirements and high validation rates indicate strong data quality despite heterogeneous participant backgrounds. Together, these elements show that Map the Giants can generate robust, scalable data on giant coral colonies while simultaneously engaging the public, providing a methodological reference for future studies and similar large-scale monitoring initiatives.
Journal Article
Adaptive energy-efficient and secure clustering-based routing architecture for underwater wireless sensor networks in marine environmental and ecosystem monitoring
IntroductionReliable long-term monitoring of coral reefs and other marine ecosystems is limited by the harsh underwater environment, restricted battery capacity of sensor nodes, and the high energy cost of acoustic communication. Underwater Wireless Sensor Networks (UWSNs) have emerged as a promising solution for marine environmental monitoring; however, challenges related to energy efficiency, secure communication, and reliable data collection remain significant.MethodsThis study proposes an integrated architecture for UWSNs that enhances energy efficiency, security, and data reliability. The framework combines a hybrid Adaptive Swarm Fitness Optimization–Golden Eagle Optimizer with K-Medoids clustering (ASFO–GEO–KM) for optimal cluster head selection, a Tiny Security (TinySec)-enabled Energy-aware Coral-Environmental Reliable Path (E-CERP) routing protocol, and Autonomous Underwater Vehicle (AUV)-assisted data collection. The ASFO–GEO–KM algorithm selects cluster heads based on residual energy, underwater link quality, and node density to improve load balancing and cluster stability. TinySec-enabled E-CERP provides authenticated, energy-aware multi-hop routing while accounting for underwater path loss and propagation delay. AUVs periodically collect aggregated data from cluster heads to reduce long-range acoustic transmissions and conserve node energy.ResultsSimulation results conducted in a realistic 3D marine environment demonstrate that the proposed framework outperforms existing approaches, including DEDG, AP, ALP, HECRA, GSA, and CTRGWO-CRP. The proposed system achieves a longer network lifetime, a higher packet delivery ratio, and significantly reduced routing overhead.DiscussionBy enabling secure, energy-efficient, and reliable underwater sensing, the proposed architecture supports long-term coral reef monitoring and marine ecosystem observation. It facilitates early detection of environmental stressors, such as thermal anomalies and turbidity spikes, thereby improving marine ecosystem protection and supporting conservation-oriented decision-making.
Journal Article
A stratified transect approach captures reef complexity with canopy-forming organisms
On the Great Barrier Reef (GBR), persistent changes to reef communities have begun to be documented, and on inshore reefs these shifts may favour the proliferation of macroalgae. Critical to understanding changes to reef community structure in response to anthropogenic impacts is developing effective methods to accurately document the abundance of different reef organisms. Effective monitoring must be time and cost efficient, replicable, and able to sufficiently and accurately detect disturbances to allow development of strategies to mitigate their impacts. Traditional techniques to document coral reef communities (i.e. photo-quadrats, benthic intercept transects) rely on planar views, which tend to either over- or under-represent canopy-forming organisms. As canopy-forming organisms are likely to be affected by anthropogenic influences (corals negatively, algae positively), it is essential for monitoring programs to implement methods sufficient to document changes to the vertical dimension of coral reefs. Here we build on previous work to document the canopy effect in coral-dominated ecosystems and propose a new survey approach suitable for implementation in algal-dominated systems. A vertically stratified transect, modified from a traditional point intercept transect, captures benthic and canopy-forming members of reef communities and provides information on three-dimensional complexity. To test the capability of the new method to detect changes in vertical reef structure, seaweed was removed from experimental quadrats and monitoring techniques were applied before and after four months of regrowth. A stratified method more accurately captured the three-dimensional change resulting from algal canopy growth, while resolving the over- and under-representation of algal biomass in two traditional techniques. We propose that a stratified transect method improves abundance estimates of canopy-forming organisms whilst maintaining data compatibility with traditional methods.
Journal Article
Increasing coral calcification in Orbicella faveolata and Pseudodiploria strigosa at Flower Garden Banks, Gulf of Mexico
Coral reefs are globally in decline and western Atlantic reefs have experienced the greatest losses in live coral cover of any region. The Flower Garden Banks (FGB) in the Gulf of Mexico are high-latitude, remote reefs that are an outlier to this trend, as they have maintained coral cover ≥ 50% since at least 1989. Quantifying the long-term trends in coral growth of key reef-building coral species, and the underlying environmental drivers, leads to a better understanding of local sensitivities to past changes that will ultimately allow us to better predict the future of reef growth at FGB. We obtained coral cores and constructed growth records for two of the most abundant hermatypic coral species at FGB, Pseudodiploria strigosa and Orbicella faveolata. Our records cover 57 yrs of growth for P. strigosa (1957–2013) and 45 yrs for O. faveolata (1970–2014). Linear extension and calcification rates of both species have increased significantly, but skeletal density did not change over the respective time periods. Extension and calcification data of both species combined were negatively correlated with the discharge from the Atchafalaya River, but positively correlated with maximum sea surface temperatures (SST). These data provide evidence that runoff from the Atchafalaya River impacts FGB corals and is a major control on coral growth at FGB. The increase in growth at FGB can be attributed to the significant warming trend in maximum monthly SSTs. Given the warming trend and recent increase in severity of bleaching at FGB, the prognosis is that bleaching events will become more deleterious with time, which will lead to a breakdown in the positive relationship between coral growth and maximum SST. This study provides further evidence that some high-latitude, cooler reef sites have experienced a stimulation in coral growth with ocean warming.
Journal Article