Scarlett Raine

Scarlett Raine, Ross Marchant, Brano Kusy et al.

Seagrass meadows serve as critical carbon sinks, but estimating the amount of carbon they store requires knowledge of the seagrass species present. Underwater and surface vehicles equipped with machine learning algorithms can help to accurately estimate the composition and extent of seagrass meadows at scale. However, previous approaches for seagrass detection and classification have required supervision from patch-level labels. In this paper, we reframe seagrass classification as a weakly supervised coarse segmentation problem where image-level labels are used during training (25 times fewer labels compared to patch-level labeling) and patch-level outputs are obtained at inference time. To this end, we introduce SeaFeats, an architecture that uses unsupervised contrastive pre-training and feature similarity, and SeaCLIP, a model that showcases the effectiveness of large language models as a supervisory signal in domain-specific applications. We demonstrate that an ensemble of SeaFeats and SeaCLIP leads to highly robust performance. Our method outperforms previous approaches that require patch-level labels on the multi-species 'DeepSeagrass' dataset by 6.8% (absolute) for the class-weighted F1 score, and by 12.1% (absolute) for the seagrass presence/absence F1 score on the 'Global Wetlands' dataset. We also present two case studies for real-world deployment: outlier detection on the Global Wetlands dataset, and application of our method on imagery collected by the FloatyBoat autonomous surface vehicle.

Melanie Wille, Tobias Fischer, Scarlett Raine

Underwater object detection is critical for monitoring marine ecosystems but poses unique challenges, including degraded image quality, imbalanced class distribution, and distinct visual characteristics. Not every species is detected equally well, yet underlying causes remain unclear. We address two key research questions: 1) What factors beyond data quantity drive class-specific performance disparities? 2) How can we systematically improve detection of under-performing marine species? We manipulate the DUO and RUOD datasets to separate the object detection task into localization and classification and investigate the under-performance of the scallop class. Localization analysis using YOLO11 and TIDE finds that foreground-background discrimination is the most problematic stage regardless of data quantity. Classification experiments reveal persistent precision gaps even with balanced data, indicating intrinsic feature-based challenges beyond data scarcity and inter-class dependencies. We recommend imbalanced distributions when prioritizing precision, and balanced distributions when prioritizing recall. Improving under-performing classes should focus on algorithmic advances, especially within localization modules. We publicly release our code and datasets.

Scarlett Raine, Ross Marchant, Peyman Moghadam et al.

We introduce a dataset of seagrass images collected by a biologist snorkelling in Moreton Bay, Queensland, Australia, as described in our publication: arXiv:2009.09924. The images are labelled at the image-level by collecting images of the same morphotype in a folder hierarchy. We also release pre-trained models and training codes for detection and classification of seagrass species at the patch level at https://github.com/csiro-robotics/deepseagrass.

Scarlett Raine, Ross Marchant, Peyman Moghadam et al.

Underwater surveys conducted using divers or robots equipped with customized camera payloads can generate a large number of images. Manual review of these images to extract ecological data is prohibitive in terms of time and cost, thus providing strong incentive to automate this process using machine learning solutions. In this paper, we introduce a multi-species detector and classifier for seagrasses based on a deep convolutional neural network (achieved an overall accuracy of 92.4%). We also introduce a simple method to semi-automatically label image patches and therefore minimize manual labelling requirement. We describe and release publicly the dataset collected in this study as well as the code and pre-trained models to replicate our experiments at: https://github.com/csiro-robotics/deepseagrass

Melanie Wille, Dimity Miller, Tobias Fischer et al.

Domain shift, where deviations between training and deployment data distributions degrade model performance, is a key challenge in underwater environments. Existing benchmarks testing performance for underwater domain shift simulate variability through synthetic style transfer. This fails to capture intrinsic scene factors such as visibility, illumination, scene composition, or acquisition factors, limiting analysis of real-world effects. We propose a labeling framework that defines underwater domains using measurable image, scene, and acquisition characteristics. Unlike prior benchmarks, it captures physically meaningful factors, enabling semantically consistent image grouping and supporting domain-specific evaluation of detection performance including failure analysis. We validate this on public datasets, showing systematic variations across domain factors and revealing hidden failure modes.

Scarlett Raine, Ross Marchant, Brano Kusy et al.

Marine surveys by robotic underwater and surface vehicles result in substantial quantities of coral reef imagery, however labeling these images is expensive and time-consuming for domain experts. Point label propagation is a technique that uses existing images labeled with sparse points to create augmented ground truth data, which can be used to train a semantic segmentation model. In this work, we show that recent advances in large foundation models facilitate the creation of augmented ground truth masks using only features extracted by the denoised version of the DINOv2 foundation model and K-Nearest Neighbors (KNN), without any pre-training. For images with extremely sparse labels, we present a labeling method based on human-in-the-loop principles, which greatly enhances annotation efficiency: in the case that there are 5 point labels per image, our human-in-the-loop method outperforms the prior state-of-the-art by 14.2% for pixel accuracy and 19.7% for mIoU; and by 8.9% and 18.3% if there are 10 point labels. When human-in-the-loop labeling is not available, using the denoised DINOv2 features with a KNN still improves on the prior state-of-the-art by 2.7% for pixel accuracy and 5.8% for mIoU (5 grid points). On the semantic segmentation task, we outperform the prior state-of-the-art by 8.8% for pixel accuracy and by 13.5% for mIoU when only 5 point labels are used for point label propagation. Additionally, we perform a comprehensive study into the impacts of the point label placement style and the number of points on the point label propagation quality, and make several recommendations for improving the efficiency of labeling images with points.

Scarlett Raine, Frederic Maire, Niko Suenderhauf et al.

Underwater surveys provide long-term data for informing management strategies, monitoring coral reef health, and estimating blue carbon stocks. Advances in broad-scale survey methods, such as robotic underwater vehicles, have increased the range of marine surveys but generate large volumes of imagery requiring analysis. Computer vision methods such as semantic segmentation aid automated image analysis, but typically rely on fully supervised training with extensive labelled data. While ground truth label masks for tasks like street scene segmentation can be quickly and affordably generated by non-experts through crowdsourcing services like Amazon Mechanical Turk, ecology presents greater challenges. The complexity of underwater images, coupled with the specialist expertise needed to accurately identify species at the pixel level, makes this process costly, time-consuming, and heavily dependent on domain experts. In recent years, some works have performed automated analysis of underwater imagery, and a smaller number of studies have focused on weakly supervised approaches which aim to reduce the expert-provided labelled data required. This survey focuses on approaches which reduce dependency on human expert input, while reviewing the prior and related approaches to position these works in the wider field of underwater perception. Further, we offer an overview of coastal ecosystems and the challenges of underwater imagery. We provide background on weakly and self-supervised deep learning and integrate these elements into a taxonomy that centres on the intersection of underwater monitoring, computer vision, and deep learning, while motivating approaches for weakly supervised deep learning with reduced dependency on domain expert data annotations. Lastly, the survey examines available datasets and platforms, and identifies gaps, barriers, and opportunities for automating underwater surveys.

Scarlett Raine, Tobias Fischer

Marine ecosystems face increasing pressure due to climate change, driving the need for scalable, AI-powered monitoring solutions. This paper examines the rapid emergence of underwater AI as a major research frontier and analyzes the factors that have transformed marine perception from a niche application into a catalyst for AI innovation. We identify three convergent drivers: environmental necessity for ecosystem-scale monitoring, democratization of underwater datasets through citizen science platforms, and researcher migration from saturated terrestrial computer vision domains. Our analysis reveals how unique underwater challenges - turbidity, cryptic species detection, expert annotation bottlenecks, and cross-ecosystem generalization - are driving fundamental advances in weakly supervised learning, open-set recognition, and robust perception under degraded conditions. We survey emerging trends in datasets, scene understanding and 3D reconstruction, highlighting the paradigm shift from passive observation toward AI-driven, targeted intervention capabilities. The paper demonstrates how underwater constraints are pushing the boundaries of foundation models, self-supervised learning, and perception, with methodological innovations that extend far beyond marine applications to benefit general computer vision, robotics, and environmental monitoring.

Scarlett Raine, Benjamin Moshirian, Tobias Fischer

Coral reefs are on the brink of collapse, with climate change, ocean acidification, and pollution leading to a projected 70-90% loss of coral species within the next decade. Restoration efforts are crucial, but their success hinges on introducing automation to upscale efforts. We present automated deployment of coral re-seeding devices powered by artificial intelligence, computer vision, and robotics. Specifically, we perform automated substrate classification, enabling detection of areas of the seafloor suitable for coral growth, thus significantly reducing reliance on human experts and increasing the range and efficiency of restoration. Real-world testing of the algorithms on the Great Barrier Reef leads to deployment accuracy of 77.8%, sub-image patch classification of 89.1%, and real-time model inference at 5.5 frames per second. Further, we present and publicly contribute a large collection of annotated substrate image data to foster future research in this area.

Dorian Tsai, Christopher A. Brunner, Riki Lamont et al.

Coral aquaculture for reef restoration requires accurate and continuous spawn counting for resource distribution and larval health monitoring, but current methods are labor-intensive and represent a critical bottleneck in the coral production pipeline. We propose the Coral Spawn and Larvae Imaging Camera System (CSLICS), which uses low cost modular cameras and object detectors trained using human-in-the-loop labeling approaches for automated spawn counting in larval rearing tanks. This paper details the system engineering, dataset collection, and computer vision techniques to detect, classify and count coral spawn. Experimental results from mass spawning events demonstrate an F1 score of 82.4\% for surface spawn detection at different embryogenesis stages, 65.3\% F1 score for sub-surface spawn detection, and a saving of 5,720 hours of labor per spawning event compared to manual sampling methods at the same frequency. Comparison of manual counts with CSLICS monitoring during a mass coral spawning event on the Great Barrier Reef demonstrates CSLICS' accurate measurement of fertilization success and sub-surface spawn counts. These findings enhance the coral aquaculture process and enable upscaling of coral reef restoration efforts to address climate change threats facing ecosystems like the Great Barrier Reef.

Scarlett Raine, Ross Marchant, Brano Kusy et al.

Monitoring coral reefs using underwater vehicles increases the range of marine surveys and availability of historical ecological data by collecting significant quantities of images. Analysis of this imagery can be automated using a model trained to perform semantic segmentation, however it is too costly and time-consuming to densely label images for training supervised models. In this letter, we leverage photo-quadrat imagery labeled by ecologists with sparse point labels. We propose a point label aware method for propagating labels within superpixel regions to obtain augmented ground truth for training a semantic segmentation model. Our point label aware superpixel method utilizes the sparse point labels, and clusters pixels using learned features to accurately generate single-species segments in cluttered, complex coral images. Our method outperforms prior methods on the UCSD Mosaics dataset by 3.62% for pixel accuracy and 8.35% for mean IoU for the label propagation task, while reducing computation time reported by previous approaches by 76%. We train a DeepLabv3+ architecture and outperform state-of-the-art for semantic segmentation by 2.91% for pixel accuracy and 9.65% for mean IoU on the UCSD Mosaics dataset and by 4.19% for pixel accuracy and 14.32% mean IoU for the Eilat dataset.