Coral Grow-out Robotic Assessment System (CGRAS): Scaling Coral Recruit Monitoring Through Robotics and Computer Vision

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. Reef restoration is crucial, but its success hinges on introducing automation to upscale efforts. In this work, we present a highly configurable AI pipeline for the real-time deployment of coral reseeding devices. The pipeline consists of three core components: (i) the image labeling scheme, designed to address data availability and reduce the cost of expert labeling; (ii) the classifier which performs automated analysis of underwater imagery, at the image or patch-level, while also enabling quantitative coral coverage estimation; and (iii) the decision-making module that determines whether deployment should occur based on the classifier's analysis. By reducing reliance on manual experts, our proposed pipeline increases operational range and efficiency of reef restoration. We validate the proposed pipeline at five sites across the Great Barrier Reef, benchmarking its performance against annotations from expert marine scientists. The pipeline achieves 77.8% deployment accuracy, 89.1% accuracy for sub-image patch classification, and real-time model inference at 5.5 frames per second on a Jetson Orin. To address the limited availability of labeled data in this domain and encourage further research, we publicly release a comprehensive, annotated dataset of substrate imagery from the surveyed sites.

In order to design conservation and restoration strategies to counter the global decline of coral reefs, ecological monitoring of reefs needs to be scaled up dramatically. Computer vision methods are increasingly used to tackle the vast amount of data: as the paradigm of data collection in reefs shifts from highly standardized and constrained survey images to unconstrained imagery on scalable platforms, it is necessary to design machine learning methods that help to get a fine-grained understanding of reefs from general-purpose reef imagery. This paper provides CoralscapesV2, an extension of the Coralscapes dataset for general-purpose visual scene understanding in reefs. CoralscapesV2 increases the dataset size, scope, label completeness and quality for semantic segmentation, and extends the number of classes from 39 to 95 fine-grained visual categories. Furthermore, CoralscapesV2 provides 65k exhaustive fish instance mask annotations, meticulously annotated to completeness by using the video, revealing that annotation of fish based on only static images is insufficient. CoralscapesV2 is the first dataset for panoptic segmentation in coral reefs, capturing a wide range of scenarios in the wild, posing a challenging benchmark for contemporary semantic segmentation and instance segmentation models. CoralscapesV2 is an important step towards general-purpose panoptic segmentation in coral reefs, which has substantial implications for scaling up coral reef monitoring, as it can be employed in a wide range of applications from benthic cover mapping from robot or handheld videos to designing methods for automated quantification and understanding of fish behavior and fish-reef interactions.

The life history of an individual coral is archived within the accreting skeleton of the colony. While reef-forming coral colonies (e.g. massive $\textit{Porites}$ sp.) may live for hundreds of years and deposit calcareous structures many metres in height and width, their living tissue is a thin outer surface layer comprised of asexually-dividing polyps that only survive a few years. To understand the rate and timing of polyp division and the consequences for colony skeletal growth, scientists need to track the skeletal corallite deposited around each polyp. Here we propose CoralLite, an annotated $μ$CT scan dataset of entire calcareous skeletons and an associated, first corallite deep learning reconstruction baseline. CoralLite combines fully quantified volumetric segmentations with cross-slice linking for visualisations of 3D models for each corallite up to colony scale. For segmentation, we propose and evaluate in detail a hybrid V-Trans-UNet architecture applicable to segmenting tiled $μ$CT virtual slabs of $\textit{Porites}$ sp. colonies. The model is pre-trained on weakly annotated data and topology-aware fine-tuned using fully annotated slice sections with 8k+ manual corallite region annotations. On unseen slices of the same colony, the resulting model reaches 0.94 topological accuracy at mean Dice scores of 0.77 on the same colony and projection axis, and 0.63 mean Dice scores on a different, biologically unrelated specimen. Whilst our experiments are limited in scale and context, our results show for the first time that visual machine learning can effectively support full 3D individual corallite modelling from $μ$CT scans of coral skeletons alone. For reproducibility and as a baseline for future research we publish our full dataset of 697 $μ$CT slices, 37 partial or full slice annotations, and all network weights and source code with this paper.