Using YOLOv5, SAHI, and GIS with Drone Mapping to Detect Giant Clams on the Great Barrier Reef

Despite the ecological importance of giant clams (Tridacninae), their effective management and conservation is challenging due to their widespread distribution and labour-intensive monitoring methods. In this study, we present an alternative approach to detecting and mapping clam density at Pioneer Bay on Goolboddi (Orpheus) Island on the Great Barrier Reef using drone data with a combination of deep learning tools and a geographic information system (GIS). We trained and evaluated 11 models using YOLOv5 (You Only Look Once, version 5) with varying numbers of input image tiles and augmentations (mean average precision—mAP: 63–83%). We incorporated the Slicing Aided Hyper Inference (SAHI) library to detect clams across orthomosaics, eliminating duplicate counts of clams straddling multiple tiles, and further, applied our models in three other geographic locations on the Great Barrier Reef, demonstrating transferability. Finally, by linking detections with their original geographic coordinates, we illustrate the workflow required to quantify animal densities, mapping up to seven clams per square meter in Pioneer Bay. Our workflow brings together several otherwise disparate steps to create an end-to-end approach for detecting and mapping animals with aerial drones. This provides ecologists and conservationists with actionable and clear quantitative and visual insights from drone mapping data.