Benchmarking an Integrated Deep Learning Pipeline for Robust Detection and Individual Counting of the Greater Caribbean Manatee

The Greater Caribbean manatee faces significant conservation challenges due to a lack of demographic data in low-visibility habitats. To address this, we present a refined automated manatee counting method pipeline integrating deep learning-based call detection with unsupervised individual counting. We resolved significant computational bottlenecks by implementing an offline feature extraction strategy, bypassing a 13-h processing lag for 43,031 audio samples. To mitigate overfitting in imbalanced bioacoustic datasets, non-parametric bootstrap resampling was employed to generate 100,000 balanced spectrograms. Benchmarking revealed that transfer learning via a VGG-16 backbone achieved a mean 10-fold cross-validation accuracy of 98.92% (±0.08%) and an F1-score of 98.08% for genuine vocalizations. Following detection, individual counting utilized k-means clustering on prioritized music information retrieval descriptors—spectral bandwidth, centroid, and roll-off—to resolve distinct acoustic signatures. This framework identified three individuals with a silhouette coefficient of 79.20%, demonstrating superior cohesion over previous benchmarks. These results confirm the automatic manatee count method as a robust, scalable framework for generating the scientific evidence required for regional conservation policies.