Analysis of Biological Images and Quantitative Monitoring Using Deep Learning and Computer Vision

Aaron Gálvez-Salido, Francisca Robles, Rodrigo J. Gonçalves, Roberto de la Herrán, Carmelo Ruiz Rejón, Rafael Navajas-Pérez

Automated biological counting is essential for scaling wildlife monitoring and biodiversity assessments, as manual processing currently limits analytical effort and scalability. This review evaluates the integration of deep learning and computer vision across diverse acquisition platforms, including camera traps, unmanned aerial vehicles (UAVs), and remote sensing. Methodological paradigms ranging from Convolutional Neural Networks (CNNs) and one-stage detectors like You Only Look Once (YOLO) to recent transformer-based architectures and hybrid models are examined. The literature shows that these methods consistently achieve high accuracy—often exceeding 95%—across various taxa, including insect pests, aquatic organisms, terrestrial vegetation, and forest ecosystems. However, persistent challenges such as object occlusion, cryptic species differentiation, and the scarcity of high-quality, labeled datasets continue to hinder fully automated workflows. We conclude that while automated counting has fundamentally increased data throughput, future advancements must focus on enhancing model generalization through self-supervised learning and improved data augmentation techniques. These developments are critical for transitioning from experimental models to robust, operational tools for global ecological monitoring and conservation efforts.