A Tracking‐By‐Detection Framework to Automatically Count Rare and Elusive Megafauna in Aerial Video Surveys

ABSTRACT

Video surveys from drones or planes equipped with cameras have become invaluable tools for monitoring populations of rare and elusive megafauna over increasingly large spatial scales. To analyze hours of such video surveys, automated species detection approaches based on deep learning are now widely used, but simply tallying detections on the successive frames of videos leads to double counting of individuals, significantly biasing population size estimates. Here, we leverage a multiple object tracking approach that links detections across video frames to derive counts of unique individuals. Our tracking‐by‐detection framework integrates the full pipeline from aerial video surveys to automated individual count and estimation of minimum population abundance. Applied to aerial video surveys of dugongs ( Dugong dugon ) on the west coast of New Caledonia in winter, our framework automatically counted individuals with a slight negative bias of −5.7% (−15 individuals over a total of 265 ground‐truth individuals) compared to a baseline method relying on the sum of detections that led to a 48 times overestimation. Our tracking‐by‐detection framework directly estimated the number of unique individuals per flight, leading to a mean seasonal index of abundance of 42 individuals (±28 SD) in the surveyed area. Overall, 35 individuals were missed across flights, representing 13.2% of all ground‐truth individuals. Among missed individuals, two‐thirds were calves superposed to their mothers, stressing the challenge of occlusion when counting group‐living animals. Despite being applied to entire videos with very low prevalence of dugongs, our framework generated just 8% of false positives (20 instances) across all flights, mostly due to misidentifications with other species. Illustrated through the case of dugong, our tracking‐by‐detection framework more generally provides a scalable method to support digital population surveys, benefitting long‐term monitoring and conservation programs of vulnerable megafauna.