An automated approach for counting groups of flying animals applied to one of the world's largest bat colonies

Estimating animal populations is essential for conservation. Censusing large congregations is especially important since these are priorities for protection, but efficiently counting hundreds of thousands of moving animals remains a challenge. We developed a deep learning-based system using consumer cameras that not only counts but also records behavioral information for large numbers of flying animals in a range of lighting conditions including near darkness. We built a robust training set without human labeling by leveraging data augmentation and background subtraction. We demonstrate this approach by estimating the size of a straw-colored fruit bat (Eidolon helvum) colony in Kasanka National Park, Zambia with cameras encircling the colony to record evening emergence. Detection of bats was robust to deteriorating lighting conditions and changing backgrounds. Combined over five days, our population estimates ranged between 750,000 and 976,000 bats with a mean of 857,233. In addition to counts, we extracted wingbeat frequency, flight altitude, and local group polarity for 639,414 individuals. This open access method is an inexpensive but powerful approach that, in addition to radial emergences from central locations, can also be applied to unidirectional movements of flying groups, such as migratory streams of birds.