Open‐source workflow approaches to passive acoustic monitoring of bats

• Main Authors: Brinkløv, Signe M. M., Macaulay, Jamie, Bergler, Christian, Tougaard, Jakob, Beedholm, Kristian, Elmeros, Morten, Madsen, Peter Teglberg
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2023
• Subjects: Bats; Passive Acoustic Monitoring (PAM); Deep Learning Classifier; Automated Species Detection; ecological modeling; Ecology; Evolution; Behavior and Systematics; toothed whales
• Online Access: https://doi.org/10.5061/dryad.4xgxd25fh

The affordability, storage, and power capacity of compact modern recording hardware has evolved passive acoustic monitoring (PAM) of animals and soundscapes into a non-invasive, cost-effective tool for research and ecological management and is particularly effective for bats and toothed whales that consistently echolocate. The use of PAM at large scales hinges on effective automated detectors and species classifiers which, combined with distance sampling approaches, have enabled species abundance estimation of toothed whales. But standardized, user-friendly, and open-access automated detection and classification workflows are in demand for this key conservation metric to be realized for bats. We used the PAMGuard toolbox including its new deep learning classification module to test the performance of four open-source workflows for automated analyses of acoustic datasets from bats. Each workflow used a different initial detection algorithm followed by the same deep learning classification algorithm and was evaluated against the performance of an expert manual analyst. Workflow performance depended strongly on the signal-to-noise ratio and detection algorithm used: the full deep learning workflow had the best classification accuracy (≤67%) but was computationally too slow for practical large-scale bat PAM. Workflows using PAMGuard's detection module or triggers onboard an SM4BAT or AudioMoth accurately classified up to 47%, 59% and 34%, respectively, of calls to species. Not all workflows included noise sampling critical to estimating changes in detection probability over time, a vital parameter for abundance estimation. The workflow using PAMGuard's detection module was 40 times faster than the full deep learning workflow and missed as few calls (recall for both ~0.6), thus balancing computational speed and performance. We show that complete acoustic detection and classification workflows for bat PAM data can be efficiently automated using open-source software such as PAMGuard and exemplify how detection choices, ...