Automated high-frequency quantification of fish communities and biomass using computer vision
Authors: Kota Ishikawa, Takuma Masui, Keita Koeda, Rickdane Gomez, Lucas Yutaka Kimura, Michio Kondoh
Organizations: Graduate School of Life Sciences, Tohoku University, Sendai, Japan · Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), Tohoku University, Sendai, Japan · Graduate School of Science and Engineering, University of the Ryukyus, Okinawa, Japan · Faculty of Science, University of the Ryukyus, Okinawa, Japan
Abstract
Quantifying fish community structure is essential for understanding biodiversity and ecosystem responses in a changing environment, yet existing survey methods provide limited high-frequency, quantitative observations. Conventional approaches, including catch-based methods, underwater visual censuses, and environmental DNA metabarcoding, either require intensive labor or lack reliable estimates of abundance and biomass. Here, we develop an automated framework for quantifying fish communities from underwater video using computer vision. Using videos acquired with a custom-made stereo camera system, the framework integrates deep learning-based fish identification, multi-object tracking, and 3D reconstruction to estimate species-level abundance and biomass. We applied the approach to a reef fish community over a 20-day period with hourly daytime observations, revealing dynamic fluctuations in species richness, abundance, and biomass associated with changes in species composition. By comparing fish communities estimated from visual census and environmental DNA surveys, we demonstrate that our method provides complementary strengths for continuous, non-invasive, and quantitative monitoring of consistently observed species. This approach provides a scalable foundation for long-term monitoring and advances the capacity to resolve fine-scale temporal dynamics in fish communities.
We report on the continued development of CatchMonitor, resulting in a prototype computer vision system designed to automatically quantify discarded fish from video footage collected from Remote Electronic Monitoring (REM) systems on fishing trawlers. The analysis of trawler surveillance footage is a challenging problem due to the real-world conditions on board fishing vessels. Building on our prior work we improve the accuracy of species identification through the application of semi-supervised learning. We utilise a simple and robust object tracking approach, upon which we build our prototype discard quantification system. Finally we analyse the variability of manual discard quantification performed by multiple expert human analysts, using it as a benchmark against which we compare the performance of our system.
Recent advances in field technology have led to a massive influx of in-the-wild video data for ecological science. The primary bottleneck in leveraging this data is the high cost of expert annotation. While computer vision offers a potential solution, current models frequently fail when deployed in complex marine environments. To characterize these failures, we introduce WildFin, a novel benchmark for fish behavior recognition collected and annotated by ecologists. WildFin spans two critical real-world paradigms: stationary cameras monitoring groups of fish and dynamic divers following individual subjects. The dataset represents a massive curation effort, involving 1,350 hours of fieldwork and 600 hours of expert annotation to produce 9 hours of behavioral data with over 2 million frame-by-frame labels. We benchmark modern vision foundation models and quantify tradeoffs between static and spatiotemporal architectures, revealing the substantial gap that remains between current model capabilities and the demands of real-world underwater behavioral analysis. Project website: https://team-wildfin.github.io/.
Abigail G. Grassick, Jerome Tze-Hou Hsu, Ethan Lin +10
Precision aquaculture faces a "phenotyping bottleneck" in tracking high-resolution behavioral traits, as conventional methods cannot quantify instantaneous three-dimensional (3D) physical exertion. To address this, we present a high-throughput 3D behavioral phenotyping framework integrating deep learning object detection with binocular stereo vision for real-time monitoring of juvenile tilapia in high-density environments. The system automates non-contact body length estimation and reconstructs 3D swimming trajectories from absolute spatial coordinates. By eliminating 2D perspective distortions, this approach precisely quantifies 3D velocity and acceleration, marking the first estimation of true physical swimming speeds in free-roaming juveniles. Results show the framework successfully establishes circadian locomotor baselines, serving as an early warning system for physiological stress and providing an objective metric for fish vitality.