| Abstract: |
Phytoplankton are central to global biogeochemical cycles and aquatic food webs, yet their monitoring remains constrained by costly instrumentation and labor-intensive workflows. We present a modular, automated machine vision system for in situ, real-time detection, classification, and tracking of phytoplankton using the open-source AFTI-scope imaging platform. Our approach systematically benchmarks one-stage, two-stage, and transformer-based detectors, identifying YOLOv11 as the most effective balance of accuracy and efficiency for resource-constrained deployment. To improve species-level identification, we integrate an ensemble classifier (EfficientNet_B0 + Swin_T), boosting F1-scores to 0.9852, and couple this with BoT-SORT tracking to enable robust, non-redundant abundance estimation under dynamic flow conditions. Unlike prior systems, our pipeline is designed for embedded GPU hardware (Jetson AGX Orin) and validated on real-world deployments, demonstrating feasibility for scalable, autonomous plankton monitoring. This work presents an open-source flow-through imaging system with a real-time machine learning pipeline, along with integrated and standardized datasets combining public and AFTI-scope imagery. It further provides comprehensive benchmarking of detection, classification, and tracking architectures under in-situ conditions, and demonstrates in-field validation of real-time species-level monitoring with a design optimized for deployment on autonomous surface vehicles. This work provides the first embedded, low-cost platform capable of continuous, automated phytoplankton observation, supporting future large-scale marine ecosystem monitoring. |