PhenoStream: A Cyberinfrastructure for Automated and AI-Based Crop Trait Extraction from Aerial Imagery

Authors

Varela, S., Ruhter, J., Sacks, E., Zheng, X., Allen, D., Hale, A., Landry, C., Kuang, X., Long, B., Zhu, Y., Proma, S., Kaur, S., Jarquin, D., Morrison, J., Leakey, A.

Abstract

The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (GxE) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams--including remote sensing, environmental, and management data--toward data-driven decision making in agriculture.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 31 Aug 2026.

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