CropMonitor: a scalable open-source experiment management system for distributed plant phenotyping and IoT-based crop management

Abstract

Abstract Background: High-quality plant phenotyping and climate data lay the foundation of phenotypic analysis as well as genotype-by-environment interactions, which is important biological evidence not only to understand the dynamics between crop performance, genotypes, and environmental factors, but also for agronomists and farmers to monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies in recent years, many IoT-based remote sensing devices have been applied to phenotyping and crop monitoring that generate big plant-environment datasets every day; however, it is still technically challenging to calibrate, annotate, and aggregate big data effectively, especially when they were generated in multiple locations, and often at different scales. Findings: CropSurveyor is a PHP and SQL based server platform, which provides automated data collation, storage, device and experiment management through IoT-based sensors and distributed plant phenotyping workstations. It provides a two-component solution for monitoring biological experiments and networked devices, with interfaces specifically designed for distributed IoT devices and centralised data servers. Data transfer is performed automatically though an HTTP accessible RESTful API installed on both device-side and server-side of the CropSurveyor system, which synchronise daily representative crop growth images for quick and visual-based crop assessment, as well as detailed microclimate readings for GxE studies. CropSurveyor also supports the comparison of historical and ongoing crop performance whilst different experiments are being conducted. Conclusions: As an open-source experiment and data management system, CropSurveyor can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current data comparison through a single cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a PC, CropSurveyor has been used in wheat field experiments for prebreeding since 2016 and has the potential to enable scalable crop management and IoT-style agricultural practices in the near future.

Plant phenotyping relevance

分散型植物フェノタイピング設備とIoTセンサーのデータ収集・管理・比較を中核とするオープンソース基盤であり、植物生育画像や微気候データを用いた再利用可能なワークフローを提供している。

Code and data availability

The authors explicitly state that the CropSurveyor system code and the datasets supporting the paper's results (wheat phenotyping image/sensor data) are openly available on their public GitHub releases page, with a BSD-3-Clause license.