Research Article | Open Access

Volume 2025 |Article ID 100047 | https://doi.org/10.1016/j.plaphe.2025.100047

PhenoGazer: A high-throughput phenotyping system to track plant stress responses using hyperspectral reflectance, nighttime chlorophyll fluorescence and RGB imaging in controlled environments

Muhammad Adeel Hassan,^1,2 and Christine Yao-Yun Chang ¹

¹U.S. Department of Agriculture, Agricultural Research Service, Adaptive Cropping Systems Laboratory, Beltsville, MD 20705, USA
²Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA

Abstract

High throughput phenotyping for crop monitoring at both leaf and canopy scales is essential for understanding plant responses to various stresses. PhenoGazer, a high-throughput phenotyping system, enhances crop monitoring in controlled environments by integrating a portable hyperspectral spectrometer with eight fiber optics, four Raspberry Pi cameras, and blue LED lights. This system allows for comprehensive assessment of plant health and development. PhenoGazer features automated moveable upper and lower racks for continuous measurements. The lower rack, equipped with four blue LED lights and spectrometer fiber optics, captures blue light-induced chlorophyll fluorescence at night. The upper rack, carrying four spectrometer fiber optics and cameras, captures hyperspectral reflectance and RGB images during the day. This dual capability enables detailed evaluation of plant phenology, stress responses, and growth dynamics throughout the entire crop growth cycle. Fully automated and managed by a Raspberry Pi running Python scripts, PhenoGazer ensures precise control and data acquisition with minimal human intervention. Additionally, it includes continuous measurements through a datalogger to acquire photosynthetically active radiation (PAR), soil moisture and temperature, and features expansion capability for additional analog or digital sensors as desired by end users. To test the system, soybean plants representing three conditions, healthy well watered, healthy droughted, and diseased, were monitored to evaluate growth and stress responses. PhenoGazer successfully phenotyped plants under different conditions in a walk-in growth chamber. By combining nighttime blue light induced chlorophyll fluorescence, hyperspectral reflectance-based vegetation indices, and RGB imagery, PhenoGazer represented a significant advancement in plant phenotyping technology, enhancing our understanding of crop responses to environmental conditions and supporting optimized crop performance in research and agricultural applications.