ABSTRACT
Advanced plant phenotyping techniques to measure biophysical traits of crops are helping to deliver improved crop varieties faster. Phenotyping of plants using different sensors for image acquisition and its analysis with novel computational algorithms are increasingly being adapted to measure plant traits. Thermal and multispectral imagery provides novel opportunities to reliably phenotype crop genotypes tested for biotic and abiotic stresses under glasshouse conditions. However, optimization for image acquisition, pre-processing, and analysis is required to correct for optical distortion, image co-registration, radiometric rescaling, and illumination correction. This study provides a computational pipeline that optimizes these issues and synchronizes image acquisition from thermal and multispectral sensors. The image processing pipeline provides a processed stacked image comprising RGB, green, red, NIR, red edge, and thermal, containing only the pixels present in the object of interest, e.g., plant canopy. These multimodal outputs in thermal and multispectral imageries of the plants can be compared and analysed mutually to provide complementary insights and develop vegetative indices effectively. This study offers digital platform and analytics to monitor early symptoms of biotic and abiotic stresses and to screen a large number of genotypes for improved growth and productivity. The pipeline is packaged as open source and is hosted online so that it can be utilized by researchers working with similar sensors for crop phenotyping.
ABSTRACT
The phenotypic characterization of crop genotypes is an essential, yet challenging, aspect of crop management and agriculture research. Digital sensing technologies are rapidly advancing plant phenotyping and speeding-up crop breeding outcomes. However, off-the-shelf sensors might not be fully applicable and suitable for agricultural research due to the diversity in crop species and specific needs during plant breeding selections. Customized sensing systems with specialized sensor hardware and software architecture provide a powerful and low-cost solution. This study designed and developed a fully integrated Raspberry Pi-based LiDAR sensor named CropBioMass (CBM), enabled by internet of things to provide a complete end-to-end pipeline. The CBM is a low-cost sensor, provides high-throughput seamless data collection in field, small data footprint, injection of data onto the remote server, and automated data processing. The phenotypic traits of crop fresh biomass, dry biomass, and plant height that were estimated by CBM data had high correlation with ground truth manual measurements in a wheat field trial. The CBM is readily applicable for high-throughput plant phenotyping, crop monitoring, and management for precision agricultural applications.
Subject(s)
Agriculture , Triticum , Biomass , Phenotype , SoftwareABSTRACT
Recent advancements in hyperspectral remote sensing technology now provide improved diagnostic capabilities to assess vegetation health conditions. This paper uses a set of 13 vegetation health indices related to chlorophyll, xanthophyll, blue/green/red ratio and structure from airborne hyperspectral reflectance data collected around a derelict mining area in Yerranderie, New South Wales, Australia. The studied area has ten historic mine shafts with a legacy of heavy metals and acidic contamination in a pristine ecosystem now recognised as Great Blue Mountain World Heritage Area. The forest is predominantly comprised of different species of Eucalyptus trees. In addition to the airborne survey, ground-based spectra of the tree leaves were collected along the two accessible heavy metal contaminated pathways. The stream networks in the area were classified and the geospatial patterns of vegetation health were analysed along the Tonalli River, a major water tributary flowing through the National Park. Despite the inflow of contaminated water from the near-mine streams, the measured vegetation health indices along Tonalli River were found to remain unchanged. The responses of the vegetation health indices between the near-mine and away-mine streams were found similar. Based on the along-stream and inter-stream analysis of the spectral indices of vegetation health, no significant impact of the heavy metal pollution could be noticed. The results indicate the possibility of the vegetation having developed immunity towards the high levels of heavy metal pollution over a century of exposure.
