Stress Distribution Analysis on Hyperspectral Corn Leaf Images for Improved Phenotyping Quality

Development of a Target-to-Sensor Mode Multispectral Imaging Device for High-Throughput and High-Precision Touch-Based Leaf-Scale Soybean Phenotyping

Image-based spectroscopy phenotyping is a rapidly growing field that investigates how genotype, environment and management interact using remote or proximal sensing systems to capture images of a plant under multiple wavelengths of light. While remote sensing techniques have proven effective in crop phenotyping, they can be subject to various noise sources, such as varying lighting conditions and plant physiological status, including leaf orientation. Moreover, current proximal leaf-scale imaging devices require the sensors to accommodate the state of the samples during imaging which induced extra time and labor cost. Therefore, this study developed a proximal multispectral imaging device that can actively attract the leaf to the sensing area (target-to-sensor mode) for high-precision and high-throughput leaf-scale phenotyping. To increase the throughput and to optimize imaging results, this device innovatively uses active airflow to reposition and flatten the soybean leaf. This novel mechanism redefines the traditional sensor-to-target mode and has relieved the device operator from the labor of capturing and holding the leaf, resulting in a five-fold increase in imaging speed compared to conventional proximal whole leaf imaging device. Besides, this device uses artificial lights to create stable and consistent lighting conditions to further improve the quality of the images. Furthermore, the touch-based imaging device takes full advantage of proximal sensing by providing ultra-high spatial resolution and quality of each pixel by blocking the noises induced by ambient lighting variances. The images captured by this device have been tested in the field and proven effective. Specifically, it has successfully identified nitrogen deficiency treatment at an earlier stage than a typical remote sensing system. The p-value of the data collected by the device (p = 0.008) is significantly lower than that of a remote sensing system (p = 0.239).

Proximal hyperspectral sensing of abiotic stresses in plants

Recent attempts, advances and challenges, as well as future perspectives regarding the application of proximal hyperspectral sensing (where sensors are placed within 10 m above plants, either on land-based platforms or in controlled environments) to assess plant abiotic stresses have been critically reviewed. Abiotic stresses, caused by either physical or chemical reasons such as nutrient deficiency, drought, salinity, heavy metals, herbicides, extreme temperatures, and so on, may be more damaging than biotic stresses (affected by infectious agents such as bacteria, fungi, insects, etc.) on crop yields. The proximal hyperspectral sensing provides images at a sub-millimeter spatial resolution for doing an in-depth study of plant physiology and thus offers a global view of the plant's status and allows for monitoring spatio-temporal variations from large geographical areas reliably and economically. The literature update has been based on 362 research papers in this field, published from 2010, most of which are from four years ago and, in our knowledge, it is the first paper that provides a comprehensive review of the applications of the technique for the detection of various types of abiotic stresses in plants.

Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives

Plant phenomics (PP) has been recognized as a bottleneck in studying the interactions of genomics and environment on plants, limiting the progress of smart breeding and precise cultivation. High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits. Proximal and remote sensing (PRS) techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis. Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications. This progress covers most aspects of PRS application in PP, including patterns of global spatial distribution and temporal dynamics, specific PRS technologies, phenotypic research fields, working environments, species, and traits. Subsequently, we demonstrate how to link PRS to multi-omics studies, including how to achieve multi-dimensional PRS data acquisition and processing, how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance, and how to link PP to multi-omics association analysis. Finally, we identify three future perspectives for PRS-based PP: (1) strengthening the spatial and temporal consistency of PRS data, (2) exploring novel phenotypic traits, and (3) facilitating multi-omics communication.

Capturing crop adaptation to abiotic stress using image-based technologies

Farmers and breeders aim to improve crop responses to abiotic stresses and secure yield under adverse environmental conditions. To achieve this goal and select the most resilient genotypes, plant breeders and researchers rely on phenotyping to quantify crop responses to abiotic stress. Recent advances in imaging technologies allow researchers to collect physiological data non-destructively and throughout time, making it possible to dissect complex plant responses into quantifiable traits. The use of image-based technologies enables the quantification of crop responses to stress in both controlled environmental conditions and field trials. This paper summarizes phenotyping imaging technologies (RGB, multispectral and hyperspectral sensors, among others) that have been used to assess different abiotic stresses including salinity, drought and nitrogen deficiency, while discussing their advantages and drawbacks. We present a detailed review of traits involved in abiotic tolerance, which have been quantified by a range of imaging sensors under high-throughput phenotyping facilities or using unmanned aerial vehicles in the field. We also provide an up-to-date compilation of spectral tolerance indices and discuss the progress and challenges in machine learning, including supervised and unsupervised models as well as deep learning.

Modeling of Diurnal Changing Patterns in Airborne Crop Remote Sensing Images

Airborne remote sensing technologies have been widely applied in field crop phenotyping. However, the quality of current remote sensing data suffers from significant diurnal variances. The severity of the diurnal issue has been reported in various plant phenotyping studies over the last four decades, but there are limited studies on the modeling of the diurnal changing patterns that allow people to precisely predict the level of diurnal impacts. In order to comprehensively investigate the diurnal variability, it is necessary to collect time series field images with very high sampling frequencies, which has been difficult. In 2019, Purdue agricultural (Ag) engineers deployed their first field visible to near infrared (VNIR) hyperspectral gantry platform, which is capable of repetitively imaging the same field plots every 2.5 min. A total of 8631 hyperspectral images of the same field were collected for two genotypes of corn plants from the vegetative stage V4 to the reproductive stage R1 in the 2019 growing season. The analysis of these images showed that although the diurnal variability is very significant for almost all the image-derived phenotyping features, the diurnal changes follow stable patterns. This makes it possible to predict the imaging drifts by modeling the changing patterns. This paper reports detailed diurnal changing patterns for several selected plant phenotyping features such as Normalized Difference Vegetation Index (NDVI), Relative Water Content (RWC), and single spectrum bands. For example, NDVI showed a repeatable V-shaped diurnal pattern, which linearly drops by 0.012 per hour before the highest sun angle and increases thereafter by 0.010 per hour. The different diurnal changing patterns in different nitrogen stress treatments, genotypes and leaf stages were also compared and discussed. With the modeling results of this work, Ag remote sensing users will be able to more precisely estimate the deviation/change of crop feature predictions caused by the specific imaging time of the day. This will help people to more confidently decide on the acceptable imaging time window during a day. It can also be used to calibrate/compensate the remote sensing result against the time effect.

Developing a Modern Greenhouse Scientific Research Facility-A Case Study

Multidisciplinary approaches in science are still rare, especially in completely different fields such as agronomy science and computer science. We aim to create a state-of-the-art floating ebb and flow system greenhouse that can be used in future scientific experiments. The objective is to create a self-sufficient greenhouse with sensors, cloud connectivity, and artificial intelligence for real-time data processing and decision making. We investigated various approaches and proposed an optimal solution that can be used in much future research on plant growth in floating ebb and flow systems. A novel microclimate pocket-detection solution is proposed using an automatically guided suspended platform sensor system. Furthermore, we propose a methodology for replacing sensor data knowledge with artificial intelligence for plant health estimation. Plant health estimation allows longer ebb periods and increases the nutrient level in the final product. With intelligent design and the use of artificial intelligence algorithms, we will reduce the cost of plant research and increase the usability and reliability of research data. Thus, our newly developed greenhouse would be more suitable for plant growth research and production.