A time-lapse imaging platform for quantification of soil crack development due to simulated root water uptake

Plants are major drivers of soil structure dynamics. Root growth creates new macropores and provides essential carbon to soil, while root water uptake may induce crack formation around roots. Cracks can facilitate root growth as they provide pathways of least resistance and improve water infiltration and soil aeration. Due to the lack of suitable quantification methods, knowledge on the effects of root water uptake on soil crack formation remains limited. In the current study, we developed a time-lapse imaging platform that allows i) simulating root water uptake through localized soil drying and ii) quantifying the development of two-dimensional crack networks. Customized soil boxes that were 50 mm wide, 55 mm high and 5 mm deep were designed. Artificial roots made of dialysis tubes were inserted into the soil boxes and polyethylene glycol solution was circulated through the tubes. This induced a gradient in osmotic potential at the contact area (150 mm(2)) between the soil and the dialysis tubes, resulting in controlled soil drying. Drying intensity was varied by using different polyethylene glycol concentrations. Experiments were conducted with three soils that were subjected to three drying intensities for 6.5 days. We developed a time-lapse imaging system to record soil crack formation at two-minute intervals in twelve samples simultaneously. Resulting crack networks were quantified with an automated image analysis pipeline. Across soils and drying intensities, crack network development slowed down after 24-48 h of soil drying. The extent and complexity of crack networks increased with drying intensity and crack networks were larger and more complex in the clay and clay loam soil than in the silt loam soil. Smaller and less complex crack networks were better connected than larger and more complex networks. These results demonstrate that the platform developed in this study is suitable to quantify crack network development in soil due to simulated root water uptake at high temporal resolution and high throughput. Thereby, it can provide information needed to improve our understanding on how plants modify soil structure

High-resolution quantification of root dynamics in split-nutrient rhizoslides reveals rapid and strong proliferation of maize roots in response to local high nitrogen

Patches rich in nitrogen are rapidly colonized by selective root growth in maize, which was quantified at high time resolution with state-of-the-art non-invasive imaging techniques in a paper-based growth syste

NU-Spidercam: A large-scale, cable-driven, integrated sensing and robotic system for advanced phenotyping, remote sensing, and agronomic research

Field-based high throughput plant phenotyping has recently gained increased interest in the efforts to bridge the genotyping and phenotyping gap and accelerate plant breeding for crop improvement. In this paper, we introduce a large-scale, integrated robotic cable-driven sensing system developed at University of Nebraska for field phenotyping research. It is constructed to collect data from a 0.4ha field. The system has a sensor payload of 30kg and offers the flexibility to integrate user defined sensing modules. Currently it integrates a four-band multispectral camera, a thermal infrared camera, a 3D scanning LiDAR, and a portable visible near-infrared spectrometer for plant measurements. Software is designed and developed for instrument control, task planning, and motion control, which enables precise and flexible phenotypic data collection at the plot level. The system also includes a variable-rate subsurface drip irrigation to control water application rates, and an automated weather station to log environmental variables. The system has been in operation for the 2017 and 2018 growing seasons. We demonstrate that the system is reliable and robust, and that fully automated data collection is feasible. Sensor and image data are of high quality in comparison to the ground truth measurements, and capture various aspects of plant traits such as height, ground cover and spectral reflectance. We present two novel datasets enabled by the system, including a plot-level thermal infrared image time-series during a day, and the signal of solar induced chlorophyll fluorescence from canopy reflectance. It is anticipated that the availability of this automated phenotyping system will benefit research in field phenotyping, remote sensing, agronomy, and related disciplines.ISSN:0168-1699ISSN:1872-710

Phenotyping a Dynamic Trait: Leaf Growth of Perennial Ryegrass Under Water Limiting Conditions

Water limitation is one of the major factors reducing crop productivity worldwide. In order to develop efficient breeding strategies to improve drought tolerance, accurate methods to identify when a plant reduces growth as a consequence of water deficit have yet to be established. In perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf elongation is a key factor determining plant growth and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under non-stress conditions, the impact of water limitation on leaf elongation in perennial ryegrass is poorly understood. We describe a method for quantifying tolerance to water deficit based on leaf elongation in relation to temperature and soil moisture in perennial ryegrass. With decreasing soil moisture, three growth response phases were identified: first, a “normal” phase where growth is mainly determined by temperature, second a “slow” phase where leaf elongation decreases proportionally to soil water potential and third an “arrest” phase where leaf growth terminates. A custom R function was able to quantify the points which demarcate these phases and can be used to describe the response of plants to water deficit. Applied to different perennial ryegrass genotypes, this function revealed significant genotypic variation in the response of leaf growth to temperature and soil moisture. Dynamic phenotyping of leaf elongation can be used as a tool to accurately quantify tolerance to water deficit in perennial ryegrass and to improve this trait by breeding. Moreover, the tools presented here are applicable to study the plant response to other stresses in species with linear, graminoid leaf morphology

Global Wheat Head Detection 2021: an improved dataset for benchmarking wheat head detection methods

The Global Wheat Head Detection (GWHD) dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4700 RGB images acquired from various acquisition platforms and 7 countries/institutions. With an associated competition hosted in Kaggle, GWHD_2020 has successfully attracted attention from both the computer vision and agricultural science communities. From this first experience, a few avenues for improvements have been identified regarding data size, head diversity, and label reliability. To address these issues, the 2020 dataset has been reexamined, relabeled, and complemented by adding 1722 images from 5 additional countries, allowing for 81,553 additional wheat heads. We now release in 2021 a new version of the Global Wheat Head Detection dataset, which is bigger, more diverse, and less noisy than the GWHD_2020 version

Towards Wheat Yield Estimation in Plant Breeding from Inhomogeneous Lidar Point Clouds Using Stochastic Features

The world relies heavily on wheat, corn, and rice for nutrition, with global challenges such as population growth and climate change threatening food security. To tackle this, plant breeding, supported by digital technologies, focuses on improving food quality and quantity. Currently, crop yield estimation uses indirect observations through hyperspectral data and spectral indices, such as NDVI, which suffer from low sensitivity in breeding scenarios. Terrestrial laser scanners (TLS) present an alternative, allowing observations of the quantity and morphology of wheat ears from point clouds, which are directly linked to grain yield. However, exploiting these observations under field conditions presents challenges, mainly due to reduced resolution and non-homogenous properties of point clouds. In response, we propose an approach for in-field wheat yield estimation using machine learning and stochastic features of TLS point clouds that are specifically handcrafted to be less sensitive to the abovementioned phenomena. This approach avoids the need for explicit 3D reconstruction of individual plants and plant organs. Our initial results show limited success in yield estimation when posed as a regression problem. However, when framed as a classification problem focusing on detecting top- and bottom-performing plant phenotypes, we achieved a promising accuracy of 84.4% and AUC of 0.93. While encouraging, these are only the first results under relaxed conditions and further work is needed to enhance practical applicability.ISSN:1682-1750ISSN:2194-9034ISSN:1682-177

PhenoCams for Field Phenotyping: Using Very High Temporal Resolution Digital Repeated Photography to Investigate Interactions of Growth, Phenology, and Harvest Traits

Understanding the interaction of plant growth with environmental conditions is crucial to increase the resilience of current cropping systems to a changing climate. Here, we investigate PhenoCams as a high-throughput approach for field phenotyping experiments to assess growth dynamics of many different genotypes simultaneously in high temporal (daily) resolution. First, we develop a method that extracts a daily phenological signal that is normalized for the different viewing geometries of the pixels within the images. Second, we investigate the extraction of the in season traits of early vigor, leaf area index (LAI), and senescence dynamic from images of a soybean (Glycine max) field phenotyping experiment and show that it is possible to rate early vigor, senescence dynamics, and track the LAI development between LAI 1 and 4.5. Third, we identify the start of green up, green peak, senescence peak, and end of senescence in the phenological signal. Fourth, we extract the timing of these points and show how this information can be used to assess the impact of phenology on harvest traits (yield, thousand kernel weight, and oil content). The results demonstrate that PhenoCams can track growth dynamics and fill the gap of high temporal monitoring in field phenotyping experiments.ISSN:1664-462

Rapid phenotyping of crop root systems in undisturbed field soils using X-ray computed tomography

Background X-ray computed tomography (CT) has become a powerful tool for root phenotyping. Compared to rather classical, destructive methods, CT encompasses various advantages. In pot experiments the growth and development of the same individual root can be followed over time and in addition the unaltered configuration of the 3D root system architecture (RSA) interacting with a real field soil matrix can be studied. Yet, the throughput, which is essential for a more widespread application of CT for basic research or breeding programs, suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. Using available methods, root segmentation is done to a large extent manually, as it requires a lot of interactive parameter optimization and interpretation and therefore needs a lot of time. Results Based on commercially available software, this paper presents a protocol that is faster, more standardized and more versatile compared to existing segmentation methods, particularly if used to analyse field samples collected in situ. To the knowledge of the authors this is the first study approaching to develop a comprehensive segmentation method suitable for comparatively large columns sampled in situ which contain complex, not necessarily connected root systems from multiple plants grown in undisturbed field soil. Root systems from several crops were sampled in situ and CT-volumes determined with the presented method were compared to root dry matter of washed root samples. A highly significant (P < 0.01) and strong correlation (R2 = 0.84) was found, demonstrating the value of the presented method in the context of field research. Subsequent to segmentation, a method for the measurement of root thickness distribution has been used. Root thickness is a central RSA trait for various physiological research questions such as root growth in compacted soil or under oxygen deficient soil conditions, but hardly assessable in high throughput until today, due to a lack of available protocols. Conclusions Application of the presented protocol helps to overcome the segmentation bottleneck and can be considered a step forward to high throughput root phenotyping facilitating appropriate sample sizes desired by science and breeding.ISSN:1746-481