A Mixed Data-Based Deep Neural Network to Estimate Leaf Area Index in Wheat Breeding Trials

Remote and non-destructive estimation of leaf area index (LAI) has been a challenge in the last few decades as the direct and indirect methods available are laborious and time-consuming. The recent emergence of high-throughput plant phenotyping platforms has increased the need to develop new phenotyping tools for better decision-making by breeders. In this paper, a novel model based on artificial intelligence algorithms and nadir-view red green blue (RGB) images taken from a terrestrial high throughput phenotyping platform is presented. The model mixes numerical data collected in a wheat breeding field and visual features extracted from the images to make rapid and accurate LAI estimations. Model-based LAI estimations were validated against LAI measurements determined non-destructively using an allometric relationship obtained in this study. The model performance was also compared with LAI estimates obtained by other classical indirect methods based on bottom-up hemispherical images and gaps fraction theory. Model-based LAI estimations were highly correlated with ground-truth LAI. The model performance was slightly better than that of the hemispherical image-based method, which tended to underestimate LAI. These results show the great potential of the developed model for near real-time LAI estimation, which can be further improved in the future by increasing the dataset used to train the model

Crop biophysical parameter retrieval from Sentinel-1 SAR data with a multi-target inversion of Water Cloud Model

Estimation of bio-and geophysical parameters from Earth observation (EO) data is essential for developing applications on crop growth monitoring. High spatio-temporal resolution and wide spatial coverage provided by EO satellite data are key inputs for operational crop monitoring. In Synthetic Aperture Radar (SAR) applications, a semi-empirical model (viz., Water Cloud Model (WCM)) is often used to estimate vegetation descriptors individually. However, a simultaneous estimation of these vegetation descriptors would be logical given their inherent correlation, which is seldom preserved in the estimation of individual descriptors by separate inversion models. This functional relationship between biophysical parameters is essential for crop yield models, given that their variations often follow different distribution throughout crop development stages. However, estimating individual parameters with independent inversion models presume a simple relationship (potentially linear) between the biophysical parameters. Alternatively, a multi-target inversion approach would be more effective for this aspect of model inversion compared to an individual estimation approach. In the present research, the multi-output support vector regression (MSVR) technique is used for inversion of the WCM from C-band dual-pol Sentinel-1 SAR data. Plant Area Index (PAI, m2 m−2) and wet biomass (W, kg m−2) are used as the vegetation descriptors in the WCM. The performance of the inversion approach is evaluated with in-situ measurements collected over the test site in Manitoba (Canada), which is a super-site in the Joint Experiment for Crop Assessment and Monitoring (JECAM) SAR inter-comparison experiment network. The validation results indicate a good correlation with acceptable error estimates (normalized root mean square error–nRMSE and mean absolute error–MAE) for both PAI and wet biomass for the MSVR approach and a better estimation with MSVR than single-target models (support vector regression–SVR). Furthermore, the correlation between PAI and wet biomass is assessed using the MSVR and SVR model. Contrary to the single output SVR, the correlation between biophysical parameters is adequately taken into account in MSVR based simultaneous inversion technique. Finally, the spatio-temporal maps for PAI and W at different growth stages indicate their variability with crop development over the test site.This research was supported in part by Shastri Indo-Candian Institute, New Delhi, India and the Spanish Ministry of Economy, Industry and Competitiveness, in part by the State Agency of Research (AEI), in part by the European Funds for Regional Development under project TEC2017-85244-C2-1-P

Retrieval of maize leaf area index using hyperspectral and multispectral data

Field spectra acquired from a handheld spectroradiometer and Sentinel-2 images spectra were used to investigate the applicability of hyperspectral and multispectral data in retrieving the maize leaf area index in low-input crop systems, with high spatial and intra-annual variability, and low yield, in southern Mozambique, during three years. Seventeen vegetation indices, comprising two and three band indices, and nine machine learning regression algorithms (MLRA) were tested for the statistical approach while five cost functions were tested in the look-up-table (LUT) inversion approach. The three band vegetation indices were selected, specifically the modified difference index (mDId: 725; 715; 565) for the hyperspectral dataset and the modified simple ratio (mSRc: 740; 705; 865) for the multispectral dataset of field spectra and the three band spectral index (TBSIb: 665; 865; 783) for the Sentinel-2 dataset. The relevant vector machine was the selected MLRA for the two datasets of field spectra (multispectral and hyperspectral) while the support vector machine was selected for the Sentinel-2 data. When using the LUT inversion technique, the minimum contrast estimation and the Bhattacharyya divergence cost functions were the best performing. The vegetation indices outperformed the other two approaches, with the TBSIb as the most accurate index (RMSE = 0.35). At the field scale, spectral data from Sentinel-2 can accurately retrieve the maize leaf area index in the study areainfo:eu-repo/semantics/publishedVersio

Farming and earth observation: sentinel-2 data to estimate within-field wheat grain yield

Wheat grain yield (GY) is a crop feature of central importance affecting agricultural, environmental, and socioeconomic sustainability worldwide. Hence, the estimation of within-field variability of GY is pivotal for the agricultural management, especially in the current global change context. In this sense, Earth Observation Systems (EOS) are key technologies that use satellite data to monitor crop yield, which can guide the application of precision farming. Yet, novel research is required to improve the multiplatform integration of data, including data processing, and the application of this discipline in agricultural management. This article provides a novel methodological analysis and assessment of its applications in precision farming. It presents an integration of wheat GY, Global Positioning Systems (GPS), combine harvester data, and EOS Sentinel-2 multispectral bands. Moreover, it compares several indices and machine learning (ML) approaches to map within-field wheat GY. It also analyses the importance of multi-date remote sensing imagery and explores its potential applications in precision agriculture. The study was conducted in Spain, a major European wheat producer. Within-field GY data was obtained from a GPS combine harvester machine for 8 fields over three seasons (2017-2019) and consecutively processed to match Sentinel-2 10 m pixel size. Seven vegetation indices (NDVI, GNDVI, EVI, RVI, TGI, CVI and NGRDI) as well as the biophysical parameter LAI (leaf area index) retrieved with radiative transfer models (RTM) were calculated from Sentinel-2 bands. Sentinel-2 10 m resolution bands alone were also used as variables. Random forest, support vector machine and boosted regressions were used as modelling approaches, and multilinear regression was calculated as baseline. Different combinations of dates of measurement were tested to find the most suitable model feeding data. LAI retrieved from RTM had a slightly improved performance in estimating within-field GY in comparison with vegetation indices or Sentinel-2 bands alone. At validation, the use of multi-date Sentinel-2 data was found to be the most suitable in comparison with single date images. Thus, the model developed with random forest regression (e.g. R-2 = 0.89, and RSME = 0.74 t/ha when using LAI) outperformed support vector machine (R-2 = 0.84 and RSME = 0.92 t/ha), boosting regression (R-2 = 0.85 and RSME = 0.88 t/ha) and multilinear regression (R-2 = 0.69 and RSME = 1.29 t/ha). However, single date images at specific phenological stages (e.g. R-2 = 0.84, and RSME = 0.88 t/ha using random forest at stem elongation) also posed relatively high R-2 and low RMSE, with potential for precision farming management before harvest.A & nbsp;We acknowledge the support of the project PID2019-106650RB-C21 from the Ministerio de Ciencia e Innovacion, Spain. J.S. is a recipient of a FPI doctoral fellowship from the same institution (grant: PRE2020-091907) . J.L.A. acknowledges support from the Institucio Catalana de Recerca i Estudis Avancats (ICREA) , Generalitat de Catalunya, Spain) . S. C.K. is supported by the Ramon y Cajal RYC-2019-027818-I research fellowship from the Ministerio de Ciencia e Innovacion, Spain. We acknowledge the support of Cerealto Siro Group, together with Cristina de Diego and Javier Velasco, technical staff from the company, by providing the wheat yield data. This research was also supported by the COST Action CA17134 SENSECO (Optical synergies for spatiotemporal sensing of scalable ecophysiological traits) funded by COST (European Cooperation in Science and Technology, www.cost.eu)

Long-term hindcasts of wheat yield in fields using remotely sensed phenology, climate data and machine learning

Satellite remote sensing offers a cost-effective means of generating long-term hindcasts of yield that can be used to understand how yield varies in time and space. This study investigated the use of remotely sensed phenology, climate data and machine learning for estimating yield at a resolution suitable for optimising crop management in fields. We used spatially weighted growth curve estimation to identify the timing of phenological events from sequences of Landsat NDVI and derive phenological and seasonal climate metrics. Using data from a 17,000 ha study area, we investigated the relationships between the metrics and yield over 17 years from 2003 to 2019. We compared six statistical and machine learning models for estimating yield: multiple linear regression, mixed effects models, generalised additive models, random forests, support vector regression using radial basis functions and deep learning neural networks. We used a 50-50 train-test split on paddock-years where 50% of paddock-year combinations were randomly selected and used to train each model and the remaining 50% of paddock-years were used to assess the model accuracy. Using only phenological metrics, accuracy was highest using a linear mixed model with a random effect that allowed the relationship between integrated NDVI and yield to vary by year (R2 = 0.67, MAE = 0.25 t ha−1, RMSE = 0.33 t ha−1, NRMSE = 0.25). We quantified the improvements in accuracy when seasonal climate metrics were also used as predictors. We identified two optimal models using the combined phenological and seasonal climate metrics: support vector regression and deep learning models (R2 = 0.68, MAE = 0.25 t ha−1, RMSE = 0.32 t ha−1, NRMSE = 0.25). While the linear mixed model using only phenological metrics performed similarly to the nonlinear models that are also seasonal climate metrics, the nonlinear models can be more easily generalised to estimate yield in years for which training data are unavailable. We conclude that long-term hindcasts of wheat yield in fields, at 30 m spatial resolution, can be produced using remotely sensed phenology from Landsat NDVI, climate data and machine learning

High-throughput phenotyping of plant leaf morphological, physiological, and biochemical traits on multiple scales using optical sensing

Acquisition of plant phenotypic information facilitates plant breeding, sheds light on gene action, and can be applied to optimize the quality of agricultural and forestry products. Because leaves often show the fastest responses to external environmental stimuli, leaf phenotypic traits are indicators of plant growth, health, and stress levels. Combination of new imaging sensors, image processing, and data analytics permits measurement over the full life span of plants at high temporal resolution and at several organizational levels from organs to individual plants to field populations of plants. We review the optical sensors and associated data analytics used for measuring morphological, physiological, and biochemical traits of plant leaves on multiple scales. We summarize the characteristics, advantages and limitations of optical sensing and data-processing methods applied in various plant phenotyping scenarios. Finally, we discuss the future prospects of plant leaf phenotyping research. This review aims to help researchers choose appropriate optical sensors and data processing methods to acquire plant leaf phenotypes rapidly, accurately, and cost-effectively