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Remote and Proximal Assessment of Plant Traits

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A special issue of Remote Sensing (ISSN 2072-4292).

Deadline for manuscript submissions: closed (31 March 2021) | Viewed by 66007

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Special Issue Editors

Dr. Ittai Herrmann

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Guest Editor

The Plant Sensing Laboratory, The Robert H. Smith Institute for Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
Interests: remote and proximal sensing of vegetation; hyperspectral; plant traits assessment and early stress detection; precision agriculture; phenotyping
Special Issues, Collections and Topics in MDPI journals

Dr. Katja Berger

E-Mail Website
Guest Editor

1. Laboratory for Earth Observation, Image Processing Laboratory - Scientific Park, University of Valencia, C/ Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
2. Mantle Labs GmbH, Vienna, Austria
Interests: agriculture; hybrid retrieval; hyperspectral remote sensing; machine learning methods; active learning
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants are optically sensed by a variety of sensors and at different scales to answer diverse research questions and to meet practical challenges. Research in quantitative remote sensing starts at the organ scale moving to the entire plant, population, field, or biotope, up to data obtained from entire continents to explore global phenomena. The use of digital information has been abundantly exploited for more efficient cultivation of large areas and has become part of agricultural practices worldwide for irrigation and fertilization based on management zones. In addition, breeders are using high-throughput phenotyping in selection experiments for biotic and abiotic stresses as well as yield quantity and quality. Ecologists are using remotely sensed information to assess carbon footprint. Analyzing high-quality remote sensing observations is also challenging in view of upcoming hyperspectral spaceborne missions and their associated large data streams. Therefore, the development and adaptation of fast, effective, accurate, and generic retrieval algorithms for biophysical and biochemical traits is required. Methods should be provided on appropriate platforms and evaluated by plant physiologists, agronomists, and ecologists.

This Special Issue strongly encourages contributions aimed at estimating the morpho-physiological and biochemical plant traits (e.g., plant height, LAI, biomass, nutrient contents, water status, pigment concentration, photosynthetic activity, disease resistance, yield prediction, pollutants detection) from Earth Observation data in agricultural and ecological contexts to support food security and sustainability. This Special Issue aims to cover a vast range of spatial resolutions (from continent to sub-leaf or root) and spectral resolutions (RGB, multi- and hyperspectral imagery, as well as point data). Besides diverse empirical and physically based retrieval approaches, “hybrid approaches” combining the generic properties of radiative transfer models with the flexibility and efficiency of nonlinear nonparametric methods (machine learning) are welcome. Moreover, time-series analysis related to plant traits assessment can be exploited. This Special Issue is expected to demonstrate recent progress and to discuss future perspectives in plant traits sensing.

Dr. Ittai Herrmann
Dr. Katja Berger
Guest Editors

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Keywords

vegetation
biophysical and biochemical traits
high-throughput phenotyping
agriculture
radiative transfer models
machine learning
hyperspectral imagery

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Published Papers (15 papers)

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Editorial

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5 pages, 175 KiB

Open AccessEditorial

Remote and Proximal Assessment of Plant Traits

by Ittai Herrmann and Katja Berger

Remote Sens. 2021, 13(10), 1893; https://doi.org/10.3390/rs13101893 - 12 May 2021

Cited by 16 | Viewed by 2313

Abstract

The inference of functional vegetation traits from remotely sensed signals is key to providing efficient information for multiple plant-based applications and to solve related problems [...] Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

Research

Jump to: Editorial, Other

17 pages, 2598 KiB

Open AccessArticle

Understanding Growth Dynamics and Yield Prediction of Sorghum Using High Temporal Resolution UAV Imagery Time Series and Machine Learning

by Sebastian Varela, Taylor Pederson, Carl J. Bernacchi and Andrew D. B. Leakey

Remote Sens. 2021, 13(9), 1763; https://doi.org/10.3390/rs13091763 - 1 May 2021

Cited by 35 | Viewed by 6191

Abstract

Unmanned aerial vehicles (UAV) carrying multispectral cameras are increasingly being used for high-throughput phenotyping (HTP) of above-ground traits of crops to study genetic diversity, resource use efficiency and responses to abiotic or biotic stresses. There is significant unexplored potential for repeated data collection through a field season to reveal information on the rates of growth and provide predictions of the final yield. Generating such information early in the season would create opportunities for more efficient in-depth phenotyping and germplasm selection. This study tested the use of high-resolution time-series imagery (5 or 10 sampling dates) to understand the relationships between growth dynamics, temporal resolution and end-of-season above-ground biomass (AGB) in 869 diverse accessions of highly productive (mean AGB = 23.4 Mg/Ha), photoperiod sensitive sorghum. Canopy surface height (CSM), ground cover (GC), and five common spectral indices were considered as features of the crop phenotype. Spline curve fitting was used to integrate data from single flights into continuous time courses. Random Forest was used to predict end-of-season AGB from aerial imagery, and to identify the most informative variables driving predictions. Improved prediction of end-of-season AGB (RMSE reduction of 0.24 Mg/Ha) was achieved earlier in the growing season (10 to 20 days) by leveraging early- and mid-season measurement of the rate of change of geometric and spectral features. Early in the season, dynamic traits describing the rates of change of CSM and GC predicted end-of-season AGB best. Late in the season, CSM on a given date was the most influential predictor of end-of-season AGB. The power to predict end-of-season AGB was greatest at 50 days after planting, accounting for 63% of variance across this very diverse germplasm collection with modest error (RMSE 1.8 Mg/ha). End-of-season AGB could be predicted equally well when spline fitting was performed on data collected from five flights versus 10 flights over the growing season. This demonstrates a more valuable and efficient approach to using UAVs for HTP, while also proposing strategies to add further value. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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26 pages, 39413 KiB

Open AccessFeature PaperArticle

Top-of-Atmosphere Retrieval of Multiple Crop Traits Using Variational Heteroscedastic Gaussian Processes within a Hybrid Workflow

by José Estévez, Katja Berger, Jorge Vicent, Juan Pablo Rivera-Caicedo, Matthias Wocher and Jochem Verrelst

Remote Sens. 2021, 13(8), 1589; https://doi.org/10.3390/rs13081589 - 20 Apr 2021

Cited by 39 | Viewed by 4371

Abstract

In support of cropland monitoring, operational Copernicus Sentinel-2 (S2) data became available globally and can be explored for the retrieval of important crop traits. Based on a hybrid workflow, retrieval models for six essential biochemical and biophysical crop traits were developed for both S2 bottom-of-atmosphere (BOA) L2A and S2 top-of-atmosphere (TOA) L1C data. A variational heteroscedastic Gaussian process regression (VHGPR) algorithm was trained with simulations generated by the combined leaf-canopy reflectance model PROSAILat the BOA scale and further combined with the Second Simulation of a Satellite Signal in the Solar Spectrum (6SV) atmosphere model at the TOA scale. Established VHGPR models were then applied to S2 L1C and L2A reflectance data for mapping: leaf chlorophyll content (

C_{a b}

), leaf water content (

C_{w}

), fractional vegetation coverage (FVC), leaf area index (LAI), and upscaled leaf biochemical compounds, i.e., LAI ∗

C_{a b}

(laiCab) and LAI ∗

C_{w}

(laiCw). Estimated variables were validated using in situ reference data collected during the Munich-North-Isar field campaigns within growing seasons of maize and winter wheat in the years 2017 and 2018. For leaf biochemicals, retrieval from BOA reflectance slightly outperformed results from TOA reflectance, e.g., obtaining a root mean squared error (RMSE) of 6.5 μ

μ

g/cm

^{2}

(BOA) vs. 8 μ

μ

g/cm

^{2}

(TOA) in the case of

C_{a b}

. For the majority of canopy-level variables, instead, estimation accuracy was higher when using TOA reflectance data, e.g., with an RMSE of 139 g/m

^{2}

(BOA) vs. 113 g/m

^{2}

(TOA) for laiCw. Derived maps were further compared against reference products obtained from the ESA Sentinel Application Platform (SNAP) Biophysical Processor. Altogether, the consistency between L1C and L2A retrievals confirmed that crop traits can potentially be estimated directly from TOA reflectance data. Successful mapping of canopy-level crop traits including information about prediction confidence suggests that the models can be transferred over spatial and temporal scales and, therefore, can contribute to decision-making processes for cropland management. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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19 pages, 2096 KiB

Open AccessArticle

Using Unmanned Aerial Vehicle and Ground-Based RGB Indices to Assess Agronomic Performance of Wheat Landraces and Cultivars in a Mediterranean-Type Environment

by Rubén Rufo, Jose Miguel Soriano, Dolors Villegas, Conxita Royo and Joaquim Bellvert

Remote Sens. 2021, 13(6), 1187; https://doi.org/10.3390/rs13061187 - 20 Mar 2021

Cited by 8 | Viewed by 3324

Abstract

The adaptability and stability of new bread wheat cultivars that can be successfully grown in rainfed conditions are of paramount importance. Plant improvement can be boosted using effective high-throughput phenotyping tools in dry areas of the Mediterranean basin, where drought and heat stress are expected to increase yield instability. Remote sensing has been of growing interest in breeding programs since it is a cost-effective technology useful for assessing the canopy structure as well as the physiological traits of large genotype collections. The purpose of this study was to evaluate the use of a 4-band multispectral camera on-board an unmanned aerial vehicle (UAV) and ground-based RGB imagery to predict agronomic traits as well as quantify the best estimation of leaf area index (LAI) in rainfed conditions. A collection of 365 bread wheat genotypes, including 181 Mediterranean landraces and 184 modern cultivars, was evaluated during two consecutive growing seasons. Several vegetation indices (VI) derived from multispectral UAV and ground-based RGB images were calculated at different image acquisition dates of the crop cycle. The modified triangular vegetation index (MTVI2) proved to have a good accuracy to estimate LAI (R² = 0.61). Although the stepwise multiple regression analysis showed that grain yield and number of grains per square meter (NGm²) were the agronomic traits most suitable to be predicted, the R² were low due to field trials were conducted under rainfed conditions. Moreover, the prediction of agronomic traits was slightly better with ground-based RGB VI rather than with UAV multispectral VIs. NDVI and GNDVI, from multispectral images, were present in most of the prediction equations. Repeated measurements confirmed that the ability of VIs to predict yield depends on the range of phenotypic data. The current study highlights the potential use of VI and RGB images as an efficient tool for high-throughput phenotyping under rainfed Mediterranean conditions. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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20 pages, 887 KiB

Open AccessArticle

Exploring the Impact of Noise on Hybrid Inversion of PROSAIL RTM on Sentinel-2 Data

by Nuno César de Sá, Mitra Baratchi, Leon T. Hauser and Peter van Bodegom

Remote Sens. 2021, 13(4), 648; https://doi.org/10.3390/rs13040648 - 11 Feb 2021

Cited by 27 | Viewed by 4544

Abstract

Remote sensing (RS) of biophysical variables plays a vital role in providing the information necessary for understanding spatio-temporal dynamics in ecosystems. The hybrid approach to retrieve biophysical variables from RS by combining Machine Learning (ML) algorithms with surrogate data generated by Radiative Transfer Models (RTM). The susceptibility of the ill-posed solutions to noise currently constrains further application of hybrid approaches. Here, we explored how noise affects the performance of ML algorithms for biophysical trait retrieval. We focused on synthetic Sentinel-2 (S2) data generated using the PROSAIL RTM and four commonly applied ML algorithms: Gaussian Processes (GPR), Random Forests (RFR), and Artificial Neural Networks (ANN) and Multi-task Neural Networks (MTN). After identifying which biophysical variables can be retrieved from S2 using a Global Sensitivity Analysis, we evaluated the performance loss of each algorithm using the Mean Absolute Percentage Error (MAPE) with increasing noise levels. We found that, for S2 data, Carotenoid concentrations are uniquely dependent on band 2, Chlorophyll is almost exclusively dependent on the visible ranges, and Leaf Area Index, water, and dry matter contents are mostly dependent on infrared bands. Without added noise, GPR was the best algorithm (<0.05%), followed by the MTN (<3%) and ANN (<5%), with the RFR performing very poorly (<50%). The addition of noise critically affected the performance of all algorithms (>20%) even at low levels of added noise (≈5%). Overall, both neural networks performed significantly better than GPR and RFR when noise was added with the MTN being slightly better when compared to the ANN. Our results imply that the performance of the commonly used algorithms in hybrid-RTM inversion are pervasively sensitive to noise. The implication is that more advanced models or approaches are necessary to minimize the impact of noise to improve near real-time and accurate RS monitoring of biophysical trait retrieval. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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24 pages, 6773 KiB

Open AccessArticle

Monitoring the Foliar Nutrients Status of Mango Using Spectroscopy-Based Spectral Indices and PLSR-Combined Machine Learning Models

by Gopal Ramdas Mahajan, Bappa Das, Dayesh Murgaokar, Ittai Herrmann, Katja Berger, Rabi N. Sahoo, Kiran Patel, Ashwini Desai, Shaiesh Morajkar and Rahul M. Kulkarni

Remote Sens. 2021, 13(4), 641; https://doi.org/10.3390/rs13040641 - 10 Feb 2021

Cited by 41 | Viewed by 5674

Abstract

Conventional methods of plant nutrient estimation for nutrient management need a huge number of leaf or tissue samples and extensive chemical analysis, which is time-consuming and expensive. Remote sensing is a viable tool to estimate the plant’s nutritional status to determine the appropriate amounts of fertilizer inputs. The aim of the study was to use remote sensing to characterize the foliar nutrient status of mango through the development of spectral indices, multivariate analysis, chemometrics, and machine learning modeling of the spectral data. A spectral database within the 350–1050 nm wavelength range of the leaf samples and leaf nutrients were analyzed for the development of spectral indices and multivariate model development. The normalized difference and ratio spectral indices and multivariate models–partial least square regression (PLSR), principal component regression, and support vector regression (SVR) were ineffective in predicting any of the leaf nutrients. An approach of using PLSR-combined machine learning models was found to be the best to predict most of the nutrients. Based on the independent validation performance and summed ranks, the best performing models were cubist (R² ≥ 0.91, the ratio of performance to deviation (RPD) ≥ 3.3, and the ratio of performance to interquartile distance (RPIQ) ≥ 3.71) for nitrogen, phosphorus, potassium, and zinc, SVR (R² ≥ 0.88, RPD ≥ 2.73, RPIQ ≥ 3.31) for calcium, iron, copper, boron, and elastic net (R² ≥ 0.95, RPD ≥ 4.47, RPIQ ≥ 6.11) for magnesium and sulfur. The results of the study revealed the potential of using hyperspectral remote sensing data for non-destructive estimation of mango leaf macro- and micro-nutrients. The developed approach is suggested to be employed within operational retrieval workflows for precision management of mango orchard nutrients. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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14 pages, 2850 KiB

Open AccessFeature PaperArticle

Hyperspectral Reflectance and Indices for Characterizing the Dynamics of Crop–Weed Competition for Water

by Inbal Ronay, Jhonathan E. Ephrath, Hanan Eizenberg, Dan G. Blumberg and Shimrit Maman

Remote Sens. 2021, 13(3), 513; https://doi.org/10.3390/rs13030513 - 1 Feb 2021

Cited by 20 | Viewed by 4024

Abstract

Understanding the spectral characteristics of crops in response to stress caused by weeds is a basic step in improving the precision of agricultural technologies that manage weeds in the field. This research focused on the competition between corn (Zea mays) and redroot pigweed (Amaranthus retroflexus), a common weed that strongly reduces corn yield. The aim of this research was to characterize the physiological changes that occur in corn during early growth because of crop–weed competition and to examine the ability to detect the effect of competition through hyperspectral measurements. A greenhouse experiment was conducted, and corn plants were examined during early growth, with and without weed competition. Hyperspectral measurements were combined with physiological measurements to examine the reflectance and photosynthetic activity of corn. Changes were expected to appear mainly in the short-wave infrared region (SWIR) due to competition for water. Relative water content (RWC), chlorophyll content, photosynthetic rate, and stomatal conductance were reduced in the presence of weeds, and intercellular CO₂ levels increased. Deeper SWIR light absorption occurred in the weed treatment as expected, accompanied by spectral changes in the visible (VIS) and near infrared (NIR) ranges. The results highlight the potential of using spectral measurements as an indicator of competition for water. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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23 pages, 15053 KiB

Open AccessArticle

A Survey of Active Learning for Quantifying Vegetation Traits from Terrestrial Earth Observation Data

by Katja Berger, Juan Pablo Rivera Caicedo, Luca Martino, Matthias Wocher, Tobias Hank and Jochem Verrelst

Remote Sens. 2021, 13(2), 287; https://doi.org/10.3390/rs13020287 - 15 Jan 2021

Cited by 67 | Viewed by 6820

Abstract

The current exponential increase of spatiotemporally explicit data streams from satellite-based Earth observation missions offers promising opportunities for global vegetation monitoring. Intelligent sampling through active learning (AL) heuristics provides a pathway for fast inference of essential vegetation variables by means of hybrid retrieval approaches, i.e., machine learning regression algorithms trained by radiative transfer model (RTM) simulations. In this study we summarize AL theory and perform a brief systematic literature survey about AL heuristics used in the context of Earth observation regression problems over terrestrial targets. Across all relevant studies it appeared that: (i) retrieval accuracy of AL-optimized training data sets outperformed models trained over large randomly sampled data sets, and (ii) Euclidean distance-based (EBD) diversity method tends to be the most efficient AL technique in terms of accuracy and computational demand. Additionally, a case study is presented based on experimental data employing both uncertainty and diversity AL criteria. Hereby, a a simulated training data base by the PROSAIL-PRO canopy RTM is used to demonstrate the benefit of AL techniques for the estimation of total leaf carotenoid content (

C_{x c}

) and leaf water content (

C_{w}

). Gaussian process regression (GPR) was incorporated to minimize and optimize the training data set with AL. Training the GPR algorithm on optimally AL-based sampled data sets led to improved variable retrievals compared to training on full data pools, which is further demonstrated on a mapping example. From these findings we can recommend the use of AL-based sub-sampling procedures to select the most informative samples out of large training data pools. This will not only optimize regression accuracy due to exclusion of redundant information, but also speed up processing time and reduce final model size of kernel-based machine learning regression algorithms, such as GPR. With this study we want to encourage further testing and implementation of AL sampling methods for hybrid retrieval workflows. AL can contribute to the solution of regression problems within the framework of operational vegetation monitoring using satellite imaging spectroscopy data, and may strongly facilitate data processing for cloud-computing platforms. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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23 pages, 7275 KiB

Open AccessArticle

Semi-Automatic Method for Early Detection of Xylella fastidiosa in Olive Trees Using UAV Multispectral Imagery and Geostatistical-Discriminant Analysis

by Annamaria Castrignanò, Antonella Belmonte, Ilaria Antelmi, Ruggiero Quarto, Francesco Quarto, Sameh Shaddad, Valentina Sion, Maria Rita Muolo, Nicola A. Ranieri, Giovanni Gadaleta, Edoardo Bartoccetti, Carmela Riefolo, Sergio Ruggieri and Franco Nigro

Remote Sens. 2021, 13(1), 14; https://doi.org/10.3390/rs13010014 - 22 Dec 2020

Cited by 26 | Viewed by 4178

Abstract

Xylella fastidiosa subsp. pauca (Xfp) is one of the most dangerous plant pathogens in the world. Identified in 2013 in olive trees in south–eastern Italy, it is spreading to the Mediterranean countries. The bacterium is transmitted by insects that feed on sap, and causes rapid wilting in olive trees. The paper explores the use of Unmanned Aerial Vehicle (UAV) in combination with a multispectral radiometer for early detection of infection. The study was carried out in three olive groves in the Apulia region (Italy) and involved four drone flights from 2017 to 2019. To classify Xfp severity level in olive trees at an early stage, a combined method of geostatistics and discriminant analysis was implemented. The results of cross-validation for the non-parametric classification method were of overall accuracy = 0.69, mean error rate = 0.31, and for the early detection class of accuracy 0.77 and misclassification probability 0.23. The results are promising and encourage the application of UAV technology for the early detection of Xfp infection. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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17 pages, 16857 KiB

Open AccessFeature PaperArticle

Image-Based High-Throughput Phenotyping of Cereals Early Vigor and Weed-Competitiveness Traits

by Shlomi Aharon, Zvi Peleg, Eli Argaman, Roi Ben-David and Ran N. Lati

Remote Sens. 2020, 12(23), 3877; https://doi.org/10.3390/rs12233877 - 26 Nov 2020

Cited by 21 | Viewed by 3924

Abstract

Cereals grains are the prime component of the human diet worldwide. To promote food security and sustainability, new approaches to non-chemical weed control are needed. Early vigor cultivars with enhanced weed-competitiveness ability are a potential tool, nonetheless, the introduction of such trait in breeding may be a long and labor-intensive process. Here, two image-driven plant phenotyping methods were evaluated to facilitate effective and accurate selection for early vigor in cereals. For that purpose, two triticale genotypes differentiating in vigor and growth rate early in the season were selected as model plants: X-1010 (high) and Triticale1 (low). Two modeling approaches, 2-D and 3-D, were applied on the plants offering an evaluation of various morphological growth parameters for the triticale canopy development, under controlled and field conditions. The morphological advantage of X-1010 was observed only at the initial growth stages, which was reflected by significantly higher growth parameter values compared to the Triticale1 genotype. Both modeling approaches were sensitive enough to detect phenotypic differences in growth as early as 21 days after sowing. All growth parameters indicated a faster early growth of X-1010. However, the 2-D related parameter [projected shoot area (PSA)] is the most available one that can be extracted via end user-friendly imaging equipment. PSA provided adequate indication for the triticale early growth under weed-competition conditions and for the improved weed-competition ability. The adequate phenotyping ability for early growth and competition was robust under controlled and field conditions. PSA can be extracted from close and remote sensing platforms, thus, facilitate high throughput screening. Overall, the results of this study may improve cereal breeding for early vigor and weed-competitiveness. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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18 pages, 4348 KiB

Open AccessArticle

Qualifications of Rice Growth Indicators Optimized at Different Growth Stages Using Unmanned Aerial Vehicle Digital Imagery

by Zhengchao Qiu, Haitao Xiang, Fei Ma and Changwen Du

Remote Sens. 2020, 12(19), 3228; https://doi.org/10.3390/rs12193228 - 3 Oct 2020

Cited by 19 | Viewed by 3876

Abstract

The accurate estimation of the key growth indicators of rice is conducive to rice production, and the rapid monitoring of these indicators can be achieved through remote sensing using the commercial RGB cameras of unmanned aerial vehicles (UAVs). However, the method of using UAV RGB images lacks an optimized model to achieve accurate qualifications of rice growth indicators. In this study, we established a correlation between the multi-stage vegetation indices (VIs) extracted from UAV imagery and the leaf dry biomass, leaf area index, and leaf total nitrogen for each growth stage of rice. Then, we used the optimal VI (OVI) method and object-oriented segmentation (OS) method to remove the noncanopy area of the image to improve the estimation accuracy. We selected the OVI and the models with the best correlation for each growth stage to establish a simple estimation model database. The results showed that the OVI and OS methods to remove the noncanopy area can improve the correlation between the key growth indicators and VI of rice. At the tillering stage and early jointing stage, the correlations between leaf dry biomass (LDB) and the Green Leaf Index (GLI) and Red Green Ratio Index (RGRI) were 0.829 and 0.881, respectively; at the early jointing stage and late jointing stage, the coefficient of determination (R²) between the Leaf Area Index (LAI) and Modified Green Red Vegetation Index (MGRVI) was 0.803 and 0.875, respectively; at the early stage and the filling stage, the correlations between the leaf total nitrogen (LTN) and UAV vegetation index and the Excess Red Vegetation Index (ExR) were 0.861 and 0.931, respectively. By using the simple estimation model database established using the UAV-based VI and the measured indicators at different growth stages, the rice growth indicators can be estimated for each stage. The proposed estimation model database for monitoring rice at the different growth stages is helpful for improving the estimation accuracy of the key rice growth indicators and accurately managing rice production. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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41 pages, 12721 KiB

Open AccessArticle

Comparison of Empirical and Physical Modelling for Estimation of Biochemical and Biophysical Vegetation Properties: Field Scale Analysis across an Arctic Bioclimatic Gradient

by Blair E. Kennedy, Douglas J. King and Jason Duffe

Remote Sens. 2020, 12(18), 3073; https://doi.org/10.3390/rs12183073 - 19 Sep 2020

Cited by 6 | Viewed by 4153

Abstract

To evaluate the potential of multi-angle hyperspectral sensors for monitoring vegetation variables in Arctic environments, empirical and physical modelling using field data was implemented for the retrieval of leaf and canopy chlorophyll content (LCC, CCC) and plant area index (PAI) measured at four sites situated across a bioclimatic gradient in the Western Canadian Arctic. Field reflectance data were acquired with an ASD FieldSpec (305–1075 nm) and used to simulate CHRIS Mode1 spectra (411–997 nm). Multi-angle measurements were taken corresponding to CHRIS view zenith angles (VZA) (−55°, −36°, 0°, +36°, +55°). Empirical modelling compared parametric regression based on vegetation indices (VIs) to non-parametric Gaussian Processes Regression (GPR). In physical modelling, PROSAIL was inverted using numerical optimization and look-up table (LUT) approaches. Cross-validation of the empirical models ranked GPR as best, followed by simple ratio (SR) with optimally selected NIR and red wavelengths, and then ROSAVI using its published wavelengths (mean r²_cv = 0.62, 0.58, and 0.54, respectively across all sites, variables, and VZAs). However, the best predictive performance was achieved by SR followed by GPR and ROSAVI (NRMSE_cv = 0.12, 0.16, 0.16, respectively). PROSAIL simulated the multi-angle top-of-canopy reflectance well with numerical optimization (r² = ~0.99, RMSE = 0.004 ± 0.002), but best performing LUT models of LCC, CCC and PAI were poorer than the empirical approaches (mean r² = 0.48, mean NRMSE = 0.22). PROSAIL performed best at the high Arctic sparsely vegetated site (r² = 0.57–0.86 for all parameters). Overall, the best performing VZA was −55° for empirical modelling and 0° and ±55° for physical modelling; however, these were not significantly better than the other VZAs. Overall, this study demonstrates that, for Arctic vegetation, nadir narrowband reflectance data used to derive simple empirical VIs with optimally selected bands is a more efficient approach for modelling chlorophyll and PAI than more complex empirical and physical approaches. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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20 pages, 21777 KiB

Open AccessArticle

Joint Use of PROSAIL and DART for Fast LUT Building: Application to Gap Fraction and Leaf Biochemistry Estimations over Sparse Oak Stands

by Thomas Miraglio, Karine Adeline, Margarita Huesca, Susan Ustin and Xavier Briottet

Remote Sens. 2020, 12(18), 2925; https://doi.org/10.3390/rs12182925 - 9 Sep 2020

Cited by 12 | Viewed by 3387

Abstract

Gap Fraction, leaf pigment contents (content of chlorophylls a and b (

C_{a b}

Gap Fraction, leaf pigment contents (content of chlorophylls a and b (

C_{a b}

) and carotenoids content (Car)), Leaf Mass per Area (LMA), and Equivalent Water Thickness (EWT) are considered relevant indicators of forests’ health status, influencing many biological and physical processes. Various methods exist to estimate these variables, often relying on the extensive use of Radiation Transfer Models (RTMs). While 3D RTMs are more realistic to model open canopies, their complexity leads to important computation times that limit the number of simulations that can be considered; 1D RTMs, although less realistic, are also less computationally expensive. We investigated the possibility to approximate the outputs of a 3D RTM (DART) from a 1D RTM (PROSAIL) to generate in very short time numerous extensive Look-Up Tables (LUTs). The intrinsic error of the approximation model was evaluated through comparison with DART reference values. The model was then used to generate LUTs used to estimate Gap Fraction,

C_{a b}

, Car, EWT, and LMA of Blue Oak-dominant stands in a woodland savanna from AVIRIS-C data. Performances of the approximation model for estimation purposes compared to DART were evaluated using Wilmott’s index of agreement (

d_{r}

), and estimation accuracy was measured with coefficients of determination (

R^{2}

) and Root Mean Squared Error (RMSE). The low approximation error of the proposed model demonstrated that the model could be considered for canopy covers as low as 30%. Gap Fraction estimations presented similar performances with either DART or the approximation (

d_{r}

0.78 and 0.77, respectively), while

C_{a b}

and Car showed improved performances (

d_{r}

increasing from 0.65 to 0.77 and 0.34 to 0.65, respectively). No satisfying estimation methods were found for LMA and EWT using either models, probably due to the high sensitivity of the scene’s reflectance to Gap Fraction and soil modeling at such low LAI. Overall, estimations using the approximated reflectances presented either similar or improved accuracy. Our findings show that it is possible to approximate DART reflectances from PROSAIL using a minimal number of DART outputs for calibration purposes, drastically reducing computation times to generate reflectance databases: 300,000 entries could be generated in 1.5 h, compared to the 12,666 total CPU hours necessary to generate the 21,840 calibration entries with DART. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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15 pages, 2385 KiB

Open AccessArticle

Satellite-Based Observations Reveal Effects of Weather Variation on Rice Phenology

by Hongfei Wang, Aniruddha Ghosh, Bruce A. Linquist and Robert J. Hijmans

Remote Sens. 2020, 12(9), 1522; https://doi.org/10.3390/rs12091522 - 10 May 2020

Cited by 19 | Viewed by 4200

Abstract

Obtaining detailed data on the spatio-temporal variation in crop phenology is critical to increasing our understanding of agro-ecosystem function, such as their response to weather variation and climate change. It is challenging to collect such data over large areas through field observations. The use of satellite remote sensing data has made phenology data collection easier, although the quality and the utility of such data to understand agro-ecosystem function have not been widely studied. Here, we evaluated satellite data-based estimates of rice phenological stages in California, USA by comparing them with survey data and with predictions by a temperature-driven phenology model. We then used the satellite data-based estimates to quantify the crop phenological response to changes in weather. We used time-series of MODIS satellite data and PhenoRice, a rule-based rice phenology detection algorithm, to determine annual planting, heading and harvest dates of paddy rice in California between 2002 and 2017. At the state level, our satellite-based estimates of rice phenology were very similar to the official survey data, particularly for planting and harvest dates (RMSE = 3.8–4.0 days). Satellite based observations were also similar to predictions by the DD10 temperature-driven phenology model. We analyzed how the timing of these phenological stages varied with concurrent temperature and precipitation over this 16-year time period. We found that planting was earlier in warm springs (−1.4 days °C⁻¹ for mean temperature between mid-April and mid-May) and later in wet years (5.3 days 100 mm^-1 for total precipitation from March to April). Higher mean temperature during the pre-heading period of the growing season advanced heading by 2.9 days °C⁻¹ and shortened duration from planting to heading by 1.9 days °C⁻¹. The entire growing season was reduced by 3.2 days °C⁻¹ because of the increased temperature during the rice season. Our findings confirm that satellite data can be an effective way to estimate variations in rice phenology and can provide critical information that can be used to improve understanding of agricultural responses to weather variation. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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21 pages, 10064 KiB

Open AccessTechnical Note

Development of a Mobile Platform for Field-Based High-Throughput Wheat Phenotyping

by Majid Khak Pour, Reza Fotouhi, Pierre Hucl and Qianwei Zhang

Remote Sens. 2021, 13(8), 1560; https://doi.org/10.3390/rs13081560 - 17 Apr 2021

Cited by 3 | Viewed by 2298

Abstract

Designing and implementing an affordable High-Throughput Phenotyping Platform (HTPP) for monitoring crops’ features in different stages of their growth can provide valuable information for crop-breeders to study possible correlation between genotypes and phenotypes. Conducting automatic field measurements can improve crop productions. In this research, we have focused on development of a mechatronic system, hardware and software, for a mobile, field-based HTPP for autonomous crop monitoring for wheat field. The system can measure canopy’s height, temperature, and vegetation indices and is able to take high quality photos of crops. The system includes. developed software for data and image acquisition. The main contribution of this study is autonomous, reliable, and fast data collection for wheat and similar crops. Full article

(This article belongs to the Special Issue Remote and Proximal Assessment of Plant Traits)

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