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Applications of Spectroscopy in Agriculture and Vegetation Research

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A special issue of Remote Sensing (ISSN 2072-4292). This special issue belongs to the section "Remote Sensing in Agriculture and Vegetation".

Deadline for manuscript submissions: closed (31 May 2019) | Viewed by 84573

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Special Issue Editors

Dr. Jochem Verrelst

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Guest Editor

Laboratory for Earth Observation, Image Processing Laboratory - Scientific Park, University of Valencia, C/ Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
Interests: imaging spectroscopy; vegetation properties retrieval; FLEX; vegetation fluorescence; optical remote sensing; radiative transfer models; retrieval methods
Special Issues, Collections and Topics in MDPI journals

Dr. Tobias Hank

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Guest Editor

Senior Scientist, Department of Geography, Faculty of Geosciences, LUDWIG-MAXIMILIANS-UNIVERSITÄT München, 80333 Munich, Germany
Interests: precision agriculture; biophysical modelling; imaging spectroscopy; data assimilation

Dr. Martin Schlerf

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Guest Editor

Senior Research Associate, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
Interests: hyperspectral and thermal remote sensing; retrieval of biochemical and structural vegetation properties; water stress detection; crop nitrogen assessment
Special Issues, Collections and Topics in MDPI journals

Dr. Xia Yao

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Guest Editor

Senior Scientist, College of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: crop SIF; phenotyping on LiDAR and UAV platforms; quantification of crop properties; disease surveillance; hyperspectral remote sensing

Dr. Karolina Sakowska

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Guest Editor

Biometeorology Research Group, Institute of Ecology, University of Innsbruck, 6020 Innsbruck, Austria
Interests: remote sensing of vegetation properties; ecosystem–atmosphere exchange of carbon dioxide and carbonyl sulfide (COS); fluorescence and COS as tracers for canopy photosynthesis

Special Issue Information

Dear Colleagues,

Vegetated ecosystems are an important component of terrestrial (agro)ecosystems largely mediating gas and energy exchange at the atmosphere–biosphere–pedosphere interface. The precise spatial and temporal acquisition of information about vegetation status, health, and photosynthetic functioning is fundamental to model the dynamic response of vegetation to changing environmental conditions.

This information can probably be best obtained with imaging spectrometers, which provide a unique opportunity to collect spectrally and spatially continuous data on vegetation traits at ecologically relevant scales over wide areas. With the ongoing progress of implementing imaging spectrometers in UAVs, aircrafts, and spaceborne missions, imaging spectroscopy has become a mature technique for capturing and quantifying vegetation properties and dynamics.

Apart from the steady progress in imaging spectroscopy sensor technology, also the continuing increase of computational power and the increasing availability and democratization of spectroscopic data have nurtured the recent boost in imaging spectroscopy science, leading to a methodological expansion and a diversification in vegetation-related applications. With imaging spectroscopy science now reaching maturity, it becomes feasible to compile recent applications in a dedicated Special Issue.

This Special Issue aims to address fundamental and applied research relating the spectral properties of vegetation to agronomic and biophysical variables, genetic and phenotypic parameters, as well as diurnal and seasonal dynamics linked to light harvesting and photoprotection.

Among the ongoing initiatives in this field, the CA17134 (SENSECO) COST Action, which aims to bring together scientists working on spectroscopy in agriculture and vegetation research, is a recent and prominent one. SENSECO places emphasis on investigating the role of spatial and temporal scales, as well as on promoting the synergistic use of multiple sensors at multiple scales and streamlining data quality and traceability. These kinds of initiatives intend to unite scientists to unravel the links between plant physiology, agroecosystem functioning, and biogeochemical cycles and will strengthen the progress in terrestrial imaging spectroscopy missions dedicated to vegetation monitoring (e.g., FLEX, EnMAP).

To gather a consolidated overview about the different activities around spectroscopy applications in agriculture and vegetation research within the COST Action and in connection with dedicated campaigns and satellite mission preparation programs, we invite papers on the following non-exhaustive list of topics:

Progress made in spectroscopy studies: considering, e.g., reflectance and fluorescence data acquisition protocols and point clouds, state of the art and performance of instrumentation, retrieval methods, and modelling applications.
Quantification of agronomic biophysical and biochemical variables: proximal sensing, UAV platforms for precision farming applications such as phenotyping, assessment of crop damage, identification of diseases, pests, water and nutrient management, growth status (LAI, biomass), photosynthetic activity, grain quality, crop acreage, and productivity.
Multi-scale observations in the spatial and temporal domains to quantify and monitor leaf-to-ecosystem functioning and biogeochemical traits and cycles. Synergistic use of multiple sensors to bridge the scaling gap.
Methodological progress in retrieval methods in the domains of machine learning, physical model inversion, hybrid methods, and from experimental-towards-operational methods and coupling of models and imaging spectroscopy.
Quantification of dynamic vegetation functioning (stress, productivity) from hyperspectral reflectance, fluorescence, and point-data sources.

Dr. Jochem Verrelst
Dr. Tobias Hank
Dr. Martin Schlerf
Dr. Xia Yao
Dr. Karolina Sakowska
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Remote Sensing is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

spectroscopy
reflectance
fluorescence
vegetation
agriculture
scaling
sensor synergy
biophysical variables
quality
productivity

Published Papers (13 papers)

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Research

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39 pages, 9940 KiB

Open AccessArticle

Multitemporal Chlorophyll Mapping in Pome Fruit Orchards from Remotely Piloted Aircraft Systems

by Yasmin Vanbrabant, Laurent Tits, Stephanie Delalieux, Klaas Pauly, Wim Verjans and Ben Somers

Remote Sens. 2019, 11(12), 1468; https://doi.org/10.3390/rs11121468 - 20 Jun 2019

Cited by 22 | Viewed by 4570

Abstract

Early and precise spatio-temporal monitoring of tree vitality is key for steering management decisions in pome fruit orchards. Spaceborne remote sensing instruments face a tradeoff between spatial and spectral resolution, while manned aircraft sensor-platform systems are very expensive. In order to address the shortcomings of these platforms, this study investigates the potential of Remotely Piloted Aircraft Systems (RPAS) to facilitate rapid, low cost, and flexible chlorophyll monitoring. Due to the complexity of orchard scenery a robust chlorophyll retrieval model on RPAS level has not yet been developed. In this study, specific focus therefore lies on evaluating the sensitivity of retrieval models to confounding factors. For this study, multispectral and hyperspectral imagery was collected over pome fruit orchards. Sensitivities of both univariate and multivariate retrieval models were demonstrated under different species, phenology, shade, and illumination scenes. Results illustrate that multivariate models have a significantly higher accuracy than univariate models as the former provide accuracies for the canopy chlorophyll content retrieval of R² = 0.80 and Relative Root Mean Square Error (RRMSE) = 12% for the hyperspectral sensor. Random forest regression on multispectral imagery (R² > 0.9 for May, June, July, and August, and R² = 0.5 for October) and hyperspectral imagery (0.6 < R² < 0.9) led to satisfactory high and consistent accuracies for all months. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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26 pages, 11637 KiB

Open AccessArticle

Estimation of Soil Heavy Metal Content Using Hyperspectral Data

by Zhenhua Liu, Ying Lu, Yiping Peng, Li Zhao, Guangxing Wang and Yueming Hu

Remote Sens. 2019, 11(12), 1464; https://doi.org/10.3390/rs11121464 - 20 Jun 2019

Cited by 48 | Viewed by 5283

Abstract

Quickly and efficiently monitoring soil heavy metal content is crucial for protecting the natural environment and for human health. Estimating heavy metal content in soils using hyperspectral data is a cost-efficient method but challenging due to the effects of complex landscapes and soil properties. One of the challenges is how to make a lab-derived model based on soil samples applicable to mapping the contents of heavy metals in soil using air-borne or space-borne hyperspectral imagery at a regional scale. For this purpose, our study proposed a novel method using hyperspectral data from soil samples and the HuanJing-1A (HJ-1A) HyperSpectral Imager (HSI). In this method, estimation models were first developed using optimal relevant spectral variables from dry soil spectral reflectance (DSSR) data and field observations of soil heavy metal content. The relationship of the ratio of DSSR to moisture soil spectral reflectance (MSSR) with soil moisture content was then derived, which built up the linkage of DSSR with MSSR and provided the potential of applying the models developed in the laboratory to map soil heavy metal content at a regional scale using hyperspectral imagery. The optimal relevant spectral variables were obtained by combining the Boruta algorithm with a stepwise regression and variance inflation factor. This method was developed, validated, and applied to estimate the content of heavy metals in soil (As, Cd, and Hg) in Guangdong, China, and the Conghua district of Guangzhou city. The results showed that based on the validation datasets, the content of Cd could be reliably estimated and mapped by the proposed method, with relative root mean square error (RMSE) values of 17.41% for the point measurements of soil samples from Guangdong province and 17.10% for the Conghua district at the regional scale, while the content of heavy metals As and Hg in soil were relatively difficult to predict with the relative RMSE values of 32.27% and 28.72% at the soil sample level and 51.55% and 36.34% at the regional scale. Moreover, the relationship of the DSSR/MSSR ratio with soil moisture content varied greatly before the wavelength of 1029 nm and became stable after that, which linked DSSR with MSSR and provided the possibility of applying the DSSR-based models to map the soil heavy metal content at the regional scale using the HJ-1A images. In addition, it was found that overall there were only a few soil samples with the content of heavy metals exceeding the health standards in Guangdong province, while in Conghua the seriously polluted areas were mainly distributed in the cities and croplands. This study implies that the new approach provides the potential to map the content of heavy metals in soil, but the estimation model of Cd was more accurate than those of As and Hg. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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22 pages, 5018 KiB

Open AccessArticle

Spectral Response Analysis: An Indirect and Non-Destructive Methodology for the Chlorophyll Quantification of Biocrusts

by José Raúl Román, Emilio Rodríguez-Caballero, Borja Rodríguez-Lozano, Beatriz Roncero-Ramos, Sonia Chamizo, Pilar Águila-Carricondo and Yolanda Cantón

Remote Sens. 2019, 11(11), 1350; https://doi.org/10.3390/rs11111350 - 05 Jun 2019

Cited by 28 | Viewed by 5775

Abstract

Chlorophyll a concentration (Chla) is a well-proven proxy of biocrust development, photosynthetic organisms’ status, and recovery monitoring after environmental disturbances. However, laboratory methods for the analysis of chlorophyll require destructive sampling and are expensive and time consuming. Indirect estimation of chlorophyll a by means of soil surface reflectance analysis has been demonstrated to be an accurate, cheap, and quick alternative for chlorophyll retrieval information, especially in plants. However, its application to biocrusts has yet to be harnessed. In this study we evaluated the potential of soil surface reflectance measurements for non-destructive Chla quantification over a range of biocrust types and soils. Our results revealed that from the different spectral transformation methods and techniques, the first derivative of the reflectance and the continuum removal were the most accurate for Chla retrieval. Normalized difference values in the red-edge region and common broadband indexes (e.g., normalized difference vegetation index (NDVI)) were also sensitive to changes in Chla. However, such approaches should be carefully adapted to each specific biocrust type. On the other hand, the combination of spectral measurements with non-linear random forest (RF) models provided very good fits (R² > 0.94) with a mean root mean square error (RMSE) of about 6.5 µg/g soil, and alleviated the need for a specific calibration for each crust type, opening a wide range of opportunities to advance our knowledge of biocrust responses to ongoing global change and degradation processes from anthropogenic disturbance. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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29 pages, 10058 KiB

Open AccessArticle

Fitted PROSAIL Parameterization of Leaf Inclinations, Water Content and Brown Pigment Content for Winter Wheat and Maize Canopies

by Martin Danner, Katja Berger, Matthias Wocher, Wolfram Mauser and Tobias Hank

Remote Sens. 2019, 11(10), 1150; https://doi.org/10.3390/rs11101150 - 14 May 2019

Cited by 45 | Viewed by 6944

Abstract

Decades after release of the first PROSPECT + SAIL (commonly called PROSAIL) versions, the model is still the most famous representative in the field of canopy reflectance modelling and has been widely used to obtain plant biochemical and structural variables, particularly in the agricultural context. The performance of the retrieval is usually assessed by quantifying the distance between the estimated and the in situ measured variables. While this has worked for hundreds of studies that obtained canopy density as a one-sided Leaf Area Index (LAI) or pigment content, little is known about the role of the canopy geometrical properties specified as the Average Leaf Inclination Angle (ALIA). In this study, we exploit an extensive field dataset, including narrow-band field spectra, leaf variables and canopy properties recorded in seven individual campaigns for winter wheat (4x) and silage maize (3x). PROSAIL outputs generally did not represent field spectra well, when in situ variables served as input for the model. A manual fitting of ALIA and leaf water (EWT) revealed significant deviations for both variables (RMSE = 14.5°, 0.020 cm) and an additional fitting of the brown leaf pigments (C_brown) was necessary to obtain matching spectra at the near infrared (NIR) shoulder. Wheat spectra tend to be underestimated by the model until the emergence of inflorescence when PROSAIL begins to overestimate crop reflectance. This seasonal pattern could be attributed to an attenuated development of ALIA_opt compared to in situ measured ALIA. Segmentation of nadir images of wheat was further used to separate spectral contributors into dark background, ears and leaves + stalks. It could be shown that the share of visible fruit ears from nadir view correlates positively with the deviations between field spectral measurement and PROSAIL spectral outputs (R² = 0.78 for aggregation by phenological stages), indicating that retrieval errors increase for ripening stages. An appropriate model parameterization is recommended to assure accurate retrievals of biophysical and biochemical products of interest. The interpretation of inverted ALIA as physical leaf inclinations is considered unfeasible and we argue in favour of treating it as a free calibration parameter. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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23 pages, 5091 KiB

Open AccessArticle

SPA-Based Methods for the Quantitative Estimation of the Soil Salt Content in Saline-Alkali Land from Field Spectroscopy Data: A Case Study from the Yellow River Irrigation Regions

by Sijia Wang, Yunhao Chen, Mingguo Wang, Yifei Zhao and Jing Li

Remote Sens. 2019, 11(8), 967; https://doi.org/10.3390/rs11080967 - 23 Apr 2019

Cited by 27 | Viewed by 3908

Abstract

The problem of soil salinization has always been a global problem involving resource, environmental, and ecological issues, and is closely related to the sustainable development of the social economy. Remote sensing provides an effective technical means for soil salinity identification and quantification research. This study focused on the estimation of the soil salt content in saline-alkali soils and applied the Successive Projections Algorithm (SPA) method to the estimation model; twelve spectral forms were applied in the estimation model of the spectra and soil salt content. Regression modeling was performed using the Partial Least Squares Regression (PLSR) method. Proximal-field spectral measurements data and soil samples were collected in the Yellow River Irrigation regions of Shizuishan City. A total of 60 samples were collected. The results showed that application of the SPA method improved the modeled determination coefficient (R²) and the ratio of performance to deviation (RPD), and reduced the modeled root mean square error (RMSE) and the percentage root mean square error (RMSE%); the maximum value of R² increased by 0.22, the maximum value of RPD increased by 0.97, the maximum value of the RMSE decreased by 0.098 and the maximum value of the RMSE% decreased by 8.52%. The SPA–PLSR model, based on the first derivative of reflectivity (FD), the FD–SPA–PLSR model, showed the best results, with an R² value of 0.89, an RPD value of 2.72, an RMSE value of 0.177, and RMSE% value of 11.81%. The results of this study demonstrated the applicability of the SPA method in the estimation of soil salinity, by using field spectroscopy data. The study provided a reference for a subsequent study of the hyperspectral estimation of soil salinity, and the proximal sensing data from a low distance, in this study, could provide detailed data for use in future remote sensing studies. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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26 pages, 3136 KiB

Open AccessArticle

A Random Forest Machine Learning Approach for the Retrieval of Leaf Chlorophyll Content in Wheat

by Syed Haleem Shah, Yoseline Angel, Rasmus Houborg, Shawkat Ali and Matthew F. McCabe

Remote Sens. 2019, 11(8), 920; https://doi.org/10.3390/rs11080920 - 16 Apr 2019

Cited by 211 | Viewed by 13105

Abstract

Developing rapid and non-destructive methods for chlorophyll estimation over large spatial areas is a topic of much interest, as it would provide an indirect measure of plant photosynthetic response, be useful in monitoring soil nitrogen content, and offer the capacity to assess vegetation structural and functional dynamics. Traditional methods of direct tissue analysis or the use of handheld meters, are not able to capture chlorophyll variability at anything beyond point scales, so are not particularly useful for informing decisions on plant health and status at the field scale. Examining the spectral response of plants via remote sensing has shown much promise as a means to capture variations in vegetation properties, while offering a non-destructive and scalable approach to monitoring. However, determining the optimum combination of spectra or spectral indices to inform plant response remains an active area of investigation. Here, we explore the use of a machine learning approach to enhance the estimation of leaf chlorophyll (Chl_t), defined as the sum of chlorophyll a and b, from spectral reflectance data. Using an ASD FieldSpec 4 Hi-Res spectroradiometer, 2700 individual leaf hyperspectral reflectance measurements were acquired from wheat plants grown across a gradient of soil salinity and nutrient levels in a greenhouse experiment. The extractable Chl_t was determined from laboratory analysis of 270 collocated samples, each composed of three leaf discs. A random forest regression algorithm was trained against these data, with input predictors based upon (1) reflectance values from 2102 bands across the 400–2500 nm spectral range; and (2) 45 established vegetation indices. As a benchmark, a standard univariate regression analysis was performed to model the relationship between measured Chl_t and the selected vegetation indices. Results show that the root mean square error (RMSE) was significantly reduced when using the machine learning approach compared to standard linear regression. When exploiting the entire spectral range of individual bands as input variables, the random forest estimated Chl_t with an RMSE of 5.49 µg·cm⁻² and an R² of 0.89. Model accuracy was improved when using vegetation indices as input variables, producing an RMSE ranging from 3.62 to 3.91 µg·cm⁻², depending on the particular combination of indices selected. In further analysis, input predictors were ranked according to their importance level, and a step-wise reduction in the number of input features (from 45 down to 7) was performed. Implementing this resulted in no significant effect on the RMSE, and showed that much the same prediction accuracy could be obtained by a smaller subset of indices. Importantly, the random forest regression approach identified many important variables that were not good predictors according to their linear regression statistics. Overall, the research illustrates the promise in using established vegetation indices as input variables in a machine learning approach for the enhanced estimation of Chl_t from hyperspectral data. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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21 pages, 18307 KiB

Open AccessArticle

Using Hyperspectral Crop Residue Angle Index to Estimate Maize and Winter-Wheat Residue Cover: A Laboratory Study

by Jibo Yue, Qingjiu Tian, Xinyu Dong, Kaijian Xu and Chengquan Zhou

Remote Sens. 2019, 11(7), 807; https://doi.org/10.3390/rs11070807 - 03 Apr 2019

Cited by 21 | Viewed by 4432

Abstract

Crop residue left in the field after harvest helps to protect against water and wind erosion, increase soil organic matter, and improve soil quality, so a proper estimate of the quantity of crop residue is crucial to optimize tillage and for research into environmental effects. Although remote-sensing-based techniques to estimate crop residue cover (CRC) have proven to be good tools for determining CRC, their application is limited by variations in the moisture of crop residue and soil. In this study, we propose a crop residue angle index (CRAI) to estimate the CRC for four distinct soils with varying soil moisture (SM) content and crop residue moisture (CRM). The current study uses laboratory-based tests ((i) a dry dataset (air-dried soils and crop residues, n = 392); (ii) a wet dataset (wet soils and crop residues, n = 822); (iii) a saturated dataset (saturated soils and crop residues, n = 402); and (iv) all datasets (n = 1616)), which allows us to analysis the soil and crop residue hyperspectral response to varying SM/CRM. The CRAI combines two features that reflect the moisture content in soil and crop residue. The first is the different reflectance of soil and crop residue as a function of moisture in the near-infrared band (833 nm) and short-wave near-infrared band (1670 nm), and the second is different reflectance of soils and crop residues to lignin, cellulose, and moisture in the bands at 2101, 2031, and 2201 nm. The effects of moisture and soil type on the proposed CRAI and selected traditional spectral indices ((i) hyperspectral cellulose absorption index; (ii) hyperspectral shortwave infrared normalized difference residue index; and (iii) selected broad-band spectral indices) were compared by using a laboratory-based dataset. The results show that the SM/CRM significantly affects the broad-band spectral indices and all other spectral indices investigated are less correlated with CRC when using all datasets than when using only the dry, wet, or saturated dataset. Laboratory study suggests that the CRAI is promising for estimating CRC with the four soils and with varying SM/CRM. However, because the CRAI was only validated by a laboratory-based dataset, additional field testing is thus required to verify the use of satellite hyperspectral remote-sensing images for different crops and ecological areas. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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18 pages, 3090 KiB

Open AccessArticle

Laboratory Visible and Near-Infrared Spectroscopy with Genetic Algorithm-Based Partial Least Squares Regression for Assessing the Soil Phosphorus Content of Upland and Lowland Rice Fields in Madagascar

by Kensuke Kawamura, Yasuhiro Tsujimoto, Tomohiro Nishigaki, Andry Andriamananjara, Michel Rabenarivo, Hidetoshi Asai, Tovohery Rakotoson and Tantely Razafimbelo

Remote Sens. 2019, 11(5), 506; https://doi.org/10.3390/rs11050506 - 02 Mar 2019

Cited by 36 | Viewed by 6205

Abstract

As a laboratory proximal sensing technique, the capability of visible and near-infrared (Vis-NIR) diffused reflectance spectroscopy with partial least squares (PLS) regression to determine soil properties has previously been demonstrated. However, the evaluation of the soil phosphorus (P) content—a major nutrient constraint for crop production in the tropics—is still a challenging task. PLS regression with waveband selection can improve the predictive ability of a calibration model, and a genetic algorithm (GA) has been widely applied as a suitable method for selecting wavebands in laboratory calibrations. To develop a laboratory-based proximal sensing method, this study investigated the potential to use GA-PLS regression analyses to estimate oxalate-extractable P in upland and lowland soils from laboratory Vis-NIR reflectance data. In terms of predictive ability, GA-PLS regression was compared with iterative stepwise elimination PLS (ISE-PLS) regression and standard full-spectrum PLS (FS-PLS) regression using soil samples collected in 2015 and 2016 from the surface of upland and lowland rice fields in Madagascar (n = 103). Overall, the GA-PLS model using first derivative reflectance (FDR) had the best predictive accuracy (R² = 0.796) with a good prediction ability (residual predictive deviation (RPD) = 2.211). Selected wavebands in the GA-PLS model did not perfectly match wavelengths of previously known absorption features of soil nutrients, but in most cases, the selected wavebands were within 20 nm of previously known wavelength regions. Bootstrap procedures (N = 10,000 times) using selected wavebands also confirmed the improvements in accuracy and robustness of the GA-PLS model compared to those of the ISE-PLS and FS-PLS models. These results suggest that soil oxalate-extractable P can be predicted from Vis-NIR spectroscopy and that GA-PLS regression has the advantage of tuning optimum bands for PLS regression, contributing to a better predictive ability. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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15 pages, 1837 KiB

Open AccessArticle

Spectral Heterogeneity Predicts Local-Scale Gamma and Beta Diversity of Mesic Grasslands

by H. Wayne Polley, Chenghai Yang, Brian J. Wilsey and Philip A. Fay

Remote Sens. 2019, 11(4), 458; https://doi.org/10.3390/rs11040458 - 23 Feb 2019

Cited by 13 | Viewed by 4556

Abstract

Plant species diversity is an important metric of ecosystem functioning, but field assessments of diversity are constrained in number and spatial extent by labor and other expenses. We tested the utility of using spatial heterogeneity in the remotely-sensed reflectance spectrum of grassland canopies to model both spatial turnover in species composition and abundances (β diversity) and species diversity at aggregate spatial scales (γ diversity). Shannon indices of γ and β diversity were calculated from field measurements of the number and relative abundances of plant species at each of two spatial grains (0.45 m² and 35.2 m²) in mesic grasslands in central Texas, USA. Spectral signatures of reflected radiation at each grain were measured from ground-level or an unmanned aerial vehicle (UAV). Partial least squares regression (PLSR) models explained 59–85% of variance in γ diversity and 68–79% of variance in β diversity using spatial heterogeneity in canopy optical properties. Variation in both γ and β diversity were associated most strongly with heterogeneity in reflectance in blue (350–370 nm), red (660–770 nm), and near infrared (810–1050 nm) wavebands. Modeled diversity was more sensitive by a factor of three to a given level of spectral heterogeneity when derived from data collected at the small than larger spatial grain. As estimated from calibrated PLSR models, β diversity was greater, but γ diversity was smaller for restored grassland on a lowland clay than upland silty clay soil. Both γ and β diversity of grassland can be modeled by using spatial heterogeneity in vegetation optical properties provided that the grain of reflectance measurements is conserved. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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17 pages, 2221 KiB

Open AccessArticle

Soil Moisture Retrieval Model for Remote Sensing Using Reflected Hyperspectral Information

by Jing Yuan, Xin Wang, Chang-xiang Yan, Shu-rong Wang, Xue-ping Ju and Yi Li

Remote Sens. 2019, 11(3), 366; https://doi.org/10.3390/rs11030366 - 12 Feb 2019

Cited by 39 | Viewed by 4951

Abstract

The variation and the spatial–temporal distribution of soil water content have significant effects on heat balance, agricultural moisture, etc. A soil moisture (SM) retrieval model can provide a theoretical basis for realizing a rapid test and revealing the spatial–temporal variation of the surface water. However, remote sensors do not measure soil water content directly. Therefore, it is of great importance to establish a SM retrieval model. In this paper, the relationship between SM and diffuse reflectance was first derived using the absorption coefficient and scattering coefficient related to SM. Then, based on Kubelka–Munk (KM) theory, the SM retrieval model using reflectance information was further derived, which is a semi-empirical model with an unknown parameter obtained either from fitting or from experimental measurements. The validity and reliability of the model were confirmed with the validation set. The results showed that the root mean square errors of prediction (RMSEPs) of four soils were generally less than 0.017, while the coefficients of determination (R²s) of four soils were generally more than 0.85, and the ratios of the performance to deviation (RPDs) of four soils were greater than 2.5 (470–2400 nm). Therefore, the model has high prediction accuracy, and can be well applied to the prediction of water content in different sorts of soils. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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15 pages, 1798 KiB

Open AccessArticle

Evaluation of Informative Bands Used in Different PLS Regressions for Estimating Leaf Biochemical Contents from Hyperspectral Reflectance

by Jia Jin and Quan Wang

Remote Sens. 2019, 11(2), 197; https://doi.org/10.3390/rs11020197 - 20 Jan 2019

Cited by 26 | Viewed by 4687

Abstract

Partial least squares (PLS) regression models are widely applied in spectroscopy to estimate biochemical components through hyperspectral reflected information. To build PLS regression models based on informative spectral bands, rather than strongly collinear bands contained in the full spectrum, is essential for upholding the performance of models. Yet no consensus has ever been reached on how to select informative bands, even though many techniques have been proposed for estimating plant properties using the vast array of hyperspectral reflectance. In this study, we designed a series of virtual experiments by introducing a dummy variable (C_d) with convertible specific absorption coefficients (SAC) into the well-accepted leaf reflectance PROSPECT-4 model for evaluating popularly adopted informative bands selection techniques, including stepwise-PLS, genetic algorithms PLS (GA-PLS) and PLS with uninformative variable elimination (UVE-PLS). Such virtual experiments have clearly defined responsible wavelength regions related to the dummy input variable, providing objective criteria for model evaluation. Results indicated that although all three techniques examined may estimate leaf biochemical contents efficiently, in most cases the selected bands, unfortunately, did not exactly match known absorption features, casting doubts on their general applicability. The GA-PLS approach was comparatively more efficient at accurately locating the informative bands (with physical and biochemical mechanisms) for estimating leaf biochemical properties and is, therefore, recommended for further applications. Through this study, we have provided objective evaluations of the potential of PLS regressions, which should help to understand the pros and cons of PLS regression models for estimating vegetation biochemical parameters. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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Review

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24 pages, 661 KiB

Open AccessReview

Challenges and Future Perspectives of Multi-/Hyperspectral Thermal Infrared Remote Sensing for Crop Water-Stress Detection: A Review

by Max Gerhards, Martin Schlerf, Kaniska Mallick and Thomas Udelhoven

Remote Sens. 2019, 11(10), 1240; https://doi.org/10.3390/rs11101240 - 24 May 2019

Cited by 155 | Viewed by 13997

Abstract

Thermal infrared (TIR) multi-/hyperspectral and sun-induced fluorescence (SIF) approaches together with classic solar-reflective (visible, near-, and shortwave infrared reflectance (VNIR)/SWIR) hyperspectral remote sensing form the latest state-of-the-art techniques for the detection of crop water stress. Each of these three domains requires dedicated sensor technology currently in place for ground and airborne applications and either have satellite concepts under development (e.g., HySPIRI/SBG (Surface Biology and Geology), Sentinel-8, HiTeSEM in the TIR) or are subject to satellite missions recently launched or scheduled within the next years (i.e., EnMAP and PRISMA (PRecursore IperSpettrale della Missione Applicativa, launched on March 2019) in the VNIR/SWIR, Fluorescence Explorer (FLEX) in the SIF). Identification of plant water stress or drought is of utmost importance to guarantee global water and food supply. Therefore, knowledge of crop water status over large farmland areas bears large potential for optimizing agricultural water use. As plant responses to water stress are numerous and complex, their physiological consequences affect the electromagnetic signal in different spectral domains. This review paper summarizes the importance of water stress-related applications and the plant responses to water stress, followed by a concise review of water-stress detection through remote sensing, focusing on TIR without neglecting the comparison to other spectral domains (i.e., VNIR/SWIR and SIF) and multi-sensor approaches. Current and planned sensors at ground, airborne, and satellite level for the TIR as well as a selection of commonly used indices and approaches for water-stress detection using the main multi-/hyperspectral remote sensing imaging techniques are reviewed. Several important challenges are discussed that occur when using spectral emissivity, temperature-based indices, and physically-based approaches for water-stress detection in the TIR spectral domain. Furthermore, challenges with data processing and the perspectives for future satellite missions in the TIR are critically examined. In conclusion, information from multi-/hyperspectral TIR together with those from VNIR/SWIR and SIF sensors within a multi-sensor approach can provide profound insights to actual plant (water) status and the rationale of physiological and biochemical changes. Synergistic sensor use will open new avenues for scientists to study plant functioning and the response to environmental stress in a wide range of ecosystems. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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Open AccessLetter

Model-Based Optimization of Spectral Sampling for the Retrieval of Crop Variables with the PROSAIL Model

by Katja Berger, Clement Atzberger, Martin Danner, Matthias Wocher, Wolfram Mauser and Tobias Hank

Remote Sens. 2018, 10(12), 2063; https://doi.org/10.3390/rs10122063 - 19 Dec 2018

Cited by 32 | Viewed by 4756

Abstract

Satellite hyperspectral Earth observation missions have strong potential to support sustainable agriculture by providing accurate spatial and temporal information of important vegetation biophysical and biochemical variables. To meet this goal, possible error sources in the modelling approaches should be minimized. Thus, first of all, the capability of a model to reproduce the measured spectral signals has to be tested before applying any retrieval algorithm. For an exemplary demonstration, the coupled PROSPECT-D and SAIL radiative transfer models (PROSAIL) were employed to emulate the setup of future hyperspectral sensors in the visible and near-infrared (VNIR) spectral regions with a 6.5 nm spectral sampling distance. Model uncertainties were determined to subsequently exclude those wavelengths with the highest mean absolute error (MAE) between model simulation and spectral measurement. The largest mismatch could be found in the green visible and red edge regions, which can be explained by complex interactions of several biochemical and structural variables in these spectral domains. For leaf area index (LAI, m²·m⁻²) retrieval, results indicated only a small improvement when using optimized spectral samplings. However, a significant increase in accuracy for leaf chlorophyll content (LCC, µg·cm⁻²) estimations could be obtained, with the relative root mean square error (RMSE) decreasing from 26% (full VNIR range) to 15% (optimized VNIR) for maize and from 77% to 29% for soybean, respectively. We therefore recommend applying a specific model-error threshold (MAE of ~0.01) to stabilize the retrieval of crop biochemical variables. Full article

(This article belongs to the Special Issue Applications of Spectroscopy in Agriculture and Vegetation Research)

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