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Keywords: Soil organic matter (SOM) plays an important role in the soil-plant system, increasing the search for faster and
Hyperspectral non-destructive methods for detecting this attribute. For this purpose, the use of hyperspectral imaging sensors is
PLSR promising. This study aimed to evaluate the possibility of predicting organic matter through hyperspectral im
Soil organic matter
ages in the laboratory associated with multivariate regression modeling procedures. There were 384 soil samples
Linear discriminant
collected at eight depths in an Oxisol, in the State of Paraná, Brazil. Principal component and linear discriminant
analysis were applied to the spectrum to group the sets according to depth. The hyperspectral imaging technique
combined with the model’s regression coefficient was used to classify the images relative to the content of
organic matter. The partial least squares regression (PLSR) model was developed to correlate spectral data from
the sensor with SOM contents acquired by the conventional method. The results obtained in the prediction were
R2 = 0.75, r = 0.87 and RPD = 2.1. These results suggest that the model generated by the image sensor was able
to discriminate the organic matter contents of the soil at different depths by capturing spectral variations.
* Corresponding author.
E-mail address: reisamanda89@gmail.com (A.S. Reis).
https://doi.org/10.1016/j.rsase.2021.100492
Received 16 November 2020; Received in revised form 3 March 2021; Accepted 3 March 2021
Available online 9 March 2021
2352-9385/© 2021 Elsevier B.V. All rights reserved.
A.S. Reis et al. Remote Sensing Applications: Society and Environment 22 (2021) 100492
compromised (Mo et al., 2013; Sahoo et al., 2015). 2. Material and methods
Although these data can be measured using a spectroradiometer, for
example, such ground-based measurements are limited to a few numbers 2.1. Soil and sampling
of field locations and cannot capture spatial variability over large areas.
In contrast, hyperspectral imaging sensors are more convenient for The study area is located at the Experimental Station of the COAMO,
acquiring the spatial variability of spectral information in a region (Lu in Campo Mourão, Paraná State (24◦ 05′ 41.6′′ S, 52◦ 21’ 31.5” W) in
et al., 2020). However, for that, more information is needed in the South Brazil (Fig. 1). The climate type is Cfa––humid subtropical mes
laboratory so that they can be applied to the field on the properties of the othermic (Köppen), with an average annual temperature of 20.1 ◦ C and
soil that are being studied. Publications related to hyperspectral images an annual rainfall of 1601 mm.
on short-range platforms are recent and have grown in the last four To extract soil organic matter (SOM), soil samples were collected at
years, as shown by the review by Lu et al. (2020). This indicates the eight different depths (0–0.05, 0.05–0.10, 0.10–0.15, 0.15–0.20,
interest in finding more objective and quick answers for conventional 0.20–0.25, 0.25–0.30, 0.30–0.35, and 0.35–0.40 m). Since 2001, no-
methodologies. tillage systems with different combinations of soy, maize, wheat, and
Associated with the hyperspectral analysis of SOM, a modeling cover crops in winter and summer have been present. The soil order of
method is increasingly used that has presented high precision values in the area is an Oxisol according to Soil Taxonomy. Soil collection
several studies (Shen et al., 2020). Several multivariate statistical occurred in March 2019.
methods can be used to classify dependent and independent variables,
making it possible to discriminate species as well as predict pigment
concentration and nutritional status in addition to estimating produc 2.2. Chemical and spectral analysis
tivity (Blackburn, 2007; Calviñ o-Cancela and Mart í n-Herrero, 2016;
Gitelson and Solovchenko, 2018; Nanni et al., 2018; Rodrigues et al., The steps for obtaining and processing data at the laboratory level
2020). In this study, principal component analysis (PCA), linear are demonstrated in the flowchart in Fig. 2. A total of 384 soil samples
discriminant analysis (LDA), and partial least squares regression (PLSR) were collected, dried, and ground to pass through a 2-mm sieve. Each
were used. The aim was to evaluate whether the model generated sample was divided into two parts: one was for spectral measurement
through data obtained by the hyperspectral imaging sensor could and the other was for chemical analysis. To obtain the SOM content (%),
discriminate soil organic matter content. This study demonstrates the the carbon organic of soil was first determined using the colorimetric
ability of this technique to predict and discriminate the content of method (Raij et al., 2001) by reading on a spectrophotometer with a
organic matter through hyperspectral images, which may be an alter maximum transmission filter of 650 nm. Afterward, the conversion
native in the future to replace conventional techniques. factor 1.724 was applied to the results, obtaining the values for SOM.
For spectral measurement, each sample was placed in a Petri dish 9
cm in diameter and 1.5 cm high. The AisaFENIX sensor was attached to a
platform (Single Core Scanner) at a height of 0.50 m and the images of
soil samples were acquired by scanning. To scan all samples, eight im
ages were needed (Fig. 3).
For each pixel, 624 bands were obtained. In the 380–970 nm region,
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A.S. Reis et al. Remote Sensing Applications: Society and Environment 22 (2021) 100492
Fig. 2. Flowchart for obtaining and processing data at the laboratory level. PCA: Principal component analysis, LDA: Linear discriminant analysis, PLSR: Partial least
squares regression.
Fig. 3. Structure assembled with the AisaFENIX sensor and the scanning belt (A) and Sequence of samples (B).
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A.S. Reis et al. Remote Sensing Applications: Society and Environment 22 (2021) 100492
the spectral resolution was 3.5 nm, and in the 970–2506 nm region, the To develop the statistical model, 384 samples were divided randomly
spectral resolution was 12 nm. Calibration with the standard whiteboard into two sets: calibration (70%) and validation (30%). One set composed
was performed before each image capture. For radiometric corrections, of 269 samples was used to calibrate the models and cross-validation
the CaliGeoPRO 2.3.1software (Specim Inc, 2017) was used. To generate testing. 115 samples were used to validate the built models (Nanni
radiometrically corrected images, the software was fed with the raw et al., 2018). The PLSR method (p ≤ 0.05) was implemented, and all
data (.raw) generated by the AisaFENIX sensor, the sensor calibration processing was conducted in Unscrambler software version 10.4
files (.cal and the .LUT), and the dark reference file (.hdr). For image (CAMO, Inc., Oslo, Norway).
processing, a specific algorithm provided by the manufacturer AisaFE Because it is a nonparametric regression method based on factor
NIX was used and applied by the software ENVI Classic 5.3. To convert analysis, PLSR is commonly used for spectrum analysis that has suffi
the image from radiance units to reflectance units in the option “Scan cient independent variable validation (Li et al., 2016). The performance
Normalization” the radiance file (radiance.dat) was added together with of the model was assessed using the coefficient of determination (R2),
the dark reference file (.hdr) and the type of radiometric correction was the root mean square error (RMSE), the standard error (SE), the sys
selected. Because of this processing, reflectance images were generated. tematic error (bias), and the residual predictive deviation (RPD). For
After processing, the data was read in the ENVI Classic software to create greater precision of the model, the values of R2 and RPD must be high,
a region of interest (ROI) on each Petri dish, using the ROY_Type ellipse but the values of RMSE must be low. The RPD parameter provides a basis
function. Each ROI presented, on average, 1500 pixels, and the spectral for standardizing SEP, and the standard deviation (SD) of conventional
curve was obtained through the average of these pixels, minimizing methods of original data is used (Williams and Sobering, 2001; Fearn,
possible variations in the spectra. There were 48 ROI’s sampled over all 2002). The RPD parameter between 2 and 3 is considered “good”, 1.5 to
eight images. In the “statistics” option of the ENVI software, the average 2, average and < than 1.5, poor (D’Acqui et al., 2010).
of each pixel was calculated and the spectral reflectance curve was Subsequently, the values of the regression coefficients of the PLSR
generated. models were applied to the hypercube image, and the converted images
were reconstructed as two-dimensional PLS images. The content pixel of
2.3. Statistical analysis the PLSR model of organic matter was isolated using a classification
algorithm. The PLSR developed model has a regression coefficient,
2.3.1. Principal component analysis which is expressed as shown in Equation (1):
Principal Component Analysis (PCA) was used to reduce the redun
C = B0 + (B1X1 + B2X2 + … + BnXn) (Equation 1)
dant information of hyperspectral imaging. The PCA (p-value≤0.05)
was performed to verify the separability of the samples in depth and the Where C is the predicted organic matter concentration, B0 is a constant
possible overlap between them by means of two-dimensional graphics coefficient, B1 - Bn are coefficients for each wavelength reading, and Xn
with PCA components (first component vs. second component). This is the reflectance by the different spectra (Selige et al., 2006).
method is an indicator of whether the variance of the reflectance spectra
between samples within each set of spectral data can be explained and 3. Results and discussion
how effectively the depths can be grouped. PCA was performed with
spectral curves using the XLSTAT supplement for Excel software 3.1. Descriptive analysis of soil sample and spectral characteristics
(Addinsoft, 2016). The degree of explanation is attributed using the first
two components (PC1 and PC2) before obtaining discriminant linear The descriptive statistics of SOM derived from conventional methods
models. Defined as the correlation of each variable (wavelength) with are shown in Table 1. Content varied from 13.21 g kg− 1 to 52.32 g kg− 1.
the principal component, the loadings describe the importance of each The coefficient of variation was 0.27, indicating low to medium vari
wavelength to the PC’s (Holden and Ledrew, 1998). ability (Qi-Yong et al., 2014). Soil reflectance was influenced by the
organic matter content and the composition of organic constituents
2.3.2. Linear discriminant analysis across the spectrum. Accordingly, when soil organic matter increases,
The discriminant functions were obtained using the proc STEPDISC soil reflectance decreases (Feng et al., 1989).
algorithm, applying the STEPWISE method available in the Statistical Fig. 4 shows a difference in the albedo of the curves in the visible
Analysis System® software (SAS Institute, Inc. North Carolina, USA). region. Soil reflectance in this region is primarily associated with ab
Wavelengths were selected according to the Wilk’s Lambda value and sorption in minerals containing Fe (Mortimore et al., 2004; DRĂGUŢ
following likelihood criteria and partial F-value input (Draper and and Dornik, 2016). However, as found by Baumgardner et al. (1970),
Smith, 2014; Falcioni et al., 2017). Variables with p-value <0.05 organic matter contents greater than 2% tend to mask the effect of iron
(defined a priori) were added and not removed in/from the function. oxides. As the minimum organic matter content in this study was 1.3%,
The wavelengths that best explained the differences were subjected to a the difference in the visible region can be seen in Fig. 4. In the SWIR
discriminant analysis using the proc DISCRIM routine available in the band, inflections were observed in 1400, 1900, and 2200 nm due to the
SAS® software, to create predictive models through linear combinations vibration of water molecules present in clay minerals. The absorption
of predictor variables (wavelengths). The obtained models were then wavelengths near 1400 nm (1395 and 1415 nm) are due to overtones of
simulated through the proc FREQ using 60% of the spectral curves and the O–H stretch, while those near 2200 nm (2165 and 2207 nm) are due
tested with the 40% remaining curves. This procedure was indepen to Al–OH bend plus O–H stretch combinations (Stenberg et al., 2010).
dently tested 50 times in a randomized mode to predict the chance of Shonk et al. (1991) found results indicating that soils containing
success based on the selected spectral bands. Thus, only wavelengths more than 6% organic matter would be increasingly difficult to
able to discriminate all depths were selected (da Silva Junior et al.,
2017).
Table 1
2.3.3. Partial least squares regression and regression coefficient Minimum, maximum, average, standard deviation (SD), and coefficient of
For the model construction, the border bands at 379–449 nm were variation (CV) values to soil organic matter content in sample soil (g kg− 1), for
eliminated because presented great noise in the spectra, leaving the conventional method.
451–2506 nm. For the final prediction results and to obtain improved ORGANIC Minimum (g. Maximum (g. Average (g. SD CV
spectra, Savitzky-Golay (Savitzky and Golay, 1964) smoothing com MATTER kg− 1) kg− 1) kg− 1)
13.21 52.32 26.32 7.13 0.27
bined with the first derivative transformation was chosen. This pre
processing is essential to improve model accuracy (Qiao et al., 2017). SD: standard deviation; CV: coefficient of variation.
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organic matter.
Fig. 5. Principal component analysis (PCA) of spectral curves from different depths. The letters correspond to the depths at which the readings were taken, in meters.
(a) 0.05, (b) 0.10, (c) 0.15, (d) 0.20, (e) 0.25, (f) 0.30, (g) 0.35, (h) 0.40.
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A.S. Reis et al. Remote Sensing Applications: Society and Environment 22 (2021) 100492
Table 2
Output from the DISCRIM analysis using selected reflectance data wavelengths, indicating the error percentage and acceptance based on the model estimated using
60% of data selected randomly among depths.
Depths (m) 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 TOTAL
Green shading indicates the highest accepted value from discriminating between depths by model.
the organic matter content of the soil. The regression coefficients values
Table 3
of the PLSR models are shown in Fig. 6. Highly positive or highly
Statistical parameters of the PLSR model.
negative coefficients indicate wavebands that strongly influence the
PLSR R R2 RMSE SE Bias PLSR model, and some of the wavebands corresponding to these highly
Calibration 0.93 0.86 2.56 2.57 0 positive or negative coefficients match the signature absorption bands of
Cross-validation 0.92 0.85 2.68 2.69 0.003 organic matter. As can be seen, wavelengths in the green and NIR ranges
Prediction 0.87 0.75 3.44 3.40 0.583
were important in estimating the variable as indicated by the STEPDISC
r: correlation coefficient; R2: coefficient of determination; RMSE: Root Mean method.
Square Error, SE: Standard Error; n = 384; p-value ≤ 0.05. The values of the regression coefficients of the PLSR models were
applied to the hypercube images using equation (1) and the converted
(RMSEc = 2.56 and RMSEcv = 2.68). In the model validation estimated images were reconstructed as two-dimensional PLS images. Fig. 7 il
by the root mean square error of prediction (RMSEP), the data confirm lustrates the PLS image for the data set resulting from the applied model.
the quality by adjusting the RMSEC (Table 3), i.e., these data presented In this image, it is possible to observe the color change with increasing
satisfactory predictive abilities as obtained by hyperspectral sensors depth, showing that the model was able to identify different levels of
using curves of reflectance. The values of bias in calibration and cross- organic matter in the soil. All the plates that contained soil at a depth of
validation indicated no tendency in the model (Cezar et al., 2019; 5 cm were darker (above 4% of the organic matter), which is equivalent
Mark and Workman, 2017). Another parameter used for evaluating the to the organic matter content found in the laboratory. In addition, after
model is RPD. The value found in the study was 2.10, indicating that a 0.20 m, there is no clear difference between colors, following the results
good prediction model, from 2 to 3, according to D’Acqui et al., (2010). found by PCA and LDA, where the superficial depths were possible to
When using PLSR associated with the spectral response to predict soil separate into groups.
attributes in transition lithologies, Nanni et al. (2018) found for soil A methodology similar to that used in our research was found in Lim
organic matter values of low coefficients of determination and RPD in et al. (2016). However, the authors used hyperspectral images of the
the calibration step. On the other hand, Cezar et al. (2019), studying infrared region to detect melanin in powdered milk and observed that as
hyperspectral remote sensing as an alternative to correlate data from soil the melamine concentration increased, the number of suspicious mel
constituents, found a coefficient of 0.65 for organic matter. Jacq et al. amine pixels in binary images also increased, suggesting that this tech
(2019), found a model with a r prediction of 0.95 (p < 0.05) when using nique would be effective in the detection of melamine in powdered milk.
a hyperspectral image to predict the concentration of organic matter. In another study, Mo et al. (2013) developed a viability assessment
method for cucumber (Cucumis sativus) seed using hyperspectral
reflectance images. But these authors used the 400–1000 nm range
3.4. Applicability of the PLS model in the estimation of soil organic matter obtained using blue, green and red LED lighting. Using images based on
content the PLS model, the discrimination accuracy for viable and non-viable
seeds was 100% and 99%, respectively.
Since the general model found was relevant by the analyzed pa Nevertheless, application of this technique was not found in the
rameters (Table 2), we applied it to the hyperspectral image to estimate
Fig. 6. Regression coefficients of the PLSR model developed using AisaFENIX sensor reflectance spectra (B0 = 31.47027).
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A.S. Reis et al. Remote Sensing Applications: Society and Environment 22 (2021) 100492
Acknowledgements
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