Using Machine-Learning Algorithms to Predict Soil Organic Carbon Content from Combined Remote Sensing Imagery and Laboratory Vis-NIR Spectral Datasets
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area and Soil Sampling
2.2. Laboratory Reflectance Measurements
2.3. Sentinel-1 and Sentinel-2 Data Pre-Processing
2.4. Sentinel-1 Soil Moisture and Indices Retrieval
2.5. Retrieval and Analysis of Spectral Indices
2.6. Prediction Models and Accuracy Assessment
2.6.1. Partial Least Squares Regression
2.6.2. Random Forest
2.6.3. Deep Neural Networks
2.6.4. Model Accuracy
3. Results
3.1. Data Description and Analysis
3.1.1. Descriptive Statistics of Measured SOC Content
3.1.2. Sentinel-2 and Laboratory Spectral and Sentinel-1 Soil Moisture Information Analysis
3.2. Model Performance and Comparison
3.2.1. Sentinel-2 Bands Prediction Performance
3.2.2. Prediction Performance of Sentinel-2 Bands Combined with Sentinel-2 and Sentinel-1 Indices and Sentinel-1 Soil Moisture
3.2.3. Prediction Performance of Sentinel-2 Bands Combined with Laboratory Spectral Indices
4. Discussion
4.1. Factors That Influenced Sentinel-2 Soil Surface Reflectance Spectra
4.2. Performance of Calibrated Models Using Only Sentinel-2 Bands: DNN vs. PLS and RF
4.3. Effects of Additional Information on Model Calibration and Validation
4.4. Utility of Including Sentinel-2 Spectral Indices
4.5. Utility of Including Sentinel-1-Derived Data
4.6. Effects of Including Laboratory Spectral Indices
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Abbreviation | Index | Equation | Reference |
---|---|---|---|
Vegetation indices | |||
AFRI16 | Aerosol free vegetation index 2.1 | [79] | |
AFRI21 | Aerosol free vegetation index 2.1 | [79] | |
ARI | Anthocyanin reflectance index | [123] | |
ARVI2 | Atmospherically Resistant vegetation index2 | [80] | |
BRI | Browning reflectance index | [124] | |
BWDRVI | Blue-wide dynamic range vegetation index | [125] | |
CCCI | Canopy chlorophyll content index | [126] | |
EVI | Enhanced vegetation index | [127] | |
EVI2 | Enhanced vegetation index2 | [128] | |
GARI | Green atmospherically resistant vegetation index | [129] | |
GLI | Green leaf index | [130] | |
GNDVI | Green normalized difference vegetation index | [129] | |
GVMI | Global vegetation moisture index | [81] | |
Maccioni | Maccioni vegetation index | [82] | |
NBR | Normalized burn ratio | [83] | |
NBR2 | Normalized burned Ratio 2 | [84,85] | |
NDVI | Normalized difference vegetation index | [70] | |
NSSI | NPV-soil separation index | [131] | |
OSAVI | Optimized soil-adjusted vegetation index | [132] | |
PANDVI | Pan normalized difference vegetation index | [133] | |
SIWSI | Shortwave infrared water stress index | [86] | |
TSAVI | Soil-adjusted vegetation index | [87] | |
Soil indices | |||
BI | Brightness index | [89,134] | |
BSI | Bare soil index | [90] | |
FI | Form index | [135] | |
Hue | Hue index | [135] | |
RedI | Redness index | [89] | |
SI | Saturation index | [135] | |
S2WI | Soil moisture index | [32] | |
STI | Soil tillage index | [136] | |
Geology indices | |||
Fe2 | Ferrous iron index | [137] | |
Fe3 | Ferric iron index | [137] | |
FO | Ferric oxides index | [137] | |
FS | Ferrous silicates index | [137] | |
Gossan | Gossan index | [137] | |
Water indices | |||
AWEI | Automated water extraction index not dominant shadow | [121] | |
AWEI2 | Automated water extraction index dominant shadow | [138] | |
MNDWI | Modified normalized difference water index | [139] | |
NDMI | Normalized difference moisture index | [91] | |
NDWI | Normalized difference water index | [140] |
Appendix B
Input | PLS | RF | DNN | |||
---|---|---|---|---|---|---|
It. | Factors | Scale | Max_Features | Max_Depth | Num_Layers | |
a | (1) | 6 | True | 0.60 | 70 | 12 |
(2) | 5 | False | auto | 10 | 8 | |
(3) | 6 | True | 0.60 | 70 | 7 | |
a + b | (1) | - | - | 0.75 | 20 | 10 |
(2) | - | - | 0.60 | 30 | 5 | |
(3) | - | - | 0.85 | 70 | 12 | |
a + c | (1) | - | - | 0.95 | 50 | 12 |
(2) | - | - | 0.85 | 10 | 11 | |
(3) | - | - | 0.85 | 10 | 12 | |
a + d | (1) | - | - | 0.6 | None | 5 |
(2) | - | - | 0.85 | 10 | 9 | |
(3) | - | - | 0.60 | None | 9 | |
a + e | (1) | - | - | 0.60 | 70 | 13 |
(2) | - | - | 0.60 | 30 | 13 | |
(3) | - | - | 0.60 | None | 13 |
Calibration | Validation | ||||||||
---|---|---|---|---|---|---|---|---|---|
Alg. | It. | R2 | RMSECV | RPD | RPIQ | r2 | RMSEP | RPD | RPIQ |
PLS | (1) | 0.15 | 3.27 | 1.08 | 0.79 | 0.13 | 3.58 | 1.07 | 0.93 |
(2) | 0.15 | 3.21 | 1.08 | 0.83 | 0.06 | 3.88 | 1.03 | 0.77 | |
(3) | 0.17 | 3.67 | 1.1 | 0.77 | −0.10 | 2.61 | 0.95 | 1.15 | |
RF | (1) | 0.73 | 1.82 | 1.94 | 1.41 | 0.09 | 3.65 | 1.05 | 0.91 |
(2) | 0.75 | 1.73 | 2.00 | 1.54 | 0.02 | 3.96 | 1.01 | 0.76 | |
(3) | 0.79 | 1.85 | 2.17 | 1.53 | −0.34 | 2.88 | 0.86 | 1.04 | |
DNN | (1) | 0.81 | 1.55 | 2.29 | 1.67 | 0.65 | 2.28 | 1.69 | 1.46 |
(2) | 0.85 | 1.36 | 2.55 | 1.96 | 0.62 | 2.47 | 1.62 | 1.21 | |
(3) | 0.86 | 1.53 | 2.63 | 1.86 | 0.18 | 2.25 | 1.11 | 1.33 |
RF | DNN | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Calibration | Validation | Calibration | Validation | ||||||||||||||
Input | It. | R2 | RMSECV | RPD | RPIQ | r2 | RMSEP | RPD | RPIQ | R2 | RMSE | RPD | RPIQ | r2 | RMSEP | RPD | RPIQ |
a | (1) | 0.73 | 1.82 | 1.94 | 1.41 | 0.09 | 3.65 | 1.05 | 0.91 | 0.81 | 1.55 | 2.29 | 1.67 | 0.65 | 2.28 | 1.69 | 1.46 |
(2) | 0.75 | 1.73 | 2.00 | 1.54 | 0.02 | 3.96 | 1.01 | 0.76 | 0.85 | 1.36 | 2.55 | 1.96 | 0.62 | 2.47 | 1.62 | 1.21 | |
(3) | 0.79 | 1.85 | 2.17 | 1.53 | −0.34 | 2.88 | 0.86 | 1.04 | 0.86 | 1.53 | 2.63 | 1.86 | 0.18 | 2.25 | 1.11 | 1.33 | |
a + b | (1) | 0.76 | 1.74 | 2.03 | 1.48 | 0.18 | 3.47 | 1.11 | 0.96 | 0.86 | 1.33 | 2.66 | 1.94 | 0.56 | 2.55 | 1.51 | 1.31 |
(2) | 0.72 | 1.83 | 1.90 | 1.46 | 0.13 | 3.73 | 1.07 | 0.8 | 0.81 | 1.53 | 2.27 | 1.74 | 0.43 | 3.01 | 1.33 | 0.99 | |
(3) | 0.8 | 1.78 | 2.26 | 1.60 | −0.30 | 2.83 | 0.88 | 1.06 | 0.97 | 0.70 | 5.87 | 4.08 | 0.02 | 2.46 | 1.02 | 1.22 | |
a + c | (1) | 0.43 | 2.67 | 1.33 | 0.97 | 0.04 | 3.76 | 1.02 | 0.89 | 0.82 | 1.51 | 2.35 | 1.71 | 0.44 | 2.87 | 1.34 | 1.16 |
(2) | 0.74 | 1.78 | 1.96 | 1.50 | −0.02 | 4.04 | 0.99 | 0.74 | 0.78 | 1.64 | 2.11 | 1.62 | 0.46 | 2.93 | 1.37 | 1.02 | |
(3) | 0.77 | 1.93 | 2.08 | 1.47 | −0.44 | 2.98 | 0.83 | 1.00 | 0.97 | 0.67 | 6.02 | 4.25 | −0.11 | 2.61 | 0.95 | 1.14 | |
a + d | (1) | 0.72 | 1.87 | 1.90 | 1.38 | 0.09 | 3.66 | 1.05 | 0.91 | 0.86 | 1.33 | 2.67 | 1.94 | 0.59 | 2.47 | 1.56 | 1.35 |
(2) | 0.73 | 1.80 | 1.93 | 1.49 | 0.03 | 3.92 | 1.02 | 0.76 | 0.89 | 1.15 | 3.01 | 2.32 | 0.63 | 2.44 | 1.64 | 1.23 | |
(3) | 0.78 | 1.89 | 2.13 | 1.51 | −0.30 | 2.84 | 0.87 | 1.05 | 0.9 | 1.26 | 3.2 | 2.26 | 0.13 | 2.32 | 1.07 | 1.29 | |
a + e | (1) | 0.75 | 1.78 | 1.99 | 1.45 | 0.16 | 3.51 | 1.09 | 0.95 | 0.81 | 1.56 | 2.28 | 1.66 | 0.31 | 3.2 | 1.21 | 1.04 |
(2) | 0.77 | 1.66 | 2.10 | 1.61 | 0.09 | 3.81 | 1.05 | 0.78 | 0.98 | 0.50 | 7.01 | 5.38 | 0.4 | 3.08 | 1.30 | 0.97 | |
(3) | 0.79 | 1.84 | 2.18 | 1.54 | −0.37 | 2.91 | 0.85 | 1.03 | 0.81 | 1.75 | 2.3 | 1.63 | −0.06 | 2.56 | 0.97 | 1.17 |
Input | RF | DNN | ||
---|---|---|---|---|
It. | Max_Features | Max_Depth | Num_Layers | |
a | (1) | 0.60 | 70 | 12 |
(2) | auto | 10 | 8 | |
(3) | 0.60 | 70 | 7 | |
a + 1 | (1) | auto | 70 | 11 |
(2) | Auto | 10 | 10 | |
(3) | auto | 20 | 10 | |
a + 2 | (1) | 0.85 | 10 | 7 |
(2) | auto | 30 | 6 | |
(3) | auto | 30 | 12 | |
a + 3 | (1) | 0.58 | 50 | 12 |
(2) | auto | 30 | 11 | |
(3) | auto | 70 | 3 | |
a + 4 | (1) | auto | 10 | 11 |
(2) | 0.95 | None | 12 | |
(3) | 0.95 | None | 12 | |
a + 5 | (1) | auto | 20 | 13 |
(2) | auto | 30 | 9 | |
(3) | 0.95 | 30 | 5 |
RF | DNN | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Calibration | Validation | Calibration | Validation | ||||||||||||||
Input | It. | R2 | RMSECV | RPD | RPIQ | r2 | RMSEP | RPD | RPIQ | R2 | RMSE | RPD | RPIQ | r2 | RMSEP | RPD | RPIQ |
a | (1) | 0.73 | 1.82 | 1.94 | 1.41 | 0.09 | 3.65 | 1.05 | 0.91 | 0.73 | 1.55 | 2.29 | 1.67 | 0.65 | 2.28 | 1.69 | 1.46 |
(2) | 0.75 | 1.73 | 2.00 | 1.54 | 0.02 | 3.96 | 1.01 | 0.76 | 0.75 | 1.36 | 2.55 | 1.96 | 0.62 | 2.47 | 1.62 | 1.21 | |
(3) | 0.79 | 1.85 | 2.17 | 1.53 | −0.34 | 2.88 | 0.86 | 1.04 | 0.79 | 1.53 | 2.63 | 1.86 | 0.18 | 2.25 | 1.11 | 1.33 | |
a + 1 | (1) | 0.81 | 1.53 | 2.32 | 1.69 | 0.43 | 2.89 | 1.33 | 1.15 | 0.96 | 0.69 | 5.18 | 3.76 | 0.65 | 2.27 | 1.7 | 1.47 |
(2) | 0.82 | 1.45 | 2.39 | 1.84 | 0.53 | 2.74 | 1.46 | 1.09 | 0.96 | 0.67 | 5.17 | 3.97 | 0.59 | 2.56 | 1.56 | 1.17 | |
(3) | 0.86 | 1.50 | 2.68 | 1.90 | 0.44 | 1.87 | 1.33 | 1.60 | 0.94 | 0.95 | 4.23 | 2.99 | 0.04 | 2.43 | 1.02 | 1.23 | |
a + 2 | (1) | 0.83 | 1.47 | 2.42 | 1.76 | 0.57 | 2.52 | 1.52 | 1.32 | 0.96 | 0.69 | 5.14 | 3.75 | 0.82 | 1.64 | 2.35 | 2.03 |
(2) | 0.79 | 1.58 | 2.20 | 1.69 | 0.67 | 2.30 | 1.74 | 1.30 | 0.88 | 1.20 | 2.91 | 2.23 | 0.77 | 1.92 | 2.09 | 1.56 | |
(3) | 0.86 | 1.46 | 2.74 | 1.94 | 0.87 | 0.88 | 2.82 | 3.40 | 0.90 | 1.25 | 3.22 | 2.27 | 0.52 | 1.72 | 1.45 | 1.74 | |
a + 3 | (1) | 0.79 | 1.61 | 2.21 | 1.61 | 0.58 | 2.50 | 1.54 | 1.33 | 0.87 | 1.27 | 2.79 | 2.02 | 0.8 | 1.73 | 2.22 | 1.92 |
(2) | 0.82 | 1.45 | 2.40 | 1.84 | 0.70 | 2.20 | 1.81 | 1.36 | 0.97 | 0.62 | 5.60 | 4.30 | 0.78 | 1.86 | 2.16 | 1.61 | |
(3) | 0.87 | 1.44 | 2.79 | 1.97 | 0.87 | 0.89 | 2.79 | 3.36 | 0.92 | 1.16 | 3.46 | 2.44 | 0.63 | 1.50 | 1.66 | 1.99 | |
a + 4 | (1) | 0.84 | 1.41 | 2.52 | 1.83 | 0.61 | 2.39 | 1.61 | 1.39 | 0.95 | 0.78 | 4.54 | 3.30 | 0.92 | 1.10 | 3.51 | 3.04 |
(2) | 0.83 | 1.41 | 2.46 | 1.89 | 0.72 | 2.11 | 1.89 | 1.42 | 0.99 | 0.40 | 8.75 | 6.72 | 0.93 | 1.02 | 3.92 | 2.92 | |
(3) | 0.88 | 1.36 | 2.96 | 2.06 | 0.94 | 0.59 | 4.21 | 5.07 | 0.96 | 0.81 | 4.98 | 3.52 | 0.76 | 1.21 | 2.05 | 2.46 | |
a + 5 | (1) | 0.84 | 1.40 | 2.53 | 1.84 | 0.60 | 2.42 | 1.59 | 1.38 | 0.99 | 0.21 | 16.74 | 12.17 | 0.95 | 0.85 | 4.51 | 3.90 |
(2) | 0.83 | 1.43 | 2.42 | 1.86 | 0.73 | 2.08 | 1.92 | 1.44 | 0.99 | 0.34 | 10.21 | 7.84 | 0.92 | 1.10 | 3.65 | 2.72 | |
(3) | 0.89 | 1.32 | 3.04 | 2.15 | 0.94 | 0.61 | 4.07 | 4.90 | 0.99 | 0.46 | 8.65 | 6.11 | 0.78 | 1.15 | 2.16 | 2.59 |
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Abbreviation | Index | Equation | Reference |
---|---|---|---|
R1 | Radar cross ratio | [74] | |
R2 | Radar ratio 2 | [74] | |
D | Radar difference | [75] |
Ab. | Index | Equation for Sentinel-2 Indices | Equation for Laboratory Spectral Indices | Ref. |
---|---|---|---|---|
Vegetation indices | ||||
AFRI21 | Aerosol free vegetation index 2.1 | [79] | ||
ARVI2 | Atmospherically resistant vegetation index2 | [80] | ||
GVMI | Global vegetation moisture index | [81] | ||
Maccioni | Maccioni vegetation index | [82] | ||
NBR | Normalized burn ratio | [83] | ||
NBR2 | Normalized burned Ratio 2 | [84,85] | ||
NDVI | Normalized difference vegetation index | [70] | ||
SIWSI | Shortwave infrared water stress index | [86] | ||
TSAVI | Soil-adjusted vegetation index | [87] | ||
Soil indices | ||||
BI | Brightness index | [88,89] | ||
BSI | Bare soil index | [90] | ||
Water indices | ||||
NDMI | Normalized difference moisture index | [91] |
n | Mean | St. Dev. | Median | Min | Max | Skewness |
---|---|---|---|---|---|---|
58 | 22.3 | 3.6 | 21.9 | 15.2 | 49.4 | 3.7 |
It. | Dataset | n | Mean | St. Dev. | Median | Min | Max | Skewness |
---|---|---|---|---|---|---|---|---|
1 | Cal | 358 | 22.2 | 3.5 | 21.9 | 15.2 | 49.4 | 3.4 |
Val | 154 | 22.3 | 3.9 | 21.9 | 17.1 | 49.4 | 4.2 | |
2 | Cal | 359 | 22.3 | 3.5 | 22.0 | 15.2 | 49.4 | 3.6 |
Val | 153 | 22.2 | 4.0 | 21.8 | 17.1 | 49.4 | 3.8 | |
3 | Cal | 358 | 22.5 | 4.0 | 22.0 | 15.2 | 49.4 | 3.8 |
Val | 154 | 21.9 | 2.5 | 21.8 | 15.2 | 30.1 | 0.4 |
Index | r |
---|---|
NBR2 | 0.85 *** |
NDVI | 0.81 *** |
ARVI2 | 0.81 *** |
Maccioni | 0.80 *** |
TSAVI | 0.79 *** |
BI | −0.46 *** |
GVMI | 0.41 *** |
NBR | 0.26 * |
BSI | 0.22 * |
NDMI | −0.16 ns |
AFRI21 | −0.20 ns |
SIWSI | −0.05 ns |
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Zayani, H.; Fouad, Y.; Michot, D.; Kassouk, Z.; Baghdadi, N.; Vaudour, E.; Lili-Chabaane, Z.; Walter, C. Using Machine-Learning Algorithms to Predict Soil Organic Carbon Content from Combined Remote Sensing Imagery and Laboratory Vis-NIR Spectral Datasets. Remote Sens. 2023, 15, 4264. https://doi.org/10.3390/rs15174264
Zayani H, Fouad Y, Michot D, Kassouk Z, Baghdadi N, Vaudour E, Lili-Chabaane Z, Walter C. Using Machine-Learning Algorithms to Predict Soil Organic Carbon Content from Combined Remote Sensing Imagery and Laboratory Vis-NIR Spectral Datasets. Remote Sensing. 2023; 15(17):4264. https://doi.org/10.3390/rs15174264
Chicago/Turabian StyleZayani, Hayfa, Youssef Fouad, Didier Michot, Zeineb Kassouk, Nicolas Baghdadi, Emmanuelle Vaudour, Zohra Lili-Chabaane, and Christian Walter. 2023. "Using Machine-Learning Algorithms to Predict Soil Organic Carbon Content from Combined Remote Sensing Imagery and Laboratory Vis-NIR Spectral Datasets" Remote Sensing 15, no. 17: 4264. https://doi.org/10.3390/rs15174264