Estimation of Soil Characteristics from Multispectral Sentinel-3 Imagery and DEM Derivatives Using Machine Learning
<p>Representation of the data used in these experiments. (<b>a</b>) shows multispectral images collected by Sentinel-3 and properly merged to cover the entire European continent. For the sake of visualization, (<b>a</b>) represents the average over all the bands, normalized between 0 and 1. (<b>b</b>) represents the digital elevation model acquired from the Copernicus Land Monitoring Service. Greenish colours represent low-elevation values (approx. −214 m), while reddish colours represent high-elevation values (approx. 5105 m).</p> "> Figure 2
<p>Violin plots of the soil properties considered in this work. (<b>a</b>) Coarse; (<b>b</b>) Clay, Silt and Sand; (<b>c</b>) pH in <math display="inline"><semantics> <mrow> <mi>C</mi> <mi>a</mi> <mi>C</mi> <msub> <mi>l</mi> <mn>2</mn> </msub> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <msub> <mi>H</mi> <mn>2</mn> </msub> <mi>O</mi> </mrow> </semantics></math>; (<b>d</b>) Organic Carbon (OC), Calcium Carbonate (CaCO<sub>3</sub>) and Nitrogen (N); (<b>e</b>) Phosphorous (P) and Potassium (K); (<b>f</b>) Cation exchange capacity (CEC). For the sake of visualization, the variables P, K and CEC are shown in a logarithmic scale.</p> "> Figure 3
<p>For a visual comparison of the results, we render through inverse distance weighting (IDW) interpolation the ground points relative to the ground-truth, the predictions, and the errors in terms of RMSE of each soil variable. The blue and yellow colors represent the minimum and the maximum values of each soil property, respectively. Colors relative to intermediate values are obtained through quantile color coding. It is worth noting that in most cases, the ground-truth (the first image of each triplet) and the prediction (the second image) are visually similar, indicating an accurate estimation of the soil properties.</p> "> Figure 4
<p>Scatter plots corresponding to the predictions of ANN Multi in relation to the soil parameters. The <span class="html-italic">x</span> axis refers to the predictions, while the <span class="html-italic">y</span> axis refers to the ground-truth values. For reference, each plot includes the perfect prediction line <math display="inline"><semantics> <mrow> <mi>y</mi> <mo>=</mo> <mi>x</mi> </mrow> </semantics></math> (dashed red) and the trend line relative to the estimations (solid orange). Each subfigure represents the scatter plot of a given soil variable.</p> "> Figure 5
<p>Feature importance of each soil property obtained using random forests. The blue bars represent the importance of the multispectral bands, while the orange bars are relative to the DEM-derivatives. (<b>a</b>) Coarse; (<b>b</b>) Sand; (<b>c</b>) Silt; (<b>d</b>) Clay; (<b>e</b>) pH in <math display="inline"><semantics> <mrow> <mi>C</mi> <mi>a</mi> <mi>C</mi> <msub> <mi>l</mi> <mn>2</mn> </msub> </mrow> </semantics></math>; (<b>f</b>) pH in <math display="inline"><semantics> <mrow> <msub> <mi>H</mi> <mn>2</mn> </msub> <mi>O</mi> </mrow> </semantics></math>.</p> "> Figure 5 Cont.
<p>Feature importance of each soil property obtained using random forests. The blue bars represent the importance of the multispectral bands, while the orange bars are relative to the DEM-derivatives. (<b>a</b>) Coarse; (<b>b</b>) Sand; (<b>c</b>) Silt; (<b>d</b>) Clay; (<b>e</b>) pH in <math display="inline"><semantics> <mrow> <mi>C</mi> <mi>a</mi> <mi>C</mi> <msub> <mi>l</mi> <mn>2</mn> </msub> </mrow> </semantics></math>; (<b>f</b>) pH in <math display="inline"><semantics> <mrow> <msub> <mi>H</mi> <mn>2</mn> </msub> <mi>O</mi> </mrow> </semantics></math>.</p> "> Figure 6
<p>Feature importance of each soil property obtained using random forests. Blue bars represent the importance of the multispectral bands, while orange bars are relative to the DEM-derivatives. (<b>a</b>) Organic Carbon (OC); (<b>b</b>) Phosphorous (P); (<b>c</b>) Potassium (K); (<b>d</b>) Nitrogen (N); (<b>e</b>) Calcium Carbonate (CaCO<sub>3</sub>); (<b>f</b>) Cation exchange capacity (CEC).</p> "> Figure 7
<p>Aggregated feature importance of each soil variable. The contributions of the multispectral and geomorphological DEM derivatives are shown in blue and orange, respectively. It is worth noting that the importance of the multispectral variables is greater than that of the DEM derivatives.</p> ">
Abstract
:1. Introduction
- We created a multisource remote sensing dataset of the European region by merging multispectral images from Sentinel-3 and DEM derivatives from the European Copernicus mission and the corresponding LUCAS samples;
- We benchmarked several machine learning methods for the estimation of the soil characteristics using multispectral signals, DEM derivatives and a combination of them;
- We proposed methods based on an artificial neural network (ANN) capable of predicting all the soil characteristics at the same time;
- We analyzed the importance of each input source (multispectral and DEM) in predicting the soil properties.
2. Methods
2.1. Explainability Investigation
3. Materials
- are the soil properties;
- are the bands of the spaceborne multispectral data;
- are the features extracted from the digital elevation model information.
3.1. Multispectral Data
3.2. Soil Data
3.3. Digital Elevation Model Data
3.4. Comparison with Existing Datasets
3.5. Data Split
4. Results
4.1. Experiments
4.2. Explainability Discussion
5. Final Discussion and Conclusions
6. Code Availability
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
MDPI | Multidisciplinary Digital Publishing Institute |
DOAJ | Directory of Open Access Journals |
TLA | Three-letter acronym |
LD | Linear dichroism |
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Stage | Operation | Output Size |
---|---|---|
Preprocessing | Input | N |
Encoding | Linear + Hardswish | 32 |
Linear + Tanhshrink | 128 | |
Linear + Hardswish | 32 | |
Linear | M | |
Total parameters |
Method | Coarse | Clay | Silt | Sand | pH | pH | SOC | CaCO | N | P | K | CEC | Area |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Meng et al. [19] | ✓ | North east China (315 samples) | |||||||||||
Forkuor et al. [13] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Rural watershed (580 km) | ||||||
Safanelli et al. [14] | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | European croplands (7142 samples) | ||||||
Trontelj et al. [22] | ✓ | ✓ | ✓ | Slovenia (350 samples) | |||||||||
Li et al. [23] | ✓ | ✓ | ✓ | 19 sampling sites (180 samples) | |||||||||
Zhou et al. [15] | ✓ | ✓ | Switzerland (150 samples) | ||||||||||
Our Proposal | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Europe (20,000 samples) |
(a) | ||||||||||||||
Type | Model | Silt | Sand | pH | pH | Coarse | Clay | P | OC | N | K | CaCO | CEC | avg |
(m) | GB | 0.13 | 0.18 | 0.42 | 0.41 | 0.05 | 0.18 | 0.08 | 0.16 | 0.11 | 0.08 | 0.25 | 0.08 | 0.18 |
RF | 0.19 | 0.25 | 0.48 | 0.47 | 0.06 | 0.26 | 0.07 | 0.13 | 0.12 | 0.10 | 0.33 | 0.11 | 0.21 | |
SVM | 0.13 | 0.19 | 0.44 | 0.44 | 0.04 | 0.14 | 0.07 | 0.11 | 0.07 | 0.04 | 0.14 | 0.02 | 0.15 | |
ANN Single | 0.23 | 0.28 | 0.54 | 0.53 | 0.11 | 0.26 | 0.13 | 0.20 | 0.17 | 0.13 | 0.37 | 0.12 | 0.26 | |
ANN Multi | 0.25 | 0.30 | 0.51 | 0.50 | 0.13 | 0.26 | 0.12 | 0.21 | 0.15 | 0.18 | 0.43 | 0.14 | 0.27 | |
() | GB | 0.22 | 0.27 | 0.47 | 0.47 | 0.14 | 0.28 | 0.13 | 0.19 | 0.13 | 0.10 | 0.33 | 0.14 | 0.24 |
RF | 0.36 | 0.41 | 0.54 | 0.54 | 0.16 | 0.39 | 0.12 | 0.20 | 0.17 | 0.12 | 0.41 | 0.22 | 0.30 | |
SVR | 0.27 | 0.32 | 0.55 | 0.54 | 0.12 | 0.31 | 0.14 | 0.19 | 0.17 | 0.10 | 0.34 | 0.17 | 0.27 | |
ANN Single | 0.33 | 0.39 | 0.57 | 0.57 | 0.17 | 0.35 | 0.12 | 0.25 | 0.20 | 0.12 | 0.46 | 0.20 | 0.31 | |
ANN Multi | 0.34 | 0.39 | 0.56 | 0.56 | 0.14 | 0.38 | 0.12 | 0.25 | 0.21 | 0.15 | 0.44 | 0.23 | 0.31 | |
(b) RMSE | ||||||||||||||
Type | Model | Silt | Sand | pH | pH | Coarse | Clay | P | OC | N | K | CaCO | CEC | avg |
() | GB | 0.96 | 0.92 | 0.76 | 0.77 | 0.96 | 0.89 | 0.87 | 0.90 | 0.95 | 1.04 | 0.88 | 0.99 | 0.91 |
RF | 0.92 | 0.88 | 0.72 | 0.73 | 0.95 | 0.84 | 0.87 | 0.91 | 0.95 | 1.03 | 0.83 | 0.97 | 0.88 | |
SVR | 0.95 | 0.91 | 0.75 | 0.75 | 0.96 | 0.91 | 0.88 | 0.93 | 0.97 | 1.07 | 0.94 | 1.02 | 0.92 | |
ANN Single | 0.90 | 0.86 | 0.67 | 0.69 | 0.91 | 0.85 | 0.85 | 0.88 | 0.92 | 1.02 | 0.80 | 0.97 | 0.86 | |
ANN Multi | 0.88 | 0.85 | 0.70 | 0.71 | 0.91 | 0.84 | 0.86 | 0.87 | 0.93 | 1.00 | 0.75 | 0.97 | 0.86 | |
() | GB | 0.90 | 0.86 | 0.73 | 0.73 | 0.91 | 0.83 | 0.85 | 0.88 | 0.94 | 1.03 | 0.83 | 0.96 | 0.87 |
RF | 0.82 | 0.78 | 0.68 | 0.68 | 0.90 | 0.77 | 0.85 | 0.88 | 0.92 | 1.02 | 0.78 | 0.91 | 0.83 | |
SVR | 0.87 | 0.84 | 0.67 | 0.68 | 0.92 | 0.82 | 0.84 | 0.88 | 0.92 | 1.04 | 0.83 | 0.94 | 0.85 | |
ANN Single | 0.84 | 0.79 | 0.66 | 0.66 | 0.90 | 0.79 | 0.86 | 0.86 | 0.91 | 1.02 | 0.75 | 0.92 | 0.83 | |
ANN Multi | 0.85 | 0.80 | 0.67 | 0.67 | 0.90 | 0.79 | 0.86 | 0.85 | 0.90 | 1.03 | 0.79 | 0.92 | 0.84 | |
(c) MAE | ||||||||||||||
Type | Model | Silt | Sand | pH | pH | Coarse | Clay | P | OC | N | K | CaCO | CEC | avg |
() | GB | 0.77 | 0.76 | 0.63 | 0.64 | 0.72 | 0.69 | 0.61 | 0.58 | 0.63 | 0.53 | 0.50 | 0.69 | 0.65 |
RF | 0.73 | 0.72 | 0.57 | 0.58 | 0.71 | 0.64 | 0.61 | 0.58 | 0.63 | 0.52 | 0.45 | 0.67 | 0.62 | |
SVR | 0.77 | 0.75 | 0.59 | 0.60 | 0.67 | 0.66 | 0.57 | 0.52 | 0.59 | 0.48 | 0.42 | 0.66 | 0.61 | |
ANN Single | 0.70 | 0.68 | 0.54 | 0.54 | 0.68 | 0.64 | 0.57 | 0.57 | 0.62 | 0.51 | 0.43 | 0.67 | 0.60 | |
ANN Multi | 0.70 | 0.68 | 0.56 | 0.57 | 0.69 | 0.65 | 0.59 | 0.54 | 0.61 | 0.52 | 0.42 | 0.66 | 0.60 | |
() | GB | 0.73 | 0.72 | 0.61 | 0.61 | 0.67 | 0.65 | 0.59 | 0.56 | 0.62 | 0.52 | 0.47 | 0.66 | 0.62 |
RF | 0.65 | 0.63 | 0.54 | 0.53 | 0.67 | 0.58 | 0.59 | 0.55 | 0.60 | 0.51 | 0.42 | 0.61 | 0.57 | |
SVR | 0.69 | 0.66 | 0.53 | 0.53 | 0.64 | 0.58 | 0.53 | 0.48 | 0.54 | 0.46 | 0.38 | 0.60 | 0.55 | |
ANN Single | 0.66 | 0.63 | 0.52 | 0.52 | 0.66 | 0.58 | 0.59 | 0.53 | 0.57 | 0.52 | 0.39 | 0.60 | 0.56 | |
ANN Multi | 0.68 | 0.65 | 0.53 | 0.53 | 0.67 | 0.59 | 0.59 | 0.53 | 0.59 | 0.52 | 0.44 | 0.61 | 0.58 |
Soil | (m) | (m,d) | ||||
---|---|---|---|---|---|---|
Parameter | RMSE | MAE | RMSE | MAE | ||
silt | ANN Multi | ANN Single | ANN Multi | RF | RF | RF |
sand | ANN Multi | ANN Multi | ANN Multi | RF | RF | RF/ANN Single |
pH | ANN Single | ANN Single | ANN Single | ANN Single | ANN Single | ANN Single |
pH | ANN Single | ANN Single | ANN Single | ANN Single | ANN Single | ANN Single |
coarse | ANN Multi | ANN Single/ANN Multi | ANN Multi | ANN Single | RF/ANN Single/ANN Multi | SVR |
clay | RF/ANN Single/ANN Multi | RF/ANN Multi | RF/ANN Single/ANN Multi | RF | RF | RF/SVR/ANN Single |
P | ANN Single | ANN Single | ANN Single | SVR | SVR | SVR |
OC | ANN Multi | ANN Multi | ANN Multi | ANN Single/ANN Multi | ANN Multi | SVR |
N | ANN Single | ANN Single | ANN Single | ANN Multi | ANN Multi | SVR |
K | ANN Multi | ANN Multi | ANN Multi | ANN Multi | RF/ANN Single | SVR |
CaCO3 | ANN Multi | ANN Multi | ANN Multi | ANN Single | ANN Single | SVR |
CEC | ANN Multi | RF/ANN Single/ANN multi | ANN Multi | ANN Multi | RF | SVR/ANN Single |
avg | ANN Multi | ANN Single/ANN Multi | ANN Multi | ANN Single/ANN Multi | RF/ANN Single | SVR |
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Piccoli, F.; Barbato, M.P.; Peracchi, M.; Napoletano, P. Estimation of Soil Characteristics from Multispectral Sentinel-3 Imagery and DEM Derivatives Using Machine Learning. Sensors 2023, 23, 7876. https://doi.org/10.3390/s23187876
Piccoli F, Barbato MP, Peracchi M, Napoletano P. Estimation of Soil Characteristics from Multispectral Sentinel-3 Imagery and DEM Derivatives Using Machine Learning. Sensors. 2023; 23(18):7876. https://doi.org/10.3390/s23187876
Chicago/Turabian StylePiccoli, Flavio, Mirko Paolo Barbato, Marco Peracchi, and Paolo Napoletano. 2023. "Estimation of Soil Characteristics from Multispectral Sentinel-3 Imagery and DEM Derivatives Using Machine Learning" Sensors 23, no. 18: 7876. https://doi.org/10.3390/s23187876
APA StylePiccoli, F., Barbato, M. P., Peracchi, M., & Napoletano, P. (2023). Estimation of Soil Characteristics from Multispectral Sentinel-3 Imagery and DEM Derivatives Using Machine Learning. Sensors, 23(18), 7876. https://doi.org/10.3390/s23187876