Combining Field and Imaging Spectroscopy to Map Soil Organic Carbon in a Semiarid Environment

Semiarid regions are especially vulnerable to climate change and human-induced land-use changes and are of major importance in the context of necessary carbon sequestration and ongoing land degradation. Topsoil properties, such as soil carbon content, provide valuable indicators to these processes, and can be mapped using imaging spectroscopy (IS). In semiarid regions, this poses difficulties because models are needed that can cope with varying land surface and soil conditions, consider a partial vegetation coverage, and deal with usually low soil organic carbon (SOC) contents. We present an approach that aims at addressing these difficulties by using a combination of field and IS to map SOC in an extensively used semiarid ecosystem. In hyperspectral imagery of the HyMap sensor, the influence of nonsoil materials, i.e., vegetation, on the spectral signature of soil dominated image pixels was reduced and a residual soil signature was calculated. The proposed approach allowed this procedure up to a vegetation coverage of 40% clearly extending the mapping capability. SOC quantities are predicted by applying a spectral feature-based SOC prediction model to image data of residual soil spectra. With this approach, we could significantly increase the spatial extent for which SOC could be predicted with a minimal influence of a vegetation signal compared to previous approaches where the considered area was limited to a maximum of, e.g., 10% vegetation coverage. As a regional example, the approach was applied to a 320 km2 area in the Albany Thicket Biome, South Africa, where land cover and landuse changes have occurred due to decades of unsustainable land management. In the generated maps, spatial SOC patterns were interpreted and linked to geomorphic features and land surface processes, i.e., areas of soil erosion. It was found that the chosen approach supported the extraction of soil-related spectral image information in the semiarid region with highly varying land cover. However, the quantitative prediction of SOC contents revealed a lack in absolute accuracy

Combining Field and Imaging Spectroscopy to Map Soil Organic Carbon in a Semiarid Environment

Semiarid regions are especially vulnerable to climate change and human-induced land-use changes and are of major importance in the context of necessary carbon sequestration and ongoing land degradation. Topsoil properties, such as soil carbon content, provide valuable indicators to these processes, and can be mapped using imaging spectroscopy (IS). In semiarid regions, this poses difficulties because models are needed that can cope with varying land surface and soil conditions, consider a partial vegetation coverage, and deal with usually low soil organic carbon (SOC) contents. We present an approach that aims at addressing these difficulties by using a combination of field and IS to map SOC in an extensively used semiarid ecosystem. In hyperspectral imagery of the HyMap sensor, the influence of nonsoil materials, i.e., vegetation, on the spectral signature of soil dominated image pixels was reduced and a residual soil signature was calculated. The proposed approach allowed this procedure up to a vegetation coverage of 40% clearly extending the mapping capability. SOC quantities are predicted by applying a spectral feature-based SOC prediction model to image data of residual soil spectra. With this approach, we could significantly increase the spatial extent for which SOC could be predicted with a minimal influence of a vegetation signal compared to previous approaches where the considered area was limited to a maximum of, e.g., 10% vegetation coverage. As a regional example, the approach was applied to a 320 km2 area in the Albany Thicket Biome, South Africa, where land cover and landuse changes have occurred due to decades of unsustainable land management. In the generated maps, spatial SOC patterns were interpreted and linked to geomorphic features and land surface processes, i.e., areas of soil erosion. It was found that the chosen approach supported the extraction of soil-related spectral image information in the semiarid region with highly varying land cover. However, the quantitative prediction of SOC contents revealed a lack in absolute accuracy

Trooppisen korkeusgradientin maaperän hiilen arviointi kuvantavalla spektroskopialla näkyvän valon ja lähi-infrapunan alueella

Maaperä on suurin aktiivisesti kiertävä maanpäällinen hiilivarasto, joka on heikentynyt suuresti viimeisen 100-200 vuoden aikana ihmistoiminnan seurauksena. Tilanteen parantamiseksi vaaditaan laajamittaista maaperän hiilen seurantaa ja kehittyneempiä metodeja tätä varten. Tässä tutkimuksessa demonstroidaan näkyvän valon ja infrapunan aallonpituuksilla toimivan hyperspektrikameran toimivuutta maaperän orgaanisen hiilen ennustamisessa. Tähän käytetään kahta monimuuttujamenetelmää, PLS-regressiota, sekä lasso regressiota, jota ei ole aikaisemmin tähän tarkoitukseen käytetty. 191 maaperänäytettä kerättiin Taitavuorilta Keniasta trooppiselta seudulta nousevan rinteen ympäriltä, viiden eri maankäytön alueelta, jotka ovat: peltometsäviljely, pelto, metsä, pensasmaa sekä sisal plantaasi. Näytteet kuvattiin hyperspektrikamera Specim IQ:lla sekä laboratoriossa, että kentällä. Kuvista tuotettiin kolme datasettiä, yksi kuvien keskiarvoisella spektrillä, toinen segmentoitujen kuvien osien keskiarvoisilla spektreillä ja kolmas segmentoitujen kuvien osien keskiarvoisilla spektreillä siten, että ääriarvot suodatettiin pois. Sekä PLS-regressio- sekä lasso regressiomallit antoivat hyviä tuloksia kaikilla dataseteillä (PLSR: R2min = 0.85, RMSEmin = 0.78, lasso: R2min=0.85, RMSEmin=0.80) viitaten sekä laitteen tuottaman datan, että lasso regression soveltuvan maaperän orgaanisen hiilen mallintamiseen. Segmentoitujen osa-kuvien käyttö mallien opettamisessa paransi tuloksia PLSR malleissa, mutta ei vaikuttanut merkittävästi lasso regressiomallien tuloksiin. Vaikka laboratoriossa kuvannettu data antoikin hyviä tuloksia, kenttäolosuhteissa kuvaaminen oli haasteellista ja tulokset tällä datalla olivat heikkoja. Tulevien tutkimusten tulisikin keskittyä kenttämenetelmien kehittämiseen ja löytämään ratkaisuja maaperän hiilen luotettavaan mittaamiseen suoraan maasta, tai lähellä tutkittavaa kohdetta siirreltävien laboratorio järjestelyiden avulla. Tämä parantaisi hiilimittausten saavutettavuutta ja mahdollistaisi niiden paremman hyödyntämisen esimerkiksi täsmäviljelyssä.Soil is the largest actively cycling terrestrial carbon pool, which has been severely distrubed in the last 100-200 years by human actions. To improve the situation, extensive monitoring of soil carbon and new methods for monitoring are required. This study demonstrates the capability of a portable hyperspectral device operating in the visible-near infrared (VIS-NIR) spectrum for soil organic carbon (SOC) prediction. Two multivariate methods, partial least squares regression (PLSR) and for this purpose previously untested lasso regression were used for prediction. 191 soil samples were collected from Taita Hills, Kenya. The samples represent a tropical altitudinal gradient with five land uses: agroforestry, field, forest, shrubland and sisal plantation. The samples were imaged with hyperspectral camera, Specim IQ in laboratory and in field conditions, and the carbon content of the samples was determined with a dry-oxidization analyzer. Three datasets were derived from the images, one containing the mean spectra of the complete imaged samples, one with segmented sub-image spectra and one with segmented sub-image spectra where outlier spectra were removed. Both multivariate methods were tested with all three datasets with good prediction accuracies (PLSR: R2min = 0.85, RMSEmin = 0.78, lasso: R2min=0.85, RMSEmin=0.80), demonstrating the feasibility of both the device and lasso regression as SOC prediction tools. Using the segmented sub-image datasets improved the results with PLSR but had no significant effect on lasso regression prediction results. While good results were gained with laboratory imagery, the field imaging conditions were difficult, and the data performed poorly. Future research should focus on finding solutions to reliably estimate SOC content in situ or with portable laboratory setups to make SOC measurements more widely accessible and agile for e.g. precision agriculture purposes

Quantitative Mapping of Soil Property Based on Laboratory and Airborne Hyperspectral Data Using Machine Learning

Soil visible and near-infrared spectroscopy provides a non-destructive, rapid and low-cost approach to quantify various soil physical and chemical properties based on their reflectance in the spectral range of 400–2500 nm. With an increasing number of large-scale soil spectral libraries established across the world and new space-borne hyperspectral sensors, there is a need to explore methods to extract informative features from reflectance spectra and produce accurate soil spectroscopic models using machine learning. Features generated from regional or large-scale soil spectral data play a key role in the quantitative spectroscopic model for soil properties. The Land Use/Land Cover Area Frame Survey (LUCAS) soil library was used to explore PLS-derived components and fractal features generated from soil spectra in this study. The gradient-boosting method performed well when coupled with extracted features on the estimation of several soil properties. Transfer learning based on convolutional neural networks (CNNs) was proposed to make the model developed from laboratory data transferable for airborne hyperspectral data. The soil clay map was successfully derived using HyMap imagery and the fine-tuned CNN model developed from LUCAS mineral soils, as deep learning has the potential to learn transferable features that generalise from the source domain to target domain. The external environmental factors like the presence of vegetation restrain the application of imaging spectroscopy. The reflectance data can be transformed into a vegetation suppressed domain with a force invariance approach, the performance of which was evaluated in an agricultural area using CASI airborne hyperspectral data. However, the relationship between vegetation and acquired spectra is complicated, and more efforts should put on removing the effects of external factors to make the model transferable from one sensor to another.:Abstract I Kurzfassung III Table of Contents V List of Figures IX List of Tables XIII List of Abbreviations XV 1 Introduction 1 1.1 Motivation 1 1.2 Soil spectra from different platforms 2 1.3 Soil property quantification using spectral data 4 1.4 Feature representation of soil spectra 5 1.5 Objectives 6 1.6 Thesis structure 7 2 Combining Partial Least Squares and the Gradient-Boosting Method for Soil Property Retrieval Using Visible Near-Infrared Shortwave Infrared Spectra 9 2.1 Abstract 10 2.2 Introduction 10 2.3 Materials and methods 13 2.3.1 The LUCAS soil spectral library 13 2.3.2 Partial least squares algorithm 15 2.3.3 Gradient-Boosted Decision Trees 15 2.3.4 Calculation of relative variable importance 16 2.3.5 Assessment 17 2.4 Results 17 2.4.1 Overview of the spectral measurement 17 2.4.2 Results of PLS regression for the estimation of soil properties 19 2.4.3 Results of PLS-GBDT for the estimation of soil properties 21 2.4.4 Relative important variables derived from PLS regression and the gradient-boosting method 24 2.5 Discussion 28 2.5.1 Dimension reduction for high-dimensional soil spectra 28 2.5.2 GBDT for quantitative soil spectroscopic modelling 29 2.6 Conclusions 30 3 Quantitative Retrieval of Organic Soil Properties from Visible Near-Infrared Shortwave Infrared Spectroscopy Using Fractal-Based Feature Extraction 31 3.1 Abstract 32 3.2 Introduction 32 3.3 Materials and Methods 35 3.3.1 The LUCAS topsoil dataset 35 3.3.2 Fractal feature extraction method 37 3.3.3 Gradient-boosting regression model 37 3.3.4 Evaluation 41 3.4 Results 42 3.4.1 Fractal features for soil spectroscopy 42 3.4.2 Effects of different step and window size on extracted fractal features 45 3.4.3 Modelling soil properties with fractal features 47 3.4.3 Comparison with PLS regression 49 3.5 Discussion 51 3.5.1 The importance of fractal dimension for soil spectra 51 3.5.2 Modelling soil properties with fractal features 52 3.6 Conclusions 53 4 Transfer Learning for Soil Spectroscopy Based on Convolutional Neural Networks and Its Application in Soil Clay Content Mapping Using Hyperspectral Imagery 55 4.1 Abstract 55 4.2 Introduction 56 4.3 Materials and Methods 59 4.3.1 Datasets 59 4.3.2 Methods 62 4.3.3 Assessment 67 4.4 Results and Discussion 67 4.4.1 Interpretation of mineral and organic soils from LUCAS dataset 67 4.4.2 1D-CNN and spectral index for LUCAS soil clay content estimation 69 4.4.3 Application of transfer learning for soil clay content mapping using the pre-trained 1D-CNN model 72 4.4.4 Comparison between spectral index and transfer learning 74 4.4.5 Large-scale soil spectral library for digital soil mapping at the local scale using hyperspectral imagery 75 4.5 Conclusions 75 5 A Case Study of Forced Invariance Approach for Soil Salinity Estimation in Vegetation-Covered Terrain Using Airborne Hyperspectral Imagery 77 5.1 Abstract 78 5.2 Introduction 78 5.3 Materials and Methods 81 5.3.1 Study area of Zhangye Oasis 81 5.3.2 Data description 82 5.3.3 Methods 83 5.3.3 Model performance assessment 85 5.4 Results and Discussion 86 5.4.1 The correlation between NDVI and soil salinity 86 5.4.2 Vegetation suppression performance using the Forced Invariance Approach 86 5.4.3 Estimation of soil properties using airborne hyperspectral data 88 5.5 Conclusions 90 6 Conclusions and Outlook 93 Bibliography 97 Acknowledgements 11