UAV-Based Hyperspectral Imagery for Detection of Root, Butt, and Stem Rot in Norway Spruce

Numerous species of pathogenic wood decay fungi, including members of the genera Heterobasidion and Armillaria, exist in forests in the northern hemisphere. Detection of these fungi through field surveys is often difficult due to a lack of visual symptoms and is cost-prohibitive for most applications. Remotely sensed data can offer a lower-cost alternative for collecting information about vegetation health. This study used hyperspectral imagery collected from unmanned aerial vehicles (UAVs) to detect the presence of wood decay in Norway spruce (Picea abies L. Karst) at two sites in Norway. UAV-based sensors were tested as they offer flexibility and potential cost advantages for small landowners. Ground reference data regarding pathogenic wood decay were collected by harvest machine operators and field crews after harvest. Support vector machines were used to classify the presence of root, butt, and stem rot infection. Classification accuracies as high as 76% with a kappa value of 0.24 were obtained with 490-band hyperspectral imagery, while 29-band imagery provided a lower classification accuracy (~60%, kappa = 0.13).publishedVersio

Benchmarking environmental machine-learning models: methodological progress and an application to forest health

Geospatial machine learning is a versatile approach to analyze environmental data and can help to better understand the interactions and current state of our environment. Due to the artificial intelligence of these algorithms, complex relationships can possibly be discovered which might be missed by other analysis methods. Modeling the interaction of creatures with their environment is referred to as ecological modeling, which is a subcategory of environmental modeling. A subfield of ecological modeling is SDM, which aims to understand the relation between the presence or absence of certain species in their environments. SDM is different from classical mapping/detection analysis. While the latter primarily aim for a visual representation of a species spatial distribution, the former focuses on using the available data to build models and interpreting these. Because no single best option exists to build such models, different settings need to be evaluated and compared against each other. When conducting such modeling comparisons, which are commonly referred to as benchmarking, care needs to be taken throughout the analysis steps to achieve meaningful and unbiased results. These steps are composed out of data preprocessing, model optimization and performance assessment. While these general principles apply to any modeling analysis, their application in an environmental context often requires additional care with respect to data handling, possibly hidden underlying data effects and model selection. To conduct all in a programmatic (and efficient) way, toolboxes in the form of programming modules or packages are needed. This work makes methodological contributions which focus on efficient, machine-learning based analysis of environmental data. In addition, research software to generalize and simplify the described process has been created throughout this work

Detection of leek rust disease under field conditions using hyperspectral proximal sensing and machine learning

Rust disease is an important problem for leek cultivation worldwide. It reduces market value and in extreme cases destroys the entire harvest. Farmers have to resort to periodical full-field fungicide applications to prevent the spread of disease, once every 1 to 5 weeks, depending on the cultivar and weather conditions. This implies an economic cost for the farmer and an environmental cost for society. Hyperspectral sensors have been extensively used to address this issue in research, but their application in the field has been limited to a relatively low number of crops, excluding leek, due to the high investment costs and complex data gathering and analysis associated with these sensors. To fill this gap, a methodology was developed for detecting leek rust disease using hyperspectral proximal sensing data combined with supervised machine learning. First, a hyperspectral library was constructed containing 43,416 spectra with a waveband range of 400-1000 nm, measured under field conditions. Then, an extensive evaluation of 11 common classifiers was performed using the scikit-learn machine learning library in Python, combined with a variety of wavelength selection techniques and preprocessing strategies. The best performing model was a (linear) logistic regression model that was able to correctly classify rust disease with an accuracy of 98.14%, using reflectance values at 556 and 661 nm, combined with the value of the first derivative at 511 nm. This model was used to classify unlabelled hyperspectral images, confirming that the model was able to accurately classify leek rust disease symptoms. It can be concluded that the results in this work are an important step towards the mapping of leek rust disease, and that future research is needed to overcome certain challenges before variable rate fungicide applications can be adopted against leek rust disease