Individual tree-based vs pixel-based approaches to mapping forest functional traits and diversity by remote sensing

Plant ecology and biodiversity research have increasingly incorporated trait-based approaches and remote sensing. Compared with traditional field survey (which typically samples individual trees), remote sensing enables quantifying functional traits over large contiguous areas, but assigning trait values to biological units such as species and individuals is difficult with pixel-based approaches. We used a subtropical forest landscape in China to compare an approach based on airborne LiDAR-delineated individual tree crowns (ITCs) with a pixel-based approach for assessing functional traits from remote sensing data. We compared trait distributions, trait–trait relationships and functional diversity metrics obtained by the ITC- and pixel-based approaches at changing pixel size and extent. We found that morphological traits derived from airborne laser scanning showed more differences between ITC- and pixel-based approaches than physiological traits estimated by airborne Pushbroom Hyperspectral Imager-3 (PHI-3) hyperspectral data. Pixel sizes approximating average tree crowns yielded similar results as ITCs, but 95th quantile height and foliage height diversity tended to be overestimated and leaf area index underestimated relative to ITC-based values. With increasing pixel size, the differences to ITC-based trait values became larger and less trait variance was captured, indicating information loss. The consistency of ITC- and pixel-based functional richness also decreased with increasing pixel size, and changed with the observed extent for functional diversity monitoring. We conclude that whereas ITC-based approaches in principle allow partitioning of variation between individuals, genotypes and species, high-resolution pixel-based approaches come close to this and can be suitable for assessing ecosystem-scale trait variation by weighting individuals and species according to coverage

Evaluation of the health status of Araucaria araucana trees using hyperspectral images

Revista oficial de la Asociación Española de Teledetección[EN] The Araucaria araucana is an endemic species from Chile and Argentina, which has a high biological, scientific and cultural value and since 2016 has shown a severe affection of leaf damage in some individuals, causing in some cases their death. The purpose of this research was to detect, from hyperspectral images, the individuals of the Araucaria species (Araucaria araucana (Molina and K. Koch)) and its degree of disease, by isolating its spectral signature and evaluating its physiological state through indices of vegetation and positioning techniques of the inflection point of the red edge, in a sector of the Ralco National Reserve, Biobío Region, Chile. Seven images were captured with the HYSPEX VNIR-1600 hyperspectral sensor, with 160 bands and a random sampling was carried out in the study area, where 90 samples of Araucarias were collected. In addition, from the remote sensing techniques applied, spatial data mining was used, in which Araucarias were classified without symptoms of disease and with symptoms of disease. A 55.11% overall accuracy was obtained in the classification of the image, 53.4% in the identification of healthy Araucaria and 55.96% in the identification of affected Araucaria. In relation to the evaluation of their sanitary status, the index with the best percentage of accuracy is the MSR (70.73%) and the one with the lowest value is the SAVI (35.47%). The positioning technique of the inflection point of the red edge delivered an accuracy percentage of 52.18% and an acceptable Kappa index.[ES] La Araucaria araucana es una especie endémica de Chile y Argentina, presenta un alto valor biológico, científico, cultural y desde el año 2016 ha evidenciado una severa afección del daño foliar en algunos individuos, causando en ciertos casos su muerte. Esta investigación tiene por objetivo detectar a partir de imágenes hiperespectrales, los individuos de la especie Araucaria (Araucaria araucana (Molina y K. Koch)) y su grado de afección, mediante el aislamiento de su firma espectral y la evaluación de su estado sanitario mediante índices de vegetación y técnicas de posicionamiento del punto de inflexión del red edge, en un sector de la Reserva Nacional Ralco, Región del Biobío, Chile. Se capturaron siete imágenes con el sensor hiperespectral HYSPEX VNIR-1600, con 160 bandas y se realizó un muestreo aleatorio en el área de estudio, donde se recolectaron 90 muestras de Araucarias. Además, de las técnicas de teledetección aplicadas, se utilizó minería de datos espaciales, que permitió clasificar las Araucarias con y sin síntomas de afección. Se logró un 55,11% de exactitud global en la clasificación de la imagen, un 53,4% en la identificación de Araucarias sanas y un 55,96% en la identificación de Araucarias afectadas. En relación a la evaluación de su estado sanitario, el índice con mejor porcentaje de exactitud es el MSR (70,73%) y el con menor porcentaje de exactitud es el SAVI (35,47%). La técnica de posicionamiento del punto de inflexión del red edge entregó un porcentaje de exactitud de 52,18% y un índice de Kappa aceptable.Este artículo se ha realizado en el contexto de fin de grado del Magíster en Teledetección, Facultad de Ciencias de la Universidad Mayor y en el mar-co del Proyecto “Prospección fitosanitaria para determinar los niveles de afección de daño foliar en bosques de Araucaria araucana de las regiones del Biobío, Araucanía y Los Ríos, 2017/ID: 633-32-LE16, financiado por la Corporación Nacional Forestal (CONAF) de Chile. 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Distinguishing forest types in restored tropical landscapes with UAV-borne LIDAR

Forest landscape restoration is a global priority to mitigate negative effects of climate change, conserve biodiversity, and ensure future sustainability of forests, with international pledges concentrated in tropical forest regions. To hold restoration efforts accountable and monitor their outcomes, traditional strategies for monitoring tree cover increase by field surveys are falling short, because they are labor-intensive and costly. Meanwhile remote sensing approaches have not been able to distinguish different forest types that result from utilizing different restoration approaches (conservation versus production focus). Unoccupied Aerial Vehicles (UAV) with light detection and ranging (LiDAR) sensors can observe forests` vertical and horizontal structural variation, which has the potential to distinguish forest types. In this study, we explored this potential of UAV-borne LiDAR to distinguish forest types in landscapes under restoration in southeastern Brazil by using a supervised classification method. The study area encompassed 150 forest plots with six forest types divided in two forest groups: conservation (remnant forests, natural regrowth, and active restoration plantings) and production (monoculture, mixed, and abandoned plantations) forests. UAV-borne LiDAR data was used to extract several Canopy Height Model (CHM), voxel, and point cloud statistic based metrics at a high resolution for analysis. Using a random forest classification model we could successfully classify conservation and production forests (90% accuracy). Classification of the entire set of six types was less accurate (62%) and the confusion matrix showed a divide between conservation and production types. Understory Leaf Area Index (LAI) and the variation in vegetation density in the upper half of the canopy were the most important classification metrics. In particular, LAI understory showed the most variation, and may help advance ecological understanding in restoration. The difference in classification success underlines the difficulty of distinguishing individual forest types that are very similar in management, regeneration dynamics, and structure. In a restoration context, we showed the ability of UAV-borne LiDAR to identify complex forest structures at a plot scale and identify groups and types widely distributed across different restored landscapes with medium to high accuracy. Future research may explore a fusion of UAV-borne LiDAR with optical sensors , include successional stages in the analyses to further characterize , distinguish forest types and their contributions to landscape restoration

Exploring the Potential of Feature Selection Methods in the Classification of Urban Trees Using Field Spectroscopy Data

Mapping of vegetation at the species level using hyperspectral satellite data can be effective and accurate because of its high spectral and spatial resolutions that can detect detailed information of a target object. Its wide application, however, not only is restricted by its high cost and large data storage requirements, but its processing is also complicated by challenges of what is known as the Hughes effect. The Hughes effect is where classification accuracy decreases once the number of features or wavelengths passes a certain limit. This study aimed to explore the potential of feature selection methods in the classification of urban trees using field hyperspectral data. We identified the best feature selection method of key wavelengths that respond to the target urban tree species for effective and accurate classification. The study compared the effectiveness of Principal Component Analysis Discriminant Analysis (PCA-DA), Partial Least Squares Discriminant Analysis (PLS-DA) and Guided Regularized Random Forest (GRRF) in feature selection of the key wavelengths for classification of urban trees. The classification performance of Random Forest (RF) and Support Vector Machines (SVM) algorithms were also compared to determine the importance of the key wavelengths selected for the detection of the target urban trees. The feature selection methods managed to reduce the high dimensionality of the hyperspectral data. Both the PCA-DA and PLS-DA selected 10 wavelengths and the GRRF algorithm selected 13 wavelengths from the entire dataset (n = 1523). Most of the key wavelengths were from the short-wave infrared region (1300-2500 nm). SVM outperformed RF in classifying the key wavelengths selected by the feature selection methods. The SVM classifier produced overall accuracy values of 95.3%, 93.3% and 86% using the GRRF, PLS-DA and PCA-DA techniques, respectively, whereas those for the RF classifier were 88.7%, 72% and 56.8%, respectively

A robust dynamic classifier selection approach for hyperspectral images with imprecise label information

Supervised hyperspectral image (HSI) classification relies on accurate label information. However, it is not always possible to collect perfectly accurate labels for training samples. This motivates the development of classifiers that are sufficiently robust to some reasonable amounts of errors in data labels. Despite the growing importance of this aspect, it has not been sufficiently studied in the literature yet. In this paper, we analyze the effect of erroneous sample labels on probability distributions of the principal components of HSIs, and provide in this way a statistical analysis of the resulting uncertainty in classifiers. Building on the theory of imprecise probabilities, we develop a novel robust dynamic classifier selection (R-DCS) model for data classification with erroneous labels. Particularly, spectral and spatial features are extracted from HSIs to construct two individual classifiers for the dynamic selection, respectively. The proposed R-DCS model is based on the robustness of the classifiers’ predictions: the extent to which a classifier can be altered without changing its prediction. We provide three possible selection strategies for the proposed model with different computational complexities and apply them on three benchmark data sets. Experimental results demonstrate that the proposed model outperforms the individual classifiers it selects from and is more robust to errors in labels compared to widely adopted approaches

Tree Species Traits Determine the Success of LiDAR-based Crown Mapping in a Mixed Temperate Forest

Automated individual tree crown delineation (ITCD) via remote sensing platforms offers a path forward to obtain wall-to-wall detailed tree inventory/information over large areas. While LiDAR-based ITCD methods have proven successful in conifer dominated forests, it remains unclear how well these methods can be applied broadly in deciduous broadleaf (hardwood) dominated forests. In this study, I applied five common automated LiDAR-based ITCD methods across fifteen plots ranging from conifer- to hardwood- dominated at the Harvard Forest in Petersham, MA, USA, and assess accuracy against manually delineation crowns. I then identified basic tree- and plot-level factors influencing the success of delineation techniques. My results showed that automated crown delineation shows promise in closed canopy mixed-species forests. There was relatively little difference between crown delineation methods (51-59% aggregated plot accuracy), and despite parameter tuning, none of the methods produce high accuracy across all plots (27 – 90% range in plot-level accuracy). I found that all methods delineate conifer species (mean 64%) better than hardwood species (mean 42%), and that accuracy of each method varied similarly across plots and was significantly related to plot-level conifer fraction. Further, while tree-level factors related to tree size (DBH, height and crown area) all strongly influenced the success of crown delineations, the influence of plot-level factors varied. Species evenness (relative species abundance) was the most important plot-level variable controlling crown delineation success, and as species evenness decreased, the probability of successful delineation increased. Evenness was likely important due to 1) its negative relationship to conifer fraction and 2) a relationship between evenness and increased canopy space filling efficiency. Overall, my work suggests that the ability to delineate crowns is not strongly driven by methodological differences, but instead driven by differences in functional group (conifer vs. hardwood) tree size and diversity and how crowns are displayed in relation to each other. While LiDAR-based ITCD methods are well suited for conifer dominated plots with distinct canopy structure, they remain less reliable in hardwood dominated plots. I suggest that future work focus on integrating phenology and spectral characteristics with existing LiDAR approaches to better delineate hardwood dominated stands

The Burning Bush: Linking LiDAR-derived Shrub Architecture to Flammability

Light detection and ranging (LiDAR) and terrestrial laser scanning (TLS) sensors are powerful tools for characterizing vegetation structure and for constructing three-dimensional (3D) models of trees, also known as quantitative structural models (QSM). 3D models and structural traits derived from them provide valuable information for biodiversity conservation, forest management, and fire behavior modeling. However, vegetation studies and 3D modeling methodologies often only focus on the forest canopy, with little attention given to understory vegetation. In particular, 3D structural information of shrubs is limited or not included in fire behavior models. Yet, understory vegetation is an important component of forested ecosystems, and has an essential role in determining fire behavior. In this dissertation, I explored the use of TLS data and quantitative structure models to model shrub architecture in three related studies. In the first study, I present a semi-automated methodology for reconstructing architecturally different shrubs from TLS LiDAR. By investigating shrubs with different architectures and point cloud densities, I showed that occlusion, shrub complexity, and shape greatly affect the accuracy of shrub models. In my second study, I assessed the 3D architectural drivers of understory flammability by evaluating the use of architectural metrics derived from the TLS point cloud and 3D reconstructions of the shrubs. I focused on eight species common in the understory of the fire-prone longleaf pine forest ecosystem of the state of Florida, USA. I found a general tendency for each species to be associated with a unique combination of flammability and architectural traits. Novel shrub architectural traits were found to be complementary to the direct use of TLS data and improved flammability predictions. The inherent complexity of shrub architecture and uncertainty in the TLS point cloud make scaling up from an individual shrub to a plot level a challenging task. Therefore, in my third study, I explored the effects of lidar uncertainty on vegetation parameter prediction accuracy. I developed a practical workflow to create synthetic forest stands with varying densities, which were subsequently scanned with simulated terrestrial lidar. This provided data sets quantitatively similar to those created by real-world LiDAR measurements, but with the advantage of exact knowledge of the forest plot parameters, The results showed that the lidar scan location had a large effect on prediction accuracy. Furthermore, occlusion is strongly related to the sampling density and plot complexity. The results of this study illustrate the potential of non-destructive lidar approaches for quantifying shrub architectural traits. TLS, empirical quantitative structural models, and synthetic models provide valuable insights into shrub structure and fire behavior

Inferring plant–plant interactions using remote sensing

Rapid technological advancements and increasing data availability have improved the capacity to monitor and evaluate Earth's ecology via remote sensing. However, remote sensing is notoriously ‘blind’ to fine-scale ecological processes such as interactions among plants, which encompass a central topic in ecology. Here, we discuss how remote sensing technologies can help infer plant–plant interactions and their roles in shaping plant-based systems at individual, community and landscape levels. At each of these levels, we outline the key attributes of ecosystems that emerge as a product of plant–plant interactions and could possibly be detected by remote sensing data. We review the theoretical bases, approaches and prospects of how inference of plant–plant interactions can be assessed remotely. At the individual level, we illustrate how close-range remote sensing tools can help to infer plant–plant interactions, especially in experimental settings. At the community level, we use forests to illustrate how remotely sensed community structure can be used to infer dominant interactions as a fundamental force in shaping plant communities. At the landscape level, we highlight how remotely sensed attributes of vegetation states and spatial vegetation patterns can be used to assess the role of local plant–plant interactions in shaping landscape ecological systems. Synthesis. Remote sensing extends the domain of plant ecology to broader and finer spatial scales, assisting to scale ecological patterns and search for generic rules. Robust remote sensing approaches are likely to extend our understanding of how plant–plant interactions shape ecological processes across scales—from individuals to landscapes. Combining these approaches with theories, models, experiments, data-driven approaches and data analysis algorithms will firmly embed remote sensing techniques into ecological context and open new pathways to better understand biotic interactions

Identifier les arbres du Québec grâce à la spectroscopie foliaire : différenciation fonctionnelle et phylogénétique des espèces

La spectroscopie représente un puissant outil en conservation grâce à la possibilité d’effectuer le suivi de la diversité végétale à travers de larges étendues géographiques. La réflectance spectrale montre un potentiel certain pour l’identification des espèces d’arbres et même des taxons inférieurs, mais ceci a rarement été testé sur un grand nombre d’espèces. J’examine la qualité de la classification de 45 espèces d’arbres des forêts tempérées du Québec à partir de plus de 3500 spectres de réflectance foliaires (400-2400 nm). Nous évaluons cette classification sur la base de la variation spectrale des espèces, de même qu’à partir des distances fonctionnelles et phylogénétiques mesurées. Nos résultats indiquent un taux de classification très satisfaisant (κ = 0.736, ±0.005). Nous observons des erreurs de classification plus fréquentes entre les espèces évolutivement proches, alors qu’il semble que la distance fonctionnelle établisse un seuil voulant qu'au-delà d’une certaine distinction fonctionnelle globale, il soit peu probable que deux espèces soient confondues. Ces résultats viennent renforcer le lien entre la diversité spectrale et l’organisation taxonomique des espèces, ajoutant à la valeur de substitution de la première pour la diversité phylogénétique. Cela suggère par contre que de fortes convergences fonctionnelles peuvent faire obstacle à l’identification des espèces à partir de la réflectance spectrale. Cette étude est prometteuse pour la classification de spectres foliaires non préalablement identifiés, et améliore notre compréhension du lien entre les données spectrales et la différenciation des espèces, d’une grande importance pour assurer la validité des estimations de la biodiversité à partir de données de télédétection.Imaging Spectroscopy is a powerful tool for conservation due to its ability to monitor plant diversity over broad geographic areas. Increasing evidence suggests that spectral reflectance can be used to identify trees at the species level, and even below. However, most studies focus on only a few species. Here, we use foliar reflectance (400-2400 nm) to discriminate among 45 temperate forest tree species from southern Quebec, using over 3500 leaf-level spectra. Furthermore, we connect those classification results to functional and phylogenetic distinctiveness, as well as to intraspecific variation. We find that spectral reflectance shows a very good discriminatory power even with an extensive set of species (κ = 0.736, ±0.005). We find that close phylogenetic species get mistaken for one another more frequently than distantly related species, while functional variation acts as a threshold, beyond which misclassifications are unlikely. These results reinforce the link between spectral diversity and taxonomic organization or phylogenetic diversity, but also reiterate the potential confounding effects of functional convergences on species identification from hyperspectral reflectance. We believe these findings hold promise for the classification of unknown spectra and further improve the link between ground truth and remotely sensed data for biodiversity assessments

Fusion Approaches to Individual Tree Species Classification Using Multi-Source Remotely Sensed Data

Tree species information plays essential roles in urban ecological management and sustainable development, and thus tree species classification has been an active research topic over the years. This study investigated fusion approaches deployed with Support Vector Machine (SVM) and Random Forest (RF) algorithms to incorporating multispectral imagery (MSI), a very high spatial resolution panchromatic image (PAN), and Light Detection and Ranging (LiDAR) data for five object-based tree species classification in an urban environment. The results demonstrated that 3D structural features contributed more to tree species with broad crowns, such as honey locust and Austrian pine, whereas textural features were more effective in differentiating trees in narrow crowns, such as spruce. Among all the possible classification schemes based on multi-source features in combinations, decision fusion achieved the best overall accuracies (0.86 for SVM and 0.84 for RF), slightly outperforming the feature fusion approach (0.85 for SVM and 0.83 for RF). Both fusion approaches significantly improved tree species classifications produced by MSI (0.7), PAN (0.74), and LiDAR (0.8) individually