A Robust Stepwise Clustering Approach to Detect Individual Trees in Temperate Hardwood Plantations Using Airborne LiDAR Data

Precise tree inventory plays a critical role in sustainable forest planting, restoration, and management. LiDAR-based individual tree detection algorithms often focus on finding individual treetops to discern tree positions. However, deliquescent tree forms (broad, flattened crowns) in deciduous forests can make these algorithms ineffective. In this study, we propose a stepwise tree detection approach, by first identifying individual trees using horizontal point density and then analyzing their vertical structure profiles. We first project LiDAR data onto a 2D horizontal plane and apply mean shift clustering to generate candidate tree clusters. Next, we apply a series of structure analyses on the vertical phase, to overcome local variations in crown size and tree density. This study demonstrates that the horizontal point density of LiDAR data provides critical information to locate and isolate individual trees in temperate hardwood plantations with varied densities, while vertical structure profiles can identify spreading branches and reconstruct deliquescent crowns. One challenge of applying mean shift clustering is training a dynamic search kernel to identify trees of different sizes, which usually requires a large number of field measurements. The stepwise approach proposed in this study demonstrated robustness when using a constant kernel in clustering, making it an efficient tool for large-scale analysis. This stepwise approach was designed for quantifying temperate hardwood plantation inventories using relatively low-density airborne LiDAR, and it has potential applications for monitoring large-scale plantation forests. Further research is needed to adapt this method to natural stands with diverse tree ages and structures

Stand Delineation of Pinus sylvestris L. Plantations Suffering Decline Processes Based on Biophysical Tree Crown Variables: A Necessary Tool for Adaptive Silviculture

Many planted Pinus forests are severely affected by defoliation and mortality processes caused by pests and droughts. The mapping of forest tree crown variables (e.g., leaf area index and pigments) is particularly useful in stand delineation for the management of declining forests. This work explores the potential of integrating multispectral WorldView-2 (WV-2) and Airborne Laser Scanning (ALS) data for stand delineation based on selected tree crown variables in Pinus sylvestris plantations in southern Spain. Needle pigments (chlorophyll and carotenes) and leaf area index (LAI) were quantified. Eight vegetation indices and ALS-derived metrics were produced, and seven predictors were selected to estimate and map tree crown variables using a Random Forest method and Gini index. Chlorophylls a and b (Chla and Chlb) were significantly higher in the non-defoliated and moderately defoliated trees than in severely defoliated trees (F = 14.02, p < 0.001 for Chla; F = 13.09, p < 0.001 for Chlb). A similar response was observed for carotenoids (Car) (F = 14.13, p < 0.001). The LAI also showed significant differences among the defoliation levels (F = 26.5, p < 0.001). The model for the chlorophyll a pigment used two vegetation indices, Plant Senescence Reflectance Index (PSRI) and Carotenoid Reflectance Index (CRI); three WV-2 band metrics, and three ALS metrics. The model built to describe the tree Chlb content used similar variables. The defoliation classification model was established with a single vegetation index, Green Normalized Difference Vegetation Index (GNDVI); two metrics of the blue band, and two ALS metrics. The pigment contents models provided R2 values of 0.87 (Chla, RMSE = 12.98%), 0.74 (Chlb, RMSE = 10.39%), and 0.88 (Car, RMSE = 10.05%). The cross-validated confusion matrix achieved a high overall classification accuracy (84.05%) and Kappa index (0.76). Defoliation and Chla showed the validation values for segmentations and, therefore, in the generation of the stand delineation. A total of 104 stands were delineated, ranging from 6.96 to 54.62 ha (average stand area = 16.26 ha). The distribution map of the predicted severity values in the P. sylvestris plantations showed a mosaic of severity patterns at the stand and individual tree scales. Overall, the findings of this work underscore the potential of WV-2 and ALS data integration for the assessment of stand delineation based on tree health status. The derived cartography is a relevant tool for developing adaptive silvicultural practices to reduce Pinus sylvestris mortality in planted forests at risk due to climate change

Benchmarking airborne laser scanning tree segmentation algorithms in broadleaf forests shows high accuracy only for canopy trees

Individual tree segmentation from airborne laser scanning data is a longstanding and important challenge in forest remote sensing. Tree segmentation algorithms are widely available, but robust intercomparison studies are rare due to the difficulty of obtaining reliable reference data. Here we provide a benchmark data set for temperate and tropical broadleaf forests generated from labelled terrestrial laser scanning data. We compared the performance of four widely used tree segmentation algorithms against this benchmark data set. All algorithms performed reasonably well on the canopy trees. The point cloud-based algorithm AMS3D (Adaptive Mean Shift 3D) had the highest overall accuracy, closely followed by the 2D raster based region growing algorithm Dalponte2016 +. However, all algorithms failed to accurately segment the understory trees. This result was consistent across both forest types. This study emphasises the need to assess tree segmentation algorithms directly using benchmark data, rather than comparing with forest indices such as biomass or the number and size distribution of trees. We provide the first openly available benchmark data set for tropical forests and we hope future studies will extend this work to other regions

A Density-Based Algorithm for the Detection of Individual Trees from LiDAR Data

Nowadays, LiDAR is widely used for individual tree detection, usually providing higher accuracy in coniferous stands than in deciduous ones, where the rounded-crown, the presence of understory vegetation, and the random spatial tree distribution may affect the identification algorithms. In this work, we propose a novel algorithm that aims to overcome these difficulties and yield the coordinates and the height of the individual trees on the basis of the point density features of the input point cloud. The algorithm was tested on twelve deciduous areas, assessing its performance on both regular-patterned plantations and stands with randomly distributed trees. For all cases, the algorithm provides high accuracy tree count (F-score > 0.7) and satisfying stem locations (position error around 1.0 m). In comparison to other common tools, the algorithm is weakly sensitive to the parameter setup and can be applied with little knowledge of the study site, thus reducing the effort and cost of field campaigns. Furthermore, it demonstrates to require just 2 points·m^−2 as minimum point density, allowing for the analysis of low-density point clouds. Despite its simplicity, it may set the basis for more complex tools, such as those for crown segmentation or biomass computation, with potential applications in forest modeling and management

Tree crown segmentation in three dimensions using density models derived from airborne laser scanning

This article describes algorithms to extract tree crowns using two-dimensional (2D) and three-dimensional (3D) segmentation. As a first step, a 2D-search detected the tallest trees but was unable to detect trees located below other trees. However, a 3D-search for local maxima of model fits could be used in a second step to detect trees also in lower canopy layers. We compared tree detection results from ALS carried out at 1450 m above ground level (high altitude) and tree detection results from ALS carried out at 150 m above ground level (low altitude). For validation, we used manual measurements of trees in ten large field plots, each with an 80 m diameter, in a hemiboreal forest in Sweden (lat. 58 degrees 28' N, long. 13 degrees 38' E). In order to measure the effect of using algorithms with different computational costs, we validated the tree detection from the 2D segmentation step and compared the results with the 2D segmentation followed by 3D segmentation of the ALS point cloud. When applying 2D segmentation only, the algorithm detected 87% of the trees measured in the field using high-altitude ALS data; the detection rate increased to 91% using low-altitude ALS data. However, when applying 3D segmentation as well, the algorithm detected 92% of the trees measured in the field using high-altitude ALS data; the detection rate increased to 99% using low-altitude ALS data. For all combinations of algorithms and data resolutions, undetected trees accounted for, on average, 0-5% of the total stem volume in the field plots. The 3D tree crown segmentation, which was using crown density models, made it possible to detect a large percentage of trees in multi-layered forests, compared with using only a 2D segmentation method

Site index estimation using airborne laser data in Eucalyptus dunnii Maide stands in Uruguay

Premio extraordinario de Trabajo Fin de Máster curso 2020/2021. Máster en Geomática, Teledetección y Modelos Espaciales Aplicados a la Gestión ForestalThe estimation of forest variables to support a forest inventory can be approached through the use of different technologies. Although field sampling is the most widely implemented technique, the development of remote sensing techniques increases the possibilities of action in this field. One of these technologies is the airborne LiDAR scanner (ALS). In this study, linear models and non-parametric models with Random Forest imputation were generated to estimate the total height (HT) and site index (SI) of Eucalyptus dunnii Maide, based on LiDAR metrics. High spatial resolution continuous rasters for HT and SI were created with these models. The use of a semi-automatic object-oriented segmentation algorithm for stand delimitation based on the SI raster was then carried out. To evaluate the performance of these models, the One Leave One cross-validation technique was implemented, determining for each model the ratio between the RMSE of the model and the RMSE of the cross-validation (RMSEcv). Linear models for HT estimation presented a better fit (R2=0.84, RMSE=0.84 m, MAPE=0.039, Bias=0.002) than the Random Forest (R2=0.85, RMSE=1.26 m, MAPE=7.19, Bias=-0.173) model including only independent variable the 99th percentile. The RMSE/RMSEcv ratio presented a higher value for the linear model (0.93) than Random Forest (0.75). For the estimation of the site index (SI), the Random Forest model was applied, which included the LiDAR metrics corresponding to the 99th percentile and the 80th bicentile. This model had an R2 value of 0.65 and an RMSE value of 1.62 m. Then, on the SI raster generated by the Random Forest model, automatic segmentation was applied, generating segments with high internal homogeneity and low homogeneity between segments. The methodology developed in this work provides accurate estimates and mapping of HT and SI at stand scale based on LiDAR data. In addition, an automatic segmentation method was applied, generating stands based on the SI. This segmentation is very useful for the sector as it is a tool that will improve forest management in terms of harvesting and future plantations

Three-dimensional Segmentation of Trees Through a Flexible Multi-Class Graph Cut Algorithm (MCGC)

Developing a robust algorithm for automatic individual tree crown (ITC) detection from airborne laser scanning datasets is important for tracking the responses of trees to anthropogenic change. Such approaches allow the size, growth and mortality of individual trees to be measured, enabling forest carbon stocks and dynamics to be tracked and understood. Many algorithms exist for structurally simple forests including coniferous forests and plantations. Finding a robust solution for structurally complex, species-rich tropical forests remains a challenge; existing segmentation algorithms often perform less well than simple area-based approaches when estimating plot-level biomass. Here we describe a Multi-Class Graph Cut (MCGC) approach to tree crown delineation. This uses local three-dimensional geometry and density information, alongside knowledge of crown allometries, to segment individual tree crowns from airborne LiDAR point clouds. Our approach robustly identifies trees in the top and intermediate layers of the canopy, but cannot recognise small trees. From these three-dimensional crowns, we are able to measure individual tree biomass. Comparing these estimates to those from permanent inventory plots, our algorithm is able to produce robust estimates of hectare-scale carbon density, demonstrating the power of ITC approaches in monitoring forests. The flexibility of our method to add additional dimensions of information, such as spectral reflectance, make this approach an obvious avenue for future development and extension to other sources of three-dimensional data, such as structure from motion datasets.Jonathan Williams holds a NERC studentship [NE/N008952/1] which is a CASE partnership with support from Royal Society for the Protection of Birds (RSPB). David Coomes was supported by an International Academic Fellowship from the Leverhulme Trust. Carola-Bibiane Schoenlieb was supported by the RISE projects CHiPS and NoMADS, the Cantab Capital Institute for the Mathematics of Information and the Alan Turing Institute. We gratefully acknowledge the support of NVIDIA Corporation with the donation of a Quadro P6000 GPU used for this research

Quantifying the urban forest environment using dense discrete return LiDAR and aerial color imagery for segmentation and object-level biomass assessment

The urban forest is becoming increasingly important in the contexts of urban green space and recreation, carbon sequestration and emission offsets, and socio-economic impacts. In addition to aesthetic value, these green spaces remove airborne pollutants, preserve natural resources, and mitigate adverse climate changes, among other benefits. A great deal of attention recently has been paid to urban forest management. However, the comprehensive monitoring of urban vegetation for carbon sequestration and storage is an under-explored research area. Such an assessment of carbon stores often requires information at the individual tree level, necessitating the proper masking of vegetation from the built environment, as well as delineation of individual tree crowns. As an alternative to expensive and time-consuming manual surveys, remote sensing can be used effectively in characterizing the urban vegetation and man-made objects. Many studies in this field have made use of aerial and multispectral/hyperspectral imagery over cities. The emergence of light detection and ranging (LiDAR) technology, however, has provided new impetus to the effort of extracting objects and characterizing their 3D attributes - LiDAR has been used successfully to model buildings and urban trees. However, challenges remain when using such structural information only, and researchers have investigated the use of fusion-based approaches that combine LiDAR and aerial imagery to extract objects, thereby allowing the complementary characteristics of the two modalities to be utilized. In this study, a fusion-based classification method was implemented between high spatial resolution aerial color (RGB) imagery and co-registered LiDAR point clouds to classify urban vegetation and buildings from other urban classes/cover types. Structural, as well as spectral features, were used in the classification method. These features included height, flatness, and the distribution of normal surface vectors from LiDAR data, along with a non-calibrated LiDAR-based vegetation index, derived from combining LiDAR intensity at 1064 nm with the red channel of the RGB imagery. This novel index was dubbed the LiDAR-infused difference vegetation index (LDVI). Classification results indicated good separation between buildings and vegetation, with an overall accuracy of 92% and a kappa statistic of 0.85. A multi-tiered delineation algorithm subsequently was developed to extract individual tree crowns from the identified tree clusters, followed by the application of species-independent biomass models based on LiDAR-derived tree attributes in regression analysis. These LiDAR-based biomass assessments were conducted for individual trees, as well as for clusters of trees, in cases where proper delineation of individual trees was impossible. The detection accuracy of the tree delineation algorithm was 70%. The LiDAR-derived biomass estimates were validated against allometry-based biomass estimates that were computed from field-measured tree data. It was found out that LiDAR-derived tree volume, area, and different distribution parameters of height (e.g., maximum height, mean of height) are important to model biomass. The best biomass model for the tree clusters and the individual trees showed an adjusted R-Squared value of 0.93 and 0.58, respectively. The results of this study showed that the developed fusion-based classification approach using LiDAR and aerial color (RGB) imagery is capable of producing good object detection accuracy. It was concluded that the LDVI can be used in vegetation detection and can act as a substitute for the normalized difference vegetation index (NDVI), when near-infrared multiband imagery is not available. Furthermore, the utility of LiDAR for characterizing the urban forest and associated biomass was proven. This work could have significant impact on the rapid and accurate assessment of urban green spaces and associated carbon monitoring and management

Stand Characterization of Eucalyptus spp. Plantations in Uruguay Using Airborne Lidar Scanner Technology

Airborne lidar scanner (ALS) technology is used in a variety of applications, including forestry. ALS has enormous potential for the estimation of relevant biometric parameters in forest plantations. This study investigates the use of an object-oriented semi-automated segmentation algorithm for stands delineation, based on modeling ALS data, in plantations of Eucalyptus grandis and E. dunnii in Uruguay. The results show that non-parametric methods delivered more accurate and less biased results for total volume (TV) with R2 0.93, RMSE 20.04 m3 h−1 for E. grandis and R2 0.93, RMSE 18.43 m3 h−1 for E.dunnii; and above ground biomass (AGB) with R2 0.95, RMSE 70.2 kg h−1 for E. grandis and R2 0.96, RMSE: 71.2 Kg h−1 for E. dunnii. Parametric methods performed better for dominant height (Ho) with R2 0.98, RMSE 0.67 m and R2: 0.96, RMSE: 0.8 m for E. grandis and E. dunnii, respectively. The most informative ALS metrics for the estimation of AGB and TV were metrics related to the elevation in parametric models (Elev.70 and Elev.75), while for the non-parametric models (k-NN) they were Elev.75 and canopy density. For Ho, the ALS metrics selected were also related to elevation both in the parametric (Elev.90 and Elev.99) and random forest models (Elev.max and Elev.75). The segmentation methodology proposed here matched closely the segments delineated by human operators, and provides a low-cost, cost-effective, easy to apply and update model aimed at generating AGB or TV maps for harvest tasks, based on rasters derived from ALS metrics. The present research shows the capacity of ALS metrics to improve extensive strategic inventories; validating and promoting the adoption of ALS technology for inventory forest stands of Eucalyptus spp. in Uruguay

Individual tree detection using template matching of multiple rasters derived from multispectral airborne laser scanning data

Multispectral airborne laser scanning (MS-ALS) provides information about 3D structure as well as the intensity of the reflected light and is a promising technique for acquiring forest information. Data from MS-ALS have been used for tree species classification and tree health evaluation. This paper investigates its potential for individual tree detection (ITD) when using intensity as an additional metric. To this end, rasters of height, point density, vegetation ratio, and intensity at three wavelengths were used for template matching to detect individual trees. Optimal combinations of metrics were identified for ITD in plots with different levels of canopy complexity. The F-scores for detection by template matching ranged from 0.94 to 0.73, depending on the choice of template derivation and raster generalization methods. Using intensity and point density as metrics instead of height increased the F-scores by up to 14% for the plots with the most understorey trees