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The rapid and accurate assessment of above ground biomass (AGB) of woody vegetation is a critical component of climate mitigation strategies, land management practices and process-based models of ecosystem function. This is especially true of semi-arid ecosystems, where the high variability in precipitation and disturbance regimes can have dramatic impacts on the global carbon budget by rapidly transitioning AGB between live and dead pools. Measuring regional AGB requires scaling ground-based measurements using remote sensing, an inherently challenging task in the sparsely-vegetated, spatially-heterogeneous landscapes characteristic of semi-arid regions. Here, we test the ability of canopy segmentation and statistic generation based on aerial LiDAR (light detection and ranging)-derived 3D point clouds to derive AGB in clumps of vegetation in a juniper savanna in central New Mexico. We show that single crown segmentation, often an error-prone and challenging task, is not required to produce accurate estimates of AGB. We leveraged the relationship between the volume of the segmented vegetation clumps and the equivalent stem diameter of the corresponding trees (R2 = 0.83, p < 0.001) to drive the allometry for J. monosperma on a per segment basis. Further, we showed that making use of the full 3D point cloud from LiDAR for the generation of canopy object statistics improved that relationship by including canopy segment point density as a covariate (R2 = 0.91). This work suggests the potential for LiDAR-derived estimates of AGB in spatially-heterogeneous and highly-clumped ecosystems.

Individual tree crown (ITC) segmentation is an approach to isolate individual tree from the background vegetation and delineate precisely the crown boundaries for forest management and inventory purposes. ITC detection and delineation have been commonly generated from canopy height model (CHM) derived from light detection and ranging (LiDAR) data. Existing ITC segmentation methods, however, are limited in their efficiency for characterizing closed canopies, especially in tropical forests, due to the overlapping structure and irregular shape of tree crowns. Furthermore, the potential of 3-dimensional (3D) LiDAR data is not fully realized by existing CHM-based methods. Thus, the aim of this study was to develop an efficient framework for ITC segmentation in tropical forests using LiDAR-derived CHM and 3D point cloud data in order to accurately estimate tree attributes such as the tree height, mean crown width and aboveground biomass (AGB). The proposed framework entails five major steps: (1) automatically identifying dominant tree crowns by implementing semi-variogram statistics and morphological analysis; (2) generating initial tree segments using a watershed algorithm based on mathematical morphology; (3) identifying “problematic” segments based on predetermined set of rules; (4) tuning the problematic segments using a modified distance-based algorithm (DBA); and (5) segmenting and counting the number of individual trees based on the 3D LiDAR point clouds within each of the identified segment. This approach was developed in a way such that the 3D LiDAR points were only examined on problematic segments identified for further evaluations. 209 reference trees with diameter at breast height (DBH) ≥ 10 cm were selected in the field in two study areas in order to validate ITC detection and delineation results of the proposed framework. We computed tree crown metrics (e.g., maximum crown height and mean crown width) to estimate aboveground biomass (AGB) at tree level using previously published allometric equations. Accuracy assessment was performed to calculate percentage of correctly detected trees, omission and commission errors. Our method correctly identified individual tree crowns with detection accuracy exceeding 80 percent at both forest sites. Also, our results showed high agreement (R2 > 0.64) in terms of AGB estimates using 3D LiDAR metrics and variables measured in the field, for both sites. The findings from our study demonstrate the efficacy of the proposed framework in delineating tree crowns, even in high canopy density areas such as tropical rainforests, where, usually the traditional algorithms are limited in their performances. Moreover, the high tree delineation accuracy in the two study areas emphasizes the potential robustness and transferability of our approach to other densely forested areas across the globe.

Precise monitoring of individual crop growth and health status is crucial for precision agriculture practices. However, traditional inspection methods are time-consuming, labor-intensive, prone to human error, and may not provide the comprehensive coverage required for the detailed analysis of crop variability across an entire field. This research addresses the need for efficient and high-resolution crop monitoring by leveraging Unmanned Aerial Vehicle (UAV) imagery and advanced computational techniques. The primary goal was to develop a methodology for the precise identification, extraction, and monitoring of individual corn crops throughout their growth cycle. This involved integrating UAV-derived data with image processing, computational geometry, and machine learning techniques. Bi-weekly UAV imagery was captured at altitudes of 40 m and 70 m from 30 April to 11 August, covering the entire growth cycle of the corn crop from planting to harvest. A time-series Canopy Height Model (CHM) was generated by analyzing the differences between the Digital Terrain Model (DTM) and the Digital Surface Model (DSM) derived from the UAV data. To ensure the accuracy of the elevation data, the DSM was validated against Ground Control Points (GCPs), adhering to standard practices in remote sensing data verification. Local spatial analysis and image processing techniques were employed to determine the local maximum height of each crop. Subsequently, a Voronoi data model was developed to delineate individual crop canopies, successfully identifying 13,000 out of 13,050 corn crops in the study area. To enhance accuracy in canopy size delineation, vegetation indices were incorporated into the Voronoi model segmentation, refining the initial canopy area estimates by eliminating interference from soil and shadows. The proposed methodology enables the precise estimation and monitoring of crop canopy size, height, biomass reduction, lodging, and stunted growth over time by incorporating advanced image processing techniques and integrating metrics for quantitative assessment of fields. Additionally, machine learning models were employed to determine relationships between the canopy sizes, crop height, and normalized difference vegetation index, with Polynomial Regression recording an R-squared of 11% compared to other models. This work contributes to the scientific community by demonstrating the potential of integrating UAV technology, computational geometry, and machine learning for accurate and efficient crop monitoring at the individual plant level.

Accurate detection and delineation of individual trees and their crowns in dense forest environments are essential for forest management and ecological applications. This study explores the potential of combining leaf-off and leaf-on structure from motion (SfM) data products from unoccupied aerial vehicles (UAVs) equipped with RGB cameras. The main objective was to develop a reliable method for precise tree stem detection and crown delineation in dense deciduous forests, demonstrated at a structurally diverse old-growth forest in the Hainich National Park, Germany. Stem positions were extracted from the leaf-off point cloud by a clustering algorithm. The accuracy of the derived stem co-ordinates and the overall UAV-SfM point cloud were assessed separately, considering different tree types. Extracted tree stems were used as markers for individual tree crown delineation (ITCD) through a region growing algorithm on the leaf-on data. Stem positioning showed high precision values (0.867). Including leaf-off stem positions enhanced the crown delineation, but crown delineations in dense forest canopies remain challenging. Both the number of stems and crowns were underestimated, suggesting that the number of overstory trees in dense forests tends to be higher than commonly estimated in remote sensing approaches. In general, UAV-SfM point clouds prove to be a cost-effective and accurate alternative to LiDAR data for tree stem detection. The combined datasets provide valuable insights into forest structure, enabling a more comprehensive understanding of the canopy, stems, and forest floor, thus facilitating more reliable forest parameter extraction.

Broad scale remote sensing promises to build forest inventories at unprecedented scales. A crucial step in this process is to associate sensor data into individual crowns. While dozens of crown detection algorithms have been proposed, their performance is typically not compared based on standard data or evaluation metrics. There is a need for a benchmark dataset to minimize differences in reported results as well as support evaluation of algorithms across a broad range of forest types. Combining RGB, LiDAR and hyperspectral sensor data from the USA National Ecological Observatory Network’s Airborne Observation Platform with multiple types of evaluation data, we created a benchmark dataset to assess crown detection and delineation methods for canopy trees covering dominant forest types in the United States. This benchmark dataset includes an R package to standardize evaluation metrics and simplify comparisons between methods. The benchmark dataset contains over 6,000 image-annotated crowns, 400 field-annotated crowns, and 3,000 canopy stem points from a wide range of forest types. In addition, we include over 10,000 training crowns for optional use. We discuss the different evaluation data sources and assess the accuracy of the image-annotated crowns by comparing annotations among multiple annotators as well as overlapping field-annotated crowns. We provide an example submission and score for an open-source algorithm that can serve as a baseline for future methods.

Precision agriculture-based orchard management relies heavily on the accurate delineation of tree canopies, especially for high-value crops like mangoes. Traditional GIS and remote sensing methods, such as Object-Based Imagery Analysis (OBIA), often face challenges due to overlapping canopies, complex tree structures, and varied light conditions. This study aims to enhance the accuracy of mango orchard mapping by developing a novel deep-learning approach that combines fine-tuned object detection and segmentation techniques. UAV imagery was collected over a 65-acre mango orchard in Multan, Pakistan, and processed into an RGB orthomosaic with a 3 cm ground sampling distance. The You Only Look Once (YOLOv7) framework was trained on an annotated dataset to detect individual mango trees. The resultant bounding boxes were used as prompts for the segment anything model (SAM) for precise delineation of canopy boundaries. Validation against ground truth data of 175 manually digitized trees showed a strong correlation (R2 = 0.97), indicating high accuracy and minimal bias. The proposed method achieved a mean absolute percentage error (MAPE) of 4.94% and root mean square error (RMSE) of 80.23 sq ft against manually digitized tree canopies with an average size of 1290.14 sq ft. The proposed approach effectively addresses common issues such as inaccurate bounding boxes and over- or under-segmentation of tree canopies. The enhanced accuracy can substantially assist in various downstream tasks such as tree location mapping, canopy volume estimation, health monitoring, and crop yield estimation.

Accurate individual tree crown delineation (ITCD), which can be used to estimate various forest parameters such as biomass, stem density, and carbon storage, stands as an essential component of precision forestry. Currently, raster data such as the canopy height model derived from airborne light detection and ranging (LiDAR) data have been widely used in large-scale ITCD. However, the accuracy of current existing algorithms is limited due to the influence of understory vegetation and variations in tree crown geometry (e.g., the delineated crown boundaries consistently extend beyond their actual boundaries). In this study, we achieved more accurate crown delineation results based on an expansion process. First, the initial crown boundaries were extracted through watershed segmentation. Then, a “from the inside out” expansion process was guided by a novel gradient feature to obtain accurate crown delineation results across different forest conditions. Results show that our method produced much better performance (~75% matched on average) than other commonly used methods across all test forest plots. The erroneous situation of “match but over-grow” is significantly reduced, regardless of forest conditions. Compared to other methods, our method demonstrates a notable increase in the precisely matched rate across different plot types, with an average increase of 25% in broadleaf plots, 18% in coniferous plots, 23% in mixed plots, 15% in high-density plots, and 32% in medium-density plots, without increasing over- and under- segmentation errors. Our method demonstrates potential applicability across various forest conditions, facilitating future large-scale ITCD tasks and precision forestry applications.

The ability to automatically delineate individual tree crowns using remote sensing data opens the possibility to collect detailed tree information over large geographic regions. While individual tree crown delineation (ITCD) methods have proven successful in conifer-dominated forests using Light Detection and Ranging (LiDAR) data, it remains unclear how well these methods can be applied in deciduous broadleaf-dominated forests. We applied five automated LiDAR-based ITCD methods across fifteen plots ranging from conifer- to broadleaf-dominated forest stands at Harvard Forest in Petersham, MA, USA, and assessed accuracy against manual delineation of crowns from unmanned aerial vehicle (UAV) imagery. We then identified tree- and plot-level factors influencing the success of automated delineation techniques. There was relatively little difference in accuracy between automated crown delineation methods (51–59% aggregated plot accuracy) and, despite parameter tuning, none of the methods produced high accuracy across all plots (27—90% range in plot-level accuracy). The accuracy of all methods was significantly higher with increased plot conifer fraction, and individual conifer trees were identified with higher accuracy (mean 64%) than broadleaf trees (42%) across methods. Further, while tree-level factors (e.g., diameter at breast height, height and crown area) strongly influenced the success of crown delineations, the influence of plot-level factors varied. The most important plot-level factor was species evenness, a metric of relative species abundance that is related to both conifer fraction and the degree to which trees can fill canopy space. As species evenness decreased (e.g., high conifer fraction and less efficient filling of canopy space), the probability of successful delineation increased. Overall, our work suggests that the tested LiDAR-based ITCD methods perform equally well in a mixed temperate forest, but that delineation success is driven by forest characteristics like functional group, tree size, diversity, and crown architecture. While LiDAR-based ITCD methods are well suited for stands with distinct canopy structure, we suggest that future work explore the integration of phenology and spectral characteristics with existing LiDAR as an approach to improve crown delineation in broadleaf-dominated stands.

Australia's terrestrial ecosystems are critical to the global carbon cycle, yet they face numerous environmental pressures such as forest degradation and biodiversity loss. Accurate monitoring of vegetation dynamics is crucial to mitigating these challenges and informing sustainable management strategies. Individual Tree Segmentation (ITS) methods, powered by deep learning, enable large-scale mapping of tree crowns, which is vital for assessing above-ground biomass and carbon stocks across vast landscapes. Despite their promise, inconsistencies in algorithmic performance arise due to varying vegetation types, point cloud densities, and dataset-specific characteristics, which limit the generalizability of supervised models.This study evaluates the performance of different ITS and Canopy Height Model (CHM) algorithms for generating large tree crown datasets using LiDAR-derived data from across Australia. We applied these methods to 37 representative airborne LiDAR point clouds across 15 vegetation classes, representing a range of ecosystems from rangelands to tropical forests.Our analysis reveals that the effectiveness of tree detection and crown delineation varies significantly across vegetation types and point cloud densities. The Pit-Free CHM algorithm generally outperforms others, yielding higher match rates in the delineation of tree crowns. Additionally, the DalPonte ITS algorithm provides the most accurate results, especially in sparsely vegetated areas such as rangelands, which are critical for mapping and monitoring. In contrast, closed-canopy forests present challenges, particularly due to crown clumping and multi-layered vegetation structures. This study highlights the importance of selecting the appropriate ITS and CHM methods for different vegetation types and emphasizes the need for algorithm optimization in complex environments, such as tropical and eucalypt forests. Ultimately, these findings provide valuable insights into enhancing large-scale vegetation monitoring and improving model generalization for tree crown detection.

Accurate estimation of canopy cover (CC) and its delineation in tree-grass ecosystems (TGE) such as savannas and silvopastoral systems are crucial to analyze and model the functioning of these systems and the role of trees at different scales. At large-scale, remote sensing is a key tool, and assessments of land use and landscape elements often rely on satellite and aircraft sensor imagery and light detection and ranging (LiDAR) data. This study addresses automatic mapping of CC in TGE using high-resolution infrared orthophotographs and low-density LiDAR data from the Spanish Aerial Orthophoto National Plan (PNOA). Canopy cover mapping was performed in two areas with different structural complexity (with or without shrub layer) by an object based image analysis (OBIA) approach applied on canopy height model (CHM) generated by the LiDAR point cloud, infrared imagery, and both sources combined (LiDAR-imagery fusion). Overall accuracy (OA) was more than 91% with the two separated methods and more than 95% combining them. The results show that low-density LiDAR data is not a reliable source for the automatic mapping of canopy of scattered tree in TGE, OBIA on high-resolution infrared orthophotographs allows a more accurate automatic delineation of tree canopy, and the combined approach was the only way to obtain acceptable mapping in shrub-encroached stands, where errors were still greater than 15% with single-source based methods.