Exploring trees in three dimensions: VoxR, a novel voxel-based R package dedicated to analysing the complex arrangement of tree crowns

Lecigne, Bastien; Delagrange, Sylvain; Messier, Christian

doi:10.1093/aob/mcx095

Cited by 62 publications

(53 citation statements)

References 27 publications

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“…Voxel-based method: The crown points were divided into voxels of size 0.2 m × 0.2 m × 0.2 m and the crown volume was calculated as product of the voxel size and the number of voxels containing at least one tree count LiDAR point [25,45,59].…”

Section: Comparison Of Five Crown Volume Calculation Methodsmentioning

confidence: 99%

“…Theoretically, the alpha shape approach uses an optimal alpha value to approximate crown shape; however, a solution to this optimal value is very difficult [10,44]. Although the voxel-based method is considered to produce the best approximations of true crown shape [9,25,45,46], the calculated crown volume depends on the voxel size and the approach involves a large cost in terms of time [9,49]. The geometric calculation method involves construction of a geometry based on 3D scatter data obtained by applying a LiDAR system to the crown; the volume of the geometry is used to calculate the tree crown volume.…”

Section: Literature Reviewmentioning

confidence: 99%

“…Depending on the range of this point cloud, extreme values in the X-, Y-, and Z-directions are determined and the grid is divided according to the cell spacing on each coordinate axis to produce a set small cubes called voxels [32,35]. The volumes of the voxels containing at least one data point are summed to obtain the crown volume [9,25,45]. Hosoi and Omasa [46] applied a voxel-based method to reconstruct a precise 3D model of a crown that included its interior.…”

Section: Literature Reviewmentioning

confidence: 99%

“…Korhonen et al [10] used 3D alpha shape and 3D convex hull techniques to extract tree crown volumes from ALS data, with the results showing that the LiDAR-based estimates were highly correlated with the field-measured tree crown volumes (best R 2 = 0.83). Lecigne et al [25] developed a voxel-based R package to analyze complex tree crown arrangements from terrestrial laser scanner (TLS) data. They noted that the voxel division size had a significant influence on the calculated crown volume and that the choice of voxel size should depend on the research objectives and the quality of the TLS data.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

A Concave Hull Methodology for Calculating the Crown Volume of Individual Trees Based on Vehicle-Borne LiDAR Data

et al. 2019

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Crown volume is an important tree factor used in forest surveys as a prerequisite for estimating biomass and carbon stocks. This study developed a method for accurately calculating the crown volume of individual trees from vehicle-borne laser scanning (VLS) data using a concave hull by slices method. CloudCompare, an open-source three-dimensional (3D) point cloud and mesh processing software package, was used with VLS data to segment individual trees from which single tree crowns were extracted by identifying the first branch point of the tree. The slice thickness and number to be fitted to the canopy point cloud were adaptively determined based on the change rate in area with height, with the area of each slice calculated using the concave hull algorithm with portions of the crown regarded as truncated cones. The overall volume was then calculated as the sum of all sub-volumes. The proposed method was experimentally validated on 30 urban trees by comparing the crown volumes calculated using the proposed method with those calculated using five existing methods (manual measurement, 3D convex hull, 3D alpha shape, convex hull by slices, and voxel-based). The proposed method produced the smallest average crown volume. Gaps and holes in the point cloud were regarded as part of the crown by the manual measurement, 3D convex hull, and convex hull by slices method, resulting in the calculated volume being higher than the true value; the proposed method reduced this effect. These results indicate that the concave hull by slices method can more effectively calculate the crown volume of a single tree from VLS data.

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Section: Comparison Of Five Crown Volume Calculation Methodsmentioning

confidence: 99%

Section: Literature Reviewmentioning

confidence: 99%

Section: Literature Reviewmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A Concave Hull Methodology for Calculating the Crown Volume of Individual Trees Based on Vehicle-Borne LiDAR Data

et al. 2019

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“…Tree modelling is relevant in other fields, e.g., planning tree growth in agricultural projects, accurate representation of trees for video games, and tree models for urban planning (Bournez et al, 2017). Several algorithms, such as PlantScan3D (Boudon et al, 2014), TreeArchitecture (Landes et al, 2015), SimpleTree (Hackenberg et al, 2015a), and VoxR (Lecigne et al, 2018) were developed throughout these years and served different purposes.…”

Section: The Art Of Tree Modellingmentioning

confidence: 99%

Assessing biomass and architecture of tropical trees with terrestrial laser scanning

Sarmiento¹,

Ivan²

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Chapter 1 Introduction 1 Chapter 2 Estimation of above-ground biomass of large tropical trees with Terrestrial LiDAR Chapter 3 Tropical tree biomass equations from terrestrial LiDAR: A case study in Guyana Chapter 4 Quantifying branch architecture of tropical trees using terrestrial LiDAR and 3D modelling Chapter 5 Estimating architecture-based metabolic scaling exponents of tropical trees using terrestrial LiDAR and 3D modelling Chapter 6 Synthesis 115 References 129

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Abiotic and biotic drivers of tree trait effects on soil microbial biomass and soil carbon concentration

Beugnon

Bruelheide

et al. 2023

Ecological Monographs

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Forests are ecosystems critical to understanding the global carbon budget, due to their carbon sequestration potential in both aboveground and belowground compartments, especially in species‐rich forests. Soil carbon sequestration is strongly linked to soil microbial communities, and this link is mediated by the tree community, likely due to modifications of microenvironmental conditions (i.e., biotic conditions, soil properties, and microclimate). We studied soil carbon concentration and the soil microbial biomass of 180 local neighborhoods along a gradient of tree species richness ranging from 1 to 16 tree species per plot in a Chinese subtropical forest experiment (BEF‐China). Tree productivity and different tree functional traits were measured at the neighborhood level. We tested the effects of tree productivity, functional trait identity, and dissimilarity on soil carbon concentrations, and their mediation by the soil microbial biomass and microenvironmental conditions. Our analyses showed a strong positive correlation between soil microbial biomass and soil carbon concentrations. In addition, soil carbon concentration increased with tree productivity and tree root diameter, while it decreased with litterfall C:N content. Moreover, tree productivity and tree functional traits (e.g., fungal root association and litterfall C:N ratio) modulated microenvironmental conditions with substantial consequences for soil microbial biomass. We also showed that soil history and topography should be considered in future experiments and tree plantations, as soil carbon concentrations were higher at sites where historical (i.e., at the beginning of the experiment) carbon concentrations were high, themselves being strongly affected by the topography. Altogether, these results implied that the quantification of the different soil carbon pools is critical for understanding microbial community–soil carbon stock relationships and their dependence on tree diversity and microenvironmental conditions.

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Exploring trees in three dimensions: VoxR, a novel voxel-based R package dedicated to analysing the complex arrangement of tree crowns

Cited by 62 publications

References 27 publications

A Concave Hull Methodology for Calculating the Crown Volume of Individual Trees Based on Vehicle-Borne LiDAR Data

A Concave Hull Methodology for Calculating the Crown Volume of Individual Trees Based on Vehicle-Borne LiDAR Data

Assessing biomass and architecture of tropical trees with terrestrial laser scanning

Abiotic and biotic drivers of tree trait effects on soil microbial biomass and soil carbon concentration

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