Dryad
Published July 13, 2023 | Version v1
Software Open

Data from: Leveraging a new branch-based taper curve and form factor from terrestrial laser scanning proxies

Authors/Creators

  • 1. University of Göttingen

Description

Modeling branch taper curve and form factor contributes to increasing the efficiency of tree crown reconstruction: the branch taper, defined as the sequential measure of diameters along the course of the branch, is pivotal to accurately estimate key branch variables such as biomass and volume. Branch diameters or volumes have commonly been estimated from terrestrial laser scanning (TLS) based on automatized voxelization or cylinder-fitting approaches, given the whole branch length is sufficiently covered by laser reflections. The results are, however, often affected by ample variations in point cloud characteristics caused by varying point density, occlusions, and noise. As these characteristics of TLS have been difficult to be sufficiently controlled or eliminated in automatized-techniques, we proposed a new branch-based taper curve model and form factor (BFF), which can be employed directly from the laser reflections and under variable point cloud characteristics.

In this paper, the approach is demonstrated on primary branches using a set of TLS-derived diameter datasets from a sample of 20 trees of 6 species. The result shows an improvement in the accuracy of the diameter estimates and, at best, enabled for predicting encompassing finer branch scales (<10 cm), with R2 of 0.86 and a mean relative absolute error of 1.03 cm (29%) when validated with field-measured diameters. This approach was also capable of retrieving branch diameters for a large percentage of explicitly identified primary branches (>85%) directly from the filtered points when validated with panoramic images acquired concurrently with laser scanning. Frequently used automatized crown reconstructions from the quantitative structural model (QSM), on the other hand, was largely obscured by discrepancies in the point clouds, with the crown-tops and finer branches being the most critical.

Furthermore, our approach provides mean BFF of 0.35 and 0.49 with the diameters determined from 5% and 10% of the total branch length, respectively, which may have the potential to produce branch volume information with reasonable accuracy from only knowing the length and respective diameter.

Although our model can be regarded as a first approximation to the taper curve and form factor for the primary branches on a relatively small set of samples, the approach can further our understanding of alternative ways to improve the accuracy of the assessment of branch diameter and volume. The approach may also be extended to other branch orders. This could expand the horizon for volumetric calculations and biomass estimates from non-destructive TLS proxies in tree crowns.

Notes

Column Name

Description

Unit

Source

Calculation or Measurement Methods

Software

 

Data1.csv

 

 

 

 

 

 

Species

The scientific name of the scanned trees

 

 

 

 

Scan_Code

Given code during scanning

 

 

 

 

Branch_ID

Isolated sample branch in each tree. Repetition of similar ID numbers indicates the series point slices taken along the corresponding branch.

 

 

 

 

BP

 

Branch position, indicating where the sample branch was positioned across the crown profile:

LCB – lower crown branch

MCB – middle crown branch

UCB – upper crown branch

 

 

 

 

BO

Branch order, where all the analysis was made for primary branches (BO 01)

 

 

 

 

DBH

Branch diameter at breast height

cm

Field

Diameter tape

 

H

Height of the tree. The vertical distance between the base of the trunk and the tree-top

m

Point Cloud

Zmax – Zmin

R Programming Language

H1

Crown base height. The vertical distance between the base of the trunk and the lowest live branch

m

Point Cloud

Zfirst-live-branch – Zmin

CloudCompare

H2

Crown length. Distance between the base of the lowest live branch and tree-top

m

Point Cloud

Zmax – Zfirst-live-branch

or H – H1

CloudCompare

CR

Crown ratio. The ratio of the crown length to the tree height

 

Point Cloud

H2/H

 

BH

Branch base height. Height of the primary branch attachment to the trunk from the base of the stump

m

Point Cloud

Zprimary-branch-base-point – Zmin

CloudCompare

BRH

Branch base relative height. Height of the base of the primary branch relative to the tree height

 

Point Cloud

BH/H

 

 

Data2.csv

 

 

 

 

 

 

Species – BRH

Similar to Data1.csv

 

 

 

 

BL

Branch length. The total length of the primary branch

m

Point Cloud

Manual length measurement from laser reflections

 

CloudCompare

BSL

Branch slices length. Absolute length of each branch slice (BS) (used for series of diameter determination with circle fitting) from the base of the primary branch

m

Point Cloud

Manual length measurement from laser reflections

 

CloudCompare

BRL

Branch relative length. The relative length of each BSL from the BL

 

Point Cloud

Normalized in [0 - 1] scale (BSL/BL)

 

BBD

Branch basal diameter

cm

Point Cloud

Determined directly from laser reflections using a circular fit for the cross-section of the points just above the point of attachment to the trunk

R Programming Language

D_TLS

Series of branch diameters along the course of the branch. The diameters served as a non-destructive TLS-based dataset to fit the branch taper curve and calculate the branch form factor

cm

Point Cloud

Determined diameters at 0.50 m intervals along the branch. Circle fitting using the RANSAC algorithm was executed for each thin point slice derived from 0.50 m intervals.

R Programming Language

D_Relative

Relative branch diameter

 

Point Cloud

Normalized in [0 -1] scale using the BBD (D-TLS/ BBD)

 

D_TaperModel_Relative

Predicted relative branch diameter from the taper curve model

 

Taper Curve

Diameter prediction in normalized [0 -1] scale

R Programming Language

D_TaperModel

Predicted diameters from the taper curve model

cm

Taper Curve

Series of diameter depicted from the taper curve regression model (D_TaperModel_Relative*BBD)

 

 

Data3. xlsx

 

 

 

 

 

 

BRL

Branch relative length (As described and derived in Data2.csv)

 

Field, Taper Curve, QSM

Normalized in [0 - 1] scale (BSL/BL)

 

Reference Diameter

 

cm

Field

Field measurements of branch diameters using a caliper

 

Predicted Diameter

 

cm

Taper Curve, QSM

Predicted diameters from the Taper curve and QSM

R Programming Language; SimpleForest

Prediction Approach

The approach of the diameter estimation:  Taper curve and QSM model

 

Taper Curve, QSM

 

 

Absolute Error (AE)

 

cm

Field, Taper Curve, QSM

 

 

Relative Absolute Error (RAE)

 

%

Field, Taper Curve, QSM

RAE = |Prediction Diameters from Taper Curve or QSM – Reference Diameters|/ Reference Diameters * 100

 

 

Data4.csv

 

 

 

 

 

 

Species_Code; Scan_Code; Species; Branch_Sample

As described in Data1.csv

 

 

 

 

Branch_Volume

The volume of the branch

cm3

Point cloud; Taper Curve

Calculated based on fitted taper curves. Summation of the volumes calculated at every 0.1 m section

R Programming Language

CylinderVolume0.05

Assuming the volume of the cylinder

cm3

Point cloud

Considering the volume of the cylinder over the length of reference diameter, i.e., from 5% (relative length of 0.05) of the total branch length

R Programming Language

CylinderVolume0.10

Assuming the volume of the cylinder

cm3

Point cloud

Considering the volume of the cylinder over the length of reference diameter, i.e., from 10% (relative length of 0.1) of the total branch length

R Programming Language

BFF0.05

Branch form factor with a reference diameter estimation at 5% if the branch length

 

Point cloud; Taper Curve

Branch_Volume/CylinderVolume0.05

 

BFF0.10

Branch form factor with a reference diameter estimation at 10% if the branch length

 

Point cloud; Taper Curve

Branch_Volume/CylinderVolume0.10

 

 

Point Clouds

 

 

 

PSP28.asc;

PSP28.las;

APS30.asc;

APS30.las

Examples of filtered tree point clouds (Platanus species and Acer platanoides)

Any software used for point cloud visualization

 

QSM Scripts

 

 

MN-QSM-asc.xsct2;

MN-QSM-las.xsct2

Examples of QSM scripts

SimpleForest

 

Pipeline Model (QSM Cylinders)

 

 

PSP28.ply;

APS30.ply

Examples of the reconstructed branch cylinders (based on the provided QSM Scripts)

CloudCompare
Reference

CloudCompare. (2021). CloudCompare Software, 3D point cloud and mesh processing Project, Open Source (Version 2.12.0). https://www.danielgm.net/cc/

Computree. (2021). Computree: a platform for processing 3D point clouds (version 5.0). http://rdinnovation.onf.fr/projects/computree/wiki

de Conto, T. (2020). TreeLS: Terrestrial Point Cloud Processing of Forest Data (R package version 2.0.4.). https://mran.microsoft.com/snapshot/2020-02-16/web/packages/TreeLS/index.html

Fischler, M. A., & Bolles, R. C. (1981). Random Sample Consensus: A Paradigm for Model Fitting with Applications to Image Analysis and Automated Cartography. Communications of the ACM, 24(6), 381–395. https://doi.org/10.1145/358669.358692

Hackenberg, J., Spiecker, H., Calders, K., Disney, M., & Raumonen, P. (2015). SimpleTree —An Efficient Open Source Tool to Build Tree Models from TLS Clouds. Forests, 6(11), 4245–4294. https://doi.org/10.3390/f6114245

RStudio. 2021 RStudio: A language and environment for statistical computing. Boston, MA. https://www.rstudio.com/

SimpleForest. (2021). SimpleForest: a 3D tree modelling software from point cloud data (version 5.3.2). https://www.simpleforest.org/

Trimble Inc., Sunnyvale, CA, U. (2021). Trimble TX5 Scanner: A 3D laser instrument. https://www.laserscanning-europe.com/de/glossar/trimble-tx5-scanner

Funding provided by: German Academic Exchange Service
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100021828
Award Number: 91732538

Files

Files (1.1 MB)

Name Size Download all
md5:76832ec9e053bafa0076baf9fae76921
481.1 kB Download
md5:dcb47bcbceabb5ca6904e846aed5273d
600.2 kB Download
md5:369d9479ea0e8001ef0889663938c2a1
7.6 kB Download

Additional details

Related works

Is source of
10.5061/dryad.nzs7h44x1 (DOI)