MR.

JOSE GONZALEZ DE TANAGO MENACA (Orcid ID : 0000-0001-5461-8250)

DR. MAT DISNEY (Orcid ID : 0000-0002-2407-4026)

Accepted Article
Article type : Research Article

Editor : Prof. Darren Kriticos

Estimation of above-ground biomass of large tropical trees with

Terrestrial LiDAR

Jose Gonzalez de Tanago Menaca1, Alvaro Lau1, Harm Bartholomeusm1, Martin Herold1, Valerio
Avitabile1, Pasi Raumonen2, Christopher Martius3, Rosa Goodman4, Mat Disney5, Solichin Manuri6,
Andrew Burt7, Kim Calders8

1
Wageningen University & Research, Laboratory of Geo-Information Science and Remote Sensing;
Center for International Forestry Research

2
Tampere University of Technology, Laboratory of Mathematics

3
Center for International Forestry Research (CIFOR)

4
Swedish University of Agricultural Sciences (SLU), Department of Forest Ecology and Management

5
University College London, Geography; Natural Environment Research Council, National Center for
Earth Observation (NCEO)

6
Australian National University Fenner School of Environment and Society

7
University College London, Geography

8
University College London, Department of Geography;National Physical Laboratory, Earth
Observation, Climate and Optical group

Corresponding author mail id:- [email protected]

This article has been accepted for publication and undergone full peer review but has not
been through the copyediting, typesetting, pagination and proofreading process, which may
lead to differences between this version and the Version of Record. Please cite this article as
doi: 10.1111/2041-210X.12904
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 Abstract

1. Tropical forest biomass is a crucial component of global carbon emission estimations.

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However, calibration and validation of such estimates require accurate and effective methods
to estimate in-situ above ground biomass (AGB). Present methods rely on allometric models
that are highly uncertain for large tropical trees. Terrestrial laser scanning (TLS) tree
modelling has demonstrated to be more accurate than these models to infer forest AGB.
Nevertheless, applying TLS methods on tropical large trees is still challenging. We propose a
method to estimate AGB of large tropical trees by 3D tree modelling of TLS point clouds.
2. Twenty-nine plots were scanned with a TLS in three study sites (Peru, Indonesia and
Guyana). We identified the largest tree per plot (mean DBH of 73.5 cm), extracted its point
cloud and calculated its volume by 3D modelling its structure using quantitative structure
models (QSM) and converted to AGB using species-specific wood density. We also estimated
AGB using pantropical and local allometric models. To assess the accuracy of our and
allometric methods, we harvest the trees and took destructive measurements.
3. AGB estimates by the TLS-QSM method showed the best agreement in comparison to
destructive harvest measurements (28.37% CV-RMSE and Concordance Correlation
Coefficient (CCC) of 0.95), outperforming the pantropical allometric models tested (35.6 to
54.95% CV-RMSE and CCC of 0.89 to 0.73). TLS-QSM showed also the lowest bias (overall
underestimation of 3.7%) and stability across tree size range, contrasting with the allometric
models that showed a systematic bias (overall underestimation ranging 15.2 to 35.7%)
increasing linearly with tree size. The TLS-QSM method also provided accurate tree wood
volume estimates (CV RMSE of 23.7%) with no systematic bias regardless the tree structural
characteristics.
4. Our TLS-QSM method accounts for individual tree biophysical structure more effectively
than allometric models, providing more accurate and less biased AGB estimates for large
tropical trees, independently of their morphology. This non-destructive method can be further
used for testing and calibrating new allometric models, reducing the current
underrepresentation of large trees in, and enhancing present and past estimates of forest
biomass and carbon emissions from tropical forests.

Keywords:

Modelling (Population Ecology) < Population Ecology, GIS < Population

Ecology, Surveys < Population Ecology

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 1. INTRODUCTION

The above-ground carbon in tropical forests represents 40% of the total carbon stocked in forests
globally (Gibbs et al. 2007). However, the estimation of tropical forest carbon stocks presents large
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uncertainties (Mitchard et al. 2013, 2014). Forest carbon stocks are not measured directly, but
derived either from interpolation or extrapolation of point estimates of the above-ground biomass
(AGB) contained in forest inventory plots, or from measurements of remote sensing proxies
calibrated with plot-based AGB estimates (Gibbs et al. 2007).

The only way to truly and directly measure forest AGB implies cutting and weighing the mass of all
trees in the plot, which is costly and causes a negative impact, and is thus seldom executed (Clark &
Kellner 2012). Instead, plot AGB is estimated from aggregation of individual tree AGB estimates.
These tree AGB estimates are indirectly derived from easily measured tree parameters (diameter at
breast height (DBH), height and wood density derived from tree species identification) by means of
allometric models, which relate these tree parameters with real tree AGB measured in destructive
sampling studies (Chave et al. 2005). This indirect estimation approach introduces an error
propagation chain. The biggest source of error is derived from the allometric models, hence its
appropriate selection is the most important aspect to improve the accuracy of AGB estimates (Molto
et al. 2013).

The uncertainty in the tree AGB estimation is even greater for large tropical trees (DBH >70cm)
because AGB in large trees varies more than in small trees (Chave et al. 2005; Slik et al. 2013;
Goodman et al. 2014; Ploton et al. 2016), and due to the presence of buttresses is prone to larger
measurement error (Chave et al. 2014). Moreover, it is particularly relevant to accurately estimate
AGB of large trees because of their major influence on the tropical forest AGB variation (Stegen et al.
2011; Slik et al. 2013).

As an alternative, remote sensing systems can be used to estimate tropical forest carbon stocks. One
of the most promising remote sensing approaches to estimate forest AGB is via light detection and
ranging (LiDAR), either via spaceborne platforms (e.g. ICESat), airborne laser scanning (ALS) or
terrestrial laser scanning (TLS). Laser pulses from LiDAR instruments can penetrate the forest canopy
providing good estimates of forest canopy heights and structure, from which AGB along the vertical
profile and canopy cover can be estimated (Goetz & Dubayah 2011).

TLS data provide the highest level of three-dimensional (3D) detail of forest and tree structure
(Newnham et al. 2015). Currently, TLS data are being used to model 3D structure of individual trees
allowing direct measurements of forest and tree structural parameters such as DBH (Bauwens et al.
2016), tree height (Király & Brolly 2007), crown dimensions (Holopainen et al. 2011) and individual
branches (Raumonen et al. 2011). Several review articles provide additional information about the
characteristics of TLS and its use for forestry surveying (Newnham et al. 2015).

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 Several approaches estimate forest AGB by exploiting the capability of TLS data to characterize
forest structure at tree level. A simple approach is to measure tree structural parameters from a TLS
3D point cloud and apply allometric models to relate the measured parameters with AGB (e.g. Yao et
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al. (2011)). However, this method still relies on allometric models. A different kind of approach has
been developed to reconstruct the complete 3D tree architecture from TLS data rather than a single
or few structural parameters. Quantitative structure models (QSMs) (Raumonen et al. 2013;
Delagrange et al. 2014; Hackenberg et al. 2015) are architectural tree models reconstructed from
the TLS point cloud of individual trees and allow volume measurements. The estimated tree volume
is converted to tree AGB by multiplying it by the specific wood density (Hackenberg et al. 2015;
Calders et al. 2015b). Thus, this method estimates AGB based on the biophysical modelling of
specific tree structure rather than the allometric models which are based on empirical relationships
from a sample of trees and rely on a limited number of tree structural parameters.

The QSM reconstruction method developed by Raumonen et al. (2013) has been applied for wood
volume estimation and AGB estimation in boreal and temperate forest (Raumonen et al. 2015) and
in more structurally complex tropical forests in Gabon (Disney et al. 2014). AGB estimates derived
from this approach in Australia showed a higher agreement with reference values from destructive
sampling (CV RMSE = 16.1%) compared to AGB estimates derived by allometric models (CV RMSE =
46.2 to 57%) (Calders et al. 2015b). However, the accuracy of AGB estimates in tropical forest trees
has not been investigated yet with reference data.

Several challenges arise when one wants to estimate tree AGB in a tropical forest using QSM. First,
for very large and complex trees there is a lack of reference data to validate the 3D reconstruction
models from TLS. Further, the structural complexity of a tropical forest can potentially have a large
influence on acquired TLS data. This requires careful design of an appropriate scanning pattern to
diminish vegetation occlusion and to allow accurate reconstruction of the 3D structure of trees
(Wilkes et al. 2016).

Here, we assess the potential and accuracy of volume reconstruction using QSMs for estimating AGB
of large tropical forest trees. For this, 29 plots were scanned with TLS and one large tree per plot was
destructively sampled afterwards. With the TLS data acquired, we (i) optimized the QSM tree volume
reconstruction method based on a subsample of nine of the 29 trees. After each tree was scanned
and harvested, we (ii) performed in situ destructive measurements to independently estimate tree
volume for comparison with model estimates and calculate their accuracy. Finally, using the
independent tree dataset (remaining 20 trees non-used in point (i)) we (iii) compared the accuracy
of the AGB estimates based on QSMs with the accuracy of the AGB estimates based on pantropical
and local allometric models.

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 2. MATERIAL AND METHODS

2.1. Study area

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We acquired field data from 29 plots across three tropical forest sites in: Peru, Indonesia and
Guyana. Table 1 shows the description of each site.

Table 1. Study sites description

Peruvian Site Indonesian Site Guyanese Site
Number of plots 9 10 10
Forest type Lowland tropical moist Peat swamp forest Lowland tropical moist
terra firme forest forest
Region Madre de Dios. South Mentaya River (Central Vaitarna Holding’s
western Amazon Kalimantan) concession
Lat/long -12.27 lat -69.10 long -2.41 lat 113.13 long 6.04 lat -58.70 long
Mean elevation 312 masl 22 masl 117 masl
Mean yearly rainfall* 2,074 mm 2,616 mm 2,195 mm
Mean stem density (trees 565 stems/ha 1,314 stems/ha 516 stems/ha
with DBH >10 cm)
Mean DBH harvested 90.0 cm (22.2 cm) 58.4 cm (18.2 cm) 73.7 cm (12.0 cm)
trees (Standard Dev.)
*From Muñoz & Grieser (Muñoz & Grieser 2006)

2.2. TLS sampling and field data collection

Plots were established around a tree to be harvested after the laser scanning. Plot spatial design and
tree selection are detailed in Supporting Information (S1). Once the plots were set up, we scanned
the plot with TLS, performed a forest inventory, harvested the selected tree, and measured the
geometric structure of the harvested tree.

2.2.1.TLS data acquisition

TLS datasets were acquired using a RIEGL VZ-400 3D® terrestrial laser scanner (RIEGL Laser
Measurement Systems GmbH, Horn, Austria). This scanner is a discretized multiple-return LiDAR
scanner and its specifications are shown in Table 2. Details of the sampling design are described in
the Supporting Information (S2).

Table 2. Terrestrial laser scanning specifications

Wavelength 1550 nm
Beam divergence 0.35 mrad
Scan range 360 in azimuth
100 in zenith
Scan resolution 0.06°

2.2.2.Forest inventory data collection

For each tree we measured DBH (or diameter above buttresses), tree height, height of first branch
and crown width. We measured DBH with a forestry tape and tree height with a Nikon “Forestry-

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 Pro” laser hypsometer with precisions of 0.01m and 0.2 m respectively. An experienced taxonomist
(specialist of the local flora) identified the trees at species level.

2.2.3.Harvested tree reference measurements

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We measured the geometry of the stem, buttresses, and branches of each harvested tree. As in
Figure 1.1, tree stem diameters (1a) were measured at every meter along the stem (1b) following
the approach of Kankare et al. (2013). For trees with buttresses or major irregularities we measured
as in Figure 1.2. Finally, we measured all branches until tapered diameter ≤10 cm by measuring each
internode independently as in Figure 1.3.

Figure 1. Tree geometry measurements. (1) Stem diameter (1a) every meter (1b) until start of first branch. For
trees with buttresses (2): diameter in two orthogonal directions (2a) and for each buttress horizontal length
(from the furthest point to the stem, (2b); width (mean width between the tip and the buttress intersection
with the stem, (2c); and height (from the ground to the highest insertion point of the buttress into the stem,
(2d). For branches (3): proximal diameter at the base of each internode and above flaring (3a), distal diameter
at the tip of each internode and below flaring of the next node (3b) and branch length from the base to the tip
of each internode (3c).

2.3. Volume and biomass estimation

2.3.1.Tree wood volume estimation from 3D QSM

We co-registered each individual TLS scan into a single plot pointcloud using RiScan Pro software
[RIEGL Laser Measurement Systems GmbH, Horn, Austria, www.riegl.com, version 2.0] and the
accuracy of our co-registration was kept below 1 cm.

We reconstructed the woody structure of trees using the QSM method developed by Raumonen et
al. (2013) and further developed by Calders et al. (2015b) and Raumonen et al. (2015). The method
first segments the TLS point cloud reconstructing the whole tree topological branching architecture
and then reconstructs the surface and volume of the segments by fitting cylinders to each of the
segments (Figure 2). The resulting cylinder models are used for automatic calculation of the volume
of the whole woody fraction of individual trees (trunk and branches). More details are provided in
Supporting Information (S3).

Figure 2. Example of one tree TLS pointcloud from Guyana dataset (left, in dark red), and the same tree
modelled by QSM (right, in green). Figure from Gonzalez de Tanago et al. (2016).

We filtered out cylinders with diameter <10 cm from resulting QSMs to be consistent with the
reference volume estimation and we calculated the total tree volume by summing the volume of all
remaining cylinders. Due to the random generation of the QSM patches (point cloud partition into

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 small segments) (Raumonen et al. 2015; Calders et al. 2015b), for each parameter set used we
reconstructed 20 QSM’s and averaged the volume of the 20 model realizations.
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2.3.2.Sensitivity analysis and independent estimation of QSM accuracy.
We split our tree population into two independent sub-datasets using stratified random sampling
without replacement: a tree dataset of nine trees (three from each study area) for the sensitivity
analysis of a QSM parameter value, and a second tree dataset of 20 trees (the remaining six trees for
Peru and seven for Guyana and Indonesia) for independent estimation of tree volume and AGB
estimates accuracy.

The reconstruction of the QSMs requires a few input parameters, of which the size of the point cloud
segments -expressed by the “surface patches diameter” (hereafter “PatchDiam”)- had the most
influence on the outcome (Calders et al. 2015b). A detailed explanation of the QSM parameters and
QSM sensitivity to them is provided in Supporting Information and in Raumonen et al (2013, 2015)
and Calders et al (2015b).

Our sensitivity analysis consisted on the evaluation of the QSMs optimal PatchDiam value, which
gives the most accurate volume estimate among the different PatchDiam values tested (1, 2.5, 5,
7.5, 10, and 15 cm). For each tree in the sensitivity analysis tree dataset we compared the mean
estimated volume (from the 20 QSM realizations per PatchDiam) against the tree volume obtained
from the destructive measurements. We computed tree volume estimation Root Mean Square Error
(RMSE). The optimal PatchDiam was chosen as the one that minimized the RMSE.

Once the optimal PatchDiam was found, we assessed the stability of the optimization procedure. We
replicated the stratified random sampling 1000 times and analysed the frequency of optimal
PatchDiam’s obtained (the one providing the smallest RMSE in each of the 1000 samples) as well as
the variability of the RMSE results (range, mean and standard deviation) for all samples with a given
optimal PatchDiam.

Finally, the optimized PatchDiam was used to run QSM for the independent estimation dataset (20
trees) and to calculate the tree volume following the same procedure described above. We used
MATLAB (The MathWorks Inc. 2014) for QSM reconstruction and “R” (R Core Team 2013) for further
calculations.

2.3.3.Tree volume estimation from reference measurements

We used the reference geometric measurements (‎2.2.3) from each harvested tree to determine the
tree reference volume. We applied the Smalian formula as in Nogueira et al. (2005) to estimate
volume of stem sections and individual branches until 10 cm diameter while for the buttresses we
applied a general prism volume formula. Detailed information can be found in Supporting
Information (S4). Total tree wood volume was calculated as the sum of volumes of main stem, large
branches (>10 cm diameter), and buttresses.

As in Berger et al (2014), any misrepresentation of the main stem and branches volumes by the
Smalian approximation and any measurement error taken were considered negligible and ignored.

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 Further, the sum of all cylinders was assumed to represent the true tree volume with no error and
that the wood volume was measured without error.
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2.3.4.Tree AGB estimation from volume models and wood density
We calculated individual tree above ground biomass by multiplying individual tree wood volume
estimates by the specific basic wood density (ρ). Values of ρ were assigned to the finest taxonomic
level possible (species, genus, or family) according to the Global Wood Density Database (Zanne et
al. 2009; Chave et al. 2009) and tree species identified in the field. We applied an expansion factor
accounting for small branches (≤10 cm diameter). The expansion factor related the volume of small
branches to the one of large branches (>10 cm diameter). We calculated an expansion factor of
0.255 using data from biomass destructive sampling of 51 trees in a nearby Peruvian Amazon forest
site (Goodman et al. 2013, 2014). We used the same value for Peru and Guyana (0.255) while we
calculated the expansion factor for Indonesia (0.28) from our own collected data. The final
contribution of small branches to tree volume was 10, 14 and 7% for Guyana, Peru and Indonesia
respectively.

2.3.5.Tree AGB estimation from allometric models

We estimated AGB using 12 allometric models, of which 8 were locally-calibrated and 4 pantropical
(See Supporting Information S5). The pantropical allometric models used were developed by Chave
et al. (2005), which have been recently improved (Chave et al. 2014).

The local allometric models used for the Peruvian trees were developed by Goodman et al. (2014)
while allometric models for Indonesian trees were developed by Manuri et al. (2014) and Jaya et al.
(2007). No suitable local allometric model could be found for Guyana. The details of the allometric
models used to estimate AGB for the harvested trees are described in the Supporting Information.

2.4. AGB estimation models accuracies and uncertainty assessment

We used the 20 trees in the dataset reserved for the independent estimation to compare the
accuracy of AGB estimates from our TLS-QSM approach (against reference AGB) versus the accuracy
obtained from allometric models (against reference AGB). The model error was calculated for each
tree and for the mean of the 20 trees using several metrics. The AGB estimation error (Residual, in
Mg) (Equation 1) and Individual tree Relative Error (in %) (Equation 2) were calculated for each tree
while model bias (in %) (Equation 3) was calculated as the mean of the Estimation Errors divided by
the mean of reference AGB.

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 Equation 1

Equation 2
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Equation 3

Where is the AGB estimated by the model and is the AGB observed (AGB
calculated from destructive measurements).

As general indicators of model accuracy, RMSE (in m3 and Mg), Coefficient of Variation of RMSE (CV
RMSE, in %) and Mean Relative Error (in %) were calculated. Slope and Intercept values of
orthogonal regression models between AGB modelled and reference values were used to identify
departure from the 1:1 line, and the R-squared (hereafter R2) was used to judge the fitting of these
regressions. Finally, the Concordance Correlation Coefficient (CCC) was calculated to compare
agreement of AGB model estimates with AGB reference and to previously reported agreement using
the QSM method (Calders et al. 2015b).

To assess the uncertainty in the tree AGB estimations, we used the error propagation approach
(Equation 4) to account for the uncertainties in the models components. We combined them and
assumed that the uncertainties were statistically independent (not correlated and with a Gaussian
distribution). We used Equation 4 expressing model uncertainties in percentage terms:

Equation 4

Where is the propagated uncertainty (as percentage) from the model components, and
are the uncertainties (as percentage) from each component (IPCC 2006).

For AGB estimations from QSM volume models, the model uncertainty components considered were
the wood volume and wood density. The uncertainty in tree wood volume by QSM is provided by
the standard deviation of the 20 QSM realizations per tree. For the estimation of wood densities
uncertainties, we assumed for all species the same standard deviation of 10% of the mean as used
by Chave et al (2004). Likewise, to assess the uncertainty in the tree AGB estimation from allometric
models, we used the uncertainties reported for each model (See Supporting Information S5). To
assess the uncertainty in the tree AGB estimation from reference volume estimates we considered
two components: wood density (as described for QSM) and expansion factor. For the expansion
factor we assumed an error of 12.5% as reported in Segura & Kanninen (2005).

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 3. RESULTS

3.1. Tree volume estimation with QSM

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The results of the tree volume modelling with the TLS-QSM approach are divided in two steps: (i)
QSM sensitivity analysis with 9 trees to determine QSM optimal parameters; and then (ii) an
independent assessment of the tree volume estimation accuracy with an independent sample of 20
trees.

3.1.1.Sensitivity analysis of QSM tree volume modelling

The TLS-QSM tree volume estimation error (RMSE) when compared with the reference volume
measurements decreased with decreasing PatchDiam (Table 3) until it reached a minimum error for
PatchDiam of 2.5 cm, and then it increased again for smaller PatchDiam. This is in line with the
results of the sensitivity analysis in Calders et al. (2015). Therefore, 2.5 cm was considered the
optimal PatchDiam, and thus selected for the tree volume estimation of the remaining tree dataset.

Table 3. QSM volume sensitivity analysis

Mean
PatchDiam 3
RMSE (m ) CV RMSE (%) Relative
(cm)
Error (%)

1.0 3.42 27.56 10.31

2.5 2.98 23.92 17.67

5.0 4.60 36.97 31.87

7.5 7.11 57.17 49.42

10.0 9.06 72.81 65.07

15.0 13.32 107.09 98.05

The stability assessment of PatchDiam optimization procedure showed that in 75% of the 1000
random sampling replicates the optimal PatchDiam was 2.5 cm. Despite the relatively small sample
reserved for the sensitivity analysis (9 out of 29 trees), the optimal PatchDiam was relatively stable
regardless of the characteristics of the randomly selected trees.

3.1.2.Independent assessment of tree volume estimation from TLS-QSM

To assess the accuracy of the tree wood volume estimation by the TLS-QSM we compared the
volume estimates by the TLS-QSM with the reference volume estimates from destructive
measurements (Figure 3).

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 Figure 3. Scatterplot of tree volume estimation by TLS-QSM (y axis) against reference measurements (x
axis). The solid black line depicts the 1:1 line. Error bars are the standard deviation of the 20 QSM model
realizations per tree. Symbols and colours denote values per study site. The blue line depicts the fitted
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linear regression model between QSM volume estimates and reference volume estimates, and grey
bands show the 95% confidence interval of this regression. Coefficient “a” denotes tree with buttresses
and “b” tree with no buttresses.

The R2 of the linear model describing the agreement of both datasets (Figure 3 blue line) was 0.9. Its
slope was 0.93 indicating that the QSMs slightly underestimated the tree volume for the largest
trees. The RMSE was 3.29 m3, compared with the mean tree volume of 15.13 m3, leading to a CV
RMSE of 23.7%. Figure 3 shows that the TLS-QSM performed similarly throughout the three different
sites, despite the three study areas contained different tree species, sizes and shapes. Results differ
between “small trees” (DBH ≤ 70 cm, corresponding approximately with 9 Mg, hereafter small trees)
and “large trees” (DBH >70 cm, hereafter large trees). For small trees -which were mostly part of the
Indonesian dataset- TLS-QSM models showed less uncertainty and less deviation from the reference
compared to large trees.

Figure 4 Analysis of volume estimation residuals. Trees with DBH ≤ 70 cm were classified as small size
trees (red colour) and trees with DBH >70 cm were classified as large trees (blue colour). Coefficient “a”
denotes tree with buttresses while coefficient “b” denotes absence of tree buttresses.

On the other hand, the analysis of the residuals (Figure 4) reveals that for small trees and large trees
the model did not systematically tend to overestimate nor underestimate the volume. Despite the
larger uncertainty in the volume estimation for large trees, there was no large systematic bias for
larger tree size (Figure 4).

Buttresses were predominately absent in small trees, which had a better agreement with the
reference data than trees with buttresses. Our QSM modelling did not perform a detailed buttress
modelling, but a cylinder fitting, which might be the cause of the higher residuals in the trees with
buttresses.

3.2. Comparison of AGB estimation accuracies: TLS-QSM vs. Allometric models

3.2.1.Overall accuracy across study sites: TLS-QSM vs. Pantropical allometric models
Figure 5 shows the agreement between the AGB estimates by TLS-QSM and allometric models
(modelled) and derived from the destructive measurements (reference) for the independent
assessment tree dataset. The high level of agreement with the AGB-reference provided by the TLS-
QSM approach (CCC = 0.95) contrasts with the systematic AGB underestimation of the allometric
models for large trees (CCC = 0.73 – 0.89).

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 Figure 5. Scatterplot of AGB estimates by TLS-QSM approach and pantropical allometric models (Y axis) against
the AGB reference values (X axis). The 1:1 line is depicted as a black solid line. The dashed lines represent the
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fitted orthogonal models between AGB estimates by TLS-QSM or pantropical allometric models and AGB
reference, with colours corresponding the colour used for the model estimates. Vertical bars show the
estimated uncertainty (standard deviation) for each model estimate and horizontal bars show the uncertainty
for the reference AGB estimates.

Table 4 shows the statistical indicators of the accuracy of AGB estimations based on the TLS-QSM
approach and pantropical allometric models for the mean of the 20 trees in the independent
assessment dataset.

Table 4. Accuracies of AGB estimations across sites by the TLS-QSM approach and by pantropical allometric
models. Sample size = 20 trees.

RMSE CV RMSE Relative 2 Intercept

Model Bias (%) R Slope CCC
(Mg) (%) error (%) (Mg)

TLS-QSM 2.89 28.37 -3.68 -0.33 0.90 1.06 -1.03 0.95

a
Chave05.m.1.3 3.63 35.60 -15.22 -0.76 0.88 0.77 0.82 0.89

Chave14.eq.7 4.52 44.35 -24.50 -10.49 0.88 0.66 0.94 0.82

Chave05.m.1.6 5.47 53.65 -34.99 -24.91 0.85 0.62 0.33 0.75

b
Chave14.eq.4 5.60 54.95 -35.67 -24.41 0.85 0.60 0.49 0.73
a
most accurate allometric model
b
least accurate allometric model

The TLS-QSM method had the lowest RMSE, which was respectively 20% and almost 50% lower than
the most accurate (Chave05.m.1.3) and the least accurate allometric model (Chave14.eq.4). The TLS-
QSM approach also had the lowest bias, 75% and 90% lower than the most and the least accurate
allometric models respectively. The TLS-QSM AGB estimates also showed the most consistent
agreement with the reference AGB (CCC = 0.95) along the range of AGB reference values with no
major systematic deviation to the 1:1 line (slope of 1.06), whereas the best allometric model (slope
of 0.77) showed a systematic increasing underestimation of AGB for large trees and a lower
agreement with reference AGB (CCC = 0.89). The trend of systematic increasing underestimation of
AGB for larger trees was even more pronounced for less accurate allometric models (slopes ranging
from 0.66 to 0.60) showing a lower agreement compared to reference AGB (CCC = 0.73 – 0.82).

3.2.2.Overall accuracy within study sites: TLS-QSM vs. Local allometric models

Figure 6 displays the agreement between the AGB-modelled based on the TLS-QSM approach and
local allometric models (Y axis) against AGB-reference (X axis) for the sites where local allometric
models were available.

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 Figure 6. Scatterplot of AGB estimates by TLS-QSM approach and local allometric models (Y axis) against the
AGB reference values (X axis) for Peruvian study site (left) and Indonesian study site (right). The 1:1 line is
depicted as a black solid line. The dashed lines represents the fitted orthogonal models between AGB
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estimates by TLS-QSM or local allometric models and AGB reference, with colours corresponding the colour
used for the model estimates. Vertical bars show the estimated uncertainty (standard deviation) for each
model estimate and horizontal bars show the uncertainty for the reference AGB estimates. Grey box on the
left graph shows where the Indonesian values would fit in the Peruvian Graph.

For the Peruvian study area the TLS-QSM approach is the closest to the 1:1 line, whereas the
deviation from the 1:1 line is clearly larger for the three local allometric models tested, which
systematically underestimate the AGB of large trees. The TLS-QSM approach showed 10% and 50%
lower RMSE and 80% and 85% lower bias than the most- and least- accurate local allometric model.
The agreement between TLS-QSM estimates and reference values expressed as CCC is higher (0.96)
compared to the most- and least- accurate allometric model (0.76 – 0.92).

Table 5. Accuracies of AGB estimations for Peruvian trees, by the TLS-QSM and by Local allometric models.
Sample size = 6 trees.

RMSE Relative 2 Intercept

Model CV RMSE (%) Bias (%) R Slope CCC
(Mg) error (%) (Mg)

TLS-QSM 3.68 24.27 3.72 -3.87 0.93 1.16 -1.84 0.96

a
Goodman.II.1 4.09 26.97 -18.37 -16.87 0.97 0.78 0.54 0.92

Goodman.I.1.C
b 7.27 47.98 -26.2 -6.42 0.94 0.54 3.19 0.76
R
a
most accurate allometric model
b
least accurate allometric model

For the Indonesian study area, unlike for the Peruvian site, the local allometric models showed lower
RMSE and bias than the TLS-QSM for this particular subset of trees. The best local allometric model
had a 44% smaller RMSE than the TLS-QSM, was closer to the 1:1 line and had a higher agreement
with reference values (CCC = 0.96) than our approach (0.92).

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 Table 6. Accuracies of AGB estimations for Indonesian trees, by TLS-QSM approach and by local allometric
models. Sample size = 7 trees.
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RMSE CV RMSE Relative 2 Intercept
Model Bias (%) R Slope CCC
(Mg) (%) error (%) (Mg)

TLS-QSM 1.67 37.13 21.36 19.08 0.96 1.29 -0.34 0.92

Manuri.DBH.WD.H.
a 0.94 20.82 0.63 11.88 0.94 0.88 0.58 0.96
mix
b
Jaya07 1.52 33.93 -19.33 -12.12 0.95 0.71 0.41 0.89
a
most accurate allometric model
b
least accurate allometric model

4. DISCUSSION

4.1. Consistent and accurate AGB estimation of tropical trees from QSMs

We found that the TLS-QSM approach can provide reliable and accurate AGB estimates for large
tropical trees (DBH >70 cm), outperforming the accuracy of all the pantropical allometric models
tested. To the best of our knowledge, this is the first study assessing the accuracy of tropical trees
AGB estimates using QSMs from TLS point clouds of trees across different tropical forest regions. A
previous study by Disney et al. (2014) presented a proof of concept for the use of TLS-QSM for tree
AGB estimation of tropical trees in Gabon, but in their research no tropical trees were harvested,
thus the accuracy of its AGB estimates could not be assessed but only compared to the AGB
estimates provided by allometric models. Our study showed that AGB estimations by allometric
models often are not a reliable indicator of AGB for large tropical trees. This issue was also
addressed by Clark and Kellner (2012), Calders et al. (2015b) and Ploton et al. (2016). Clark and
Kellner (2012) and Calders et al. (2015b) both noted that large trees are under-represented in
calibration of allometric models, therefore these models may produce large absolute errors for large
trees, which is supported by our findings. Ploton et al. (2016) identified an increase in the estimation
error of pantropical allometric models with the increase of tree mass. Clark and Kellner (2012) also
point out that large trees inherently span a larger range of AGB values for a given DBH, thus
exacerbating this problem of under sampling.

4.1.1.AGB estimations by TLS-QSM vs pantropical allometric models

Across the three sites the TLS-QSM method to estimate AGB was more accurate than the most
accurate pantropical allometric model evaluated (Chave05m1.3, in Supporting Information S5), with
an absolute improvement of 7.2 % less CV RMSE (Table 4). This accuracy improvement, was even
more pronounced in terms of bias reduction. Moreover, TLS-QSM showed a higher agreement with
reference values (CCC= 0.95) compared to the most accurate pantropical allometric model (CCC =
0.89). Calders et al. (2015b) found a comparable trend of higher accuracy for their TLS-QSM method

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 in relation to allometric models for estimating AGB of eucalyptus trees in Australia. The accuracy of
the AGB estimates by TLS-QSM in our study was lower than the accuracy reported by Calders et al.
(2015b), and our agreement (CCC = 0.95) was lower than the agreement found by Calders et al (CCC
Accepted Article
= 0.98). This is likely due to the greater structural complexity and vegetation occlusion of the tropical
very dense forest in our study areas compared to the open eucalyptus forest studied by Calders et
al. (2015b). In relation to the updated and widely-used pantropical allometric models of Chave et al.
(2014), our method achieved an absolute improvement of 16% and 27% lower CV RMSE, which is
comparable to the error decrease reported by Calders et al. (2015b).

It should be noted that the models accuracies were estimated by comparing each model AGB
estimates with AGB reference estimates derived from destructive geometric measurements, rather
than with AGB weighted. The uncertainties introduced in measuring stems, buttresses, and branches
volumes were taken into account, but -as in Kankare et al. (2013) and Berger et al. (2014)- the
uncertainty due to the use of Smalian formula for estimating true volume was assumed to be
negligible. Furthermore, the uncertainty introduced in the correction factor for small branches
volume, and in the application of a single species-specific wood density value for each tree instead of
discriminating wood density for different woody fractions, both were not measured but taken from
literature. Moreover, models uncertainties increasing with tree size indicates heteroscedasticity
effects, which should be considered with caution when developing allometric models. This reinforces
the need for improved methods for estimating large trees biomass, and for further research with
larger datasets to assess the uncertainty on large trees biomass estimation.

4.1.2.AGB estimations by QSM models vs local allometric models in Indonesia and Peru

The TLS-QSM method also produced AGB estimates more accurate than the local allometric models
for the Peruvian dataset, with a higher agreement (CCC = 0.96) with reference data than the local
allometric models in Peru (CCC = 0.76 - 0.92). However, several local allometric models
outperformed our method for the Indonesian dataset, which trees were predominately smaller than
10 Mg. In this case, several local allometric models had better agreement, ranging from 0.89 to 0.96,
while TLS-QSM approach had an agreement of 0.92.

For both cases, at pantropical or regional-local level, there are large implications related to the
choice of which allometric model one should use for AGB estimation of tropical trees. While some
allometric models presented here performed with similar accuracy than our method for some trees;
other allometric models proposed for the same region and by the same authors provided
significantly larger errors on the same trees.

4.2. Reconstructing 3D woody structure of tropical forest trees using QSMs

We showed that the TLS-QSM method can be used to accurately estimate volume from 3D
reconstructed structure of large tropical trees from scans in very dense forest with leaf-on
conditions. The tree structure reconstructions for these large tropical trees contained larger
uncertainty (higher variance on the QSM outcomes) than in previous studies (Calders et al. 2013,
2015b; Raumonen et al. 2015) which evaluated smaller trees and were located in more open forest
conditions and less occluded trees. For the smallest trees in our study, the 3D reconstruction
uncertainty values were closer to those previously reported by Calders et al. (2015b).

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 Consistent with previous QSM studies (Calders et al. 2013, 2015b; Raumonen et al. 2013; Disney et
al. 2014) we optimized the reconstruction process based on the PatchDiam parameter, which was
reported to be the most influential parameter (Calders et al. 2013). The main difference compared
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to Calders et al. (2015b) is in the method for judging the optimal reconstruction.

Our sample of tropical trees was characterized by being among the most challenging conditions for a
3D tree reconstruction method because the target trees were among the tallest trees in each plot
and having the largest crown size and complexity. The combination of these limiting factors
contributes to increased occlusion, in combination with very dense understory, resulting in under-
sampled areas in the tree crowns, and larger uncertainties in the QSM reconstructions. For these low
density point cloud areas the QSM’s presented some unrealistic branching reconstructions. The low
density point cloud issue was also addressed by Raumonen et al. (2011, 2013). They stated that the
reconstruction method was quite sensitive to low point cloud density and therefore, reliability of
cylinders reconstructing small branches could be very low. Therefore, we discarded all branches with
a diameter < 10 cm and applied the expansion factor to account for their volume.

Alternatively, Calders et al. (2015a) recently proposed an automated method for QSM
parameterization. This method optimized the PatchDiam value based on the maximum match of
QSM cylinders diameter with point cloud circle fitting diameter at four different heights along the
main trunk. This approach focuses on comparing the reconstructed main trunk, regardless of the
quality of the reconstructed tree crown. However, recent studies (Goodman et al. 2014; Ploton et al.
2016) showed the important contribution of the crown biomass to the total tree biomass for large
tropical trees. Similarly, for the trees in our study, the crown contribution to the total tree biomass
was 50% on average and even larger for the trees above 10 Mg (60% of the total tree biomass).
Therefore, we decided not to implement the method of Calders et al. (2015b) for our study.

Future research should focus on developing an automated QSM optimization which optimizes the
reconstruction of the entire tree and does not focus on the tree trunk alone. Automated
optimization of this sort might enable to improve even further the accuracy of tree volume and AGB
estimates of tropical trees from TLS data at large scale without harvesting trees.

5. CONCLUSIONS

We present an approach to estimate tree wood volume and AGB for large tropical trees that relies
on estimates of tree volume based on 3D data from Terrestrial Laser Scanner (TLS) and basic wood
density. We show that tree volume estimation of these large tropical trees based on TLS data and
Quantitative Structure Models (QSM) provided a CV RMSE of 23.7% in comparison to destructive
harvest measurements. Tree AGB estimates derived from TLS-QSM provided better agreement with
AGB reference data (28.4% CV RMSE, CCC = 0.95) than AGB estimates based on traditional forest
inventory data and pantropical allometric models (33.5 to 54.9% CV RMSE, CCC = 0.73 – 0.82). The
allometric models considered in this study showed a systematic underestimation for large trees
(DBH >70cm), increasing with tree size, contrasting with the largely smaller and non-systematic
deviation for the TLS-QSM.

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 It is important to remark that our results are based on a limited sample size of 29 trees across three
ecosystems; while Calders et al. (2015b) harvested 65 trees in one ecosystem. Despite this, our
results confirmed a recent trend showing that TLS scanning and QSM are able to account for
Accepted Article
individual tree structure more effectively than allometric models, thus providing tree volume and
AGB estimates which are likely to be unbiased by tree size.

This approach can be further used for testing and calibrating new allometric models, since allometric
models often have large absolute errors for large trees, which are usually underrepresented in
destructive sampling studies. This opens up the opportunity for QSMs derived from TLS
measurements to be used in the future for building improved allometric models that might enhance
present and past estimates of forest biomass and carbon emissions from tropical forest.

6. ACKNOWLEDGMENTS

This research is part of CIFOR's Global Comparative Study on REDD+. The funding partners whose
support is greatly appreciated include the Norwegian Agency for Development Cooperation (Norad),
the Australian Department of Foreign Affairs and Trade (DFAT), the European Union (EU), the
International Climate Initiative (IKI) of the German Federal Ministry for the Environment, Nature
Conservation, Building and Nuclear Safety (BMUB), and the CGIAR Research Program on Forests,
Trees and Agroforestry (CRP-FTA) with financial support from the donors to the CGIAR Fund. The
study received further support from a SilvaCarbon research project (14-IG-11132762-350) on
Measuring forest degradation for REDD+: a synthesis study across five SilvaCarbon countries. We
acknowledge the collaboration of scientist and technicians from CIFOR and associated consultants,
and the Guyana Forestry Commission for their support: Louis Verchot, Shijo Joseph, Emilio Perales,
John Janovec, I.E. Wiyono, Garik Cruise, Uji Pribadi, Hans Sukhdeo, Walter Huaraca, Filio Farfán,
Cesar Vela, Angel Balarezo, Javier Huinga; and many local villagers who participate in the field work
in Peru, Indonesia and Guyana. M.D. acknowledges support from the UK NERC National Centre for
Earth Observation (NCEO).

All the authors declare no conflict of interest.

DATA ACCESSIBILITY

The individual trees TLS point cloud, QSM cylinder models, forest inventory, and destructive
sampling measurement data used for this research can be accessed in the LUCID repository
(http://lucid.wur.nl/datasets/terrestrial-lidar-of-tropical-forest). These datasets are owned by the
Centre for International Forestry Research (CIFOR) and Wageningen University. The datasets are free
to download and available for any use as long as the proper reference, as specified in the portal, is
applied For collaborations or questions please contact: [email protected],
[email protected] or [email protected].

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 AUTHORS CONTRIBUTIONS

JGT and AL equally co-led the entire study. JGT, AL, HB, VA and MH conceived the ideas and
designed methodology; JGT, AL, RG and SM collected the data; JGT and AL analysed the data; JGT, AL
Accepted Article
and HB led the writing of the manuscript. All authors contributed critically to the drafts and gave
final approval for publication.

SUPPORTING INFORMATION

Additional Supporting Information available in the online version of this article:

Supporting Information S1. Field data acquisition.

Supporting Information S2. Plot spatial design and laser scanning sampling.

Supporting Information S3. Quantitative Structure Models.

Supporting Information S4. Equations used for volume estimation from reference measurements.

Supporting Information S5. Equations used for tree above ground biomass estimation with
allometric models.

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