https://doi.org/10.20965/ijat.2021.

p0313
Forest Data Collection by UAV Lidar-Based 3D Mapping:
Segmentation of Individual Tree Information from 3D Point Clouds

Technical Paper:

Forest Data Collection by UAV Lidar-Based 3D Mapping:

Segmentation of Individual Tree Information
from 3D Point Clouds
Taro Suzuki∗1,† , Shunichi Shiozawa∗2 , Atsushi Yamaba∗3 , and Yoshiharu Amano∗4
∗1 Chiba Institute of Technology

2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan

† Corresponding author, E-mail: taro@furo.org
∗2 Terra Drone Corporation, Tokyo, Japan
∗3 Forestry Research Center, Hiroshima Prefectural Technology Research Institute, Miyoshi, Japan
∗4 Waseda University, Tokyo, Japan

[Received November 11, 2020; accepted February 12, 2021]

In this study, we develop a system for efficiently mea-
suring detailed information of trees in a forest envi-
ronment using a small unmanned aerial vehicle (UAV)
equipped with light detection and ranging (lidar). The
main purpose of forest measurement is to predict the
volume of wood for harvesting and delineating for-
est boundaries by tree location. Herein, we pro-
pose a method for extracting the position, number of
trees, and vertical height of trees from a set of three-
dimensional (3D) point clouds acquired by a UAV lidar
system. The point cloud obtained from a UAV is dense
in the tree’s crown, and the trunk 3D points are sparse
because the crown of the tree obstructs the laser beam.
Therefore, it is difficult to extract single-tree infor-
mation from 3D point clouds because the characteris-
tics of 3D point clouds differ significantly from those
of conventional 3D point clouds using ground-based
laser scanners. In this study, we segment the forest
point cloud into three regions with different densities
of point clouds, i.e., canopy, trunk, and ground, and
process each region individually to extract the target
information. By comparing a ground laser survey and
the proposed method in an actual forest environment,
it is discovered that the number of trees in an area
measuring 100 m × 100 m is 94.6% of the total num-
ber of trees. The root mean square error of the tree
position is 0.3 m, whereas that of the vertical height
is 2.3 m, indicating that single-tree information can be
measured with sufficient accuracy for forest manage-
ment.
Keywords: remote sensing, 3D point cloud, UAV, seg-
mentation
1. Introduction
Japan is an eminent forest country, with forest areas
constituting 68% of the entire country. 41% of the for-
est area is artificial forest with needle-leaved trees. Many
of such artificially expanded forests, which are currently
at their harvest time, are left unharvested as they do not
generate any profit. Various capacities of aged trees have
been degraded not only to render them vulnerable to ty-
phoon damage, but also to reduce their water-sustaining
capacities to cause natural disasters such as landslides. In
addition, Japan’s declining birthrates and young people’s
increasing exodus to urban areas have rapidly reduced
the forestry workforce, whereas efficient forest manage-
ment and measurements remain to be addressed. From
the perspective of sustainable forest management, indi-
vidual management by which to manage single trees in-
dividually would be more suitable than areawide forest
management [1]. However, as most forests are distributed
in mountainous areas, measuring single trees individually
in a sloped environment in a wide range of mountains will
impose significant burden on workers.
Meanwhile, small unmanned aerial vehicles (UAVs)
have been applied for measuring objects from the sky as
an affordable and easy method to replace conventional air-
borne measurements using aircraft. In particular, three-
dimensional (3D) measurements using light detection and
ranging (lidar) are expected to replace conventional pho-
tographic measurements [2]. In measuring a forest, single
trees used for measurements by ground-based lidar, are
often obstructed by their branches and leaves, rendering it
difficult to acquire the tree crown point clouds that work-
ers are compelled to repetitively move using their mea-
suring devices; hence, the burden on workers remains an
issue to be addressed [3, 4].
The aim of this study is to build a system to efficiently
measure single-tree information for artificial forest man-
agement. Fig. 1 shows the tree information used in this
study. The height of a tree is defined as the height of
the trunk at 1.2 m above the ground (the terrain on the
mountain side in the case of a slope). The measured ver-
tical height from the top of the tree to the terrain is known
as the vertical height, and the trunk’s cross-sectional cen-
ter refers to the location of the tree in the forest. The
tree locations used for the land’s boundary information,
the number of trees used as an index for thinning, and

Int. J. of Automation Technology Vol.15 No.3, 2021 313

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Suzuki, T. et al.
Top
Tree canopy
Number of trees
Position of tree
Vertical height
1.2m
Fig. 1. Target single-tree information to be extracted from
3D point cloud using proposed method.
the vertical heights used to estimate tree volumes provide
the most important information for single-tree measure-
ments. As the distance between standing trees in a well-
maintained forest is approximately 2–4 m, we aim to es-
timate the horizontal positions of single trees with an ac-
curacy of 0.5 m or less.
In this study, we developed a small UAV equipped
with lidar and created 3D point clouds of a wide range
of forests including their absolute coordinates. We fur-
ther propose a method for processing 3D point clouds
to extract and measure the numbers, locations, and verti-
cal heights from the numerous 3D point clouds acquired.
Three-dimensional point clouds acquired by a small UAV
from the sky are particularly sparse in the trunk region,
unlike those measured using the conventional ground-
based lidar. As a small UAV flies at a low altitude, signifi-
cant differences in density occur between the point clouds
immediately under the flight path and those distant from
it because of the difference in the angle of incidence of
the laser. Therefore, in this study, we propose a single-
tree segmentation method for 3D point clouds acquired
using a small UAV equipped with lidar. We expect the
proposed method to enable us to reduce the measurement
time and mitigate human burden. Furthermore, we eval-
uated the proposed method by comparing the measure-
ments yielded by it with single-tree information acquired
by ground-based lidar in the field of an actual forest.
2. Related Studies
The conventional forest measurement and manage-
ment method uses ground-based lidar for forest measure-
ments [3]. It can acquire 3D point clouds that are as dense
as 100,000 or more points per square meter, enabling
not only the measurements of the locations, heights, and
trunk diameters of trees, but also the determination of tree
shapes. Furthermore, it can measure the height of a tree
314
with an accuracy of 0.25–1.5 m by defining a tree top as
the maximum point in the planar region estimated from
terrain point clouds acquired near it [4]. The measure-
ment of tree heights using ground laser is often hindered
by the tree branches and leaves, rendering it difficult to
acquire tree top point clouds that cannot be measured cor-
rectly using their vertical heights. Moreover, ground laser
can only measure a limited range at a time.
In the currently prevailing airborne laser surveys, high-
accuracy lidar equipped on medium- or large-sized air-
craft irradiates the terrain to measure a wide range [5–
9]. It can measure the digital surface model (DSM) for
the branches and leaves by directly irradiating laser from
the sky, as well as the digital terrain model (DTM) from
point clouds that are transmitted through the branches and
leaves to reach the ground. Hence, we can calculate the
digital canopy height model from the difference between
the DSM and DTM. In areas where the forests to be mea-
sured are distinctly bounded, approximate quantities of
trees can be measured using airborne surveys. However,
in an airborne survey where laser is irradiated immedi-
ately under a high altitude, the trunk point clouds can
barely be acquired, and the tree crown point clouds are
as sparse as four points per square meters. Therefore, the
numbers of trees cannot be determined correctly, nor can
individual information regarding each tree be measured;
these issues remain to be addressed [10].
Visiblelight and near-infrared radiation images taken
by a camera have been applied to forest surveys. As cam-
eras are relatively lightweight compared with lidars, they
are used not only in aircraft, but also in small UAVs [11–
13]. We can create a DSM by applying the structure from
motion method to images that have been continuously
photographed from the sky; however, DTM information
cannot be obtained because it is difficult to acquire terrain
and trunk information from such images.
UAV laser surveys using UAVs equipped with lidar
have recently garnered increasing attention. They survey
forests from the sky, thereby improving work efficiency
compared with conventional single-tree forest measure-
ments using ground laser. Furthermore, airborne laser
surveys can acquire detailed point clouds by flying at low
altitudes over forests [14]. Despite the many operational
advantages of laser surveys by small UAVs, they are not
used extensively for forest surveys. To create precise 3D
point clouds using a UAV equipped with lidar, the position
and attitude of lidar in flight must be estimated with high
accuracy. Conventionally, a composite system comprising
a global navigation satellite system (GNSS) and an iner-
tial navigation system (INS) has been used to estimate the
position and attitude of lidar [15]. Because a composite
GNSS/INS system is expensive and requires some initial-
izing flights, it poses problems when operating in moun-
tainous areas that are limited in space. In a few previous
studies [14, 16–18], forests were measured using a GNSS
equipped with lidar. However, the measurements did not
include detailed single-tree data.
Our contributions from the current study are as follows:
Int. J. of Automation Technology Vol.15 No.3, 2021

Segmentation of Individual Tree Information from 3D Point Clouds
Fig. 2. UAV 3D mapping system with multiple GNSS re-
ceivers and lidar.
• We develop a UAV equipped with multiple GNSSs
and lidar and build a 3D point cloud mapping sys-
tem capable of measuring forests with an accuracy
of 10 cm.
• To measure single trees from their 3D point clouds,
which are characteristically uneven in density and
sparse on the trunk, we propose a method for extract-
ing composite tree information by segmenting a tree
into a tree crown and trunk.
• Considering the shape characteristics of trees, we
propose a method to cluster their 3D point clouds
using their vertical compressions.
• We acquire data from an actual forest environment
to comparatively evaluate single-tree measurements
obtained by ground lidar and the proposed method,
which uses a UAV equipped with lidar.
3. 3D Mapping System
3.1. Overview
Figure 2 shows the developed hexacopter-type UAV
equipped with multiple GNSS antennas. We used
Matrice 600 from DJI Inc. as the UAV platform. The
mapping system comprising multiple GNSSs and lidar
was separated from the UAV and installed via a passive
damper.
Figure 3 shows an enlarged photograph of the mapping
system: it comprises six GNSS antennas installed approx-
imately 1.8 m apart from each other; it uses VLP-16 of
Velodyne Inc. for lidar; it uses NEO-M8T of u-biox Inc.,
a one-frequency GNSS receiver capable of outputting the
GNSS carrier wave phase, as a receiver for real-time kine-
matic (RTK)-GNSS; it uses TW2712 of Tallysman Inc.
for its six GNSS antennas; all the installed equipment,
Int. J. of Automation Technology Vol.15 No.3, 2021
Forest Data Collection by UAV Lidar-Based 3D Mapping:
Lidar GNSS Receivers
(Velodyne VLP16) (u-blox NEO M8T)
Fig. 3. Lidar and GNSS receivers equipped with UAV.
such as the GNSS receivers, antennas, and lidar, weigh
approximately 3.5 kg in total [19].
The developed system combining RTK-GNSS with
the installed multiple low-cost one-frequency GNSS re-
ceivers and antennas can estimate the UAV’s position and
attitude with high accuracy. The use of multiple GNSS
antennas and their RTK-GNSS processing enables us to
directly measure the 3D attitude of the UAV from the ge-
ometrical arrangement of the GNSS antennas without us-
ing any expensive INS. In estimating the position of the
UAV, for which one GNSS receiver is typically used, the
developed system uses six GNSS receivers to acquire the
UAV’s position, thereby allowing the redundancy of the
installed GNSS receivers to be utilized to improve the ac-
curacy of the RTK-GNSS, using low-cost one-frequency
GNSS receivers. Moreover, the developed system can di-
rectly measure the UAV’s 3D attitude from the installed
multiple GNSS antennas, thereby obviating the necessity
for any initial flights to estimate the UAV’s attitude, which
is required in conventional similar systems. Therefore,
the developed system becomes more suitable for measure-
ments in mountainous areas with limited space. For more
details, please refer to [20].
3.2. 3D Point Clouds
Figure 4 shows an example of 3D point clouds of a
forest acquired using the developed UAV equipped with
lidar, where the point clouds are shown in different colors
based on their elevations. The abovementioned example
represents the data of approximately 30 million points in
a 100-m square acquired by a UAV flying at an altitude of
60 m. Fig. 5 shows the cross-sectional views of the above-
mentioned 3D point clouds of the forest, from which one
can observe that as the laser was irradiated on the ground
surface through the clearance of the trees and leaves, the
acquired ground surface 3D point clouds became sparse.
Furthermore, as the point clouds of the trunk were ex-
tremely sparse compared with those of the tree crown, the
density of acquired point clouds differed among the trees.
Next, we describe our proposed method for estimating the
locations, numbers, and vertical heights of trees from 3D
point clouds acquired by a UAV equipped with lidar.
315
Suzuki, T. et al.

3D mapping by
UAV Lidar
3D pointcloud of
3D pointcloud trees
Extraction terrain pointcloud Principal component
by Progressive analysis and b-spline
Morphological Filter fitting
Terrain Tree canopy Tree trunk
pointcloud pointcloud pointcloud

Segmentation
Local maximum
B-spline fitting using vertical
computation
compression
Terrain model Tree top
Tree trunk model
Tree top

Fig. 4. Example of 3D point cloud in forest acquired by Estimation of Integrtation of tree canopy and
proposed UAV 3D mapping system. vertical height trunk information

Vertical height 3D location Number of trees

Fig. 6. Proposed measurement flow for number, position,

and vertical height of single tree from forest 3D point cloud.

We first segmented the point clouds in the terrain region

and then defined the curvilinear surface passing through
the bottom face of the tree crown via B-spline fitting us-
ing principal component analysis. Hence, we segmented
the tree 3D point clouds, excluding the point clouds in
the terrain region, into point clouds in the tree crown and
tree trunk regions. We extracted each tree top informa-
tion from the point clouds in the tree crown region. The
tree locations were extracted from the point clouds in the
trunk region via the segmentation method using their ver-
tical compressions; subsequently, we integrated such in-
formation to calculate the numbers, locations, and vertical
heights of trees.
Fig. 5. Cross-sectional view of acquired forest point cloud.

4.2. Tree Top Detection

4. Proposed Method
4.1. Overview
The algorithm to be used for extracting single-tree in-
formation from the point clouds acquired by ground laser
identifies a single tree by fitting its tree crown modeled
into a cone and its trunk modeled into a column [3].
Meanwhile, the point clouds to be acquired by a small
UAV that irradiates laser from the sky are characteristi-
cally dense for the tree crown and sparse for the trunk
because the laser is obstructed by the tree crown. In many
cases, some of the point cloud data of the trunk are un-
available. It is difficult to extract a single tree by model
fitting such point clouds. Therefore, in this study, we seg-
mented the forest’s 3D point clouds into regions of tree
crown, tree trunk, and terrain, the point cloud densities of
which differ from each other; subsequently, we processed
these three regions separately. Fig. 6 shows the flow of
extracting single-tree information from 3D point clouds.
First, we extracted the point clouds in the terrain re-
gion from the acquired 3D point clouds. To detect the
point clouds that pass through the tree crowns and trunks
to arrive at the terrain, we removed the point clouds of
ground objects other than the terrain (non-terrain point
clouds), such as trees, using the progressive morphologi-
cal filter proposed by Zhang et al. [21]. The progressive
morphological filter removes non-terrain point clouds by
open processing, where they are first expansion processed
and then contraction processed. The filter removes ground
objects whose width is smaller than the window region w.
Ground objects of different widths can be removed more
precisely by gradually changing the window width from
a small value to a large one to sequentially process them
and distinguish ground objects from the terrain based on
height changes between adjacent points. Subsequently, to
calculate the intersection between the vertical line from
the tree top and the terrain to determine the vertical height,
we created a curvilinear surface representing the terrain
by B-spline fitting [22] the terrain point clouds.

316 Int. J. of Automation Technology Vol.15 No.3, 2021


Segmentation of Individual Tree Information from 3D Point Clouds
Fig. 7. Estimation of boundary plane of crown and trunk 3D
points from 3D tree point cloud.
In the B-spline fitting, we determined a B-spline curvi-
linear surface that fits the input point clouds through
repetitive calculations using point distance minimization,
which minimizes the residual distance between the cre-
ated curvilinear surface and the input point clouds [22–
24]. B-spline fitting was performed as follows [22, 23]:
1. An appropriate initial shape of B-spline curvilinear
surface was specified.
2. The distance to the curvilinear surface at every input
point cloud as well as the error function were calcu-
lated.
3. A control point to minimize the error function was
identified, and the B-spline curvilinear surface was
updated.
4. Steps 2 and 3 were repeated until the prespecified
error threshold was obtained.
Next, the entire-tree point clouds were segmented, ex-
cluding the terrain point clouds, into point clouds in the
tree crown and trunk regions. In mountainous areas with
diverse terrains, the shape of the curvilinear surface that
separates the tree crown and trunk is complex. Therefore,
in this study, we determined the curvilinear surface that
separates the tree crown from the trunk using B-spline fit-
ting.
First, we downsampled the entire-tree point clouds in
advance using a voxel grid filter [25]. The voxel grid filter
separates the point clouds by an arbitrary grid size and
replaces the point clouds in a grid with one point in the
center of gravity.
Next, we defined the third principal component vector
in the principal component analysis of the entire tree point
clouds as its normal vector and calculated the plane that
will pass through the center of gravity of the point cloud
data as the initial plane in the B-spline fitting. As we can
assume that the tree crown of a needle-leaved tree is cone
shaped, the density of the bottom part of the point clouds
in the tree crown region is higher in the entire forest, and
the plane to be acquired by the principal component anal-
ysis constitutes an approximate average plane of the tree
bottom faces (light gray line in Fig. 7). Fig. 8 shows an
example of the plane estimated via principal component
analysis in an actual forest, from which it is clear that the
plane passed slightly above the bottom part of the tree
crown.
Int. J. of Automation Technology Vol.15 No.3, 2021
Forest Data Collection by UAV Lidar-Based 3D Mapping:
Fig. 8. Example of initial plane estimated using PCA.
Fig. 9. Example of boundary plane of crown and trunk 3D
points via B-spline fitting.
Next, we estimated by the abovementioned B-spline fit-
ting a curvilinear surface separating the tree crown from
the trunk (gray line in Fig. 7). Using the plane acquired
via principal component analysis as an initial shape for
the B-spline fitting, we estimated a curvilinear surface that
minimizes the distance residuals between the curvilinear
surface and the entire-tree point clouds. Because the den-
sity of the point clouds near the bottom part of the tree
crown is higher than that of the trunk and top parts of
the tree, as described above, the final curvilinear surface
passed through the tree’s bottom face.
Figure 9 shows an example of a plane that separates the
tree crown from the trunk as estimated from actual forest
point cloud data. As shown, the B-spline fitting method
can estimate a curvilinear surface that separates the tree
crown from the trunk. By setting the tree’s bottom face
determined by B-spline fitting as a boundary, we defined
the point clouds above the boundary as point clouds in the
tree crown region and those below the boundary as point
clouds in the trunk region.
Finally, we detected the tree top as the local maximum
point in the region diameter D in the height direction. To
avoid this, for cases involving two or more trees within the
region diameter D, the tree top of a tree inferior in height
may be detected as excessively small. Therefore, we set
the region diameter D as the minimum distance between
trees in the forest for detecting the tree top. We extracted
the tree top from the acquired 3D point clouds using the
abovementioned processes.
317
Suzuki, T. et al.
ε
D
Fig. 10. Segmentation of trunk points including crown points.
4.3. Trunk Detection
In measuring a forest using ground-based laser, tree
trunks were detected by columnar-fitting or circular arc-
fitting entire-tree 3D point clouds [26]. In measuring a
forest by a UAV, however, laser is irradiated on tree trunks
at angles that are extremely small for generating sufficient
reflection intensities to acquire trunk point clouds from
the sky. Moreover, because the laser beam was obstructed
by tree crowns, the trunk point clouds became sparser.
Hence, the abovementioned forest measuring method is
not suitable for the detection of tree trunks.
Therefore, in this study, we segmented the entire-tree
point clouds into point clouds in the tree crown and trunk
regions. Additionally, we segmented the point clouds in
the trunk region into one segment per trunk based on Eu-
clidean cluster expansion [27]. Euclidean cluster expan-
sion is a representative clustering method for classifying
adjacent point clouds within radius ε into the same seg-
ment. As described in the preceding section, the tree
crown point clouds were separated from the trunk point
clouds by setting the B-spline curvilinear surface as their
boundary. In cases where some trees were extremely low
compared with the neighbors, the tree’s bottom face might
not completely correspond to the boundary curvilinear
surface because the tree crown point clouds remained in
the trunk region. Fig. 10 shows the tree crown point
clouds remaining in the trunk region; point clouds in the
tree crown and trunk regions are indicated in gray and
black, respectively.
Therefore, in this study, exploiting the characteristics of
needle-leaved trees wherein their trunks grow vertically,
we processed the point cloud density in the height direc-
tion such that they are virtually dense; consequently, the
adjacent trunks can be separated appropriately into differ-
ent segments. Fig. 11 shows the flow of the proposed seg-
mentation method. First, to prevent the horizontally dense
tree crown point clouds that remained in the trunk region
from being combined into the same segment with the ad-
jacent trunk segment, we downsampled the point clouds
in the trunk region using a voxel grid filter. We used the
318
Input trunk Voxel grid filter Vertical compression and Vertical
pointcloud clustering decompression
Fig. 11. Flow of segmentation of trunk 3D points.
ε
D
Input trunk Voxel grid filter Vertical compression and Vertical
pointcloud clustering decompression
Fig. 12. Examples of trunk segmentation failures.
minimum distance D between trees in the object position
measuring range as the downsampling grid size such that
adjacent trunk point clouds exhibit the largest size within
the limits that prevent them from appearing in the same
grid and become filtered.
Subsequently, the point clouds aligned in the vertical
direction were compressed to obtain their vertical coordi-
nate values 1/d times such that they can appear within the
radius to be determined in the same segment. We set the
compression coefficient d to satisfy Eq. (1) such that the
compressed vertical distance between the points is smaller
than the segmentation radius ε and the horizontal distance
between points is larger than ε .
D
<ε <D
d
D
∴ d> . . . . . . . . . . . . . . (1)
ε
The Euclidean cluster extraction of vertically com-
pressed point clouds enables us to segment the trunk point
clouds sparsely in the height direction into the same seg-
ment. After the trunk point clouds were segmented, they
were decompressed such that their vertical coordinate val-
ues would be d-times and trunk detection can be com-
pleted.
In the proposed method, it is important to segment the
point clouds into point clouds in the tree crown and trunk
regions in advance. Fig. 12 shows an example of seg-
menting the entire-tree point clouds using the proposed
method. To detect the trunks by downsampling them with
a voxel and by vertically compressing them without sep-
arating the tree crown point clouds from the trunk point
clouds in advance, some point clouds will remain be-
tween adjacent trunks after vertical compression; there-
fore, the segmentation will not separate the trunks from
each other. Trunks can be accurately detected by separat-
ing point clouds in the tree crown region from those in the
trunk region, as well as by reducing the tree crown point
clouds remaining in the trunk region.
Int. J. of Automation Technology Vol.15 No.3, 2021
 Forest Data Collection by UAV Lidar-Based 3D Mapping:
Segmentation of Individual Tree Information from 3D Point Clouds

4.4. Estimate Numbers, Locations, and Vertical

Heights of Trees
We estimated the number, location, and vertical height
of trees by combining the detection results of the tree
tops and trunk segments. First, the tree top was de-
signed to correspond to the trunk segment by searching
the N-dimensional nearest neighboring point through the
Delauny division [28]. Subsequently, we calculated the
number of trees by assuming that the same tree is repre-
sented if the horizontal coordinate residuals of the tree
crown and trunk segment are within the minimum dis-
tance between trees D. Furthermore, if the tree top or
trunk segment is detected from one tree, then it is detected
as a single tree. Hence, we can detect trees of inferior
height whose tops are obstructed by the tree crowns of Fig. 13. UAV flight path and reference data acquired using
other trees or trees whose trunk point clouds cannot be ground-based laser scanner.
acquired in the dense tree area.
As the horizontal position of a tree can be defined by
its breast-height position at 1.2 m above the ground, if the
trunk segment has been successfully detected, the nearest
point at 1.2 m above the ground should be selected among
the point clouds of the detected trunk segment as the tree’s
estimated position. In this study, however, by assuming
that the trees are positioned nearly upright, we regarded
the center of gravity of the trunk segment point clouds as
the tree’s horizontal position.
As the vertical height is defined by the vertical distance
from the top of the tree to the ground surface, we calcu-
lated the vertical distance from the point determined as
the top of each tree to the terrain polygon to determine
the vertical height of the tree.
Using the abovementioned processes, we extracted the
numbers, locations, and vertical heights of trees from for-
est 3D point clouds acquired by a small UAV equipped
with lidar.

5. Experiments Fig. 14. Examples of 3D point cloud of single tree acquired

5.1. Overview
On September 5, 2017, we conducted forest measur-
ing experiments in the mountainous area of Mount Kan-
muri in Hatsukaichi City, Hiroshima Prefecture. Fig. 13
shows an aerial photograph of the experimental environ-
ment. The measurement object was an artificial forest of
Japanese cedar trees that were measured approximately
25 m in vertical height; they were planted around 1965
and qualitatively thinned by approximately 600 trees/ha.
In a measurement area of approximately 200 m × 200 m,
the UAV automatically flew approximately 60 m above
the ground at a speed of 2.0 m/s for 9 min and 51 s on
the path indicated in white in Fig. 13. For the refer-
ence data pertaining to the measured trees, we used the
locations, numbers, and vertical heights measured using
ground-based laser in 2014 as true values in the evaluation
experiments. We evaluated the proposed method by com-
paring the UAV-airborne measurements with those for an
area of 100 m × 100 m, indicated in the black square re-
using proposed UAV 3D mapping system.
gion in Fig. 13. Ground-based laser can be used to mea-
sure trees with the following accuracies: 0.01 and 1.1 m
in position and vertical height accuracies, respectively.
5.2. Experimental Results
5.2.1. 3D Point Clouds
Figure 13 shows the laser point clouds acquired in
the experiments (indicated by white points). The num-
ber of acquired point clouds was approximately 30 mil-
lion, and the point cloud density was approximately
1,300 points/m2 . Fig. 14 shows an example of a 3D point
cloud of a single tree extracted from the entire point cloud.
The tree crown point clouds were extremely dense com-
pared with the trunk point clouds. In regions with dense
trees, the point clouds of the trunk below the tree crown
and those of ground were sparse. It was difficult to apply

Int. J. of Automation Technology Vol.15 No.3, 2021 319

Suzuki, T. et al.
Fig. 15. Detection of tree top from crown point cloud.
Fig. 16. Extraction and segmentation results of tree trunk
point cloud.
any cylindrical model as used in the ground laser mea-
surements to trunk point clouds that were discontinuous
owing to the different tree densities.
5.2.2. Detection Results of Tree Tops and Trunks
Figure 15 shows the tree top point clouds detected us-
ing the local maximization method after separating the
point clouds by the B-spline curvilinear surface that con-
stitutes a boundary between the tree crown and trunk re-
gions. The minimum distance between trees D in the veri-
fication area was 1.0 m. Fig. 16 shows the point clouds in
the trunk region created by removing the tree crown point
clouds and terrain point clouds, followed by segmentation
performed using the proposed method. Because the max-
imum diameter of the trunks to be measured was 0.7 m,
we set the radius ε of the distance between points to be
placed in the same segment as 0.8 m and the depth d to
10. The abovementioned detection results prove that the
proposed method can detect tree tops and trunks from 3D
point clouds with uneven densities.
5.3. Evaluations
5.3.1. Number of Trees
We evaluated the detection of number of trees in terms
of the following three criteria: correct detection, in which
the number of trees is correctly detected; misdetection, in
which trees that are not present are detected as trees; un-
detected, in which trees that are present are not detected.
Table 1 shows the evaluation results for the detection of
trees from the tree top only, from the trunk segment only,
320
and from both the tree top and the trunk, as in the pro-
posed method. Fig. 17 shows the tree locations measured
via ground lidar, the tree top positions, and the trunk po-
sitions detected using the proposed method.
Among 514 trees within an area measuring 100 m ×
100 m, approximately 60 trees were undetected by the es-
timations from the tree top and trunk information. Mean-
while, the proposed method undetected 28 trees, which
represents an improved detection rate. Among the total
number of trees within the reference area, 94.6% was cor-
rectly detected. The undetected trees were either trees of
inferior height whose crowns were positioned lower than
the surrounding trees, or trees that were located lower than
the boundary set for separating the tree top from the trunk
and whose top point clouds remained in the trunk region.
Most of the trees undetected from both the tree top and
trunk segments by the proposed method were short and
obstructed by other trees; therefore, their point clouds
were not sufficiently acquired. Approximately 2.7% of
the total trees were misdetected; this occurs when the tree
crown point clouds are not sufficiently acquired in the
sparse point cloud region and other point clouds within
the local searching distance D [m] are scarce.
5.3.2. Location
Among the three trees whose trunk segments were un-
detected in the evaluation area, the tree top of one tree
was detected; hence, we were able to calculate its loca-
tion. Excluding one tree whose location has been calcu-
lated from the tree top, the proposed method utilized the
trunk segment’s position. We compared the 3D tree lo-
cations with the true values acquired by the ground laser
to obtain a locational root mean square error (RMSE) of
0.3 m.
5.3.3. Vertical Height
We only evaluated the vertical heights of trees whose
tops were detected. As the ground laser measured them
as a height above sea level, including the geoid height,
and the measurement values were calculated as an ellip-
soidal height on the GPS coordinate system, we added the
geoid height of the measurement area to the measurement
values to obtain the height above sea level. Fig. 18 shows
the histogram of the vertical height residuals between the
estimated height hest and the actual measured height href .
The average height residual was 1.34 m. The standard
deviation was 0.94 m, and the RMSE was 2.28 m.
6. Discussion
The 3D point clouds acquired by the small UAV were
dense for the tree crown point clouds and sparse for the
trunk point clouds because the laser beam was obstructed
by the tree crowns. The proposed method segmented the
acquired 3D point clouds into tree crown, trunk, and ter-
rain data, extracted tree information from each dataset,
and combined such tree information to obtain improved
Int. J. of Automation Technology Vol.15 No.3, 2021
 Forest Data Collection by UAV Lidar-Based 3D Mapping:
Segmentation of Individual Tree Information from 3D Point Clouds

Table 1. Number of detected trees and detection rates.

Proposal method Detection

Number of trees Reference Top Trunk (Top and Trunk) rate [%]
Total 514 464 482 510 99.2
Correct detection – 458 474 486 94.6
Undetection – 56 60 28 5.4
Misdetection – 6 8 14 2.7

䕿 ZĞĨĞƌĞŶĐĞ 㽢 dŽƉ 䠇 dƌƵŶŬ from many different angles.

䢷䢲 The proposed method can be used to estimate tree loca-
tions with an accuracy sufficient for forest management.
䢶䢲
As the trunk point clouds are low in density, we calculated
䢵䢲
the tree locations from the center of gravity of the point
clouds segmented as trunk point clouds. If we can im-
䢴䢲 prove the density of 3D point clouds as described above,
then the location estimation accuracy can be improved by
䢳䢲
applying a trunk model, which can also be used for bent
trees. Furthermore, improvements in the point cloud den-
䣛䣯

䢲
sity will enable us to estimate the tree trunk shapes, i.e.,
䢯䢳䢲 a task that used to be difficult to perform without using
ground-based lidar.
䢯䢴䢲
The low accuracy in measuring the vertical heights of
䢯䢵䢲 trees may be attributed to the reference data acquired by
ground laser, which often measures the vertical heights
䢯䢶䢲 at positions lower than the tree tops when it cannot ob-
tain their unobstructed views. Moreover, as the reference
䢯䢷䢲
䢯䢷䢲 䢯䢶䢲 䢯䢵䢲 䢯䢴䢲 䢯䢳䢲 䢲 䢳䢲 䢴䢲 䢵䢲 䢶䢲 䢷䢲 data represent the actual values measured more than three
䣚䢢䣯
years ago, the Japanese cedar trees subject to be measured
in this study appeared to have grown taller. Japanese cedar
Fig. 17. Comparison of estimated locations of trees using
proposed method. tree, which varies significantly with soil conditions, forest
age, tree density, and tree height, is estimated to grow by
0.4–1.3 m annually. Hence, the vertical heights measured
using the proposed method in 2017 were 1.34 m higher
(on average) than those measured using ground laser in
2014.
In 2014, an entire woodland of approximately 6 ha in
area, which included the area investigated in this study,
was measured; this activity was performed by two per-
sons and required two days to complete. Generally, the
work efficiency in measuring forests by laser is approx-
imately 2.5 ha per day. Measuring efficiency on ground
depends on the environment; in particular, on a sloped
ground, the work efficiency declines significantly. The
proposed method for measuring forests by a UAV suc-
cessfully measured the measurement area (1 ha) by fly-
m
ing for approximately 15 min, which would otherwise re-
Fig. 18. Histogram of vertical height residuals. quire half a day. Compared with the ground-based laser
measurement method, using a UAV for the measurements
reduced the required operation hours by approximately
24 times. Hence, it is demonstrated that the proposed
detection rates. Because most of the undetected tree point method is superior in terms of work efficiency and pro-
clouds were for short trees that were obstructed by other ductivity.
trees and remained undetected, the density of the 3D point
clouds can be increased and the detection accuracy fur-
ther increased by lowering the UAV’s flying altitude and
setting its flight path such that lidar data can be acquired

Int. J. of Automation Technology Vol.15 No.3, 2021 321

Suzuki, T. et al.
7. Conclusion
Herein, we proposed a system to efficiently measure
detailed tree information in a forest environment using a
UAV equipped with lidar. Forest measurements are pri-
marily aimed at estimating tree volumes for thinning and
harvesting, as well as to clarify the boundaries by tree
locations. We proposed a method for extracting the lo-
cations, numbers, and vertical heights of trees from 3D
point clouds acquired using a UAV equipped with lidar.
The point clouds acquired by a small UAV were dense
for the tree crowns and sparse for the trunks. This oc-
curred because the laser beam was obstructed by the tree
crowns, rendering it difficult to extract single-tree infor-
mation from 3D point clouds acquired by the UAV, un-
like the 3D point clouds acquired by the conventional
ground-based laser because of the large difference in char-
acteristics between them. Therefore, in this study, we
segmented the forest 3D point clouds into three regions:
tree crown, trunk, and terrain, with different point cloud
densities. Subsequently, we processed the three regions
separately to extract the target information. We com-
pared the measurement results in the actual forest envi-
ronment obtained using the ground laser and the proposed
method. It was discovered that the proposed method cor-
rectly detected 94.6% of the 514 trees present in an area
of 100 m × 100 m. The RMSEs of the tree locations and
vertical heights were 0.3 and 2.3 m, respectively. This
proves that the proposed method measured single-tree in-
formation with an accuracy sufficient for forest manage-
ment.
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Int. J. of Automation Technology Vol.15 No.3, 2021
 Forest Data Collection by UAV Lidar-Based 3D Mapping:
Segmentation of Individual Tree Information from 3D Point Clouds

Name: Name:
Taro Suzuki Atsushi Yamaba

Affiliation: Affiliation:
Chief Researcher, Future Robotics Technology Chief Researcher, Forestry Research Center, Hi-
Center, Chiba Institute of Technology roshima Prefectural Technology Research Insti-
tute

Address:
2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
Brief Biographical History:
2015- Assistant Professor, Waseda University
2019- Future Robotics Technology Center, Chiba Institute of Technology
Main Works:
• T. Suzuki, “Time-Relative RTK-GNSS: GNSS Loop Closure in Pose
Graph Optimization,” IEEE Robotics and Automation Letters, Vol.5, No.3,
pp. 4735-4742, July 2020.
Membership in Academic Societies:
• Japan Society of Mechanical Engineers (JSME)
• Robotics Society of Japan (RSJ)
• Society of Instrument and Control Engineers (SICE)
Address:
4-6-1 Toukaichi-higashi, Miyoshi, Hiroshima 728-0013, Japan
Brief Biographical History:
1996- Forestry Technical Staff, Hiroshima Prefectural Government
2000 Received Ph.D. from Hiroshima University
2004- Researcher, Hiroshima Prefectural Forestry Research Center
Main Works:
• “Forest Ownership Patterns Impacting on Landscape Structure of
Vegetation in a Mountainous Farm Village, Western Japan,” S. K. Hong
and N. Nakagoshi (Eds.), “Landscape Ecology for Sustainable Society,”
pp. 309-319, Springer, 2017.
Membership in Academic Societies:
• Japanese Forest Society (JFS)
• Japan Forest Engineering Society (JFES)

Name:
Shunichi Shiozawa Name:
Yoshiharu Amano
Affiliation:
Division Manager, Terra Drone Corporation Affiliation:
Professor, Department of Applied Mechanics
and Aerospace Engineering, Waseda University

Address:
2-14-13 Shibuya, Shibuya-ku, Tokyo 150-0002, Japan
Brief Biographical History:
2016 Received Bachelor of Engineering degree from Waseda University
2018 Received Master of Engineering degree from Waseda University
2018- Terra Drone Corporation
Address:
17 Kikui-cho, Shinjuku-ku, Tokyo 162-0044, Japan
Brief Biographical History:
2000-2002 Assistant Professor, Research Institute for Science and
Engineering, Waseda University
2002-2007 Associate Professor, Research Institute for Science and
Engineering, Waseda University
2008- Professor, Faculty of Science and Engineering, Waseda University
2008- Visiting Professor, École Polytechnique Fédérale de Lausanne
(EPFL)
Main Works:
• Development of automated energy management system for smart grid
through digital communication standards
• Development of autonomous sensing systems of 3D environment for
smart society
Membership in Academic Societies:
• Society of Instrument and Control Engineers (SICE)
• American Society of Mechanical Engineers (ASME)
• Japan Society of Mechanical Engineers (JSME)
• Japan Forest Engineering Society (JFES)

Int. J. of Automation Technology Vol.15 No.3, 2021 323

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