Int J Appl 

Earth Obs Geoinformation 92 (2020) 102173

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Int J Appl Earth Obs Geoinformation

journal homepage: www.elsevier.com/locate/jag

Tree species classification using UAS-based digital aerial photogrammetry T

point clouds and multispectral imageries in subtropical natural forests
Zhong Xua,1, Xin Shena,1, Lin Caoa,*, Nicholas C. Coopsb, Tristan R.H. Goodbodyb, Tai Zhongc,
Weidong Zhaoc, Qinglei Sunc, Sang Bac, Zhengnan Zhanga, Xiangqian Wua
a
Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, 159 Longpan Road, Nanjing, Jiangsu, 210037 China
b
Faculty of Forestry, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4 Canada
c
Yunnan Baima Snow Mountain National Nature Reserve Management Bureau, 16 Kangzhu Avenue, Shangri-La, Diqing Tibetan Autonomous Prefecture, Yunnan
Province, 674499, China

A R T I C LE I N FO A B S T R A C T

Keywords: Tree species composition of forest stand is an important indicator of forest inventory attributes for assessing
UAS ecosystem health, understanding successional processes, and digitally displaying forest biodiversity. In this
Multispectral study, we acquired high spatial resolution multispectral and RGB imagery over a subtropical natural forest in
High-resolution southwest China using a fixed-wing UAV system. Digital aerial photogrammetric (DAP) technique was used to
Individual tree crown delineation
generate multi-spectral and RGB derived point clouds, upon which individual tree crown (ITC) delineation
Tree species classification
algorithms and a machine learning classifier were used to identify dominant tree species. To do so, the structure-
from-motion method was used to generate RGB imagery-based DAP point clouds. Then, three ITC delineation
algorithms (i.e., point cloud segmentation (PCS), image-based multiresolution segmentation (IMRS), and ad-
vanced multiresolution segmentation (AMRS)) were used and assessed for ITC detection. Finally, tree-level
metrics (i.e., multispectral, texture and point cloud metrics) were used as metrics in the random forest classifier
used to classify eight dominant tree species. Results indicated that the accuracy of the AMRS ITC segmentation
was highest (F1-score = 82.5 %), followed by the segmentation using PCS (F1-score = 79.6 %), the IMRS ex-
hibited the lowest accuracy (F1-score = 78.6 %); forest types classification (coniferous and deciduous) had a
higher accuracy than the classification of all eight tree species, and the combination of spectral, texture and
structural metrics had the highest classification accuracy (overall accuracy = 80.20 %). In the classification of
both eight tree species and two forest types, the classification accuracies were lowest when only using spectral
metrics, indicated that the texture metrics and point cloud structural metrics had a positive impact on the
classification (the overall accuracy and kappa accuracy increased by 1.49–4.46 % and 2.86–6.84 %, respec-
tively).

1. Introduction
Forests contribute to key ecosystem services and ecological pro-
cesses by adjusting local and regional climate changing the latent and
sensible heat fluxes on the surface, changing the hydrological climate at
the catchment scale, and conserving runoff and altering other functions
(Bonan, 2008; Gamfeldt et al., 2013; Pan et al., 2011). At the same time,
forest ecosystems are also the largest carbon sinks in terrestrial eco-
systems; thus, playing an important role in reducing carbon dioxide and
slowing some of the impacts of global warming (Cardinale et al., 2012;
Chambers et al., 2007; Pan et al., 2011). Therefore, it is extremely
important to maintain the stability of forest ecosystems. An increasing
number of studies have shown that forest biodiversity is a sign of forest
ecosystem stability (Chen et al., 1999; Loreau and de Mazancourt,
2013; Schneider, 2001; Tilman et al., 2006). However, forest biodi-
versity is increasingly threatened by deforestation, fragmentation, cli-
mate change and other stressors (Durães et al., 2013; Laurance et al.,
2012). Trees are a main body of the forest ecosystem, and tree species
composition is an important indicator that is often used to describe
forest biodiversity. The accurate identification of tree species is essen-
tial for effective monitoring of biodiversity (Piiroinen et al., 2018). Cho
et al. (2012) mapped the composition and spatial distribution of tree
species in South African savannahs to directly assess the biodiversity in
these areas. The composition and spatial distribution of tree species are

⁎
Corresponding author.
E-mail address: lincao@njfu.edu.cn (L. Cao).
1
These authors shared first authorship.

https://doi.org/10.1016/j.jag.2020.102173
Received 23 January 2020; Received in revised form 21 May 2020; Accepted 2 June 2020
Available online 01 July 2020
1569-8432/ © 2020 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/BY-NC-ND/4.0/).
Z. Xu, et al.
important parameters that can be used to address various ecological
problems, such as mapping availability of wildlife habitat (Davies et al.,
2017; Loarie et al., 2013; McDermid et al., 2009; Nijland et al., 2015).
Therefore, in natural mixed forests with diverse tree species and com-
plex distributions, the ability to accurately obtain the information on
the spatial distribution of dominant tree species has important ecolo-
gical significance for the study of forest ecosystems. Traditional forest
ecosystem surveys and assessments often rely on field surveys to collect
tree species information (Fassnacht et al., 2016). Because of the high
costs associated with field surveys, it is difficult to assess detailed in-
formation on tree species over large areas using this approach. There-
fore, more effective and rapid approaches are needed.
Traditionally, most of the remote sensing spectral and structural
data were acquired from satellites or manual airplanes, which always
have course spatial resolution (> 1 m) (Goodbody et al., 2017; Shen
et al., 2016; Torresan et al., 2017). Moreover, with the influences of
aerosol and water vapour in the air, remote sensing signals must be
calibrated and corrected before application. Unmanned aerial system
(UAS) is a multi-purpose platform operated at very low altitude, which
provide a solution for ultra-high spatial resolution data acquisition and
enhanced forestry inventory, such as tree species classification
(Pierzchała et al., 2018), individual stem detection(Wallace et al.,
2014), and biomass estimation (Kachamba et al., 2016; Christensen,
2015; Otero et al., 2018). Franklin and Ahmed (2018) classified de-
ciduous tree species using a machine learning algorithm with multi-
spectral data from UASs, with an overall classification accuracy reached
78 %. Ahmed et al. (2017) compared data from three UAS-based mul-
tispectral cameras and obtained a total accuracy of up to 89 % for se-
quoia classification. Digital aerial photogrammetry (DAP) point clouds
generated by structural-from-motion algorithms from high dense
overlapped imagery, have been considered as alternatives to LiDAR
data for three-dimensional metrics of forest structure because of their
cheap, efficient and high-precision characteristics (Goodbody et al.,
2017; White et al., 2016). Unlike the LiDAR data, DAP point cloud
derived from optical imagery has three-dimensional structural in-
formation as well as spectral attributes. Shen et al. (2019) estimated
forest structural attributes using spectral and structural metrics from
the multi-spectral imagery and point clouds, and the models had a high
accuracy (R2 = 0.82−0.93). Jones et al. (2010) combined DAP point
cloud and spectral metrics for forest inventory attributes and found that
the highest increasement in accuracy for models was observed with
RMSE decreasing 0.23 %–1.75 %.
Compared with field-based survey research, remote sensing tech-
nology provides a cost-effective and feasible method for mapping tree
species (Axelsson et al., 2018; Gini et al., 2018). In recent years, remote
sensing data have been widely applied to classify species of various
types of forests (Franklin et al., 2017; Immitzer et al., 2012; Ke et al.,
2010; Lin et al., 2015). Airborne platforms are capable of acquiring
high-spatial resolution data because of low flying height, and these
platforms can be combined with multispectral and hyperspectral sen-
sors to obtain spectrally rich data for the classification of tree species
(Dalponte et al., 2014; Maschler et al., 2018; Shen and Cao, 2017).
Chan and Paelinckx (2008) compared the classification accuracy of
AdaBoost and random forest (RF) classification algorithms based on
hyperspectral data and showed that the overall accuracy of two algo-
rithms were almost identical. Buddenbaum et al. (2005) used hyper-
spectral data from forests in western Germany and used geo-statistical
methods to classify the species in coniferous forests, with a final clas-
sification accuracy of 74 %. In all of these cases, however, the spatial
resolution of the imagery was coarse, with multiple crowns per pixel
making individual species level classification challenging. When high
spatial resolution imagery is utilized individual tree scale approaches,
which rely on the spectral characteristics of each individual tree crown
(ITC) can be used (Chen et al., 2018; Clark and Roberts, 2012; Erikson
and Olofsson, 2005; Sun et al., 2014). Clark and Roberts (2012) found
that tree species classification based on the individual tree had a higher
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Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
overall accuracy of 7% than pixel-based. Similarly, many studies have
shown that the tree species classification at the individual tree scale
exhibited higher precision than that at the pixel level (Cho et al., 2010;
Palace et al., 2008).
For remote sensing imagery either from airplanes and satellites,
most of the individual tree crown detection algorithms were based on
the brightness of image pixels or geometric shape of tree (Yancho et al.,
2019). In high-resolution spectral images, there are mainly two cate-
gories of segmentation techniques: edge-based and region-based seg-
mentation. Edge-based segmentation methods are boundary based
methods and region-based segmentation methods which based on their
spectral similarity of adjacent pixels (Saini and Arora, 2014). For ex-
ample, Drǎgu et al. (2010) used the multiresolution segmentation al-
gorithm to treat each pixel as a separate region based on a combination
of spectral and shape properties to extract ITCs at multiple scales. Tilton
et al. (2006) proposed a hierarchical segmentation algorithm that al-
ternates between region growth and spectral clustering. LiDAR tech-
nology also cloud be applied in extracting tree crown. Yao et al. (2012)
extracted the individual tree using the full-waveform LiDAR data by a
stem detection method, and the result showed that the classification
accuracy of forest types based on object was 95 %. Wu et al. (2018)
mapped individual tree species along the urban roads using LiDAR data,
and the result showed that the overall accuracies of tree species clas-
sification was to 78 %. With the 3D structural information, DAP point
cloud had a significant advancement in individual tree crown seg-
mentation. Most of the delineation algorithms developed from LiDAR
point cloud can be used for DAP point cloud segmentation, such as
watershed (Reitberger et al., 2009), region growing (Li et al., 2012) and
nearest neighbour (Silva et al., 2016). Nevalainen et al. (2017) acquired
dense point clouds, which were generated by image matching algorithm
using high quality aerial photogrammetry images, and the accuracy of
single tree segmentation was distributed from 40 % to 95 %. Nuijten
et al. (2019) compared the results of individual tree segmentation in
deciduous stands during different seasons using DAP point clouds and
UASs, and the highest ITC segmentation accuracy reached 77.1 %. The
acquisition of the individual tree information is necessary for improving
the accuracy of the tree species classification. Clark et al., 2005 found
that the overall accuracy of tree species classification was 4% higher
than that of pixel level at crown level.
Previous studies have confirmed that the combination of spectral
and structural data can improve the tree species classification accuracy
(Heinzel and Koch, 2012; Holmgren et al., 2008; Puttonen et al., 2011;
Sedliak et al., 2017). In general, the combination of these two datasets
were conducted at decision- and feature-level (Jones et al., 2010). With
the combination, the differences of tree species presented in spectral
and structural information were easier to be recognised. Compared with
only using multispectral data to identify conifer forests and broad-leaf
forests, Sedliak et al. (2017) combined LiDAR and aerial multispectral
data to identify conifer forests and broad-leaf forests and compared the
results with those based on only multispectral data; the accuracies of
conifer forests and broad-leaf forests were respectively improved by
2.80 % and 6.37 %. Cho et al. (2012) used LiDAR data to extract the
height of trees which were used with spectral data to classify tree
species, and the classification accuracy was improved by 14 %.
However, in the case of individual tree detection or tree species
classification, previous studies mostly have based on one data source
and did not simultaneously consider the spectral and three-dimensional
structural information of tree species. In this study, we acquired high
spatial resolution multi-spectral and RGB imageries from a fixed-wing
UAS. Three-dimensional structural information was used to combine
with vegetation indices for segmentation and classification of the
dominant tree species in a natural subtropical forest. We compared the
accuracy of tree species classification using spectral and structural data
alone and in combination. Moreover, the performance of three in-
dividual tree segmentation algorithms were assessed and compared.
The main objectives of this paper are as follows: 1) to generate RGB-
Z. Xu, et al.
Fig. 1. The workflow containing general steps for the classification of tree species from raw RGB and multispectral imageries acquired from UASs.
based DAP point clouds based on structure-from-motion technology; 2)
to compare high-resolution RGB images, DAP point clouds as well as the
composited CHM and high-resolution RGB imagery for the detection of
ITCs; and 3) to classify the dominant tree species in natural forests using
the combination of multispectral and structural information.
2. Materials and methods
The workflow containing general steps of this study is shown in
Fig. 1. In this study, we acquired multi-spectral imagery from fixed-
wing UASs combined with ITC delineation algorithms and a machine
learning classifier to identify the dominant tree species in the natural
forests of southwest China. First, the structure-from-motion method was
used to generate DAP point clouds. Second, three ITC delineation al-
gorithms (i.e., point cloud segmentation (PCS), image-based multi-
resolution segmentation (IMRS), and advanced multiresolution seg-
mentation (AMRS)) were used and assessed for ITC detection. Finally,
tree-level metrics (i.e., multispectral, texture and point cloud metrics)
were used as indicators for discriminating eight dominant tree species
at two levels (eight tree species and two forest types) with random
forest classifiers.
2.1. Study area
Xiangguqing (XGQ) is located in the southern part of the town of
Diqing, in the north-western part of Yunnan Province, China, and the
southern end of the Baima Snow Mountain National Nature Reserve
(99°21′3.9′′E, 27°39′14′′N) (Fig. 2). The study area extents approxi-
mately 3 × 3.5 km, and ranges in elevation between 2300–3500 m
above sea level. The research area is located in the plateau mountain
monsoon climate, which is divided into dry and wet seasons in one
year. The annual rainfall is 1370.7 mm, and the annual average tem-
perature is 9.8 °C. There are a small number of villages and farmlands in
the area, and the dominant tree species can be subdivided into conifers
and broad-leaved trees.
2.2. Field measurements
According to the tree species information based on historical data
from the XGQ study site, the dominant conifer species can be divided
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Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
into two types: (i) conifer species: Yunnan pine (Pinus yunnanensis),
hemlock (Tsuga chinensis), spruce (Picea asperata); (ii) broadleaf species:
Cyclobalanopsis glauca (Cyclobalanopsis oxyodon), Oriental white oak
(Quercus aliena), maple (Acer forrestii), Nepal alder (Alnus nepalensis)
and aspen (Populus davidiana).
The study selected a total of 502 trees, including each of the
dominant tree species that were spatially evenly distributed for field
measurements. Field data was collected in October 29 - November 4,
2018. The measurements included individual tree position, species, and
diameter at breast height (DBH), tree top height, and crown width in
both cardinal directions. The position of the individual tree was mea-
sured by a Trimble® real-time kinematic (RTK) R4 GNSS receiver, re-
sulting in centimetre-level accuracy. A diameter tape was used for the
measurement of DBH. A Vertex IV® hypsometer was used for the
measurement of the tree top height. The average of two values mea-
sured in two perpendicular directions were calculated to get the crown
widths. The statistics for three tree species types and eight dominant
tree species parameters are aggregated in Table 1.
2.3. Remote sensing data
All multispectral imageries were obtained using a fixed-wing UAS
(Fig. 3) in October 29 – October 30, 2018. The weather condition was
clear with the thin clouds. Two cameras were mounted on the UAS for
data acquisition. The multispectral imagery parameters are shown in
Table 2.
In addition to the multispectral data, LiDAR data were acquired
from a CW-30 on a JOUAV series fixed-wing UAS with the Riegl VUX®-1
LR sensor. The UAS fuselage length was 2.1 m, the wingspan was 4.0 m,
the maximum take-off weight was 34.5 kg, and it was equipped with an
80 cc carburettor engine. The take-off and landing modes were VTOL
(Vertical Take-Off and Landing). The data acquisition time was
December 16, 2018. The detailed parameters of acquiring LiDAR data
are provided in Table 3.
2.4. Data pre-processing
Multispectral data was collected by two-type of cameras. The first
camera is an RGB sensor, the second camera is a mica-sense sensor
which has RGB and additional two NIR bands. Both multispectral and
Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 2. Overview of the Xiangguqing (XGQ) study site with the locations of field-measured trees, false colour images (near-infrared, red, green) and a digital terrain
model (DTM). a. The location of the study site in Yunnan Province, high-resolution RGB ortho-imageries and the distribution of eight dominant tree species as
determined by field work; b. the ortho-imagery of the multispectral image of the study site composited by three bands (near-infrared, red and green); c. the DTM
created using LiDAR data by filtering, smoothing and interpolation. (For interpretation of the references to colour in this figure legend, the reader is referred to the
web version of this article).

RGB data were processed in Pix4Dmapper Professional (Pix4D, 2018). imageries.

The spatial resolution of the multispectral imagery was 0.5 m and the
RGB imagery was 0.1 m. First, images were aligned using in-flight in-
ternal GPS data and inertial measurement units (IMUs), and the aligned
images could be stitched together to create an ortho-mosaic (Goodbody
et al., 2017). Second, 200 GCPs were selected from the RGB and mul-
tispectral ortho-imageries to register the multispectral ortho-imageries
to the RGB ortho-imagery using the spline algorithm (Vercauteren
et al., 2009) (the mean RMSE in the X and Y orientation was less than
0.01 m). Finally, the nearest neighbour pixel method was used for re-
sampling to obtain spatially matched multispectral and RGB ortho-
To derived DAP point clouds the structure-from-motion (SfM) al-
gorithm was used in the RGB module of Pix4Dmapper to generate high-
density DAP point clouds. First, RGB images were aligned using in-
flight internal GPS data and IMUs, followed by the generation of tie
points in overlapping images as the skeleton of the point cloud
(Goodbody et al., 2017). The RGB-based DAP dense point clouds were
generated based on SfM technology (the point density was 42.25 p/m2).
Second, Clear points such as buildings and road intersections in the
study area were chosen as GCPs. A total of 200 GCPs were selected and
the polynomial algorithm was applied for creating the DAP point cloud

Table 1
Summary statistics of the trees measured.
Forest Type Scientific Name N DBH (cm) Height (m) Crown width (m)

Mean SD Mean SD Mean SD

Coniferous Pinus yunnanensis (P.Y.) 162 36.26 15.83 20.13 12.03 6.20 1.94
Picea asperata (P.A.) 39 53.95 18.90 28.67 10.37 7.47 2.43
Tsuga chinensis (T.C.) 46 57.97 27.73 24.14 7.90 8.51 2.98
Broadleaved Cyclobalanopsis oxyodon (C.O.) 59 53.37 35.84 20.55 7.09 7.25 3.02
Acer forrestii (A.F.) 32 55.83 50.18 17.70 5.30 8.15 2.71
Populus davidiana (P.D.) 30 27.04 8.24 16.72 4.08 5.21 2.31
Quercus aliena (Q.A.) 83 34.83 13.53 15.71 3.83 6.90 2.52
Alnus nepalensis (A.N.) 51 32.74 11.12 16.64 5.58 6.56 2.49

Note: DBH: diameter at breast height (cm); H: height (m); SD: standard deviation; N: number of trees; Alnus nepalensis = A.N.; Quercus aliena = Q.A.; Cyclobalanopsis
oxyodon = C.O.; Acer forrestii = A.F.; Tsuga chinensis = T.C.; Populus davidiana = P.D.; Pinus yunnanensis = P.Y.; Picea asperata = P.A.

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Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 3. The UAS multispectral, RGB imageries and LiDAR system used in this study. a. Fixed-wing UAS platform with multispectral and RGB systems, b. the CW-30
UAS with a LiDAR system and generated DEM.

Table 2 models (DSMs) were produced from points with maximum heights.
Imagery acquisition parameters. Finally, the normalized DAP point clouds were used for the generation
Parameters MicaSense RedEdge Sony ILCE-6000
of a CHM (the spatial resolution is 0.1 m) by using the natural neigh-
bourhood interpolation algorithm.
Flight height (m) 800 800
Flight speed (m/s) 30 20
Forward overlap (%) 80 80
2.5. Individual tree detection
Lateral overlap (%) 80 70
Spectral bands Blue, Green, Red, Red-edge Blue, Green and Red
and Near-infrared In this study, three methods were applied for individual tree deli-
Optimal resolution 1280 × 960 6000 × 4000 neation detection. Method 1: Image segmentation was performed on
ground sample distance 0.5 0.1 high spatial resolution RGB ortho-imagery to obtain ITCs by the mul-
(m)
Image format 16-bit TIFF (Tagged Image 24-bit TIFF
tiresolution segmentation (MRS) algorithm based on edge detection
File Format) (Benz et al., 2004). The MRS algorithm starts from a single pixel and the
calculations were separate from its neighbours. If two adjacent objects
and the combined heterogeneity index is smaller than the given domain
Table 3 value, they are merged; otherwise, they remain distinct. This study
LiDAR acquisition parameters. implemented the MRS algorithm using eCognition Development 9.0
Parameters Summary (Trimble) software. Method 2: DAP point cloud data were processed
using the PCS algorithm of Li et al. to extract position and crown in-
Flight height (m) 900 formation for individual tree. This algorithm segmented trees which
Flight speed (m/s) 27
based on three parameters: the spacing threshold, minimum spacing
Strip spacing (m) 400
Laser wave length 1550nm
rule, and horizontal profile of the tree shape, which can be modified or
Divergence (mrad) 0.5 extended depending on the characteristics of the trees to be segmented
Pulse emission frequency (KHz) 50−820 (Li et al., 2012). This study implemented the PCS algorithm in the
Scanning frequency (KHz) 100 software called LiForest (GreenValley International, Berkeley, CA,
Point density (p/m2) 0.627
USA). Method 3: The same segmentation algorithm used in Method 1
(MRS) was utilized, but the difference was that the segmented data
and the de-noised LiDAR point cloud three-dimensional registration were the composition of CHM and RGB ortho-imageries. The composite
with an error of less than 0.05 m. LiDAR point clouds were justified image resolution was 0.1 m.
ground and non-ground points by the progressive triangulated irregular The results of segmentation were vector polygons that described the
network densification filtering algorithm improved by Zhao et al. boundary of each tree, and each vector polygon which containing the
(2016). Ground points were used for the normalization of DAP point trees identification. The tree position was extracted by algorithm and
clouds and digital terrain model (DTM) creation with a resolution of combined with the tree position of the field measurements to evaluate
0.5 m using the natural field interpolation method, while digital surface algorithm accuracy. The correct position happens when the tree posi-
tion by algorithms was located within the crown of the field

5
Z. Xu, et al.
measurement tree. Three measures are compared to assess the accuracy
of individual tree segmentation: recall (r, represents the rate of tree
detection), precision (p, represents the detected trees precision) and F1-
score (F1, presents the overall accuracy). The equations are as follow
(Goutte and Gaussier, 2005; Sokolova et al., 2006):
Nt
r=
Nt + No (1)
Nt
p=
Nt + Nc (2)
2(r × p)
F1 =
r+p (3)
Nt is the number of detected trees that exist in the field position, No
is the number of the trees that were omitted by the algorithm, and Nc is
the number of detected trees that did not exist in the field.
2.6. Sensitivity analysis
In this study, three methods were used to extract the ITCs. The
segmentation algorithm used for image segmentation in Method 1 and
Method 3 was multiresolution segmentation (MRS). MRS is affected by
four parameters: scale, shape, precision and the weight of the input
layer (Benz et al., 2004). The segmentation size is mainly controlled by
the parameter of scale. This study will explore the impact of segmen-
tation scale on object-oriented segmentation, so the remaining three
parameters were given constant values (1, 0.5, and 0.5). Three different
scales were used in the two methods (Method 1: 30, 60, 90; Method 3:
15, 25, 35) to compare and determine the most suitable segmentation
scale. The segmentation algorithm of Method 2 directly faced the dis-
tance judgement segmentation, which is mainly determined by two
parameters of a height threshold and an interval threshold. In this
study, a uniform height threshold of 2 m was set, and sensitivity ana-
lysis (0.5 m, 1 m, 2 m) was performed for different interval thresholds.
The results were compared to determine the most appropriate interval
threshold.
2.7. Spectral metrics calculation
Once tree crowns were delineated, we extracted spectral data from
the multispectral imagery and computed spectral indices. The multi-
spectral module in Pix4Dmapper was used to generate images with the
five bands (blue, green, red, red, near-infrared) at the highest resolu-
tion; then, a set of vegetation indices was calculated according to the
formula. Then, a high-resolution RGB image was used to calculate 8
texture features for each band for a total of 24 features. The meanings
and calculation formulas for the spectral characteristic variables and
texture features are shown in Table 4a and 4b.
2.8. Point cloud metrics calculation
The point cloud metrics were extracted using normalized DAP point
clouds in fusion software. A grid with a cell size of 1 m was placed in the
study area, and the point cloud metrics in each 1 m cell were counted,
and a raster was generated via interpolation. The meanings of the point
cloud metrics are shown in Table 5.
2.9. RF classification
We used a Random Forest model which is a combination of tree
predictors such that each tree depends on the values of a random in-
dependently sampled vector and with the same distribution for all trees
in the forest (Breiman, 2001). The training dataset was used to train RF
classifiers, and the validation dataset was used to assess the accuracy of
the classification. The proportions used for the training dataset and the
validation dataset for each tree species were 60 % and 40 %,
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Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
respectively, which were randomly allocated by RF classifiers. The
values of overall accuracy and kappa accuracy were used to assess the
accuracies of the classification.
First, the datasets for tree species and forest types were divided into
three groups: (i) using spectral metrics (n = 25, 5 raw bands and 20
vegetation indices) for the classification of tree species (S); (ii) using
spectral metrics (n = 25) and texture metrics (n = 24) to classify tree
species (ST); (iii) using spectral metrics (n = 25), texture metrics
(n = 24) and point cloud metrics (n = 9) to classify tree species (STP).
Then, the classification of all the features (5 raw bands, 20 vegetation
indices, 24 texture metrics and 9 point cloud metrics) of the best ITC
was extracted before the classification. The metrics were added to the
RF classifier and sorted metrics by contribution size to model. Finally,
the tree species over the study area were mapped and counted.
3. Results
3.1. Individual tree detection
The results of the single tree segmentation using the algorithm of
PCS in a square with length of 50 m. On the whole, the algorithm could
segment the natural forest which can been inspected visually. A nor-
malized tree point cloud for one plot using DAP technology is shown by
the tree height in Fig. 4a. The results of segmentation using the PCS
algorithm are shown in Fig. 4b, and each individual tree corresponds to
one colour.
Fig. 5 shows the results of sensitivity analysis of individual tree
segmentation using the image-based MRS algorithm for one typical plot
(50 × 50 m2). Fig. 5a, b, c show the RGB ortho-imagery of a plot seg-
mented at three different scales (30, 60, 90, Method 1). Fig. 5d, e, f
show the composited CHM and RGB ortho-imagery of a plot segmented
at three different scales (15, 25, 35, Method 2). In Method 1, the results
suggest that when the scale factor was 30, over-segmentation of tree
crowns occurred; when the scale factor was 90, fewer segments are
apparent; when the scale factor was 60, the tree segmentation exhibited
best match the existing field data tree locations. In Method 3, the fig-
ures indicate that when the scale factor was 25 and 35, the segmenta-
tion phenomena were prominent; when the scale factor was 15, the tree
segmentation exhibited the best visual effect. For further comparative
analysis, the scale used for Method 1 in this research was 60, and the
scale used for Method 3 was 15.
In total, 80.3 %, 83.5 %, and 84.5 % of the field-measured trees
were correctly detected by the three methods. The commission error
(the trees detected by algorithms but not exist according to field mea-
surement) that resulted from using only ultra-high RGB imagery (23.1
%) was greater than that obtained when normalized DAP point clouds
were used (24.0 %), and segmentation using CHM and ultra-high RGB
imagery exhibited the lowest commission error (19.5 %). The F1-score
of the segmentation using composited imagery was highest (82.5 %),
followed by the segmentation using normalized DAP point clouds (79.6
%), and the segmentation using RGB imagery had the lowest F1-score
(78.6 %) (Table 6). This result may be because the composited imagery
contained both the spectral information and structural information of
the tree, which greatly improved the segmentation result.
Fig. 6 shows a normalized DAP point cloud displayed in RGB colour
with the CHM and high-resolution RGB imageries with the location of
trees (test data), tree tops and tree crowns detected by the three
methods within three plots (50 × 50 m2, the numbers of trees in the
three plots are 22, 38, and 51). The following phenomena can be found
in the Fig. 1) High-density DAP point clouds can visually represent the
canopy structure information of plots, and a high-quality CHM can be
obtained through the interpolation algorithm; 2) the comparison of the
segmentation effects of the three methods in the three plots indicates
that the ITCs extracted using only high-resolution RGB images have
more mis-segmentation, especially for adjacent trees. DAP point clouds
can extract the crowns of single trees most accurately (Fig. 6i and n);
Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Table 4a
The summary of the vegetation indices with respective equations and references.
Metrics Equation Reference

Vegetation Index
Atmospherically Resistant Vegetation Index (ARVI) (ρnir - ρrb)/(ρnir + ρrb), ρrb = ρred - γ (ρblue - ρred), γ = 0.5 (Kaufman and Tanré, 1996)
Difference Vegetation Index (DVI) ρnir - ρred (Ju et al., 2010)
Enhanced Vegetation Index (EVI) 2.5(ρnir - ρred)/(ρnir + 6ρred - 7.5ρblue +1) (Huete et al., 2002)
Green Normalized Difference Vegetation Index (GNDVI) (ρnir - ρgreen)/(ρnir + ρgreen) (Verstraete and Pinty, 1996)
Infrared Percentage Vegetation Index (IPVI) ρnir/(ρnir + ρred) (Kandare et al., 2017)
Red Green Ratio Index (RGRI) ρred /ρgreen (Gamon and Surfus, 1999)
Modified Soil Adjusted Vegetation Index (MSAVI) [2ρnir + 1 - [(2ρnir + 1)2 - 8(ρnir - ρred)]0.5]/2 (Haboudane et al., 2004)
Modified Simple Ratio Vegetation Index (MSR) ρred/(ρnir/ρred + 1)0.5 (Haboudane et al., 2004)
Normalized Difference Vegetation Index (NDVI) (ρnir - ρred)/(ρnir + ρred) (Haboudane et al., 2004)
Optimized Soil Adjusted Vegetation Index (OSAVI) (ρnir - ρred)/(ρnir + ρred + 0.16) (Yuan et al., 2007)
Renormalized Difference Vegetation Index (RDVI) (ρnir - ρred)/(ρnir + ρred) 0.5 (Haboudane et al., 2004)
Ratio Vegetation Index (RVI) ρred/ρnir (Darvishzadeh et al., 2009)
Soil and Atmospherically Resistant Vegetation Index (SARVI) (1 + 0.5)(ρnir - ρrb)/(ρnir + ρrb + 0.5), ρrb = ρred - γ(ρblue -ρred), γ = 0.5 (Haboudane et al., 2004)
Soil Adjusted Vegetation Index (SAVI) (1 + 0.5)(ρnir - ρred)/(ρnir + ρred + 0.5) (Haboudane et al., 2004)
Simple Ration Vegetation Index (SR) ρnir/ρred (Peñuelas et al., 1993)
Simple Ratio × Normalized Difference Vegetation Index (SR × NDVI) (ρnir2 - ρred)/(ρnir + ρred2) (Thomas et al., 2011)
G/R (GR) ρgreen/ρred (Fraser et al., 2017)
Brightness (BI) ρgreen + ρred + ρblue (Fraser et al., 2017)
Normalized Greenness (Norm G) ρgreen/(ρgreen + ρred + ρblue) (Fraser et al., 2017)
Normalized Green-Red Ratio (Norm GR) (ρgreen - ρred)/(ρgreen + ρred) (Fraser et al., 2017)

Note: The vegetation indices were calculated using raw imagery bands; ρni =Blue band, ρgreen=Green band, ρred=Red band, ρnir=Near infrared band.

Table 4b 3.3. Classification and accuracy evaluation

The summary of the texture metrics with respective equations and reference.
Metrics Equation
The importance of the ten most important variables in the RF
models used to classify tree species is shown in Fig. 8. Different para-
Texture metrics meters in different classification models had relatively large im-
Correlation (CR) N −1
CR=∑i, j = 0 i⋅Pi, j |
(i − ME )(j − ME )
| portance. As shown in Fig. 8a, the spectral metrics Atmospherically
VAiVAj
Contrast (CO) N =1 Resistant Vegetation Index (ARVI), normalized greenness (NormG), and
CO = / ∑i, j = 0 n2 Pi, j /
Band Red were most important for the classification. When texture
Dissimilarity (DI) N −1
DI=∑i, j = 0 i⋅Pi, j / i − j/ metrics were added for classification, the mean value of the blue band
Entropy (EN) N −1
EN=∑i, j = 0 i⋅Pi, j (-lnPi, j ) (Blue_ME) became the most important metric for classification, and
Homogeneity (HO) N −1 Pi, j other texture metrics played relatively important roles (Fig. 8b). The
HO=∑i, j = 0 i⋅
1 + (i − j )2 point cloud structure metrics, such as H95, H50, H25, and Hcv also had a
Mean (ME) N −1
ME=∑i, j = 0 i⋅Pi, j positive effect in the RF model with all metrics (Fig. 8c).
Second moment (SM) N −1
SM=∑i, j = 0 i⋅Pi2, j As shown in Table 7 and 8, the confusion matrix of eight dominant
Variance (VA) N −1 tree species and two forest types using three groups of metrics, re-
VA=∑i, j = 0 i⋅Pi, j (i -ME )
spectively. In general, the accuracy of tree type classification was
higher than that of tree species, and the combination of spectral, texture
and structural metrics produced the best result (Overall Accuracy:
however, incorrect segmentation occurred for broad-leaf tree species
80.20 %, Kappa Accuracy: 60.37 %). In the classification of both the
that were close to each other. Image segmentation using the composited
eight tree species and two forest types, the accuracy of the three models
CHM imagery and RGB ortho-imagery fusion exhibited the best per-
increased in turn, indicating that the texture metrics and point cloud
formance (Fig. 6e, j and o).
structure metrics had positive impacts on the classification results (the
overall accuracy and kappa accuracy increased by 1.49–4.46 % and
3.2. Metric extraction and analysis 2.86–6.84 %, respectively). Classification using spectral, texture and
point cloud metrics exhibited the highest accuracy in the classification
The spectral reflectance from the multi-spectral imagery for each of of the eight tree species (OA = 66.34 %, kappa accuracy = 58.53 %).
the delineated crown averaged by species are shown in Fig. 7. At The distribution of tree species throughout the study site and in a
850 nm, the maple (A.F.) species was easily distinguished from all other partially enlarged area according to spectral metrics, texture metrics
species (Fig. 7a). For Oriental white oak (Q.A.) and Yunnan pine (P.Y.) and point cloud metrics is shown in Fig. 9. As shown in Fig. 9a, Yunnan
they are most easily separated by 720 nm (Fig. 7b). Confusion exists pine had the largest distribution area, which was consistent with the
between some species for example Cyclobalanopsis glauca (C.O.) and field measurement results. Fig. 9c and d show the classification results
hemlock (T.C.). Therefore, the vegetation index, texture features and in an enlarged map of a typical area (500 × 500 m2) of the tree species,
structural features were calculated in the study for tree species classi- and the three-dimensional results of the tree species classification in
fication.

Table 5
Summary of the point cloud metrics with descriptions.
Metrics Description

Percentile heights (H25, H50, H95) The percentiles of the canopy height distributions (25th, 50th, 95th).
The coefficient of variation of height (Hcv) The coefficient of variation of heights of all first returns.
Canopy return density (D1, D3, D5, D7 and D9) The proportion of points above the quantiles (10th, 30th, 50th, 70th and 90th) to total number of points.

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Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 4. a. Normalized DAP point cloud of a square with length of 50 m; b. the results of segmentation using the PCS algorithm (each individual tree was shown in one
colour).

two 100 × 100 m2 square areas in the area. The height distribution of Table 6
each tree species throughout the study area was calculated and is shown Accuracy assessment for the detection of individual trees of eight dominant tree
in Fig. 9b. Some tree species of the same type exhibited significant species.
differences in tree height distribution; for example, Cyclobalanopsis Nt No Nc r(%) p(%) F1(%)
glauca was significantly different from the other broad-leaved tree
species, and the tree height was significantly higher. RGB imagery 403 99 121 80.3 76.9 78.6
DAP 419 71 132 83.5 76.0 79.6
CHM and RGB imagery 424 78 103 84.5 80.5 82.5

4. Discussion
In this study, we aimed to map key species for biodiversity assess-
ment across the natural forest region. We wanted to investigate impact
of structure vs spectral on species classification. High spatial resolution
RGB ortho-imageries and point clouds generated by UAS-based imagery
matching were applied for the detection of ITCs. Dense RGB point
clouds were generated based on SfM technology, which is a method of
image matching (Dalponte et al., 2012). Sothe et al. (2019) used UAS-
based photogrammetric point clouds generated by SfM technology to
detect individual trees and confirmed its application potential. Fawcett
Note: r, represent the tree detection rate; p, represent the precision of detected
trees) and F1, present the overall accuracy taking both omission and commis-
sion in consideration).
et al. (2019) segmented individual tree canopies and estimated the
heights of oil palms from UAS-based point clouds generated by SfM
technology, reaching a detection accuracy of 98.2 %. However, most
previous studies focused on applying the derived SfM point clouds in
stands with few species or plantations. In this study, the derived point
clouds were used for canopy segmentation in a natural forest (eight

Fig. 5. Sensitivity analysis of individual tree segmentation by MRS (plot size: 50 × 50 m). a, b, c. multiresolution segmentation using the high-resolution RGB ortho-
imagery data (the scales of the display are 30, 60, and 90 respectively); d, e, f. multiresolution segmentation using a composited CHM image and high-resolution RGB
ortho-imagery data (the scales of the display are 15, 25, and 35).

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Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 6. The normalized DAP point clouds displayed in RGB colour, CHM and high-resolution RGB imageries with the locations of trees (test data), tree tops and tree
crowns detected by the three methods within three plots (50 × 50 m2, the numbers of trees in the three plots are 22, 38, and 51). a, f, k. the DAP point clouds with
different numbers of trees (22, 38, 51); b, g, l. the CHMs for the three plots; c, h, m. delineation of ITCs using high-resolution RGB images based on multiresolution
segmentation (MRS) in the three plots; d, i, n. delineation of ITCs using normalized DAP point clouds based on PCS in the three plots; e, j, o. delineation of ITCs using
the composited CHM imagery and high-resolution RGB ortho-imagery based on MRS in the three plots.

Fig. 7. The reflection values for the different spectral bands (near-infrared, red-edge, red and green) for each tree species in the study area. a. near-infrared; b. red-
edge; c. red; d. green. see Table 1 for short descriptions of the tree species. (For interpretation of the references to colour in this figure legend, the reader is referred to
the web version of this article).

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Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 8. The importance of the ten most important variables in RF models of tree species classification. a. tree species classification using spectral metrics; b. tree
species classification using spectral and texture metrics; c. tree species classification using spectral, texture and point cloud metrics. Note: Blue_ME means the mean
value of the band blue; B_VA means the variance in the band blue. (For interpretation of the references to colour in this figure legend, the reader is referred to the web
version of this article).

Table 7 Table 8
Confusion matrix (including overall accuracies, kappa accuracies) for the Confusion matrix (including overall accuracies, kappa accuracies) for the
classification of the eight dominant tree species using the validation dataset. classification of the three forest types using the validation dataset. Coniferous
Alnus nepalensis = A.N.; Quercus aliena = Q.A.; Cyclobalanopsis oxyodon = and broadleaf.
C.O.; Acer forrestii = A.F.; Tsuga chinensis = T.C.; Populus davidiana = P.D.;
Class Coniferous Broadleaved
Pinus yunnanensis = P.Y.; Picea asperata = P.A.
Class A.N. Q.A. C.O. A.F. T.C. P.D. P.Y. P.A. Spectral metrics
Spectral metrics Coniferous 80 28
Broadleaved 19 75
A.N. 15 7 1 1 2 0 5 3 Overall Accuracy: 76.73 % Kappa Accuracy: 53.53 %
Q.A. 0 19 1 1 0 0 4 0 Spectral and texture metric
C.O. 3 1 9 0 4 0 0 1 Coniferous 77 33
A.F. 1 0 1 10 0 0 0 0 Broadleaved 22 78
T.C. 0 1 3 0 4 0 6 1 Overall Accuracy: 78.22 % Kappa Accuracy: 56.42 %
P.D. 0 0 1 0 0 12 0 2 Spectral, texture and point cloud metrics
P.Y. 1 5 6 0 7 0 49 3 Coniferous 78 19
P.A. 1 0 2 0 1 0 1 6 Broadleaved 21 84
Overall Accuracy: 61.88 % Kappa Accuracy: 53.46 % Overall Accuracy: 80.20 % Kappa Accuracy: 60.37 %
Spectral and texture metric
A.N. 16 2 2 1 1 0 2 1
Q.A. 0 24 0 1 0 1 6 1 actual was common (Fig. 6b, g and l). The MRS algorithm is based on
C.O. 3 0 9 0 5 0 0 3 the assumption that a shadow on the edge is more than the canopy of
A.F. 0 0 0 11 0 0 0 0
T.C. 0 0 5 0 3 0 2 0
one tree (Drǎguţ et al., 2010). These phenomena may have been
P.D. 0 3 0 0 0 11 0 2 common because the forest information in the study site was complex,
P.Y. 1 4 8 0 8 0 54 6 and many trees were close to each other. The AMRS algorithm applied
P.A. 1 0 0 0 1 0 1 3 multiresolution segmentation to composited CHM and RGB imagery,
Overall Accuracy: 64.85 % Kappa Accuracy: 56.32 %
which showed the best results (F1 = 82.5 %). Previous studies have
Spectral, texture and point cloud metrics
A.N. 15 1 1 1 2 1 1 2 used UAS-based imagery and the DAP approach to extract ITCs. DAP
Q.A. 1 24 0 0 0 1 6 1 point clouds were applied in individual tree segmentation because they
C.O. 3 0 11 0 5 0 1 2 can intuitively reflect the three-dimensional structure of trees. The
A.F. 0 0 0 11 0 0 0 0 studies can directly segment point clouds or extract the metrics from
T.C. 0 0 2 0 2 0 2 2
point cloud for individual tree segmentation. Nevalainen et al. (2017)
P.D. 0 4 0 1 0 10 0 2
P.Y. 0 3 8 0 8 0 55 1 utilized DAP point clouds and a DTM computed from NLS ALS data to
P.A. 2 1 2 0 1 0 0 6 acquire a CHM and extracted tree crown information from the CHM
Overall Accuracy: 66.34 % Kappa Accuracy: 58.53 % using the local maxima method; they found that the probability of ac-
curately identifying trees were 64 %–96 % with a search radius of two
meters. When the results of this study were compared to the results of
dominant tree species) by using the PCS algorithm. The large difference previous studies, the tree detection rate exhibited increased accuracy.
of crown size has a bad effect on the segmentation of tree (Fig. 6d). This This increased accuracy may have occurred because previous studies
result may have occurred because natural forests are more complex either used spectral or texture metrics from the image for ITC extrac-
than the forests investigated previous studies, and the PCS algorithm tion, or three-dimensional point cloud data for ITC detection, and these
cannot provide an interval threshold for all trees in forests with large methods are based on a single type of data. However, this study used
differences in canopy size. To improve the segmentation accuracy, this composited CHM and RGB image data for ITC extraction, considering
study attempted to use image-based segmentation. When segmenting both spectral and three-dimensional structural information.
high-resolution RGB ortho-imagery with the IMRS algorithm, The The classification of tree species exhibited improved the accuracy
phenomenon that the number of trees segmented was less than the because the composition of multispectral and DAP point cloud data

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Z. Xu, et al. Int J Appl  Earth Obs Geoinformation 92 (2020) 102173

Fig. 9. a. Tree species classification image using spectral metrics, texture metrics and point cloud metrics; b. I. the height distribution of broad-leaved tree species, b.
II. the height distribution of coniferous tree species; c. tree species distribution in one plot (500 × 500 m); d. three-dimensional results of the tree species classifi-
cation in two sample plots (I, II size: 100 × 100 m) in the study area. See Table 1 for short descriptions of the tree species.

could provide not only spectral but also structure information. The
object-based classification of tree species was used in this paper. Many
studies have shown that tree species classification on the canopy scale
exhibits higher precision than pixel-level classification (Cho et al.,
2010; Palace et al., 2008). In general, the classification accuracy by tree
type was higher than that by tree species (Table 7 and Table 8), and the
combination of spectral, texture and structural metrics provided the
best results (overall accuracy = 80.20 %). This result occurred because
the information on the species type characteristic variables is compre-
hensive, and the differences between forest types are more obvious than
the differences between tree species, so the results are more accurate.
Because the data were collected in autumn, there were obvious differ-
ences between the deciduous broad-leaved tree species and other tree
species. The deciduous broad-leaved species had a richer color. For

11
Z. Xu, et al.
example, in high-resolution aerial photography, the spectral separation
of poplars is usually high (Sääjoki et al., 2008) because poplar canopies
are usually represented by bright and unique tones. There were five
main broad-leaved species in the study area, including cyclobalanopsis
glauca, riental white oak, maple, Nepal alder and aspen. It can be seen
from Fig. 7a that there was a significant difference reflectivity between
it and other species in the near infrared band (value concentrated
around 0.3). The reflectivity of cyclobalanopsis glauca, Oriental white
oak, nepal alder in the green band was significantly different (Fig. 7d).
The height of cyclobalanopsis glauca was higher than that of other
broad-leaved trees (Fig. 9b), so it can be distinguished by height
characteristics.The height of Cyclobalanopsis glauca was higher than
that of other broad-leaved trees, so it can be distinguished by height
characteristics. Texture metrics can greatly improve the OA of classi-
fication. Gini et al. (2018) used texture metrics to improve classification
results, and they proved that the use of texture increased the OA by 20
%. The 3-D structural metrics of trees can effectively improve the ac-
curacy of tree species classification. Different tree species usually have
different tree forms; thus, Hovi et al. (2016) improved tree species
classification by stratifying the data according to tree height computed
from LiDAR data. Therefore, this study used the ITC as a statistical unit
to calculate tree structure metrics from DAP point clouds, thereby im-
proving the classification accuracy.
In the ranking of variable importance of the characteristics by the
RF model, different models identified different metrics as the most
important. In the RF model of spectral metrics, the ARVI, NormG and
Band Red were the highest variables in the final classification result
(Fig. 8a). Among these vegetation indices, ARVI is a combination of
three bands of red, green and blue, which can comprehensively con-
sider spectral information. NormG is a normalized green band, and the
green band can better distinguish yellow leaves from green leaves
(Gitelson et al., 1996). The data in the study area were collected in
autumn, when there were obvious colour differences among the leaves
of the different tree species. Therefore, the green band played an im-
portant role in tree species classification by this model. Band red is an
indicator of anthocyanin content (Gamon and Surfus, 1999). Antho-
cyanin content indexes have an important influence on tree species
classification (Liu et al., 2017). The correlation and mean values of the
blue band played a large role in the classification result of the RF model
using spectral and texture metrics (Fig. 8b). The texture feature clearly
improved the classification accuracy. H95, H50, and H25 were also high
in terms of parameter importance in the RF model with spectral, texture
and structural metrics (Fig. 8c). These parameters represent the height
some percentiles of the different height distributions (95th, 50th, 25th),
and these metrics can adequately describe the three-dimensional
structures of trees. The maximum of all height points within each pixel
(Hmax) was selected to classify tree species, which increased the value of
kappa accuracy by 9% (Dalponte et al., 2012).
The data obtained from this study were clear skies and the UAV was
stable relative to the ground flight height. The external conditions for
information of different trees in the study area were consistent. The
number of conifers in the study area was relatively large, and the stu-
dies with conifer tree pointed out that there was no evidence that sunlit
crown spectra could improve the tree species classification accuracy
(François A. Gougeon, 1995; Leckie et al., 2003). The influence by solar
geometry and illumination would be considered in the future study.
There were previous studies using UAS-based imagery and the DAP
data. Weiss and Baret (2017) used the UAS to acquire RGB imagery, and
derived 3D point clouds for precision viticulture. Saarinen et al. (2018)
used UAS-based hyperspectral imagery and photogrammetric point
clouds to assess biodiversity, and the relative RMSE of indicators was
between 24.4 % and 29.3 % with semi-ITC. These studies indicated that
UAS-based imagery and the DAP data was of great application value. In
this study, we used simultaneously acquired spectral and structural data
from the fixed-wing UAS for ITC delineation, the dominant tree species
classification and make preparation for future assessments of forest
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Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
ecosystems and biodiversity in the region.The distribution maps and
statistics of the dominant tree species are important for the assessment
of forest ecosystems. Selkowitz et al. (2012) mapped canopy height by
using a multi-sensor LiDAR, multispectral and multi-angular approach
to assess boreal forest regions. Guo et al. (2017) obtained the three-
dimensional structure information of vegetation in different natural
areas of Alberta, Canada, by using airborne LiDAR and mapped the
vegetation structure of the whole study area by using cluster analysis to
obtain the related spatial distribution, which solved the basic problems
of habitat structure in biodiversity monitoring. The study area is located
in a high-altitude area of Yunnan Province, China. This area exhibits
large altitudinal differences and rich vegetation types. This region is
one of the main habitats for the golden monkey and has deep ecological
significance. The spatial distribution and statistics of dominant tree
species can provide local data for future assessments of forest ecosys-
tems and biodiversity in the region.
5. Conclusion
In this study, we used simultaneously acquired multi-source ima-
geries (i.e., highly overlapping multispectral and RGB imageries), DAP
data and LiDAR point clouds acquired from fixed-wing UASs combined
with ITC delineation algorithms and a machine learning classifier to
identify the dominant tree species in subtropical natural forests of
southwest China. The results showed the following: 1) The accuracy of
ITC segmentation using AMRS was highest (F1-score = 82.5 %), fol-
lowed by segmentation using PCS (79.6 %), and segmentation using
IMRS exhibited the lowest accuracy (F1-score = 78.6 %); 2) the tree
type classification had a higher accuracy than tree species classification,
and the combination of spectral, texture and structural metrics had the
highest classification accuracy (overall accuracy = 80.20 %). In the
classification of both eight dominant tree species and two forest types,
the classification accuracies were lowest when only spectral metrics
were used, indicated that the texture metrics and point cloud structural
metrics had a positive impact on the classification (the overall accuracy
and kappa accuracy increased by1.49–4.46 % and 2.86–6.84 %, re-
spectively).
CRediT authorship contribution statement
Zhong Xu: Writing - original draft, Methodology, Software, Formal
analysis. Xin Shen: Methodology, Investigation, Writing - review &
editing. Lin Cao: Writing - review & editing, Conceptualization,
Resources, Supervision, Funding acquisition. Nicholas C. Coops:
Writing - review & editing. Tristan R.H. Goodbody: Writing - review &
editing. Tai Zhong: Investigation. Weidong Zhao: Investigation.
Qinglei Sun: Investigation. Sang Ba: Investigation. Zhengnan Zhang:
Investigation, Writing - review & editing. Xiangqian Wu: Investigation.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influ-
ence the work reported in this paper.
Acknowledgments
We acknowledge grants from the National Natural Science
Foundation of China (grant number 31922055, 31770590) and the
Priority Academic Program Development of Jiangsu Higher Education
Institutions (PAPD). We gratefully acknowledge staff (e.g., Xinming He
and Zhonghua Yu et al.) in Yunnan Baima Snow Mountain National
Nature Reserve for assistance with data collection and sharing their rich
knowledge and working experience of the local forest ecosystems.
Z. Xu, et al.
References
Ahmed, O.S., Shemrock, A., Chabot, D., Dillon, C., Williams, G., Wasson, R., Franklin,
S.E., 2017. Hierarchical land cover and vegetation classification using multispectral
data acquired from an unmanned aerial vehicle. Int. J. Remote Sens. 38, 2037–2052.
https://doi.org/10.1080/01431161.2017.1294781.
Axelsson, A., Lindberg, E., Olsson, H., 2018. Exploring multispectral ALS data for tree
species classification. Remote Sens. 10. https://doi.org/10.3390/rs10020183.
Benz, U.C., Hofmann, P., Willhauck, G., Lingenfelder, I., Heynen, M., 2004. Multi-re-
solution, object-oriented fuzzy analysis of remote sensing data for GIS-ready in-
formation. ISPRS J. Photogramm. Remote Sens. 58, 239–258. https://doi.org/10.
1016/J.ISPRSJPRS.2003.10.002.
Bonan, G.B., 2008. Forests and climate change: forcings, feedbacks, and the climate
benefits of forests. Science(80). https://doi.org/10.1126/science.1155121.
Breiman, L., 2001. ST4_Method_Random_Forest. Mach. Learn. 45, 5–32. https://doi.org/
10.1017/CBO9781107415324.004.
Buddenbaum, H., Schlerf, M., Hill, J., 2005. Classification of coniferous tree species and
age classes using hyperspectral data and geostatistical methods. Int. J. Remote Sens.
26, 5453–5465. https://doi.org/10.1080/01431160500285076.
Cardinale, B.J., Duffy, J.E., Gonzalez, A., Hooper, D.U., Perrings, C., Venail, P., Narwani,
A., MacE, G.M., Tilman, D., Wardle, D.A., Kinzig, A.P., Daily, G.C., Loreau, M., Grace,
J.B., Larigauderie, A., Srivastava, D.S., Naeem, S., 2012. Biodiversity loss and its
impact on humanity. Nature. https://doi.org/10.1038/nature11148.
Chambers, J.Q., Asner, G.P., Morton, D.C., Anderson, L.O., Saatchi, S.S., Espírito-Santo,
F.D.B., Palace, M., Souza, C., 2007. Regional ecosystem structure and function:
ecological insights from remote sensing of tropical forests. Trends Ecol. Evol. https://
doi.org/10.1016/j.tree.2007.05.001.
Chan, J.C.W., Paelinckx, D., 2008. Evaluation of Random Forest and Adaboost tree-based
ensemble classification and spectral band selection for ecotope mapping using air-
borne hyperspectral imagery. Remote Sens. Environ. 112, 2999–3011. https://doi.
org/10.1016/j.rse.2008.02.011.
Chen, J., Saunders, S.C., Brosofske, K.D., Mroz, G.D., Crow, T.R., Naiman, R.J., Franklin,
J.F., Brookshire, B.L., 1999. Microclimate in forest ecosystem and landscape ecology:
variations in local climate can be used to monitor and compare the effects of different
management regimes. Bioscience 49, 288–297. https://doi.org/10.2307/1313612.
Chen, G., Weng, Q., Hay, G.J., He, Y., 2018. Geographic object-based image analysis
(GEOBIA): emerging trends and future opportunities. GIScience Remote Sens. 55,
159–182. https://doi.org/10.1080/15481603.2018.1426092.
Cho, M.A., Debba, P., Mathieu, R., Naidoo, L., Van Aardt, J., Asner, G.P., 2010. Improving
discrimination of savanna tree species through a multiple-endmember spectral angle
mapper approach: canopy-level analysis. IEEE Trans. Geosci. Remote Sens. 48,
4133–4142. https://doi.org/10.1109/TGRS.2010.2058579.
Cho, M.A., Mathieu, R., Asner, G.P., Naidoo, L., van Aardt, J., Ramoelo, A., Debba, P.,
Wessels, K., Main, R., Smit, I.P.J., Erasmus, B., 2012. Mapping tree species compo-
sition in South African savannas using an integrated airborne spectral and LiDAR
system. Remote Sens. Environ. 125, 214–226. https://doi.org/10.1016/j.rse.2012.
07.010.
Christensen, B.R., 2015. Use of UAV or remotely piloted aircraft and forward-looking
infrared in forest, rural and wildland fire management: evaluation using simple
economic analysis. New Zeal. J. For. Sci. 45. https://doi.org/10.1186/s40490-015-
0044-9.
Clark, M.L., Roberts, D.A., 2012. Species-level differences in hyperspectral metrics among
tropical rainforest trees as determined by a tree-based classifier. Remote Sens. 4,
1820–1855. https://doi.org/10.3390/rs4061820.
Clark, M.L., Roberts, D.A., Clark, D.B., 2005. Hyperspectral discrimination of tropical rain
forest tree species at leaf to crown scales. Remote Sens. Environ. 96, 375–398.
https://doi.org/10.1016/j.rse.2005.03.009.
Dalponte, M., Bruzzone, L., Gianelle, D., 2012. Tree species classification in the Southern
Alps based on the fusion of very high geometrical resolution multispectral/hyper-
spectral images and LiDAR data. Remote Sens. Environ. 123, 258–270. https://doi.
org/10.1016/j.rse.2012.03.013.
Dalponte, M., Ørka, H.O., Ene, L.T., Gobakken, T., Næsset, E., 2014. Tree crown deli-
neation and tree species classification in boreal forests using hyperspectral and ALS
data. Remote Sens. Environ. 140, 306–317. https://doi.org/10.1016/j.rse.2013.09.
006.
Darvishzadeh, R., Atzberger, C., Skidmore, A.K., Abkar, A.A., 2009. Leaf Area Index de-
rivation from hyperspectral vegetation indicesand the red edge position. Int. J.
Remote Sens. 30, 6199–6218. https://doi.org/10.1080/01431160902842342.
Davies, A.B., Ancrenaz, M., Oram, F., Asner, G.P., 2017. Canopy structure drives or-
angutan habitat selection in disturbed Bornean forests. Proc. Natl. Acad. Sci. U. S. A.
114, 8307–8312. https://doi.org/10.1073/pnas.1706780114.
Drǎguţ, L., Tiede, D., Levick, S.R., 2010. ESP: a tool to estimate scale parameter for
multiresolution image segmentation of remotely sensed data. Int. J. Geogr. Inf. Sci.
24, 859–871. https://doi.org/10.1080/13658810903174803.
Durães, R., Carrasco, L., Smith, T.B., Karubian, J., 2013. Effects of forest disturbance and
habitat loss on avian communities in a Neotropical biodiversity hotspot. Biol.
Conserv. 166, 203–211. https://doi.org/10.1016/j.biocon.2013.07.007.
Erikson, M., Olofsson, K., 2005. Comparison of three individual tree crown detection
methods. Mach. Vis. Appl. 16, 258–265. https://doi.org/10.1007/s00138-005-
0180-y.
Fassnacht, F.E., Latifi, H., Stereńczak, K., Modzelewska, A., Lefsky, M., Waser, L.T.,
Straub, C., Ghosh, A., 2016. Review of studies on tree species classification from
remotely sensed data. Remote Sens. Environ. 186, 64–87. https://doi.org/10.1016/j.
rse.2016.08.013.
Fawcett, D., Azlan, B., Hill, T.C., Kho, L.K., Bennie, J., Anderson, K., 2019. Unmanned
13
Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
aerial vehicle (UAV) derived structure-from-motion photogrammetry point clouds for
oil palm (Elaeis guineensis) canopy segmentation and height estimation. Int. J.
Remote Sens. 40, 7538–7560. https://doi.org/10.1080/01431161.2019.1591651.
Franklin, S.E., Ahmed, O.S., 2018. Deciduous tree species classification using object-based
analysis and machine learning with unmanned aerial vehicle multispectral data. Int.
J. Remote Sens. 39, 5236–5245. https://doi.org/10.1080/01431161.2017.1363442.
Franklin, S.E., Ahmed, O.S., Williams, G., 2017. Northern conifer forest species classifi-
cation using multispectral data acquired from an unmanned aerial vehicle.
Photogramm. Eng. Remote Sensing 83, 501–507. https://doi.org/10.14358/PERS.83.
7.501.
Fraser, R.H., van der Sluijs, J., Hall, R.J., 2017. Calibrating satellite-based indices of burn
severity from UAV-derived metrics of a burned boreal forest in NWT. Canada. Remote
Sens. 9, 279. https://doi.org/10.3390/rs9030279.
Gamfeldt, L., Snäll, T., Bagchi, R., Jonsson, M., Gustafsson, L., Kjellander, P., Ruiz-Jaen,
M.C., Fröberg, M., Stendahl, J., Philipson, C.D., Mikusiński, G., Andersson, E.,
Westerlund, B., Andrén, H., Moberg, F., Moen, J., Bengtsson, J., 2013. Higher levels
of multiple ecosystem services are found in forests with more tree species. Nat.
Commun. 4, 1034. https://doi.org/10.1038/ncomms2328.
Gamon, J.A., Surfus, J.S., 1999. Assessing leaf pigment content and activity with a re-
flectometer. New Phytol. 143, 105–117. https://doi.org/10.1046/j.1469-8137.1999.
00424.x.
Gini, R., Sona, G., Ronchetti, G., Passoni, D., Pinto, L., 2018. Improving tree species
classification using UAS multispectral images and texture measures. ISPRS Int. J.
Geo-Information 7, 315. https://doi.org/10.3390/ijgi7080315.
Gitelson, A.A., Kaufman, Y.J., Merzlyak, M.N., 1996. Use of a green channel in remote
sensing of global vegetation from EOS- MODIS. Remote Sens. Environ. 58, 289–298.
https://doi.org/10.1016/S0034-4257(96)00072-7.
Goodbody, T.R.H., Coops, N.C., Marshall, P.L., Tompalski, P., Crawford, P., 2017.
Unmanned aerial systems for precision forest inventory purposes: A review and case
study. For. Chron. 93, 71–81. https://doi.org/10.5558/tfc2017-012.
Gougeon, François A., 1995. Comparison of possible multispectral classification schemes
for tree crowns individually delineatedon high spatial resolution meis images. Can. J.
Remote Sens. 21, 1–9. https://doi.org/10.1080/07038992.1995.10874590.
Goutte, C., Gaussier, E., 2005. A probabilistic interpretation of precision, recall and F-
score, with implication for evaluation. 27th European Conference on Information
Retrieval Research (ECIR 2005) 345–359. https://doi.org/10.1007/978-3-540-
31865-1.
Guo, X., Coops, N.C., Tompalski, P., Nielsen, S.E., Bater, C.W., John Stadt, J., 2017.
Regional mapping of vegetation structure for biodiversity monitoring using airborne
lidar data. Ecol. Inform. 38, 50–61. https://doi.org/10.1016/j.ecoinf.2017.01.005.
Haboudane, D., Miller, J.R., Pattey, E., Zarco-Tejada, P.J., Strachan, I.B., 2004.
Hyperspectral vegetation indices and novel algorithms for predicting green LAI of
crop canopies: modeling and validation in the context of precision agriculture.
Remote Sens. Environ. 90, 337–352. https://doi.org/10.1016/j.rse.2003.12.013.
Heinzel, J., Koch, B., 2012. Investigating multiple data sources for tree species classifi-
cation in temperate forest and use for single tree delineation. Int. J. Appl. Earth Obs.
Geoinf. 18, 101–110. https://doi.org/10.1016/j.jag.2012.01.025.
Holmgren, J., Persson, Å., Söderman, U., 2008. Species identification of individual trees
by combining high resolution LiDAR data with multi-spectral images. Int. J. Remote
Sens. 29, 1537–1552. https://doi.org/10.1080/01431160701736471.
Hovi, A., Korhonen, L., Vauhkonen, J., Korpela, I., 2016. LiDAR waveform features for
tree species classification and their sensitivity to tree- and acquisition related para-
meters. Remote Sens. Environ. 173, 224–237. https://doi.org/10.1016/j.rse.2015.08.
019.
Huete, A., Didan, K., Miura, T., Rodriguez, E.P., Gao, X., Ferreira, L.G., 2002. Overview of
the radiometric and biophysical performance of the MODIS vegetation indices.
Remote Sens. Environ. 83, 195–213. https://doi.org/10.1016/S0034-4257(02)
00096-2.
Immitzer, M., Atzberger, C., Koukal, T., 2012. Tree species classification with Random
forest using very high spatial resolution 8-band worldView-2 satellite data. Remote
Sens. (Basel) 4, 2661–2693. https://doi.org/10.3390/rs4092661.
Jones, T.G., Coops, N.C., Sharma, T., 2010. Assessing the utility of airborne hyperspectral
and LiDAR data for species distribution mapping in the coastal Pacific Northwest.
Canada. Remote Sens. Environ. 114, 2841–2852. https://doi.org/10.1016/j.rse.
2010.07.002.
Ju, C., Tian, Y., Yao, X., Cao, W., Zhu, Y., Hannaway, D., 2010. Estimating leaf chlor-
ophyll content using red edge parameters. Pedosphere 20, 633–644. https://doi.org/
10.1016/S1002-0160(10)60053-7.
Kachamba, D.J., Ørka, H.O., Gobakken, T., Eid, T., Mwase, W., 2016. Biomass estimation
using 3D data from unmanned aerial vehicle imagery in a tropical woodland. Remote
Sens. (Basel) 8. https://doi.org/10.3390/rs8110968.
Kandare, K., Ørka, H.O., Dalponte, M., Næsset, E., Gobakken, T., 2017. Individual tree
crown approach for predicting site index in boreal forests using airborne laser
scanning and hyperspectral data. Int. J. Appl. Earth Obs. Geoinf. 60, 72–82. https://
doi.org/10.1016/j.jag.2017.04.008.
Kaufman, Y.J., Tanré, D., 1996. Strategy for direct and indirect methods for correcting the
aerosol effect on remote sensing: from AVHRR to EOS-MODIS. Remote Sens. Environ.
55, 65–79. https://doi.org/10.1016/0034-4257(95)00193-X.
Ke, Y., Quackenbush, L.J., Im, J., 2010. Synergistic use of QuickBird multispectral ima-
gery and LIDAR data for object-based forest species classification. Remote Sens.
Environ. 114, 1141–1154. https://doi.org/10.1016/j.rse.2010.01.002.
Laurance, W.F., Carolina Useche, D., Rendeiro, J., Kalka, M., Bradshaw, C.J.A., Sloan,
S.P., et al., 2012. Averting biodiversity collapse in tropical forest protected areas.
Nature 489, 290–293. https://doi.org/10.1038/nature11318.
Leckie, D.G., Gougeon, F.A., Walsworth, N., Paradine, D., 2003. Stand delineation and
composition estimation using semi-automated individual tree crown analysis. Remote
Z. Xu, et al.
Sens. Environ. 85, 355–369. https://doi.org/10.1016/S0034-4257(03)00013-0.
Li, W., Guo, Q., Jakubowski, M.K., Kelly, M., 2012. A new method for segmenting in-
dividual trees from the lidar point cloud. Photogramm. Eng. Remote Sensing 78,
75–84. https://doi.org/10.14358/PERS.78.1.75.
Lin, C., Popescu, S.C., Thomson, G., Tsogt, K., Chang, C.I., 2015. Classification of tree
species in overstorey canopy of subtropical forest using QuickBird images. PLoS One
10, 1–23. https://doi.org/10.1371/journal.pone.0125554.
Liu, L., Coops, N.C., Aven, N.W., Pang, Y., 2017. Mapping urban tree species using in-
tegrated airborne hyperspectral and LiDAR remote sensing data. Remote Sens.
Environ. 200, 170–182. https://doi.org/10.1016/j.rse.2017.08.010.
Loarie, S.R., Tambling, C.J., Asner, G.P., 2013. Lion hunting behaviour and vegetation
structure in an African savanna. Anim. Behav. 85, 899–906. https://doi.org/10.
1016/j.anbehav.2013.01.018.
Loreau, M., de Mazancourt, C., 2013. Biodiversity and ecosystem stability: a synthesis of
underlying mechanisms. Ecol. Lett. 16, 106–115. https://doi.org/10.1111/ele.
12073.
Maschler, J., Atzberger, C., Immitzer, M., 2018. Individual tree crown segmentation and
classification of 13 tree species using Airborne hyperspectral data. Remote Sens.
(Basel) 10, 1218. https://doi.org/10.3390/rs10081218.
McDermid, G.J., Hall, R.J., Sanchez-Azofeifa, G.A., Franklin, S.E., Stenhouse, G.B.,
Kobliuk, T., LeDrew, E.F., 2009. Remote sensing and forest inventory for wildlife
habitat assessment. For. Ecol. Manage. 257, 2262–2269. https://doi.org/10.1016/j.
foreco.2009.03.005.
Nevalainen, O., Honkavaara, E., Tuominen, S., Viljanen, N., Hakala, T., Yu, X., Hyyppä,
J., Saari, H., Pölönen, I., Imai, N.N., Tommaselli, A.M.G., 2017. Individual tree de-
tection and classification with UAV-Based photogrammetric point clouds and hy-
perspectral imaging. Remote Sens. (Basel) 9. https://doi.org/10.3390/rs9030185.
Nijland, W., Coops, N.C., Nielsen, S.E., Stenhouse, G., 2015. Integrating optical satellite
data and airborne laser scanning in habitat classification for wildlife management.
Int. J. Appl. Earth Obs. Geoinf. 38, 242–250. https://doi.org/10.1016/j.jag.2014.12.
004.
Nuijten, R.J.G., Coops, N.C., Goodbody, T.R.H., Pelletier, G., 2019. Examining the multi-
seasonal consistency of individual tree segmentation on deciduous stands using
Digital Aerial Photogrammetry (DAP) and unmanned aerial systems (UAS). Remote
Sens. (Basel) 11. https://doi.org/10.3390/rs11070739.
Otero, V., Van De Kerchove, R., Satyanarayana, B., Martínez-Espinosa, C., Fisol, M.A.Bin,
Ibrahim, M.R.Bin, Sulong, I., Mohd-Lokman, H., Lucas, R., Dahdouh-Guebas, F.,
2018. Managing mangrove forests from the sky: forest inventory using field data and
Unmanned Aerial Vehicle (UAV) imagery in the Matang Mangrove Forest Reserve,
peninsular Malaysia. For. Ecol. Manage. 411, 35–45. https://doi.org/10.1016/j.
foreco.2017.12.049.
Palace, M., Keller, M., Asner, G.P., Hagen, S., Braswell, B., 2008. Amazon forest structure
from IKONOS satellite data and the automated characterization of forest canopy
properties. Biotropica 40, 141–150. https://doi.org/10.1111/j.1744-7429.2007.
00353.x.
Pan, Y., Birdsey, R.A., Fang, J., Houghton, R., Kauppi, P.E., Kurz, W.A., Phillips, O.L.,
Shvidenko, A., Lewis, S.L., Canadell, J.G., Ciais, P., Jackson, R.B., Pacala, S.W.,
McGuire, A.D., Piao, S., Rautiainen, A., Sitch, S., Hayes, D., 2011. A large and per-
sistent carbon sink in the world’s forests. Science 333 (80), 988–993. https://doi.org/
10.1126/science.1201609.
Peñuelas, J., Gamon, J.A., Griffin, K.L., Field, C.B., 1993. Assessing community type,
plant biomass, pigment composition, and photosynthetic efficiency of aquatic vege-
tation from spectral reflectance. Remote Sens. Environ. 46, 110–118. https://doi.org/
10.1016/0034-4257(93)90088-F.
Pierzchała, M., Giguère, P., Astrup, R., 2018. Mapping forests using an unmanned ground
vehicle with 3D LiDAR and graph-SLAM. Comput. Electron. Agric. 145, 217–225.
https://doi.org/10.1016/j.compag.2017.12.034.
Piiroinen, R., Fassnacht, F.E., Heiskanen, J., Maeda, E., Mack, B., Pellikka, P., 2018.
Invasive tree species detection in the Eastern Arc Mountains biodiversity hotspot
using one class classification. Remote Sens. Environ. 218, 119–131. https://doi.org/
10.1016/j.rse.2018.09.018.
Puttonen, E., Jaakkola, A., Litkey, P., Hyyppä, J., 2011. Tree classification with fused
mobile laser scanning and hyperspectral data. Sensors 11, 5158–5182. https://doi.
org/10.3390/s110505158.
Reitberger, J., Schnörr, C., Krzystek, P., Stilla, U., 2009. 3D segmentation of single trees
exploiting full waveform LIDAR data. ISPRS J. Photogramm. Remote Sens. 64,
561–574. https://doi.org/10.1016/j.isprsjprs.2009.04.002.
Sääjoki, R., Packalén, P., Maltamo, M., Vehmas, M., Eerikäinen, K., 2008. Detection of
aspens using high resolution aerial laser scanning data and digital aerial images.
Sensors 8, 5037–5054. https://doi.org/10.3390/s8085037.
Saarinen, N., Vastaranta, M., Näsi, R., Rosnell, T., Hakala, T., Honkavaara, E., Wulder,
M.A., Luoma, V., Tommaselli, A.M.G., Imai, N.N., Ribeiro, E.A.W., Guimarães, R.B.,
Holopainen, M., Hyyppä, J., 2018. Assessing biodiversity in boreal forests with UAV-
based photogrammetric point clouds and hyperspectral imaging. Remote Sens. 10.
https://doi.org/10.3390/rs10020338.
Saini, S., Arora, K., 2014. A study analysis on the different image segmentation techni-
ques. Int. J. Inf. Comput. Technol. 4, 1445–1452.
Schneider, D.C., 2001. The rise of the concept of scale in ecology. Bioscience 51, 545.
https://doi.org/10.1641/0006-3568(2001)051[0545:trotco]2.0.co;2.
Sedliak, M., Sackov, I., Kulla, L., 2017. Classification of tree species composition using a
14
Int J Appl  Earth Obs Geoinformation 92 (2020) 102173
combination of multispectral imagery and airborne laser scanning data. Cent. Eur.
For. J. 63, 1–9. https://doi.org/10.1515/forj-2017-0002.
Selkowitz, D.J., Green, G., Peterson, B., Wylie, B., 2012. A multi-sensor lidar, multi-
spectral and multi-angular approach for mapping canopy height in boreal forest re-
gions. Remote Sens. Environ. 121, 458–471. https://doi.org/10.1016/j.rse.2012.02.
020.
Shen, X., Cao, L., 2017. Tree-species classification in subtropical forests using airborne
hyperspectral and LiDAR data. Remote Sens. 9. https://doi.org/10.3390/rs9111180.
Shen, W., Li, M., Huang, C., Wei, A., 2016. Quantifying live aboveground biomass and
forest disturbance of mountainous natural and plantation forests in Northern
Guangdong, China, based on multi-temporal landsat, PALSAR and field plot data.
Remote Sens. 8, 595. https://doi.org/10.3390/rs8070595.
Shen, X., Cao, L., Yang, B., Xu, Z., Wang, G., 2019. Estimation of forest structural attri-
butes using spectral indices and point clouds from UAS-based multispectral and RGB
imageries. Remote Sens. 11, 1–24. https://doi.org/10.3390/rs11070800.
Silva, C.A., Hudak, A.T., Vierling, L.A., Loudermilk, E.L., O’Brien, J.J., Hiers, J.K., Jack,
S.B., Gonzalez-Benecke, C., Lee, H., Falkowski, M.J., Khosravipour, A., 2016.
Imputation of individual longleaf pine (Pinus palustris mill.) tree attributes from field
and LiDAR data. Can. J. Remote Sens. https://doi.org/10.1080/07038992.2016.
1196582.
Sokolova, M., Japkowicz, N., Szpakowicz, S., 2006. Beyond accuracy, F-score and ROC: a
family of discriminant measures for performance evaluation. 19th Australian Joint
Conference on Artificial Intelligence 1015–1021. https://doi.org/10.1007/
11941439_114.
Sothe, C., Dalponte, M., de Almeida, C.M., Schimalski, M.B., Lima, C.L., Liesenberg, V.,
Miyoshi, G.T., Tommaselli, A.M.G., 2019. Tree species classification in a highly di-
verse subtropical forest integrating UAV-based photogrammetric point cloud and
hyperspectral data. Remote Sens. (Basel) 11. https://doi.org/10.3390/rs11111338.
Sun, H., Deng, T., Li, Y., 2014. Image segmentation algorithm based on the improved
watershed algorithm. Harbin Gongcheng Daxue Xuebao/J. Harbin Eng. Univ. 35,
857–864. https://doi.org/10.3969/j.issn.1006-7043.201309067.
Thomas, V., Noland, T., Treitz, P., Mccaughey, J.H., 2011. Leaf area and clumping indices
for a boreal mixed-wood forest: lidar, hyperspectral, and Landsat models. Int. J.
Remote Sens. 32, 8271–8297. https://doi.org/10.1080/01431161.2010.533211.
Tilman, D., Reich, P.B., Knops, J.M.H., 2006. Biodiversity and ecosystem stability in a
decade-long grassland experiment. Nature 441, 629–632. https://doi.org/10.1038/
nature04742.
Tilton, J.C., Lawrence, W.T., Plaza, A.J., 2006. Utilizing hierarchical segmentation to
generate water and snow masks to facilitate monitoring change with remotely sensed
image data. GIScience Remote Sens. 43, 39–66. https://doi.org/10.2747/1548-1603.
43.1.39.
Torresan, C., Berton, A., Carotenuto, F., Di Gennaro, S.F., Gioli, B., Matese, A., Miglietta,
F., Vagnoli, C., Zaldei, A., Wallace, L., 2017. Forestry applications of UAVs in Europe:
a review. Int. J. Remote Sens. 38, 2427–2447. https://doi.org/10.1080/01431161.
2016.1252477.
Vercauteren, T., Pennec, X., Perchant, A., Ayache, N., 2009. Diffeomorphic demons: ef-
ficient non-parametric image registration. Neuroimage 45. https://doi.org/10.1016/
j.neuroimage.2008.10.040.
Verstraete, M.M., Pinty, B., 1996. Designing optimal spectral indexes for remote sensing
applications. IEEE Trans. Geosci. Remote Sens. 34, 1254–1265. https://doi.org/10.
1109/36.536541.
Wallace, L., Watson, C., Lucieer, A., 2014. Detecting pruning of individual stems using
airborne laser scanning data captured from an Unmanned Aerial Vehicle. Int. J. Appl.
Earth Obs. Geoinf. 30, 76–85. https://doi.org/10.1016/j.jag.2014.01.010.
Weiss, M., Baret, F., 2017. Using 3D point clouds derived from UAV RGB imagery to
describe vineyard 3D macro-structure. Remote Sens. (Basel) 9, 111. https://doi.org/
10.3390/rs9020111.
White, J.C., Coops, N.C., Wulder, M.A., Vastaranta, M., Hilker, T., Tompalski, P., 2016.
Remote sensing technologies for enhancing forest inventories: a review. Can. J.
Remote Sens. 42, 619–641. https://doi.org/10.1080/07038992.2016.1207484.
Wu, J., Yao, W., Polewski, P., 2018. Mapping individual tree species and vitality along
urban road corridors with LiDAR and imaging sensors: point density versus view
perspective. Remote Sens. 10, 1–21. https://doi.org/10.3390/rs10091403.
Yancho, J.M.M., Coops, N.C., Tompalski, P., Goodbody, T.R.H., Plowright, A., 2019. Fine-
scale spatial and spectral clustering of UAV-Acquired digital aerial photogrammetric
(DAP) point clouds for individual tree crown detection and segmentation. IEEE J. Sel.
Top. Appl. Earth Obs. Remote Sens. 12, 1–18. https://doi.org/10.1109/jstars.2019.
2942811.
Yao, W., Krzystek, P., Heurich, M., 2012. Tree species classification and estimation of
stem volume and DBH based on single tree extraction by exploiting airborne full-
waveform LiDAR data. Remote Sens. Environ. 123, 368–380. https://doi.org/10.
1016/J.RSE.2012.03.027.
Yuan, J.G., Niu, Z., Fu, W.X., 2007. Model simulation for sensitivity of hyperspectral
indices to LAI, leaf chlorophyll and internal structure parameter - art. No. 675213.
Geoinformatics 2007 Remote. Sensed Data Information 2 (Pts 1), 6752–75213.
https://doi.org/10.1117/12.760656.
Zhao, X., Guo, Q., Su, Y., Xue, B., 2016. Improved progressive TIN densification filtering
algorithm for airborne LiDAR data in forested areas. ISPRS J. Photogramm. Remote
Sens. 117, 79–91. https://doi.org/10.1016/j.isprsjprs.2016.03.016.