UAV-BASED PHOTOGRAMMETRIC POINT CLOUDS AND HYPERSPECTRAL IMAGING FOR MAPPING BIODIVERSITY INDICATORS IN BOREAL FORESTS

Abstract

Biodiversity is commonly referred to as species diversity but in forest ecosystems variability in structural and functional characteristics can also be treated as measures of biodiversity. Small unmanned aerial vehicles (UAVs) provide a means for characterizing forest ecosystem with high spatial resolution, permitting measuring physical characteristics of a forest ecosystem from a viewpoint of biodiversity. The objective of this study is to examine the applicability of photogrammetric point clouds and hyperspectral imaging acquired with a small UAV helicopter in mapping biodiversity indicators, such as structural complexity as well as the amount of deciduous and dead trees at plot level in southern boreal forests. Standard deviation of tree heights within a sample plot, used as a proxy for structural complexity, was the most accurately derived biodiversity indicator resulting in a mean error of 0.5 m, with a standard deviation of 0.9 m. The volume predictions for deciduous and dead trees were underestimated by 32.4 m³/ha and 1.7 m³/ha, respectively, with standard deviation of 50.2 m³/ha for deciduous and 3.2 m³/ha for dead trees. The spectral features describing brightness (i.e. higher reflectance values) were prevailing in feature selection but several wavelengths were represented. Thus, it can be concluded that structural complexity can be predicted reliably but at the same time can be expected to be underestimated with photogrammetric point clouds obtained with a small UAV. Additionally, plot-level volume of dead trees can be predicted with small mean error whereas identifying deciduous species was more challenging at plot level.

Full text

UAV-BASED PHOTOGRAMMETRIC POINT CLOUDS AND HYPERSPECTRAL
IMAGING FOR MAPPING BIODIVERSITY INDICATORS IN BOREAL FORESTS
N. Saarinen a,g *, M. Vastaranta a,g, R. Näsi b, T. Rosnell b, T. Hakala b, E. Honkavaara b, M.A. Wulder c, V. Luoma a,g, A. M. G.
Tommaselli d, N. N. Imai d, E. A. W. Ribeiro e, R. B. Guimarães f, M. Holopainen a,g, J. Hyyppä b,g
a Dept. of Forest Sciences, University of Helsinki, P.O. Box 27, 00014 University of Helsinki, Finland -
firstname.lastname@helsinki.fi
b Dept. of Remote Sensing and Photogrammetry, Finnish Geospatial Research Institute FGI, National Land Survey, Geodeetinrinne
2, 04310 Masala, Finland - firstname.lastname@nls.fi
c Pacific Forestry Centre, National Resources Canada, 506 West Burnside Road, Victoria, British Columbia, V8Z 1M5, Canada -
mike.wulder@canada.ca
d Dept. of Cartography, São Paulo State University, Roberto Simonsen 305, 19060-900 Presidente Prudente, Brazil -
(tomaseli, nnimai)@fct.unesp.br
e Catarinense Federal Institute, Rodovia Duque de Caxias - km 6 - s/n, 89240-000 São Francisco do Sul, Brazil -
eduwerneck@gmail.com
f Dept. of Geography, São Paulo State University, Roberto Simonsen 305, 19060-900 Presidente Prudente, Brazil -raul@fct.unesp.br
g Centre of Excellence in Laser Scanning Research, Finnish Geospatial Research Institute FGI, National Land Survey of Finland,
04310 Masala, Finland
Commission ΙΙI, WG III/4
KEY WORDS: Spectral Imaging, Remote Sensing, Forest Ecology, Forest Mensuration, Forest Inventory, UAS, Photogrammetry
ABSTRACT:
Biodiversity is commonly referred to as species diversity but in forest ecosystems variability in structural and functional
characteristics can also be treated as measures of biodiversity. Small unmanned aerial vehicles (UAVs) provide a means for
characterizing forest ecosystem with high spatial resolution, permitting measuring physical characteristics of a forest ecosystem from
a viewpoint of biodiversity. The objective of this study is to examine the applicability of photogrammetric point clouds and
hyperspectral imaging acquired with a small UAV helicopter in mapping biodiversity indicators, such as structural complexity as
well as the amount of deciduous and dead trees at plot level in southern boreal forests. Standard deviation of tree heights within a
sample plot, used as a proxy for structural complexity, was the most accurately derived biodiversity indicator resulting in a mean
error of 0.5 m, with a standard deviation of 0.9 m. The volume predictions for deciduous and dead trees were underestimated by 32.4
m3/ha and 1.7 m3/ha, respectively, with standard deviation of 50.2 m3/ha for deciduous and 3.2 m3/ha for dead trees. The spectral
features describing brightness (i.e. higher reflectance values) were prevailing in feature selection but several wavelengths were
represented. Thus, it can be concluded that structural complexity can be predicted reliably but at the same time can be expected to be
underestimated with photogrammetric point clouds obtained with a small UAV. Additionally, plot-level volume of dead trees can be
predicted with small mean error whereas identifying deciduous species was more challenging at plot level.
* Corresponding author
1. INTRODUCTION
Monitoring biodiversity is increasingly important in sustainable
use of forest resources. Species diversity is frequently applied
approach for describing biodiversity (e.g. Gaston 2000, Huston
1994, Kimmins 1997, Rosenzweig 1995). Additionally, forest
structural and functional variety can also be used for
characterizing biodiversity. In forest environments, several
descriptive structural attributes of forests can be available upon
for assessing biodiversity, including tree size variability, canopy
cover, as well as amount of dead wood and deciduous trees
(Esseen et al. 1997, Kuuluvainen 2002, Kuusinen 1994,
Kuusinen 1996, Siitonen 2001, Willson 1974).
Remote sensing provides a means for measuring and mapping
of these structural attributes. Small unmanned aerial vehicles
(UAVs) have been used increasingly as a data collection option
to support forest sciences and applications (Goodbody et al.
2017, Pajares 2015, Torresan et al., 2017). The use of UAVs
has enabled the on-demand collection of high spatial resolution
imagery, serving to improve the resolution of photogrammetric
point clouds, and therefore offer improved characterization of
forest structure. UAV-based photogrammetric point clouds and
hyperspectral imagery provide information from forest structure
(de Oliveira et al. 2016, Puliti et al. 2015) and can be
considered complementary to traditional field plot
measurements. Although field measurements are still required,
UAV offer detailed and geolocated information on forest
structural and functional conditions that can be employed as
reference for larger area estimates represented by satellite
imagery, for example.
Recently, small UAVs have been used in depicting forest
characteristics related to biodiversity. For instance, in detecting
dead trees on the ground (Inoue et al. 2014), canopy gaps as an
indicator of biodiversity especially in natural forest where they
play vital role in regeneration (Getzin et al. 2014), and
structural heterogeneity of forests (Zahawi et al. 2015, Wallace
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-3/W3, 2017
Frontiers in Spectral imaging and 3D Technologies for Geospatial Solutions, 25–27 October 2017, Jyväskylä, Finland
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171

et al. 2016). In addition, UAV-based hyperspectral imagery has
been utilized in identifying individual tree species (Nevalainen
et al. 2017) as well as damaged and dead trees (Näsi et al.
2015).
The aim of this study is to investigate the ability of UAV-based
photogrammetric point clouds and hyperspectral imagery in
mapping biodiversity indicators for southern boreal forest
conditions as a means for enhancing the traditional field
measurements. The biodiversity indicators considered in the
study included structural complexity as well as the amount of
deciduous and dead trees.
2. MATERIALS AND METHODS
2.1 Study area and field data
The study area of an approximately 2000 ha is located in
southern Finland (61.19° N, 25.11° E) representing southern
boreal forests. The area includes both managed and natural
forests with an average stand size of slightly less than 1 ha. The
main tree species in the area are Scots pine (Pinus sylvestris L.),
Norway spruce (Picea abies (L.) Karst) as well as silver and
downy birches (Betula pendula Roth, and pubescens Ehrh.),
with a mix of aspen (Populus tremula L.) and Grey and
Common alder (Alnus incana (L.) Moench, and glutinosa (L.)
Gaertn.). Field data include 26 plots with a size of 32 m x 32 m.
The sample plots were measured in the summer of 2014. All
trees with a diameter-at-breast height (dbh) at least 5 cm were
tallied in a sample plot. Tree species, status (i.e. live or dead),
dbh and height were determined for each of these tallied trees.
Allometric functions were used to define stem volume for the
individual trees. Plot-level proxy for the biodiversity indicator
of the structural complexity was calculated as a variation in
field-measured tree heights (Hst.dev). Furthermore, stem volume
of deciduous and dead trees was aggregated from individual
tree-level information.
Attribute
Min
Max
Mean
Standard
deviation
Dg (cm)
14.0
35.1
23.3
5.7
Hg (m)
10.45
26.6
20.2
4.0
G (m2/ha)
5.8
41.7
25.1
7.4
Vtotal (m3/ha)
31.4
417.1
246.5
95.0
VDead (m3/ha)
0.00
17.2
3.1
4.2
VDeciduous (m3/ha)
1.5
287.4
61.3
67.2
N/ha
342
2871
1027
561
Hst.dev (m)
2.2
11.1
5.4
2.3
Table 1. Descriptive statistics of forest attributes of the sample
plots. Dg = basal-area weighted mean dbh, Hg = basal-area
weighted mean height, G = basal area, V = stem volume, and
Hst.dev = Standard deviation of field measured tree heights on
plot level
2.2 Data acquisition and pre-processing of UAV data
The UAV data were acquired during July of 2014. A tunable
Fabry-Pérot interferometer (FPI) based multispectral camera
manufactured by Senop Ltd. operating in the visible to near-
infrared spectral range (i.e. between 500 nm and 900 nm) was
used in the study to hyperspectral imagery with 22 spectral
bands. In addition, a Samsung NX300 RGB camera was
employed for obtaining high spatial resolution data. The two
cameras were mounted on a small, single-rotor UAV helicopter
based on Mikado Logo 600 mechanics with a 5-kg payload
capacity enabling simultaneous hyperspectral data collection
with high spatial resolution imagery required for creating a
detailed photogrammetric point cloud. A preprogrammed flight
path was flown autonomously using an autopilot DJI ACE
Waypoint. The flying altitude was 400 m, which resulted in a
ground sampling distance of 0.25 m for FPI imaging and 0.10 m
for RGB imagery. The data sets were processed using a
photogrammetric workstation, to provide image orientations and
finally the final outputs of photogrammetric point clouds with
3-dimensional (3D) information. Reflectance reference panels
were utilized to carry out transformation of digital numbers to
reflectance factors. The methods of Honkavaara et al. (2013)
were followed to radiometrically process and provide spectral
information and calibrated reflectance factors resulting in
reflectance mosaics from the FPI imaging. Finally, the
reflectance values from these mosaics were combined to the 3D
point clouds, in other words each point included the 3D
coordinates as well as reflectance values for the 22 spectral
bands used in the study.
2.3 Methodology
A digital surface model (DSM) with a resolution of 0.3 m was
created from the photogrammetric point clouds for detecting
individual tree crowns. The tree-crown delineation was carried
out by using a watershed segmentation approach.
Photogrammetric point clouds were normalized with the
national digital terrain model (DTM) with a horizontal
resolution of 2 m (NLS 2017). Metrics describing forest
structure (i.e. 3D metrics) for each segment were generated
from these normalized point clouds. The generated metrics
included maximum height (Hmax), mean height defined as the
arithmetic mean of heights (Hmean), standard deviation of
heights (Hstd) as well as the coefficient of variation of heights
(Hcv). Furthermore, quantiles for every 10% representing the
height of certain percentage of points (i.e. height percentiles)
were calculated between 10% and 90% (HP10-HP90). Similarly,
spectral features were generated for each segment by using the
reflectance values of points within a segment. The spectral
features included arithmetic mean spectra (Smean) and median
spectra (Smedian) as well as percentiles between 10% and
100% (SP10-SP100), depicting brightness of points within a
segment, for each of the 22 spectral bands.
A nearest-neighbour estimation method (Breiman 2001) was
applied in predicting simultaneously dbh, height, species, and
health status (i.e. live or dead) for each crown segment. Then
the investigated biodiversity indicators were compiled for the
sample plots as sums or averages of the tree level predictions.
Random forest classification was used for selecting the most
important 3D metrics as well as spectral features, but it was also
employed for identifying the nearest neighbour needed for the
estimations. The number of neighbours used in the predictions
was set to one to include the variability in the reference data.
Random forest was iterated ten times to define the best
performing 3D metrics for tree height and dbh. Pearson’s
correlation coefficient was used to assess the relation between
3D metrics and height and dbh. For health status and tree
species, the random forest was also iterated ten times to find the
most suitable spectral features. The within-built computing of
variable importance scores of the Random forest was used when
selecting spectral features, in other words spectral features with
scaled importance higher than 2.5 were selected for further
inspection. Pearson’s correlation coefficient was computed
between these spectral features to select the spectral features to
be included in the final modelling. Mean spectra from all the 22
The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-3/W3, 2017
Frontiers in Spectral imaging and 3D Technologies for Geospatial Solutions, 25–27 October 2017, Jyväskylä, Finland
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172

spectral bands were calculated for each tree species when only
live trees were considered and separately for dead trees.
The validation of the UAV-based mapping of the biodiversity
indicators was assessed based the mean error (ME) when
compared to the field reference. The ME was calculated by
subtracting a biodiversity indicator predicted with the UAV data
from the indicator observed in the field. The absolute value for
ME was divided by the mean of each field-observed
biodiversity indicator to obtain the relative value. In addition,
the effect of structural complexity as well as the amount of
deciduous and dead trees in a sample plot on the ME was
analysed.
3. RESULTS
3.1 Feature selection
All of the high height percentiles (i.e. HP80-HP90) and Hmax
had a Pearson’s correlation coefficients higher than 0.9 when
relationship with field-measured height and dbh was assessed.
They were, however, also highly correlated (r > 0.90) with each
other. Hmax was within the best metrics in each random forest
iteration and thus, only the Hmax was selected for the final
modelling. The spectral features were included to the search of
nearest neighbour for improving tree species and health status
estimation. All spectral features with the scaled importance
higher than 2.5 were correlated (r > 0.7) with each other.
Therefore, the spectral features with the lowest Pearson’s
correlation coefficient, namely SP90 for the bands 688, 719, and
900 as well as Smean for the band 504, were included in the
final nearest-neighbour prediction model.
Figure 2. Mean and median spectra of various tree species (only
live trees included) and dead trees
Visual inspection of the mean spectra revealed that the dead
trees had visibly lower reflectance values, especially in the near-
infrared part of the spectrum (Figure 2). Average difference
between mean and median spectra of live trees was
approximately 0.00 indicating relatively uniformly distributed
species-specific spectral values without any noteworthy outliers.
For dead trees, on the other hand, the difference between mean
and median spectra varied from 0.01 to 0.02 for wavelengths
from 719 to 775, corresponding on average 27.6% of the mean
reflectance values, indicating more variability in reflectance
values for especially the red-edge bands.
3.2 Accuracy of mapping the biodiversity indicators
The rate of identifying individual trees varied between 22.3%
and 137.1%, with a mean of 64.3%. The underestimates were
mainly caused by low detection rate of small trees under the
dominant canopy layer. On the other hand, overestimates were
present where the photogrammetric point clouds could not
penetrate to ground level to define crown boundaries and
marginal peaking in the DSM resulted in commission error (i.e.
identification of tree that is not there).
Structural complexity within a sample plot was the most
accurately derived biodiversity indicator resulting in the ME of
0.5 m (8.7%). The ME for volume of deciduous trees varied
from 11.1 m3/ha overestimates to 216.6 m3/ha underestimates
(Table 3). Although, the volume of dead trees was notably
smaller compared to deciduous trees (3.1 m3/ha and 61.3 m3/ha,
respectively), and the mean absolute ME was not as substantial,
the mean relative MEs were similar for both, in other words
52.4% for stem volume of deciduous and 54.6% for stem
volume of dead trees.
Statistics
Hst.dev,
m
VOLdead,
m3/ha
VOLdec,
m3/ha
ME
Min
-2.3
-2.6
-11.1
Max
2.5
10.9
216.6
Mean
0.5
1.7
32.4
Standard
deviation
0.9
3.2
50.2
Table 3. Accuracy of mapping biodiversity indicators. ME =
mean error, Hst.dev = standard deviation of individual tree
heights (used as a proxy for structural complexity), VOLdead =
plot-level volume of dead trees, VOLdec = plot-level volume of
deciduous trees
When the effect of the amount of deciduous and dead trees was
analysed, proportion of stem volume was used (i.e. VOL%dead
and VOL%dec). Furthermore, the mean value based on field
measurements of either Hst.dev (5.4 m), VOL%dead (1.4%), or
VOL%dec (26.7%) at a time were used to divide the plots into
two groups (i.e. plots with larger or smaller value than the
mean). The structural complexity did not affect the accuracy of
estimating either the VOLdead or VOLdec, in other words the
difference between the mean relative MEs of the plots with
Hst.dev larger or smaller than 5.4 m was not statistically
significant (p = 0.77 and p = 0.42, respectively).
On the other hand, VOL%dec affected the mapping accuracy of
VOLdec as the difference in the ME was statistically significant
(p = 0.01), when comparing sample plots with the VOL%dec
larger and smaller than the average (i.e. 26.7%). The mean
relative ME for plots with deciduous proportion larger than the
average was 63.6% whereas for plots with proportion of
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Frontiers in Spectral imaging and 3D Technologies for Geospatial Solutions, 25–27 October 2017, Jyväskylä, Finland
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173

deciduous trees less than the average, the relative ME was
31.0%. In contrast, the difference in the relative ME of dead
trees was not statistically significant (p = 0.42) between plots
with more (relative ME 53.1%) or less (relative ME 72.9%)
dead trees (i.e. proportion from stem volume) than on average
(i.e. 1.4%).
4. DISCUSSION
The suitability of UAV-based photogrammetric point clouds
and hyperspectral imaging was investigated in mapping
biodiversity indicators such as structural complexity and
volume of deciduous and dead trees. It was possible to estimate
structural complexity with a mean error of 0.5 m indicating
ability of photogrammetric point clouds in describing
biodiversity through height variation. Structural complexity
affected on the accuracy of plot-level stem volume estimates of
dead trees, implying better accuracy with smaller structural
variation.
The accuracy of individual tree detection influences the
estimated variability in tree height as suppressed trees are
problematic to identify with photogrammetric point clouds
because penetration through canopy is challenging (Vastaranta
et al. 2013, White et al. 2013, Wallace et al. 2016). Thus, a
plot-level mean height can be expected to be overestimated with
photogrammetric point clouds, which was true also in this
study. Furthermore, Hst.dev, utilized to describe structural
complexity, was also underestimated. However, the mean error
for Hst.dev of 0.5 m is similar or better compared to results of
other studies using UAV-based photogrammetric point clouds
in estimating tree height (Zarco-Tejada et al. 2014, Dandois et
al. 2015, Zahawi et al. 2015, Wallace et al. 2016). Berveglieri et
al. (2016) used photogrammetric point clouds to derive
information from vertical structure of Brazilian semideciduous
tropical forest and concluded that it was possible to classify
successional stage with this information. Based on also our
results, the accuracy of height variation could be used for
estimating biodiversity when assessed with vertical structure of
a forest. Wallace et al. (2016) estimated canopy cover and
vertical canopy structure in a native eucalypt forest in Australia.
They reported underestimates of 15% in point-cloud based
canopy cover, but 0.61 m overestimates for tree height which
could have been caused the use of DTM based on
photogrammetric point cloud.
The reflectance values for each spectral band depend on
illuminating conditions, therefore spectral features are not as
stable as the 3D metrics between sample plots and data
acquisitions (Nevalainen et al. 2017). Dandois et al. (2015)
reported likewise of the effect of cloudy vs clear days on the
canopy penetration of UAV-based photogrammetric point cloud
which suggests that tree crown identification and tree detection
can be affected by the illumination conditions. In addition, the
accuracy of classifying tree species and health status (i.e. live or
dead) influences the final results of mapping the biodiversity
indicators such as volume of dead and deciduous trees.
Although random forest provides a robust means for selecting
features for final modelling, several wavelengths across the
spectral range were represented in the selected spectral features
used for the modelling. This is in line with the results presented
by Näsi et al. (2015) and Nevalainen et al. (2017). Thus, it is
challenging to specify the relationship between the physical
characteristics of various tree species or health status and
reflectance values of the 22 bands used here. However, smaller
mean error was identified for plots where the proportion of
deciduous trees was less than the average. This indicates good
reliability for plots where small amount of deciduous trees exist
which is important as tree species variability increases overall
biodiversity. Many of the trees identified as dead in the field did
not have any or little crown and the health status dead also
included snags. When segmenting DSM to identify individual
trees, these may not have been detected as they might have been
under the dominant canopy layer or crowns of adjacent trees.
Here we classified specific tree species for each identified tree
crown which might have caused more uncertainty if simpler
classification of conifer-deciduous would have been used. In
addition, deciduous trees contribute in co-dominant canopy
layer which decreases the classification accuracy if their crowns
are not identified from a point cloud. Variation in detection
accuracy based on canopy layers could explain relatively low
estimates for volume of deciduous trees. Nevertheless, the study
increases understanding how photogrammetric point clouds and
hyperspectral imaging acquired with a small UAV can be used
in mapping biodiversity indicators. And with the potential for
temporal resolution, UAV can be utilized in producing these
kinds of data sets in monitoring changes in forest conditions
that can reveal a trend for development of biodiversity.
5. CONCLUSIONS
Photogrammetric point clouds generated from UAV was used to
characterize structural complexity of southern boreal forests and
it was possible to capture this biodiversity indicator with a level
of reliability comparable to field measurements, indicating that
UAV-based photogrammetric point clouds are suitable for
mapping biodiversity when measured through structural
variability. Hyperspectral imaging was employed in addition to
3D information from the point clouds, to estimate volume of
dead and deciduous trees. Smaller mean errors were obtained
for volume estimates for dead trees than for deciduous trees.
The results did not vary between plots of different forest
characteristics, although it was possible to estimate volume of
deciduous trees more reliably when they were mixed in conifer-
dominated forests.
ACKNOWLEDGEMENTS
The study was funded by the Academy of Finland through a
project “Unmanned Airborne Vehicle- based 4D Remote
Sensing for Mapping Rain Forest Biodiversity and Its Change
in Brazil” (Decision number 273806) and the Centre of
Excellence in Laser Scanning Research (project number
272195). The authors would also like to thank Häme University
of Applied Science for supporting our research activities at Evo
study site, Senop Oy for providing us the FPI hyperspectral
camera, and Dr Sakari Tuominen and Dr Ilkka Pölönen for their
support during the UAV data capture flights. Senior researcher
Paula Litkey is thanked for her support in generating the
photogrammetric point clouds.
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The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-3/W3, 2017
Frontiers in Spectral imaging and 3D Technologies for Geospatial Solutions, 25–27 October 2017, Jyväskylä, Finland
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The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Volume XLII-3/W3, 2017
Frontiers in Spectral imaging and 3D Technologies for Geospatial Solutions, 25–27 October 2017, Jyväskylä, Finland
This contribution has been peer-reviewed.
https://doi.org/10.5194/isprs-archives-XLII-3-W3-171-2017 | © Authors 2017. CC BY 4.0 License.
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