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remote sensing
Article
Machine Learning Techniques to Predict Soybean Plant Density
Using UAV and Satellite-Based Remote Sensing
Luthfan Nur Habibi 1, Tomoya Watanabe 2, Tsutomu Matsui 3and Takashi S. T. Tanaka 3,4 ,*
Citation: Habibi, L.N.; Watanabe, T.;
Matsui, T.; Tanaka, T.S.T. Machine
Learning Techniques to Predict
Soybean Plant Density Using UAV
and Satellite-Based Remote Sensing.
Remote Sens. 2021,13, 2548.
https://doi.org/10.3390/rs13132548
Academic Editor:
Michael Schirrmann
Received: 30 May 2021
Accepted: 28 June 2021
Published: 29 June 2021
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This article is an open access article
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conditions of the Creative Commons
Attribution (CC BY) license (https://
creativecommons.org/licenses/by/
4.0/).
1Graduate School of Natural Science and Technology, Gifu University, Gifu 5011193, Japan;
noerhabibii@gmail.com
2Graduate School of Mathematics, Kyushu University, Fukuoka 8190395, Japan;
watanabe.tomoya.713@s.kyushu-u.ac.jp
3Faculty of Applied Biological Sciences, Gifu University, Gifu 5011193, Japan; matsuit@gifu-u.ac.jp
4Artificial Intelligence Advanced Research Center, Gifu University, Gifu 5011193, Japan
*Correspondence: takashit@gifu-u.ac.jp; Tel.: +81-752-932-975
Abstract:
The plant density of soybean is a critical factor affecting plant canopy structure and
yield. Predicting the spatial variability of plant density would be valuable for improving agronomic
practices. The objective of this study was to develop a model for plant density measurement
using several data sets with different spatial resolutions, including unmanned aerial vehicle (UAV)
imagery, PlanetScope satellite imagery, and climate data. The model establishment process includes
(1) performing the high-throughput measurement of actual plant density from UAV imagery with the
You Only Look Once version 3 (YOLOv3) object detection algorithm, which was further treated as a
response variable of the estimation models in the next step, and (2) developing regression models to
estimate plant density in the extended areas using various combinations of predictors derived from
PlanetScope imagery and climate data. Our results showed that the YOLOv3 model can accurately
measure actual soybean plant density from UAV imagery data with a root mean square error (RMSE)
value of 0.96 plants m
−2
. Furthermore, the two regression models, partial least squares and random
forest (RF), successfully expanded the plant density prediction areas with RMSE values ranging from
1.78 to 3.67 plant m
−2
. Model improvement was conducted using the variable importance feature
in RF, which improved prediction accuracy with an RMSE value of 1.72 plant m
−2
. These results
demonstrated that the established model had an acceptable prediction accuracy for estimating plant
density. Although the model could not often evaluate the within-field spatial variability of soybean
plant density, the predicted values were sufficient for informing the field-specific status.
Keywords:
PlanetScope; random forest; partial least squares regression; spatial variation; spectral
reflectance; YOLOv3
1. Introduction
In soybean (Glycine max (L.) Merr.) production, ensuring a high plant density is one
of the main ways to maximize crop yield [
1
–
3
]. Plant density is a product of seedling
rates and stands establishment ratios. However, soybean establishment is highly variable
depending on climate and soil conditions [
4
,
5
]. Furthermore, there is an optimal plant
density for maximizing yield according to the environment [
6
] and genotype [
7
], because
an excessively high soybean population affects plant structure, mainly by reducing the
number of pods per plant. Thus, the quantification of plant density is an essential step to
identifying the optimal plant population, row spacing, and seed density during sowing,
which could contribute to developing better crop management practices. Given the recent
diffusion of precision agricultural technologies, such as variable-rate seeding, not only
field-specific but also within-field variability of plant density should be quantified.
Evaluating plant density can be done by manually counting the soybean stands in
the field by employing various methods, such as systematic design counting, which can
Remote Sens. 2021,13, 2548. https://doi.org/10.3390/rs13132548 https://www.mdpi.com/journal/remotesensing
Remote Sens. 2021,13, 2548 2 of 20
assess a wide range of soybean plant densities [
8
]. However, this kind of method is labor-
intensive and time-consuming. Although the optimal seeding rates have been tested in
field-scale trials [
9
,
10
], information on final plant density is mostly unavailable. Detailed
spatial information on plant density, which cannot be assessed by manual measurement,
is needed to provide better prescriptions across fields. Thus, it is essential to develop a
high-throughput measurement method for plant density.
The application of remote sensing technology has been widely addressed in agricul-
tural fields using various platforms, such as satellite, aircraft, and unmanned aerial vehicles
(UAVs), to achieve better efficiency, cost-effectiveness, and high-throughput measurement,
rather than direct monitoring on the field [
11
]. The determination of suitable remote sensing
instruments for measuring a specific variable is crucial to obtaining the appropriate method
and data set [
12
], since each platform has different specifications, namely, the spatial and
temporal resolution, flight altitude, acquisition schedule, spectral ranges, operational cost,
and others [
13
]. The measurement of plant density requires explicit information on the
individual plant canopies in high accuracy of the quantification and geographic location in
a detailed scale. The remote sensing scene can be used to access individual plant stands
with a canopy delineation process to obtain the location, size, shape, and number of plant
canopies [
14
]. In larger vegetation canopies, such as forest vegetation, satellite remote
sensing has been widely used to delineate vegetation canopy at the tree-crown scale [
15
,
16
].
However, commonly used optical satellite imagery, such as Landsat (30 m resolution),
Sentinel-2 (10 m resolution), and PlanetScope (3 m resolution), has an insufficient spatial
resolution to detect small canopy, namely, crop plants [
15
]. Crop plant density that rep-
resents the geometrical agronomic trait [
11
,
17
] is more challenging to be measured using
satellite imagery, since the majority of satellite imagery does not provide a detailed spatial
resolution that can show textures or geometrical features of crop plants; thus, it prevents
directly accessing the number of plants inside the pixels. Crop plant density usually has a
dense population in a one-meter square area that is hard to capture using either satellite-
or aircraft-based remote sensing. The limitation of the spatial resolution of satellite-based
remote sensing instruments prevents high-throughput analysis for small grain crops.
Each remote-sensing instrument and platform has different characteristics such as
spatiotemporal resolution, coverage, and spectral specifications. Thus, a multiscale remote
sensing and image analysis has been applied to compensate for each other’s shortcomings.
For instance, a synergy between satellite imagery and finer resolution imagery captured by
other platforms that can precisely observe an object can expand the observation coverage
on a global scale to break the resolution limitation in satellite imagery [
18
]. This approach
has been widely applied in forestry studies for measuring plant populations by using
airborne-based light detection and ranging (LiDAR) and satellite imagery together [
14
,
19
].
Data accessed from LiDAR can assess the individual structure of plants, such as height and
canopy area, then incorporated with satellite imagery data (e.g., spectral reflectance) to
measure plant populations in a broader coverage using regression analysis [
19
]. A similar
approach should be applied in agricultural studies for accessing crop growth status, which
is plant density; however, to the best of our knowledge, this kind of approach has not yet
been applied for soybean production. The utilization of LiDAR was also used to quantify
small grain crop plant density with great accuracy, as proposed by Saeys et al. [
20
]; however,
it has a significant shortcoming, since the sensor must be mounted on a combine harvester,
causing limited area observation. Moreover, the cost of LiDAR sensors is not affordable for
most farmers. As a substitute to LiDAR, UAV imagery can record photogrammetry scenes,
presenting geometric agricultural traits on a detailed scale.
Unmanned aerial vehicles have been widely used in scientific research for several
years with the benefits of flexible time and flight operation and cloud-free data [
21
]. Un-
manned aerial vehicles are commonly equipped with high-resolution camera sensors
that are capable of providing high spatial resolution, depending on the platform’s height.
Photogrammetry can also provide geometrical traits of vegetation similar to LiDAR. The
use of UAVs in the study of delineating or detecting a single crop plant also became a
Remote Sens. 2021,13, 2548 3 of 20
trend in the last decade with the rise of machine learning techniques. Object detection
algorithms have become a popular approach to identifying an individual crop canopy
from photogrammetry images. The combination of UAV imagery and machine learning
has been applied to accurately estimate the numbers of plants of various crops, including
soybean [
22
], rice [
23
], wheat [
24
], maize [
25
], rapeseed [
26
], and cotton [
27
], and is even
used to detect weed seedlings in cultivation fields [
28
]. The proposed methods in the
literature have utilized machine learning techniques that provide high accuracy output for
detecting individual plants in UAV imagery; thus, the quantification of field plant density
can be accurately measured. However, since previous studies only utilized a single remote
sensing instrument—namely, UAV—with the flight altitude limited to a maximum height
of 20 m to keep the high spatial resolution imagery, the area coverage became limited to
a few hectares in a single flight. Considering that farmers have broad fields, monitoring
plant density with UAV will be a challenging task.
As noted above, satellite imagery is directly incapable of identifying individual plants
because of the limited resolution; however, optical sensors of satellite imagery can provide
surface reflectance values and vegetation indices, reflecting the plant biomass and leaf
area index [
29
]. Plant biomass per unit area is a product of individual plant biomass and
plant density. Therefore, surface reflectance values and vegetation indices are hypothesized
to be indirect predictors for estimating plant density by referring to the values at the
same phenological stage as long as the individual plant biomass is almost constant. Thus,
accurately measured plant population from UAV imagery by the object detection algorithm
are expected to be a response variable for plant density estimation model, which treats
reflectance data and vegetation indices derived from satellite imagery as predictors in a
wider area coverage of observations. In addition to remote sensing data, climate data, such
as precipitation and air temperature, might be important elements in predicting the plant
density, since it could affect seedling establishment and plant growth such as leaf area
expansion [5,30,31].
The aim of this study was to develop a satellite-based model for estimating soybean
plant density through machine learning techniques. Specifically, the high-throughput
measurement of actual plant density quantified by UAV imagery and YOLOv3 models
was used as the response variable for plant density estimation models, while PlanetScope
imagery and climate data were used as predictors for the models. The prediction accuracies
of partial least squares (PLS) regression and random forest (RF) regression were compared
in developing estimation models, as these methods were reported to be robust for dealing
with remote sensing imagery data [
32
–
37
]. Finally, the spatial pattern of plant density was
further assessed using the developed model to examine the potential implications for better
crop management practices and the limitations of the satellite-based models.
2. Materials and Methods
In order to establish models to predict the plant density of soybean, we divided the
workflow of the study into three steps: (1) performing high-throughput measurement of
actual plant density of the observation fields from UAV imagery using an object detection
model based on the You Only Look Once version 3 (YOLOv3) algorithm, which was
further treated as a response variable in the regression model development; (2) performing
preprocessing of the PlanetScope imagery to fill in the gaps of missing daily spectral
reflectance data using spline smoothing, which served as predictor variables from satellite
imagery data; (3) establishing satellite-based plant density estimation models using two
regression analysis methods, PLS and RF regression, to expand the measurement of plant
density into wider area coverage. The flow chart in Figure 1summarizes all of the steps
involved in this study.
Remote Sens. 2021,13, 2548 4 of 20
Figure 1. Flow chart of the research.
2.1. Study Area
This study was conducted in 12 soybean fields in Kaizu City, Gifu, Japan. The soybean
fields were planted between the 2018 and 2020 growing seasons from July–November
for each year. The farmers in this location implemented crop rotation with three crops
(paddy rice–winter wheat–soybean) over two years, which became a challenging task to
find exactly the same fields cultivating soybean in multiple years sequentially. Thus, fields
in different locations for each year were observed for the analysis. A local leading soybean
cultivar, ‘Fukuyutaka’, was grown in all observation fields. According to a previous
study [
38
], the optimum planting date of the ‘Fukuyutaka’ cultivar was approximately
10 July. However, the sowing dates of the observed fields were varied due to the climate
conditions, as machinery cannot be used for seeding several days after heavy rain. The
differences in sowing dates and soil conditions during the seeding caused unstable seedling
establishment rate and plant density variability in fields. Thus, selected fields sown from
the optimum to late sowing dates in the three years were surveyed to cover high variations
of plant density. The detailed locations map and sowing dates for the research fields are
presented in Figure 2and Table 1.
Table 1.
Locations, sowing dates, UAV imagery acquisition dates, and the number of satellite (PlanetScope) imagery used
for all observation fields.
Field
Name
Area
(ha) Latitude Longitude Sowing Dates UAV Imagery
Acquisition Date
The Number of
PlanetScope Imagery a
Field 1 0.9 35◦11013.2” 136◦4004.8” Jul 15, 2018 6 August 2018 (22 DAS) 12
Field 2 1.16 35◦11031.2” 136◦4001.2” Jul 15, 2018 6 August 2018 (22 DAS) 12
Field 3 1.1 35◦11020.4” 136◦39054.0” Jul 17, 2019 29 July 2019 (12 DAS) 13
Field 4 1.19 35◦11020.4” 136◦39054.0” Jul 17, 2019 29 July 2019 (12 DAS) 13
Field 5 1.11 35◦11016.8” 136◦39054.0” Jul 10, 2019 30 July 2019 (20 DAS) 11
Field 6 0.94 35◦11016.8” 136◦39054.0” Jul 10, 2019 30 July 2019 (20 DAS) 11
Field 7 0.88 35◦1102.4” 136◦38016.8” Jul 25, 2019 5 August 2019 (11 DAS) 10
Field 8 0.95 35◦1102.4” 136◦3809.6” Jul 25, 2019 5 August 2020 (11 DAS) 10
Field 9 1.87 35◦11016.8” 136◦39043.2” Aug 2, 2020
19 August 2020 (17 DAS)
8
Field 10 0.73 35◦14042.0” 136◦39050.4” Jul 21, 2020 4 August 2020 (14 DAS) 6
Field 11 0.61 35◦14027.6” 136◦4001.2” Aug 5, 2020
18 August 2020 (13 DAS)
8
Field 12 0.76 35◦1004.8” 136◦39036.0” Aug 4, 2020
18 August 2020 (14 DAS)
8
aThe duration of the PlanetScope imagery acquisition was from 1 to 60 days after sowing.
Remote Sens. 2021,13, 2548 5 of 20
Figure 2. Location of study sites at Kaizu city, Gifu Prefecture, Japan. Shaded fields indicate test fields.
2.2. Imagery and Climate Data Collection
2.2.1. Acquisition of UAV Imagery
A total of 12 soybean field scenes were taken under natural daylight conditions. All
imagery was captured during the early stage of soybean growth (emergence stage) from
11 days after sowing (DAS) until 22 DAS (Table 1). The image data sets were captured
using a commercial UAV (Phantom 4 Pro, DJI, Shenzhen, China) equipped with a default
RGB camera capturing 5472
×
3648 pixel images for each scene. The number of scenes
was different for each field depending on the area coverage. Images were captured from
15 m above the surface, resulting in a ground sampling distance of approximately 3.5 mm
per pixel. The trajectory of the UAV was set to ensure a 60–70% front and side image
overlap. The coordinates of ground control points (GCPs) for registering the camera
location were measured using KlauPPK (Klau Geomatics, New South Wales, Australia) with
0.03 m precision. Using this georeferencing process, we could minimalize the geographical
error regarding the location of each soybean stand measured in the following procedure
(
Section 2.3
). The orthomosaic for each field was generated using Structure from Motion
(SfM) software (Pix4D, Pix4Dmapper version 4.6.4, Lausanne, Switzerland). The average
pixel size per field of the orthomosaics was 61,036 ×28,113 pixels.
2.2.2. PlanetScope Imagery Data
This study used the PlanetScope surface reflectance product taken with PS2 and
PS2.SD instruments (Planet Labs Inc., San Francisco, CA, USA). This product provides
ground sample distance at 3 m per pixel, captured using a four-band frame imager in-
Remote Sens. 2021,13, 2548 6 of 20
cluding blue (PS2: 455–515 nm; PS2.SD: 464–517 nm), green (PS2: 500–590 nm; PS2.SD:
547–585 nm), red (PS2: 590–670 nm; PS2.SD: 650–682 nm), and near-infrared (NIR) (PS2:
780–860 nm; PS2.SD: 846–888 nm). The imagery was already orthorectified and geomet-
rically corrected using altitude telemetry and ephemeris data with refined GCPs by the
provider to deal with geographical errors [
39
]. Moreover, all available imagery was already
atmospherically corrected by Planet Labs Inc. before they released it in their application
programming interface framework. This correction was crucial for the study, since we used
spectral reflectance values of the imagery. The PlanetScope satellite constellation is capable
of recording the land surface at a daily frequency. In this study, we used PlanetScope scenes
of the observation fields from the sowing dates until 60 DAS. However, the terrestrial
surface was sometimes covered with thick clouds, which made daily observations difficult.
Thus, we tried to download the available cloudless imagery that clearly shows the fields
and processed the imagery in the following procedure (Section 2.4) to acquire a daily
spectral reflectance value. The imagery was very limited in 2020 because of frequent bad
weather during the growing season. The number of PlanetScope scenes used for each field
is listed in Table 1.
2.2.3. Climate Data
Daily total rainfall (mm) and mean air temperature (
◦
C) were obtained from the Agro-
Meteorological Grid Square Data, NARO [
40
] (https://amu.rd.naro.go.jp/, accessed on
23 October 2020). Daily data were downloaded for the months of the soybean growing
season (July–October) in 2018–2020. The meteorological data had an approximately 1 km
2
resolution based on the reference mesh area used by the data provider. Ideally, higher-
resolution data for the climate would have been utilized to match the resolution of the
satellite imagery and to understand the spatial variations more precisely. However, such
data were not available without in situ measurement; thus, we used these data as a
substitute for the meteorological data.
2.3. Actual Plant Density Measurement from UAV Imagery Using YOLOv3
Firstly, the number of soybean plants were accurately measured to obtain the actual
plant density data of the observation fields. This data will be used as the response variable
for the plant density estimation model using satellite imagery and climate data. The high-
throughput detection of soybean plants was carried out using the YOLOv3 algorithm that
is capable of extracting the number and exact location of the plant canopies from UAV
imagery; thus, actual plant density can be evaluated by calculating the number of plants
divided by the area.
YOLOv3 is an end-to-end object detection algorithm based on a deep learning neural
network [
41
]. The YOLOv3 network contained 53 convolutional layers, known as Darknet-
53, with improved detection speed and accuracy, and was designed to be more suitable for
small object detection than the previous generation [
41
,
42
]. This feature makes YOLOv3 a
suitable algorithm for detecting individual soybean plants from UAV imagery.
The input dimensions for the YOLOv3 network were 416
×
416
×
3. To meet the input
dimension, the orthomosaics were split into 416
×
416 pixel images using the virtual raster
function in QGIS software (QGIS Development Team 2001, version 3.14), which resulted
in a total of 129,520 images. From the split images, 712 images were randomly selected
for YOLOv3 model establishment. The training, validation, and test data sets contained
278 (40%), 186 (25%), and 248 (35%) images, respectively. Each soybean plant in the split
images was annotated with a bounding box using LabelImg [
43
], as shown in Figure 3a. To
establish the best YOLOv3 model for counting the number of established soybean plants,
a confidence threshold affecting object detection accuracy was tested from 0.05 to 0.95 at
intervals of 0.05. The epoch size for the training processes was constant at 50. The batch
size was set at 4 to speed up the training process due to the limited workstation specs
(Intel Core i7-7820X, Nvidia GeForce GTX 1070, 72 GB of RAM and a Windows 10 Pro
64-bit system operation). The prediction accuracy was evaluated based on the coefficient of
Remote Sens. 2021,13, 2548 7 of 20
determination (r
2
), and root mean square error (RMSE) values obtained from calculations
between the manually and automatically counted established soybean plants from the test
data set by the developed models using a different confidence threshold value. The best
model was determined by the highest r2and lowest RMSE values.
Figure 3.
(
a
) Example of the annotation process of established soybean plants using LabelImg; (
b
) the
established soybean plants detected by the YOLOv3 model.
The final process of YOLOv3 was to conduct soybean plant detection from all available
split images. The Geospatial Data Abstraction Library (GDAL) function was used in this
process to extract the centroid coordinates of the bounding boxes of detected soybean
plants according to the world files that contained coordinates for each split image. The
detected soybean plants with coordinate data were used for further regression analysis as
described in Section 2.5.
2.4. Daily Spectral Reflectance Gap-Filling of PlanetScope
PlanetScope imagery data were used in this study to expand the high-throughput
measurement of plant density in a wider coverage based on the actual plant density ob-
tained from the YOLOv3 model (Section 2.3). PlanetScope imagery had a daily temporal
resolution that was robust for identifying plant phenology, as we tried to measure the plant
density in the later growth stages of soybean. However, due to the frequent observations
using many satellites with various illumination geometries and poor inter-sensor calibra-
tion, the temporal surface reflectance data of PlanetScope became less stable and noisy [
29
].
Figure 4shows that the raw spectral reflectance data of PlanetScope (presented as points)
were not stable throughout the growth durations. Moreover, surface reflectance derived
from satellite imagery were inherently noisy due to the variable illumination patterns and
aerosols in the atmosphere. Smoothing splines can be used to reduce the potential for noise
from the spectrum wavelength [44].
The process was started by extracting the spectral reflectance values of every pixel
within the observation field areas using the zonal statistic function in QGIS software.
The available raw spectral reflectance data of PlanetScope imagery were then processed
using the spline function implemented in the ‘stats’ package in R (R Development Core
Team 2019, version 3.5.3). As presented in Figure 4, the distribution of available spectral
reflectance data was scattered between the sowing date and 60 DAS. A smoothing spline
can also be used to interpolate spectral reflectance values of the missing date due to the
presence of thick clouds from the available data. On the other hand, the smoothness of the
spline curves can be set to make flexible curves by increasing the degree of polynomial
or the number of knots. However, increasing the number of knots can lead to overfitting,
while a small number of knots may result in restricted data that have more bias. Therefore,
four knots were used in the smoothing spline process to obtain the natural shape of the
curve. Our data set had a small range of examples, so a higher number of knots would
overfit the data.
Remote Sens. 2021,13, 2548 8 of 20
Figure 4.
Examples of preprocessing multitemporal NDVI of PlanetScope by smoothing spline in a certain pixel for Fields 1,
6, and 9. Points represent observed NDVI values at a certain day after sowing (DAS) derived from PlanetScope imagery,
and the lines represent the estimated curves from the smoothing spline.
Furthermore, we also calculated the daily normalized difference vegetation index
(NDVI) value [
45
] from the interpolated spectral reflectance of PlanetScope imagery, be-
cause it represents the most commonly used vegetation indices that are capable of assessing
a particular variable of vegetation, e.g., quantity, quality, and vegetation stage develop-
ments [
19
]. The normalized difference vegetation index was calculated using PlanetScope
bands with the equation: ((NIR
−
Red)/(NIR + Red). Data for the interpolated spectral
reflectance and NDVI value from this process were used as predictor variables in the
regression analysis (Section 2.6).
2.5. Selecting Variables
Three data sources with different spatial resolutions (UAV imagery with
0.03 ×0.03 m2
,
PlanetScope imagery with 3
×
3 m
2
, and climate data with 1
×
1 km
2
) were used to
develop the plant density prediction model. Regression analysis using statistical and
machine learning methods was used for the model. The selection of variables, both for
response and predictors, is crucial in regression analysis. The response variable for the
regression model was the soybean plant density derived from the number of plants counted
by the YOLOv3 best model (Section 2.3). For the predictors, PlanetScope imagery data
(spectral reflectance and NDVI) and climate data (precipitation and temperature) were
selected. The first predictor, the spectral reflectance values of all PlanetScope bands, was
used from every pixel in the observation field to examine the potential of each band in
explaining plant density. Second, NDVI values calculated from the spectral reflectance
value of PlanetScope imagery was used in the regression analysis. Moreover, we also
minded the temporal resolution of the satellite imagery for increasing the capability of
regression models in estimating plant density. Spectral reflectance and NDVI data were
selected every ten days, calculated from the sowing dates (10, 20, 30, and 40 DAS) to reflect
the growing process of the plants, as time series data could be valuable information for
detecting plant density in the later growth stages. The last predictor variables were derived
from climate data with the following details: (1) seven-day precipitations before and after
the sowing date calculated from daily values; (2) ten-day cumulative temperatures at
10, 20, 30, and 40 DAS, calculated from the daily mean air temperature. All data from
YOLOv3 model, PlanetScope imagery, and climate data were transformed into averaged
values within each 3
×
3 m
2
grid cell to match pixels area of PlanetScope. Details about
the predictor variables are summarized in Table 2. The data were divided into training
and test data sets by randomly selecting the observation fields. In this process, we also
considered the potential effect of different years on plan density, as the climate condition
varied largely from year to year; thus, the training and test datasets were not divided by
the years. Training data were obtained using PlanetScope pixels in Fields 1, 4, 5, 6, 7, 10,
and 12 (n= 6600), while pixels in the other five fields were used as test data (n= 5839).
Remote Sens. 2021,13, 2548 9 of 20
Table 2.
Predictor variables used in partial least squares (PLS) and random forest (RF) regression
models.
Variable Type Dataset
Reflectance values PlanetScope surface reflectance: blue, green, red, NIR at 10, 20, 30, and 40 DAS)
Vegetation indices Normalized difference vegetation index (NDVI) at 10, 20, 30, and 40 DAS
Climate data Precipitation data: seven-days before and after the sowing date
Ten-days cumulative temperature at 10, 20, 30, and 40 DAS
2.6. PLS and RF Regression
In this study, two regression models, including PLS and RF regression, were used
to establish the model for estimating plant density. These two methods are based on
different analyses, where the PLS is a representative of the statistical approach, while RF is
a representative of the machine learning technique. The main reason for using PLS and RF
regression is because these approaches can deal with highly intercorrelated data such as
the spectral reflectance data of satellite imagery. Conventional regression analysis, such as
multiple linear regression, cannot handle multi-temporal satellite imagery data due to the
fact of multi-collinearity problems [46].
Partial least squares regression is a generalized multiple linear regression that pro-
vides a multivariate approach to predicting one response variable using strongly collinear
(correlated) predictor variables [
47
,
48
]. Details of PLS regression can be found in Geladi
et al. [
49
]. A partial least squares regression model was established using the ‘pls’ package
implemented in R [
50
]. In the analysis of PLS regression, the number of components was
determined using the ‘selectNcomp’ function attached to the ‘pls’ package, according to
the one-sigma method. The one-sigma heuristic chooses the fewest components for the
model that has an accuracy of less than one standard error from the best model.
Random forest regression is one of the techniques in machine learning that can be used
to estimate the response variable, based on classification and regression tree (CART) [
51
].
This analysis is efficient in processing non-linear data, which can also be found in the data
set [
32
]. Details about RF can be found in Breiman [
51
]. A random forest regression model
was established using the ‘randomForest’ package [
52
] implemented in R. Two parameters
were adjusted to optimize the RF regression model: ntree, the number of trees grown in the
regression forest, was set at 100; mtry, the number of different predictors sampled at each
node (default = the number of predictors divided by 3).
The selection of predictors is an important process for the model’s establishment,
as it could greatly affect the prediction accuracy and facilitate a better understanding of
the relationships between predictors and response variables [
12
]. Thus, the PLS and RF
regression models were trained to estimate plant density using several possible predictor
variable combinations, as follows: (1) using spectral reflectance values only; (2) using
NDVI values only; (3) using a combination of spectral reflectance and NDVI; (4) using a
combination of PlanetScope imagery and climate data. The variable combinations were
used to test the impact of different predictors in estimating plant density.
In addition, we also examined the variable importance measurement from RF regres-
sion as a method to determine the suitable variable predictors for predicting soybean plant
density. This method has been widely used in many scientific fields to select and identify
relevant predictors for predicting response variables [
53
]. Variable importance can be
extracted from the regression trees by calculating IncNodePurity, which is the total decrease
in node impurities from the splitting on the predictors, using the importance function in
the ‘randomForest’ package. An increase in the value of IncNodePurity implies a decrease
in the mean square error, which means that the largest values represent the most important
variables to the response [
54
]. Variable importance was evaluated from the RF model with
all available predictor variables. We verified whether the variable predictors with high
values of IncNodePurity could improve the prediction capability of the developed regression
model, since the predictors with low IncNodePurity are less critical to the response variable.
The performance of all developed regression models in this section was compared based
Remote Sens. 2021,13, 2548 10 of 20
on r
2
and RMSE values to see the best-fitted model, which were further used for spatial
prediction of soybean plant density for the test fields.
3. Results
3.1. UAV Imagery and YOLOv3 Model Accuracy
We trained the YOLOv3 object detection model for high-throughput measurement
of soybean plant numbers from the UAV imagery data. The effect of various confidence
thresholds on the accuracy of the YOLOv3 model was examined to establish the most
accurate model detecting the soybean seedling in the test data set images. The established
YOLOv3 model with a 0.50 confidence threshold scored the highest accuracy with an r
2
value of 0.88 and RMSE of 0.96 plants m
−2
as shown in Figure 5. The results from the other
models with different confidence threshold values are listed in Table S1. The YOLOv3, as
the best model using the confidence threshold of 0.50, was hereafter applied for the UAV
imagery of all observation fields to measure the actual plant density value, which was
further used as the response variable of the PLS and RF regression models.
Figure 5.
Relationship between manually observed and automatically counted soybean plant density
(plants m
−2
) in the YOLOv3 best model with a confidence threshold value of 0.50 for the test dataset
(n= 248). The solid line represents a regression line. The dashed line represents a 1:1 reference line.
3.2. Accuracy of PLS and RF Regression Model
We created six models using different predictor variable combinations for the regres-
sion analysis using PLS and RF regression. The names and details of the models are listed in
Table 3. In general, the RF regression outperformed the PLS regression in all combinations
of predictors for both the training and test data sets (Table 3). The results showed that the
high accuracy in the training data set did not always represent high accuracy in the test
data set. In the test data, the PLS regression models scored an RMSE between 2.08 and
3.67 plants m
−2
(r
2
= 0.19–0.56), while the RF regression models scored between 1.78 and
1.92 plants m−2(r2= 0.60–0.67).
The partial least squares regression models with different variable combinations
showed different results in estimating plant density as presented in Figure 6. The partial
least squares regression model using variables SR + NDVI (SR + NDVI-PLS) gave the
highest accuracy to estimate the test dataset (r
2
0.56 and RMSE 2.08 plants m
−2
). Partial
least squares regression using the SR-only predictor (SR-only PLS) performed similar
results to SR + NDVI-PLS, with higher plant density variation, ranging from –0.95 to
12.41 plants m
−2
. In contrast, PLS regression using the NDVI-only predictor (NDVI-only
PLS) scored the lowest variance, ranging from 1.04 to 8.04 plants m−2.
Remote Sens. 2021,13, 2548 11 of 20
Table 3.
Comparison of partial least squares (PLS) and random forest (RF) regression models using several combinations of
predictors.
Model Combination a
PLS Regression RF Regression
Training Test Training Test
r2RMSE r2RMSE r2RMSE r2RMSE
SR only 0.71 1.81 0.50 2.17 0.84 1.37 0.63 1.82
NDVI only 0.58 2.20 0.56 2.37 0.79 1.54 0.60 1.92
SR + NDVI 0.74 1.74 0.56 2.08 0.84 1.35 0.67 1.81
SR + Climate 0.76 1.65 0.19 3.67 0.84 1.36 0.63 1.83
NDVI + Climate 0.74 1.72 0.46 2.22 0.81 1.49 0.67 1.78
SR + NDVI + Climate 0.77 1.62 0.28 2.95 0.84 1.35 0.65 1.79
a
Model combination: SR only—model using predictors from surface reflectance data of PlanetScope imagery only (number of predictors:
16); NDVI only—model only using predictors from NDVI data of PlanetScope imagery only (number of predictors: 4); SR + NDVI—model
using predictors from a combination of surface reflectance data and NDVI data of PlanetScope imagery (number of predictors: 20); SR +
Climate—model using predictors from a combination of surface reflectance data of PlanetScope imagery and climate data (number of
predictors: 22); NDVI + Climate—model using predictors from a combination of NDVI data of PlanetScope imagery and climate data
(number of predictors: 10); SR + NDVI + Climate—model using predictors from combination of all PlanetScope imagery data and climate
data (number of predictors: 26); the best models for each case are highlighted with bold letters. The best scores for each regression model
are marked in bold.
Figure 6.
Relationships between actual plant density derived from the YOLOv3 model and estimated plant density
(
plants m−2
) derived from (
a
) SR-only PLS; (
b
) NDVI-only PLS; (
c
) SR + NDVI-PLS; (
d
) SR + Climate-PLS; (
e
) NDVI +
Climate-PLS; (
f
) SR + NDVI + Climate-PLS of test data set. The red line represents a regression line. The black line represents
a 1:1 relationship. Different color points represent the field names.
The results of the RF regression models using different variable combinations pre-
sented in Figure 7. The RF model using NDVI and climate data as variable predictors
(NDVI + Climate-RF) that scored the highest accuracy was NDVI + Climate-RF (r
2
0.67
Remote Sens. 2021,13, 2548 12 of 20
and RMSE 1.78 plants m
−2
). The model with the lowest accuracy was the RF model using
NVDI only predictors (NDVI-only RF). The accuracy of RF models was surpassed the PLS
models in estimating plant density in test fields.
Figure 7.
Relationships between actual plant density derived from the YOLOv3 model and estimated plant density
(plants m−2)
derived from (
a
) SR-only RF; (
b
) NDVI-only RF; (
c
) SR + NDVI-RF; (
d
) SR + Climate-RF; (
e
) NDVI + Climate-
RF; (
f
) SR + NDVI + Climate-RF of the test data set. The red line represents a regression line. The black line represents a 1:1
relationship. Different color points represent the field names.
In addition to the RF analysis, we examined the variable importance of the RF model
using all available predictors, and the results are shown in Figure 8. The results revealed
that NIR at 40 DAS was the most influential variable for the model with more than 12,000
values of IncNodePurity, followed by precipitation before the sowing date, temperature at
10 DAS, and NIR at 30 DAS. The NDVI variables in the later DAS (40, 20, and 30 DAS)
dominated the top ten variables. The temperature variables had little impact on the model
accuracy, excluding that on DAS 10. The result indicated that most of the predictors were
less important for the model to estimate the response variable, since the IncNodePurity was
less than 20% of the highest variable, NIR at 40 DAS.
Based on the variable importance of the RF model using all available predictors,
we developed another model using the top ten variables with the highest IncNodePurity
score (10VarImp-RF). The newly developed RF regression model, 10VarImp-RF, scored
the best performance (r
2
0.68 and RMSE 1.72 plants m
−2
), as presented in Figure 9, which
outperformed the best RF regression model without variable selection, according to the
variable importance (NDVI + Climate-RF) and the best PLS regression model (SR + NDVI-
PLS) in the test dataset, as presented in Table 3, Figures 6c and 7e. The plant density
estimated by the 10VarImp-RF model ranged from 0.40 to 11.70 plants m−2.
Remote Sens. 2021,13, 2548 13 of 20
Figure 8.
Variable importance (IncNodePurity values) list of the full random forest regression model
(SR + NDVI + Climate).
Figure 9.
Relationships between actual plant density derived from the YOLOv3 model and estimated
plant density (plants m
−2
) derived from 10VarImp-RF of the test data set. The red line represents a
regression line. The black line represents a 1:1 relationship. Different color points represent the field
names.
3.3. Spatial Prediction
The plant density spatial distribution maps of the test fields were created based on
four methods: the YOLOv3 best model; SR + NDVI-PLS; NDVI + Climate-RF; 10VarImp-
RF model (Figure 10). The YOLOv3 distribution map reflects the actual plant density of
the fields, as it was measured by counting the accurate plant numbers inside the UAV
imagery. Visually, the YOLOv3 model demonstrated the spatial variability of plant density
in the test fields with a relatively wide variation in the within-field patterns, especially in
Fields 2 and 8. From this distribution map, it was also possible to highlight field-specific
Remote Sens. 2021,13, 2548 14 of 20
plant density. Overall, the distribution maps based on the listed regression models could
reflect the general pattern of the plant density spatial variability for both within-field
and field-specific patterns. The distribution maps derived from NDVI + Climate-RF and
10VarImp-RF showed almost similar results, with minor differences in a few locations due
to the higher sensitivity for small plant density in the 10VarImp-RF map, as shown in Fields
2 and 4 (Figure 10).
Figure 10.
Spatial distribution of plant density in test fields as the result of the (
a
) YOLOv3 best model; (
b
) SR + NDVI-PLS;
(
c
) NDVI + Climate-RF; (
d
) 10VarImp-RF. The resolution of the distribution maps was 3
×
3 m per pixel to match the spatial
resolution of the PlanetScope imagery.
For further analysis of the comparison between actual and estimated spatial dis-
tribution maps, residual maps were created (Figure 11). In general, the residual maps
resemble the spatial distribution of the actual plant density derived from the YOLOv3
model
(Figure 10a
), with some highlighted features on the overestimated and underesti-
mated pattern from the estimated plant density values. According to the residual map
(Figure 11), the spatial patterns showed similar tendencies, although there were differences
in degrees across the field. In Field 3, all regression models showed underestimated pat-
terns across the fields. On the other hand, in Field 9, almost two-thirds of the area of the
field had a tendency of overestimation, while small areas in the southeast of the field had a
tendency to underestimate. In Field 8, the most contrasting differences between the PLS
model and RF models was that the underestimation pattern was obvious in SR + NDVI-
PLS model. The field-specific RMSE values showed that the accuracy of the models was
different from field to field, as the RMSE values ranged between 1.38 and
3.06 plant m−2
(Table 4).
Remote Sens. 2021,13, 2548 15 of 20
Figure 11.
Residual maps for (
a
) SR + NDVI-PLS; (
b
) NDVI + Climate-RF; and (
c
) 10VarImp-RF
models compared to actual plant density data derived from YOLOv3 model.
Table 4.
RMSE values for individual fields using three different regression model (SR + NDVI-PLS;
NDVI + Climate-RF; 10VarImp-RF).
Test Field
RMSE (plant m−2)
SR + NDVI-PLS NDVI + Climate-RF 10VarImp-RF
Field 2 1.60 1.38 1.49
Field 3 2.46 2.43 2.28
Field 8 3.06 1.90 1.82
Field 9 1.49 1.39 1.38
Field 11 1.84 1.93 1.74
The best models for each field are marked in bold.
4. Discussion
4.1. Quality of Measured Actual Plant Density Using YOLOv3 Model
In the YOLOv3 model process, confidence threshold values were tuned to con-
struct the most accurate model. The developed YOLOv3 model in this study’s imagery
was capable of measuring soybean plant density accurately, as the RMSE was less than
1.0 plants m
−2(Figure 5)
. This result is in agreement with a previous study that quantified
cotton plant density using UAV imagery and a YOLOv3 model with an RMSE between
0.50 and 1.14 plants m
−2
[
17
]. Given that the detected plant density varied from 0 to
16.11 plants m−2
(Table S2), the detection accuracy of the model was considered to be
adequate for representing the actual plant density spatial variance at the emergence in
fields (Figure 10).
4.2. Factors Affecting the Accuracy of the Regression Models
Our results indicate that soybean plant density can be estimated using PlanetScope
imagery and climate data with acceptable accuracy. Overall, RF regression models outper-
Remote Sens. 2021,13, 2548 16 of 20
formed PLS regression models (Table 3). Random forest has been reported as a superior
regression model to PLS regression [
32
,
35
,
36
], which is consistent with our results. As
indicated by the r
2
and RMSE values in the RF models, the NDVI + Climate-RF and SR
+ NDVI were likely to have the best performance. The model performance significantly
decreased when predicting the test data set as compared to training data set (Table 3). Data
distribution differences between each observation field used in the training and test data set
might have caused the different output accuracy of the models. In our data sets, each field
had a unique data distribution, from low to high values of plant density, and the majority of
the field had a low variance. Thus, data variance between the training and test fields might
have become unbalanced. The details about descriptive statistics for each observation field
is presented in Table S2. Completely random data split might be a solution to improve
model performance. However, completely random data split might not be the appropriate
way in our case, because we must examine not only the overall prediction accuracy but
also the effect of observation year and within-field prediction accuracy.
The different predictor combinations in the regression model development affected
the accuracy of the estimation. The NDVI data used in the regression models might lead to
underestimated plant densities in high population values. Previous studies [
55
,
56
] reported
that there were underestimated trends in estimating biomass using NDVI but only seen
in high values of biomass. The NDVI had limitations in losing the sensitivity of the plant
canopy when the leaf area index was greater than 3 m
2
m
−2
[
57
], which corresponds to a
high plant density. According to Mutanga and Skidmore [
58
], this phenomenon is called
NDVI saturation, which subsequently contributed to a reduced accuracy in estimating
plant-related variables. Concerning another predictor, climate variables also contributed to
the inconsistent output of the regression model, especially in PLS analysis (Figure 6d–f).
This inconsistency might be due to the other environmental or edaphic factors that we
did not consider in our models, even though the same pattern did not appear on the RF
models, possibly due to the better capability of non-linear relationships.
4.3. Benefit of Variable Importance of Random Forest
In this study, the variable importance in RF analysis was used to determine important
predictor variables for developing a better estimation model and for improving prediction
accuracy. This method has been used to determine the important variable of RF regression
in predicting plant density and vegetation biomass using vegetation indices and multi-
spectral instruments [
22
,
59
,
60
]. The newly developed model based on this method, the
10VarImp-RF model, showed a better prediction value (r
2
0.68 and RMSE 1.72 plants m
−2
)
than the other regression models (Figure 9). The accuracy of the 10VarImp-RF model was
more robust compared to a previous study by Randelovi´c et al. [
22
], who also predicted
soybean plant density using RF regression treating multiple vegetation indices derived
from an RGB UAV imagery as explanatory variables (RMSE: 3.91–7.47 plants m
−2
). Thus,
the 10VarImp-RF model result may indicate that the selection of predictor variables based
on variable importance would be an effective approach. Although the variable selection
was reported to generate some bias in the classification task of RF, the potential of causing
biased results in regression tasks has not been discussed [
61
]. The results demonstrated that
variable selection might also be an essential process in enhancing the prediction accuracy
of the RF model for regression tasks.
The variable importance of the RF regression model indicated that the NIR bands at 30
and 40 DAS were the first and fifth most important variables, respectively
(Figure 8)
. Near-
infrared reflectance is sensitive to changes in vegetation structure and leaf area index [
29
],
which was also influential in predicting plant density. The normalized difference vegetation
index at 20, 30, and 40 DAS was also within the ten most important variables. Overall,
PlanetScope reflectance and NDVI values from the later growth stage that were close to
flowering time, which was approximately 30–40 DAS, played relatively important roles in
predicting plant density compared to the early growing stage. Red, green, and blue bands
did not appear in the fifth most important variables.
Remote Sens. 2021,13, 2548 17 of 20
The variable importance of RF regression further indicated that precipitation before
sowing dates affected the plant density of soybean, probably because water availability
is the main factor affecting the vegetation growth of plants [
30
]. Rainfall events could
provide favorable conditions for both seedling emergence and subsequent leaf expansion.
On the other hand, excessive soil moisture and submergence due to the heavy rain is
reported to result in low emergence rate of seedling [
5
] and to retard leaf expansion in the
early vegetative stage [
31
]. Therefore, rainfall data may have nonlinear effects on either
leaf area or plant density. The significant errors in the PLS regression models for Field 9
(Figure 6d–f) also indicate the importance of nonlinear relationships between precipitation
and plant density, because PLS regression is theoretically based on a linear assumption
between the variables. Furthermore, a suitable temperature in the early days of emergence
is also needed for seedlings to the emergence and represents the importance of cumulative
temperature at 10 DAS in the RF model. High temperatures and low precipitation rates
after sowing could promote drought, which could also decrease or delay emergence and
plant growth [
62
]. The soybean growth rate in the juvenile stage after emergence responds
strongly to temperature and water stress conditions [
63
]. Thus, climate data might have
contributed to increasing the RF model’s accuracy (Table 3). However, note that climate
data had a 1 km
2
spatial resolution, resulting in almost regionally identical values across
fields; thus, it could not contribute to increasing the prediction accuracy in terms of within-
field spatial variability of plant density. To improve the model’s capability in the future, we
should further consider including field microclimate data, including soil moisture content
and temperature, by using an in situ measurement apparatus or synthetic-aperture radar.
4.4. Plant Density Distribution Map and Future Development
The plant density distribution map can provide a better understanding of identify-
ing areas with low or high plant density dependencies for better management practices.
The distribution map derived from the YOLOv3 model (Figure 10a) clearly shows the
within-field and between-field patterns of plant density spatial variability. However, the
distribution maps derived from regression models could not always clearly evaluate the
within-field spatial variability of soybean plant density, although they might provide good
information for identifying field-specific patterns. The spatial trends in prediction residuals
(Figure 11) were not entirely at random, because each model shows similar tendencies
in the same places across the fields. Other factors, namely, edaphic factors might have
contributed to the spatial patterns, since it could affect within-field variability in individual
aboveground biomass, leaf area index, and canopy structure, thus decreasing the prediction
accuracy derived from the regression models. To improve the within-field spatial prediction
accuracy, the edaphic factors affecting plant density should be quantified and included as
predictors. As noted above, the effect of field microclimate data on the prediction accuracy
should also be quantified in further study.
5. Conclusions
This study demonstrates that the satellite-based RF regression model successfully
identified field-specific plant density. First, UAV imagery data processed using the YOLOv3
object detection model can be used to accurately measure the soybean plant density with
an RMSE value of 0.96 plants m
−2
. The area coverage for the measurement of plant density
was extended by utilizing PlanetScope imagery and climate data, which have a wider range
than UAV imagery. The regression analysis using PLS and RF was capable of predicting
the plant density of test fields with RMSE values ranging from 1.78 to 3.67 plant m
−2
. The
selection of predictor variables based on the variable importance feature in RF analysis
significantly improved the prediction accuracy with an RMSE value of 1.72 plant m
−2
(10VarImp-RF model). The satellite-based prediction model might be able to provide
farmers with useful information about field-specific variability in plant density. However,
there might be a room to improve the prediction accuracy for explaining within-field
variability in plant density because the plant density was likely to be influenced by edaphic
Remote Sens. 2021,13, 2548 18 of 20
factors that could not be quantified in this study. To the best of our knowledge, this is the
first case study establishing satellite-based estimation model for soybean plant density. The
proposed method in this study is expected to be adapted for other locations and different
crops by arranging a suitable training process. Further research is needed to examine the
potential uses of predicted plant density maps by analyzing the effects of edaphic factors
and agronomic practices.
Supplementary Materials:
The following are available online at https://www.mdpi.com/article/
10.3390/rs13132548/s1, Table S1: Comparison of the output accuracy of the YOLOv3 models with
different confidence threshold values, Table S2: Descriptive statistics of the actual plant density
data derived from YOLOv3 model for the observation fields, Table S3: Descriptive statistics of
the estimated plant density data derived from three regression models (SR + NDVI-PLS, NDVI +
Climate-RF, 10VarImp-RF) for the test fields.
Author Contributions:
Conceptualization, L.N.H., T.M. and T.S.T.T.; methodology, L.N.H., T.W. and
T.S.T.T.; software, L.N.H., T.W. and T.S.T.T.; validation, L.N.H. and T.S.T.T.; formal analysis, L.N.H.;
investigation, L.N.H. and T.S.T.T.; resources, T.M. and T.S.T.T.; data curation, L.N.H. and T.S.T.T.;
writing—original draft preparation, L.N.H.; writing—review and editing, T.M. and T.S.T.T.; visual-
ization, L.N.H.; supervision, T.M. and T.S.T.T.; project administration, T.S.T.T.; funding acquisition,
T.S.T.T. All authors have read and agreed to the published version of the manuscript.
Funding:
This research was funded by JSPS (Japan Society for the Promotion of Science) KAKENHI
Early-Career Scientists Grant 18K14452, The OGAWA Science and Technology Foundation Research
Grant, and MAFF (Ministry of Agriculture, Forestry and Fisheries, Japan) Commissioned Project
Study JP J008719.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement:
The data presented in this study are available within the manuscript
and in the Supplementary Materials.
Acknowledgments:
The authors wish to thank the farming companies ‘Fukue-eino’ and ‘Kamigiri-
eino’ for allowing the survey of their fields. The first author also acknowledges the Ministry of
Education, Culture, Sports, Science, and Technology (MEXT) for providing master’s student scholar-
ship under the Japanese Government MEXT scholarship program.
Conflicts of Interest: The authors declare no conflict of interest.
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