Plant Disease Detection using Hyperspectral Imaging
Peyman Moghadam, Daniel Ward, Ethan Goan, Srimal Jayawardena, Pavan Sikka, Emili Hernandez
Abstract— Precision agriculture has enabled significant
progress in improving yield outcomes for farmers. Recent
progress in sensing and perception promises to further enhance
the use of precision agriculture by allowing the detection of
plant diseases and pests. When coupled with robotics methods
for spatial localisation, early detection of plant diseases will al-
low farmers to respond in a timely and localised manner to dis-
ease outbreaks and limit crop damage. This paper proposes the
use of hyperspectral imaging (VNIR and SWIR) and machine
learning techniques for the detection of the Tomato Spotted
Wilt Virus (TSWV) in capsicum plants. Discriminatory features
are extracted using the full spectrum, a variety of vegetation
indices, and probabilistic topic models. These features are used
to train classifiers for discriminating between leaves obtained
from healthy and inoculated plants. The results show excellent
discrimination based on the full spectrum and comparable
results based on data-driven probabilistic topic models and
the domain vegetation indices. Additionally our results show
increasing classification performance as the dimensionality of
the features increase.
I. INTRODUCTION
Plant diseases are responsible for major economic losses in
the agricultural industry worldwide. In precision agriculture,
monitoring plant health and detecting pathogens are essential
to reduce disease spread and facilitate effective management
practices [1]. Automatic detection of plant diseases and other
crop stresses could be a valuable source of information for
improving crop management strategies and disease control
measures to prevent the development and the spread of
diseases.
The automatic plant disease detection methods can be
categorised into two main groups, direct and indirect (proxy)
methods. Molecular and serological methods are examples
of direct detection and favor high-throughput analysis of a
large number of samples. These methods provide accurate
identification of the disease-pathogen link by directly detect-
ing the disease causing pathogens [2]. Common pathogens
include bacteria, fungi and viruses. These methods require
at least couple days for sample harvest, processing, and
analysis. Indirect (proxy) methods identify plant diseases
through various parameters such as morphological change,
temperature change, transpiration rate change and volatile
organic compounds released by infected plants [2]. These
methods are mainly based on optical imaging techniques.
The optical imaging sensors provide detailed information
based on different electromagnetic spectra and thus, enable
The authors are with the Autonomous Systems, Cyber-Physical
Systems, DATA61, CSIRO, Brisbane, QLD 4069, Australia. E-mails:
firstname.lastname@data61.csiro.au Correspondence
should be addressed to peyman.moghadam@data61.csiro.au
978-1-5386-2839-3/17/$31.00 ©2017 IEEE
(a) (b)
Fig. 1: (a) An example of a hypercube. (b) Spectral re-
flectance of a healthy plant.
prediction of the plant health [3]. Thermography, fluores-
cence and hyperspectral imaging are among the most used
indirect methods for plant disease detection [4].
Hyperspectral imaging has been successfully applied for
plant disease characterisation, detection, modelling and clas-
sification [3]. Hyperspectral imaging measures reflected light
from plants in hundreds of narrow bands across the electro-
magnetic spectrum as a hypercube (Figure 1a). A typical
spectral reflectance of a healthy plant is shown in Figure 1b.
A plant’s interaction with different parts of the electromag-
netic spectrum depends on leaf biochemical compounds and
leaf anatomical structure. Healthy plants typically absorb
light in the visible range (VIS 400-700 𝑛𝑚) due to leaf
photosynthesis pigments. The amount of light scattered in
the near-infrared range (NIR 700-1000 𝑛𝑚) is strongly
sensitive to leaf cell structure. Dominant factors influencing
leaf reflectance in short-wave infrared (SWIR 1000-2500
𝑛𝑚) are leaf water and chemical contents.
When plants undergo various stresses, they react through
biophysical and biochemical variations such as degradation
of the leaf chlorophyll content or changes in leaf cell struc-
tures. Hyperspectral imaging has the advantage of detecting
these subtle changes in spectral reflectance of plants. A range
of machine learning methods have been developed based on
these spectral reflectance values for automatic classification
of plant diseases. The process usually involves extracting
features from spectral reflectance, learning a classifier model
from diseased and healthy plant images and finally apply-
ing the model to new data for the prediction of diseased
leaves [5], [6]. A common feature extraction approach is to
calculate spectral Vegetation Indices (VIs) related to specific
physiological parameters. However, these VIs are generally
not designed to discriminate between healthy and diseased
plants [7].
 In this paper, we present an automatic method to detect
plant disease using hyperspectral imaging (VNIR and SWIR)
and machine learning techniques. We evaluate the utility
of three types of features based on the hypercube - the
full spectrum, spectral Vegetation Indices (VIs) and features
generated using data driven probabilistic topic models. In
contrast to previous work [8] we propose to use a data
driven approach to build features and do not make any prior
assumptions about the topics.
The remainder of this paper is organized as follows. Sec-
tion II explains existing hyperspectral imaging and machine
learning techniques applied to plant disease detection. In
Section III we present the hyperspectral imaging system used
in this paper. Section IV explains the pre-processing steps
such as leaf segmentation and grid removal. In section IV
we propose our feature extraction techniques based on leaf
spectral indices, entire spectrum, and probabilistic topic mod-
eling from VNIR and SWIR imaging systems. Section VI
demonstrates the effectiveness of the proposed feature ex-
traction techniques for automatic plant disease classification
in greenhouse experiments. Finally, we conclude our paper
in Section VII and discuss the future directions.
II. RELATED WORK
SVM is a common choice of machine learning algorithm
for detection of plant diseases. Rumpf et al. [5] used a variety
of machine learning algorithms for early detection of plant
diseases based on hyperspectral reflectance. They showed
a SVM trained on spectral VI feature vectors calculated
from a leaf mean of 25 representative spectra to be the best
performing model in disease classification. Similarly, in our
paper, a leaf mean spectra was calculated from all pixels.
Rumpf et al. [5]s choice of VNIR VIs matched those used
in our paper with the addition of the leaf SPAD value, a
measure of chlorophyll content. Rumpf et al. [5] reported
diseased leaf classification accuracy of up to 97% using
K-fold testing. The majority of existing literature in the
field of small scale hyperspectral imaging involves VNIR
technology, furthermore the distribution of vegetation indices
across the reflectance regions strongly favors VNIR [9], [10],
[11].
More recently, Zhu et al. [12] investigated early detection
and classification of inoculated tobacco leaves based on
hyperspectral imaging. They use only a VNIR camera and
generate mean leaf spectra from a ROI rather than the all
pixels, Zhu et al. [12] reported model accuracies from 75-
98.33%. Most notably, 81.67% for an SVM with RBF kernel
and 98.33% for an extreme learning machine. Unlike this
paper, they used effective wavelengths (EWs) as features
to train all their models. EWs were found by successive
projections algorithm. The majority of literature has extracted
features from the hyperspectral images through approaches
such as PCA [12], VIs [5] and manual wavelength selection
[13].
Probabilistic Topic Modeling [14] is used extensively in
the natural language processing community as an unsuper-
vised learning technique and has been recently extended to
(a) (b)
Fig. 2: (a) Hyperspectral imaging system. (b) Closeup of the
target platform showing a leaf being imaged by the system.
hyperspectral imaging [8]. However, in contrast to previous
work, we do not make any assumptions on the nature of
the topics (healthy vs disease) and use topic modelling to
generate discriminative features for disease detection in a
data driven manner.
III. HYPERSPECTRAL IMAGING SYSTEM
The hyperspectral imaging system (Fig 2) consists of
two push-broom hyperspectral cameras from Headwall -
the VNIR A-series and the SWIR M-series. The VNIR
hyperspectral camera has a spectral range of 400-1000 𝑛𝑚
with 324 spectral bands and a spatial resolution of 1004
pixels. The SWIR hyperspectral camera provides a spectral
range of 900-2500 𝑛𝑚 with 168 spectral bands and a spatial
resolution of 384 pixels. The cameras are attached to a
frame with a linear motion stage whose axis of motion is
perpendicular to the spatial axis of the two cameras. Six 20𝑊
halogen lights are used for illuminating the leaf samples. We
use a thread grid to hold the leaf sample flat against the plate
during imaging. The entire system is controlled from a PC
running the Hyperspec III software from Headwall.
The data acquisition protocol is an important aspect of
experiment design. It was experimentally determined that
while the temperature variation is less than 5% for the
VNIR camera after it was first turned on, there is significant
variation in the SWIR camera which needs about 1 hour to
stabilise after being turned on. Another important aspect of
hyperspectral sensing is the timely collection of dark refer-
ence images which provide an estimate of the noise (i.e., dark
current noise) and white reference images which provide the
spectrum of the incident light. The dark reference is normally
obtained by capturing an image with the lens cap on (0%
reflectance) while the white reference is obtained by imaging
a standard white Teflon target (99.9% reflectance). An auto-
mated system, implementing the considerations above, was
developed for the data acquisition stage of the experiment.
It also guarded the user from errors such as leaving a lens
cap on during white reference and target leaf imaging or
leaving a lens cap off for dark reference imaging. The system
enforced the collection of meta-data and the timely collection
Fig. 3: The dataflow of the hypercube pre-processing steps
used in this paper.
of dark and white reference data (at least every 30 minutes,
configurable).
Once the raw radiance hypercubes were collected they
were calibrated to normalized reflectance hypercubes using
white and dark references images to account for drift of the
light system and thermal variations in hyperspectral imaging
sensors. Then, to improve signal to noise ratio (SNR) the
starting 58 wavelengths in VNIR (below 500 𝑛𝑚) and the
starting 1 wavelength in SWIR (900 𝑛𝑚) were discarded for
further processing in this paper. The Savitzky-Golay filter [8]
was next applied to smooth the reflectance spectrum with 11
supporting points and 2 degree polynominal.
IV. HYPERCUBE PRE-PROCESSING
Figure 3 displays the dataflow of the hypercube pre-
prossesing steps. Initially, a predefined region of interest
(ROI) is extracted from the hypercube. Next, the leaf is
automatically segmented from the background. The grid is
detected within the images and a grid mask is generated.
The final hypercube is generated by applying the relevant
grid mask to each of the leaf segmented images.
A. Leaf Segmentation
No single frequency band or combination of bands was
able to be utilized to segment the leaf from the back-
ground. This was particularly evident in some diseased leaves
where dry/dead leaf spots were commonly miss-classified as
background. Spectral profiles of vegetation exhibit a unique
spectral signature compared to other materials in the image
such as plastics and metals. One could exploit this spectral
signature to segment the leaf from the background.
In this paper, an unsupervised K-means clustering algo-
rithm was applied in the spectral domain to segment the leaf
from the background. Cluster analysis successfully classified
the image spectra into two classes using the significant
spectral profile difference between the vegetation and it’s
surroundings. The spatial location of each classified spectra
was maintained and a 2D leaf mask was generated. Then,
in order to detect the leaf and to identify any misclassified
regions, the contours of the binary mask were detected using
an algorithm proposed by Suzuki et al. [15]. The largest
of the detected contours is assumed to be the leaf, while
smaller contours were removed as misclassified pixels. The
extremities of the largest contours were located and mask
was cropped to this size with a 5% buffer on all dimensions.
(a) (b)
(c) (d)
Fig. 4: Grid removal process (a) Whitened image from SWIR
camera. (b) Centre of output of convolving the matched
filter with the whitened image. (c) Average of matched filter
output and peaks found via the CWT. (d) False colourised
representation of SWIR data with the grid removed.
It was ensured that the region of interest (ROI) cropped from
the VNIR and SWIR masks were of the same shape. Figure 3
shows an example image and the resulting leaf segmentation
mask in the leaf segmentation step of the dataflow.
B. Grid Removal
Whilst use of the grid permits holding the leaf flat and
measuring of reflectance normal to the leaves, it introduces
unwanted artifacts in hypercubes. Despite common place-
ment during the experiment, a small amount of displacement
in each grid line is caused by each individual leaf. This
makes accurate and spatially adaptive grid removal essential
to ensure that spectral measurements used for classification
pertain only to the leaf being scanned. Since the shape and
orientation of the grid remains consistent throughout scans, a
spatial matched filter approach is proposed for detection and
removal of the grid. A matched filter is an optimal filter for
detection of a known signal corrupted with additive white
noise.
For a matched filter approach to be suitable, the data
must be first be whitened. Since the spectral content of
natural images is primarily at low frequencies, a high pass
filter is applied in an effort to flatten the power spectral
density of the image. The high pass filter used is a third
order FIR Butterworth filter. An example of the output of
this filter is shown in Figure 4a. It can be seen that whilst
much of the leaf content has been attenuated, high frequency
components at the edge of the grid are still prominent. With
the whitened image, a spatially matched filter is created.
Given the dimension and orientation of the grid, the matched
filter is approximated by a column that is four pixels wide
and the same height as the image, with all elements equal to
 Algorithm 1: Grid removal algorithm
Input : Hyperspectral hypercubes, Type of camera
Output: Hypercubes with grid removed
function gridRemoval (ℎ𝑦𝑝𝑒𝑟𝑐𝑢𝑏𝑒, 𝑐𝑎𝑚𝑒𝑟𝑎);
// Select band where grid most salient
if camera = VNIR then
2DImage = hypercube[666nm]
else
2DImage = hypercube[1450nm]
end
whitened ← HPF(2DImage)
// Convolve with matched filter
gridLoc2D ← convolve(abs(whitened), matchedFilt)
gridLoc1D ← verticalMean(gridLoc2D)
gridPeaks ← findPeaksCWT(gridLoc1D)
// Use found peaks to mask out grid in
horizontal dimension 𝑥
return hypercube[𝑥 != gridPeaks, 𝑦, 𝜆]
one. This filter is then convolved with the whitened image,
and the absolute value of the output is found as shown in
Figure 4b.
Peaks in the output of the convolution are found as column
shapes in the 2D array. As only the horizontal location
of these peaks is of importance, a vertical Gaussian blur
is applied to smooth each column vertically. The output
from convolution with the spatially matched filter and the
whitened image is then averaged along the vertical axis to
create a 1D array. The peaks in this filtered 1D vector were
used to represent the horizontal position of each grid line.
The location of each grid line is indicated by a peak in
the mean vector found through the matched filter. Figure
4c shows an example of the signal obtained. To find these
peaks, the method proposed by Du et al. [16] which utilises
the Continuous Wavelet Transform (CWT) is employed. The
CWT can be expressed as,
∫ ∞
𝐶(𝑎, 𝑏) = 𝑠(𝑡)𝜓𝑎,𝑏 (𝑡) 𝑑𝑡 (1)
−∞
where 𝑠(𝑡) is a given signal, 𝜓(𝑡) is the mother wavelet, 𝑎 is
the scale and 𝑏 is the translation in the independent variable.
To find peaks, the CWT is applied at a number of different
scales and local maxima at each scale are found. Peaks found
at surrounding scales create a ridge in the coefficient matrix
at a common point of translation. For this application, the
Ricker mother wavelet is used. From the peaks found from
application of the CWT, a mask is created to indicate location
of the grid. A column with a width of nine pixels was
used to illustrate the width of each grid line as shown in
Figure 4d. The grid removal steps are further summarised in
Algorithm 1.
V. FEATURE EXTRACTION
A. Vegetation Indices
Vegetation Indices (VIs) are widely used for extracting
features from the spectral reflectance by combining two or
more wavelengths that are related to biophysical character-
istics of plants. However, most VIs have been developed for
remote sensing, and are not disease specific. As such, using a
single VI for disease discrimination is not feasible. Different
VIs relate to different biophysical plant properties. Steddom
et al. [27] amongst others, investigated the effectiveness of
using multiple VIs for disease discrimination. They found
that differences in betacyanin and carotenoid levels appeared
to be related to the investigated disease and not nitrogen con-
tent [28]. These results indicate the importance of choosing
VIs specific to the application.
Table I displays the vegetation indices which were used
in this paper as features where 𝑅 denotes a particular wave-
length reflectance value. In the VNIR range (400-1000 𝑛𝑚),
vegetation indices are mostly correlated to variation in pho-
tosynthetic pigments. The Normalized Difference Vegetation
Index (NDVI) and Simple ratio (SR) relate to stress, biomass
and leaf area [17], [18]. Structure Insensitive Pigment Index
(SIPI), Modified Chlorophyll Absorption Integral (mCAI)
and both Pigment Specific Simple Ratio (PSSR) indices
relate to chlorophyll concentration [20], [23]. Furthermore,
Anthocyanin Reflectance Index (ARI) provides an index for
anthocyanin [21] and Red Edge Position (REP) relates to
the inflection point of the red edge [22]. Those relevant to
the VNIR region, were selected from results of correlation
and regression analyses between VIs and disease severity by
Mahlein et al. [29]. The VNIR VIs are the same as those
used in a comparable study by Rumpf et al. [5].
In SWIR range (1000-2500 𝑛𝑚), majority of VIs are
related to water content and chemical compounds [30].
The Water Band Index (WBI) relates to leaf water con-
tent [24]. While Cellulose Absorption Index (CAI) provides
an indication of dried plant material [25] and Normalized
Difference Lignin Index (NDLI) and Normalized Difference
Nitrogen Index (NDNI) are normalized difference indexes of
lignin and nitrogen content respectively [26]. In this study,
all VIs for each leaf (sample) were calculated using the mean
spectra of all pixels in that leaf.
B. Full Spectrum
In order to preserve short range dependencies between
spectral wavelengths, the mean reflectance for each wave-
length for all pixels in a leaf were used as features. The
entire spectrum (feature vector length: VNIR: 268, SWIR:
167) was used to allow the models to learn complex re-
lationships between shape of the spectral reflectance rather
than limiting the model to the information within the few
bands of predefined VIs. The length of the feature vector
was dependant on the frequency range of image following
preprocessing.
C. Probabilistic Topic Modeling
In order to utilize the entire hyperspectral spectrum to
build useful features with reduced dimensions for a classifier
that predicts diseased leaves, we generate features based
on a data-driven approach using Probabilistic Topic Mod-
eling [14] which is used extensively in the natural language
 Spectral region Index Equation
𝑅800 −𝑅670
Normalised Difference Vegetation Index [17] 𝑁 𝐷𝑉 𝐼 = 𝑅800 +𝑅670
𝑅800
Simple Ratio [18] 𝑆𝑅 = 𝑅670
Structure Insensitive Pigment Index [19] 𝑆𝐼𝑃 𝐼 = 𝑅 800 −𝑅445
𝑅800 +𝑅680
VNIR Pigments Specific Simple Ratio (a) [20] 𝑃 𝑆𝑆𝑅𝑎 = 𝑅 800
𝑅680
Pigments Specific Simple Ratio (b) [20] 𝑃 𝑆𝑆𝑅𝑏 = 𝑅 800
𝑅635
1 1
Anthocyanin Reflectance Index [21] 𝐴𝑅𝐼 = ( 𝑅500 ) − ( 𝑅700 )
40(𝑅𝑅𝐸 −𝑅700 )
Red Edge Position [22] 𝑅𝐸𝑃 = 700 + (𝑅740 −𝑅700 ) , 𝑅𝑅𝐸 = 𝑅670 +𝑅 2
700

(𝑅545 +𝑅752 ) ∑𝑅752

Modified Chlorophyll Absorption Integral [23] 𝑚𝐶𝐴𝐼 = 2
.(752 − 545) − ( 𝑅545 𝑅 ∗ 1.423)
𝑅970
Water Band Index [24] 𝑊 𝐵𝐼 = 𝑅900
Cellulose Absorption Index [25] 𝐶𝐴𝐼 = 0.5 ∗ (𝑅2000 + 𝑅2200 ) − 𝑅2100
log 𝑅 1 −log 𝑅 1
SWIR Normalized Difference Lignin Index [26] 𝑁 𝐷𝐿𝐼 = 1754
log 𝑅 1
1680
+log 𝑅 1
1754 1680
log 𝑅 1 −log 𝑅 1
Normalized Difference Nitrogen Index [26] 𝑁 𝐷𝑁 𝐼 = log 𝑅
1510
1
1680
+log 𝑅 1
1510 1680

TABLE I: Vegetation indices used as features for VNIR and SWIR (VNIR indices replicated from Rumpf et al. [5]).

processing community. It is an unsupervised learning tech-

nique that models documents as words generated from topics
based on a two step generative process where each word in
a document is chosen by randomly picking a ‘topic’ and
randomly picking a ‘word’ from that topic. To apply topic
modelling to hyperspectral imaging we treat each hypercube
pixel as a document and each wavelength-reflectance pair in
the discretized reflectance spectrum is treated as a word in the
corpus [8]. The wordified hyperspectral data is used to train
a regularized Latent Dirichlet Allocation (LDA) model using
on-line Variational Bayes (VB) inference [8] on hypercube.
Similar to [8], we used 50 quantisation levels for reflectance
and apply a down-sampling factor of five. The trained model
is used to obtain topic proportions for the hyperspectral
pixels of the leaves. Fig. 5: Differences in the distributions of the leaf-wise feature
for control samples (green) vs diseased samples (red) shows
its utility as a discriminative feature. The feature is the ratio
The proportions of topics in each hyperspectral pixel of pixels in each leaf where the topic proportion is greater
can be expected to differ between inoculated and control than a threshold 𝜏 that is computed from the data. The
(healthy) leaves. Therefore the topic proportions should figure shows the feature element 𝑥19 from topic 19. Feature
form a good basis for generating data-driven discriminative elements for other topics show similar characteristics.
features. We build a feature vector 𝑥 ∈ ℝ𝑚 for each leaf
where each element 𝑥𝑖 ∈ 𝑥 contains the ratio of pixels in
the leaf where the proportion of topic 𝑖 is greater than a VI. RESULTS
threshold 𝜏 . The threshold 𝜏 is determined from the data
A. Greenhouse Experiment
by conducting a grid search to select the threshold which
gives the best classification performance on the training data The experiment were carried out in November and De-
with 5-fold cross validation. To illustrate the discriminative cember 2016 in a controlled greenhouse environment with
capability of these features, the distribution of the ratios for relative humidity of 68% (𝜎 = 13.5%) and temperature of
topic 𝑖 = 19 (𝑥19 ) have been compared across diseased and 27.8∘ C (𝜎 = 4.53∘ 𝐶). Capsicum (variety Warlock) were
control leaves in Figure 5. As shown, distributions of the used in this experiment. Plants were watered daily using a
pixel ratios between diseased and control leaves are different, drip irrigation system. 30 plants were inoculated with Tomato
making it a useful feature to discriminate between the two Spotted Wilt Virus (TSWV) when they were 8 weeks old.
classes. We are able to build a feature matrix 𝑋 ∈ ℝ𝑛×𝑚 Disease progression of TSWV was observed for 21 days
with a leaf based feature vector in each row and a label after inoculation. A further 30 plants was not inoculated and
vector 𝑦 ∈ ℝ𝑛 which can be used for supervised learning. served as control of healthy plants for this experiment.

Fig. 6: The joint overall dissimilarity values between control-
inoculated per DAI for VNIR and SWIR hypercubes.
Leaves were harvested from both plants groups (inoculated
and control) from 3 days after inoculation (DAI) till 21 DAI.
Leaves were only harvested from the new growth above the
inoculation node. In this study, a total of 216 leaves (133
inoculated leaves, 103 control leaves) were sampled on six
separate days over 18 days period. Each leaf was assessed
and labeled visually for symptoms by QDAF plant scientists.
Labels consisted of presence or absence of symptoms and
disease severity using 1-5 disease rating scale. First visual
symptoms of TSWV only appeared 10 DAI.
B. Dissimilarity Estimation using Relative Entropy
In order to make inferences from collected hyperspectral
data using any machine learning technique, we first should
measure the dissimilarity between two spectrum distributions
of inoculated and control hypercubes. We use the Kullback-
Leibler (KL) divergence, also called relative entropy, to
estimate the distances between two distributions (inoculated
and control). In this application, we use the control group
to represent the model distribution (𝑄) while the inoculated
group represents the true distribution of data (𝑃 ). The KL-
divergence between these two probability density functions
can be approximated as:
∑ 𝑃𝜆 (𝑖)
𝐷𝜆 (𝑃 ∣∣𝑄) = 𝑃𝜆 (𝑖)𝑙𝑜𝑔 (2)
𝑖
𝑄𝜆 (𝑖)
where 𝐷𝑠 (𝑃 ∣∣𝑄) denotes a dissimilarity measure between
the control group and inoculated group. A superscript in-
dicates that the respective measure is applied only to the
marginal distributions along spectrum 𝜆. The dissimilarity
values obtained for single spectrum must be combined into
a joint overall dissimilarity value as:
∑
𝐷(𝑃 ∣∣𝑄) = ( (𝐷𝜆 (𝑃 ∣∣𝑄))𝑝 )1/𝑝 (3)
𝜆
where 𝑝 = 1 is used in this work.
To evaluate dissimilarity between distributions of inocu-
lated and control hypercubes, we first randomly split the
control group per DAI by half to represent the prior proba-
bility distribution 𝑄. Then, we calculate the KL-divergence
between two marginal distributions, the selected control
leaves (𝑄) and inoculated leaves (𝑃 ) per DAI, along each
spectrum (𝜆) where 𝜆 = 1, ..., 𝑚 and 𝑚 is the number of
spectrum bands for each hyperspectral camera (VNIR and
SWIR). Finally, the dissimilarity values obtained for each
spectrum are combined into a joint overall dissimilarity value
using Equation (3). For comparison, we repeat the procedure
to measure dissimilarity between two control distributions
(50% split) per DAI. Joint overall dissimilarity between two
control distributions (control-control) shows close to zero
values (0.24). This implies that their spectrum distributions
in both SWIR and VNIR hypercubes are similarly distributed
across different days.
Figure 6 illustrates the joint overall dissimilarity values
between control-inoculated per DAI for SWIR and VNIR
hypercubes. Note that the small dissimilarity values from
DAI 3 to DAI 10 between inoculated and control spectrum
distributions in VNIR (Figure 6) are quite consistent with
the ground-truth labels in our experiments where the visual
symptoms of TSWV only appears after DAI 10.
Figure 6 indicates that dissimilarity values between inoc-
ulated and control spectrum distributions in SWIR gradually
increase over time. Except for DAI 7 and 10, where we
were not able to correlate this small reduction in SWIR
overall dissimilarity values to any plant-pathogen biophysical
interaction. This suggests that it might be linked to other
stress factors such as environmental variation during those
days.
Figure 7a and Figure 7b demonstrate which part of the
electromagnetic spectrum is mainly contributing to the joint
overall dissimilarity values. As can be seen, the key discrim-
inative spectrum ranges in VNIR (Figure 7a) are located in
green (520-580 𝑛𝑚, maximum reflectivity of leaf pigments),
red (650-680 𝑛𝑚, maximum chlorophyll absorption), and
red edge (680-720 𝑛𝑚, where changes appear between
reflectivity of stress and healthy leaves). As we expected only
DAI 12 and 21 show strong dissimilarity in these spectrum
ranges. In stressed plants, photosynthesis pigments decline
resulting in a reduction in overall green reflection and an
increase in red reflectance.
The variation in SWIR wavelengths are scattered across
spectrum range (910-2500 𝑛𝑚) and across different DAI. In
SWIR Figure 7b, the KL-divergence variability is primarily
governed by scattering and absorption characteristics of the
leaf structure, biochemical and water content. Pathogenesis
causes variation in leaf cell structure which result in different
light scattering signatures. In addition, loss of water impacts
on biological processes during pathogenesis and this can
influence the spectral reflectance in the SWIR range.
 (a) VNIR
Fig. 7: The KL-divergence between two distributions (inoculated and control group) for each spectrum in (a) VNIR and (b)
SWIR across different DAI.
C. Machine Learning
Table II presents the results of classification between
control and diseased leaves based on three types of feature
sets derived: the full spectrum, spectral Vegetation Indices
(VIs) and data driven features generated using probabilistic
topic models. The full spectrum is the result of a spatial
mean of the leaf and the VIs are derived from this. The
dataset was split 80-20% for training and testing respectively.
Results are reported for the testing set only. All models
were trained and evaluated on identical data. We trained
an SVM with RBF kernel using grid search on 80% train
data. Overall, the full spectrum based models outperformed
both the spectral Vegetation Indices (VIs) and probabilistic
topic modeling for VNIR and SWIR. The performance of
classifiers with the topic modelling based features were better
than the VI based models but lower than the full spectrum
based models. Interestingly, the dimensionality of the three
types of features considered increase in the order of VIs,
topic model based features and full spectrum based features.
Our results indicate that the performance of the classifiers
improve as the dimensionality of the features increases.
In this study, all components of the feature vectors were
equally weighted. Future investigations could further explore
this area and deep learning approaches such as neural net-
works. Mosho et al. [13] used multilayer perceptrons to
classify yellow rust in wheat VNIR leaf spectra and achieved
classification accuracy greater than 99%. Feature weighting
may also play a role in investigating different selections and
combinations of VIs. A similar trend between performance
and feature vector length is seen when VNIR models to
SWIR. The SWIR models have significantly less features
and were out performed by the VNIR models (approximately
10%). The VNIR full spectrum SVM with RBF kernel
achieved the greatest performance on the test set. Most
notably, an F1-score of 0.939 and area under the Receiver
Operator Characteristic (ROC) curve of 0.95.
The best performing model, full spectrum RBF SVM,
(b) SWIR
was 93.6% and 91.5% accurate on VNIR and SWIR images
respectfully. This is higher than the same model used by
Zhu et al. [12] which achieved 81.67% with a full spectrum
feature vector calculated from a ROI. Whether the increased
accuracy can be attributed to differing experimental condi-
tions (capsicum plants and TSWV vs. tobacco and tobacco
mosaic virus) or feature extraction (mean of all spectra vs.
ROI) requires further investigation.
The accuracy of human experts labelling the leaves as
inoculated on last DAI was 70%. This suggests that the
presented models are better than human expert classification
abilities.
VII. C ONCLUSIONS
In this paper, we have presented the results of an early
experiment in the automatic detection of plant disease us-
ing hyperspectral imaging. An experimental trial was run
to detect capsicum plants with the Tomato Spotted Wilt
Virus (TSWV). An automated system was developed to
collect hyperspectral hypercubes of plant leaves in VNIR and
SWIR spectrum ranges at regular intervals after inoculation.
The system was also used to collect associated meta-data
about the plants. The data was then analysed using image
processing and machine learning techniques to demonstrate
effective automatic discrimination of plant leaves. We trained
SVM classifiers on three types of features; vegetation indices,
features based on probabilistic topic modeling and the full
spectrum, on both VNIR and SWIR hypercubes. Our results
showed better than 90% accuracy. It is important to empha-
size that we used the full electromagnetic spectrum including
both the VNIR component (400-1000 𝑛𝑚) and the SWIR
component (900-2500 𝑛𝑚) compared to previous studies
which have mostly relied on the VNIR component only. The
work based on Topic Models is of a preliminary nature and is
very promising. Future work includes exploration of dynamic
topic models to estimate the dynamic nature of pathogen-
plant development over time.
 Spectral Range Model Accuracy
Vegetation Indices 0.830
VNIR Full Spectrum 0.936
Topic Models 0.894
Vegetation Indices 0.787
SWIR Full Spectrum 0.915
Topic Models 0.840
TABLE II: Classification results using an SVM (RBF) with vegetation indicies, full spectrum and probabilistic topic models.
ACKNOWLEDGMENT
This work has been funded by Horticulture Innovation
Australia through project VG15024 and Commonwealth Sci-
entific and Industrial Organization (CSIRO) and in collab-
oration with the Queensland Government’s Department of
Agriculture and Fisheries (QDAF). The authors gratefully
acknowledge valuable feedback from Susanne Heisswolf
through the project. The authors appreciate critical support
provided by QDAF plant scientists Andrew Manners, Denis
Persley, David Carey, Tony Cooke and Mary Firrell for
greenhouse data collection and labeling. Authors also thank
James Brett from the CSIRO.
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