INTELLIGENT DISEASE DETECTION SYSTEM FOR EARLY
BLIGHT OF TOMATO USING FOLDSCOPE: A PILOT STUDY
P. Maheswari
School of Mechanical Engineering School of Mechanical Engineering
SASTRA Deemed University SASTRA Deemed University
Thanjavur, India Thanjavur, India
maheswari@sastra.ac.in raja_sastra@yahoo.com
Abstract— Early disease identification plays an inevitable role
in modern agricultural fields to mitigate huge production losses.
This paper presents a method to identify the pathogen of
Alternaria solani, causing early blight fungal disease in tomato
leaves, using foldscope and machine learning algorithms.
Foldscope is a paper microscope invented by Manu Prakash and
his team. It is the remedy for bulky and expensive conventional
microscope. The foldscope can be attached with high resolution
mobile phone for obtaining magnified images. The images of
Alternaria solani were captured using the above mentioned set
up. Then the captured images were classified using various
machine learning algorithms. The quadratic Support Vector
Machine (SVM) classifier shows the highest classification
accuracy of 89% in prediction phase when compared to other
machine learning algorithms.
Keywords— Agriculture, foldscope, early blight disease,
Alternaria solani, machine learning algorithms, tomato crop
I. INTRODUCTION
Agriculture is the dominant sector in determining the
economic status in vast majority of the countries. The
production of crops is affected every year due to the intrusion
of pathogens, changing climatic conditions, etc. Among the
cultivated crop, tomato (Solanum lycopersicum) which is a
type of horticultural crop is one of the customary vegetable
grown all over the world. Tomato has more demand, in
worldwide due to its nutritional values. Hence, there is a need
for higher production to fulfil the consumers. Like other
crops, tomato production is also hugely affected due to
various parasitic microorganisms such as fungal, bacterial,
viral, etc., and changing environmental conditions [1].
Hence, early stage identification of disease secure the crops
and increases the yield significantly.
An integrated system that uses several methodologies (to
accumulate different data) and effectively analyse it to
increase the production in a cost effective manner is precision
agriculture [2]. Precision agriculture with image processing
and machine learning algorithms finds immense applications
in identifying the diseases on crops at its early stage [3]. The
main idea of machine learning is that it focuses on the given
input data by its own without explicit programming and
emphasize the performance of given tasks. Supervised and
unsupervised learning are the two important categories of
machine learning algorithms. In supervised learning, input
and desired output data are provided. Based on that, the
prediction is made on future data. In unsupervised learning,
only the input data are provided and algorithm predicts the
future data without any guided information. Some of the
supervised and unsupervised learning algorithms are: linear
regression, K-Nearest Neighbours (KNN), Linear
Discriminant Analysis (LDA), Artificial Neural Networks
Funding Agency: Department of Biotechnology-Government of India (Grant
No. BT/IN/Indo-US/Foldscope/39/2015)
XXX-X-XXXX-XXXX-X/XX/$XX.00 ©20XX IEEE
P. Raja N.M. Ghangaonkar
Department of Botany
Chandamal Tarachand Bora College
Shirur, Pune, India
ctborainfo68@gmail.com
(ANN), SVM, decision trees, clustering, Principal Component
Analysis (PCA) and random forests which are used in many
applications based on the requirement [4]. The four supervised
learning algorithms used in the proposed work are LDA,
KNN, linear SVM and quadratic SVM. LDA learning
algorithm is used for dimension reduction and classification
based on conventional multivariate technique. KNN is a non-
parametric as well as supervised learning algorithm used for
classification and regression [4, 5]. Image classification using
SVM provides more robustness, accuracy and effectiveness
even for the smaller set of training samples. SVMs are binary
classifiers and it can also be adapted to multiclass
classification task. [5, 6].
A. Early blight of tomato
Early blight is one of the fungal diseases which affects the
tomato plant leaves, fruit and stem. Among the common
fungal diseases, early blight is most dominant, serious and
damaging disease. The crop production is heavily affected by
the early blight disease, as they cause premature defoliation
and results in heavy losses in yield by decreasing quality and
quantity of the fruit. The symptoms of early blight on tomato
leaves are, 1. Small dark spots enlarged into circular lesions
consisting of concentric rings and 2. Leaves appear as older
foliage [7]. High rainfall, overhead irrigation, crowded
plantation, dews and extended period of leaf wetness are the
appreciative conditions for disease development [8]. Fig.1
shows the images of healthy and early blight disease of tomato
leaf.
b. Early blight disease of
a. Healthy tomato leaf
tomato leaf
Fig.1. Healthy and diseased tomato leaves
The prime causal agent of early blight is a fungus,
Alternaria solani. Fig.2 shows the morphology of Alternaria
solani causing early blight in tomato leaves.
a. Multiple Alternaria solani b. Single Alternaria solani
pathogens pathogen
Fig.2. Images of Alternaria solani captured using foldscope
 Alternaria solani reproduces asexually by conidia.
Morphologically, these conidia are bell-shaped, having
horizontal and vertical septation [7, 8].
B. Foldscope – A paper microscope
A new low-cost tool that explores the biological and non-
biological science, is foldscope, which is a paper microscope.
The biological samples (such as fungi, bacteria, etc) along
with non-biological samples (for eg. particulates detrimental
to air quality) can be visualized using foldscope. It is portable
as well as water-proof when compared to conventional
microscope [9]. The assembly of foldscope is explained in
detail in the link [10]. The assembled foldscope (with various
parts) is shown in Fig.3.
Fig.3. Assembled foldscope
A foldscope kit consists of a punched sheet of cardstock, a
spherical glass lens, three squared magnetic couplers, a LED
and a diffuser panel, along with a watch battery that powers
the LED. At present, the lens used in the foldscope are having
the magnification of 140X and resolution of 2 microns.
Foldscope weighs just 8 grams, as a result, it can be easily
attached with the mobile phone to obtain images for
processing [11]. The foldscope attached with the mobile
phone is shown in Fig.4.
Fig.4. Foldscope attached with mobile phone
C. Feature extraction from texture
Texture is defined as the local intensity values are
arranged spatially in the given image which has the
correlation within the areas of visual scene corresponding to
surface regions. Repetition, directionality and complexity are
the three describing properties of texture. Texture manifests
some sort of periodicity of basic patterns. Gray Level Co-
occurrence Matrix (GLCM) is used for feature extraction as
it describes better texture details present in an image. The
textural descriptors such as contrast, energy, correlation and
homogeneity are the four important features that relates the
properties of texture of a given image exactly. Contrast
feature is measured to find the local variations in the GLCM
matrix. Energy estimates the summed values of squared
elements in the GLCM. Between the specified pixel pairs, the
correlation measures the occurrence of joint probability in the
GLCM. The closeness of the distribution of elements is
measured using homogeneity feature [12]. The four textural
descriptors and their corresponding formulae are given in
Table I.
TABLE I. TEXTURE FEATURES AND THEIR FORMULAE
Features Formulae
 i  j pi, j 
2
Contrast, I con
i, j
 pi, j 
2
Energy, Ie
i, j
i i  j   j pi, j 
Correlation, I corr 
i, j  i j
Homogeneity,
pi, j 
I homo 
i, j 1  i  j
where pi, j  is the probability of occurrence of pixel i
with respect to pixel j in an image. i and  j are the mean
values of ith and j th pixels and  i and  j are the
standard deviation of i and j
th th
pixels, respectively.
D. Machine learning algorithms
Image classification using machine learning algorithms is
one of the major area of focus in precision agriculture.
Machine learning is a data driven approach which learns
based on the given input data and it is the subfield of artificial
intelligence [13]. The four machine learning algorithms used
in this proposed work are briefly described below:
The machine learning algorithm, namely LDA is mostly
used for regression and classification problems. In this
method, the sample mean and covariance matrices are
computed from different groups of the training samples. In
LDA, the Fisher discriminant criteria is used and defined as
the ratio of the variance between classes to the variance
within classes. The ratio should be maximum for optimal
solution [14]. Among all the machine learning algorithms, the
simplest one is KNN. In KNN, object classification into a
particular class is performed based on its neighboring pixel
values [15].
One of the popular supervised learning algorithms is
SVM. Using kernel function in SVM, the training data is
projected nonlinearly in the input space to the property space
of higher dimensionality. Then the results are classified using
SVM classifier. Hyper-planes are constructed in SVM
classification which are used to separate the class labels of
different cases. Both regression and classification tasks are
supported by SVM along with multiple categorical and
continuous variables can be handled [16].
In linear SVM, the hyper-planes can be selected, so that
there are no points between two classes of data. Then the
effort can be performed to maximize the distance. In feature
space, there are number of hyper-planes, and one has to be
chosen which maximize the distance between datasets is
called an optimal separating hyper-plane. In quadratic SVM,
Lagrangian multiplier is used to obtain the optimal separating
hyper-plane with maximum margin [17].
Various research work has been done using image
processing implementing machine learning algorithms to
identify the diseases in tomato leaves based on the external
appearance of the leaves [18, 19]. But this is the first work
that detects the early blight fungal disease in tomato leaves
based on the pathogen identification using paper
microscope (i.e, foldscope) and machine learning
algorithms. The captured images are classified using the
above four machine learning algorithms and the
comparison by the measure of accuracy has also been
performed.
The paper is organized as follows: In section II, the
proposed method is described and section III presents the
simulation results of the machine learning algorithms. The
conclusion and future direction are described in section IV.
II. PROPOSED METHOD
In this work, the pathogen which causes early blight in
tomato leaves is identified using foldscope and machine
learning algorithms. The functional blocks of the proposed
system is shown in Fig.5.
First, the infected tomato leaves are collected from the
agricultural field. Then it undergoes proper staining
procedure. After that, the specimen slide is inserted into the
foldscope coupled with mobile phone and the pathogen is
captured. The captured images are given to the above
described learning algorithms for classification and the
performance is measured. The steps of the proposed system
are discussed in the following sections.
Input: Infected tomato
leaf Capturing of pathogen image
using foldscope with mobile
phone
Label
Training Feature
images Extraction
Training Phase
Fig.5. Functional blocks of proposed method
A. Infected leaf specimen
The infected tomato leaves from the agricultural farm are
collected. The portions having the lesion (dark spot
surrounded by concentric rings) is cut into fine bits and
staining procedure is done on the nano pieces of leaves. These
nano pieces were inoculated on the Potato Dextrose Agar
(PDA) nutrient medium aseptically. It is incubated at a
temperature of 27°C, for 10 days. The formed colonies were
analyzed by preparing slides. This fungal culture is made pure
and maintained on the PDA slants. The prepared specimen
slide is inserted into the foldscope for observation.
B. Capturing of pathogen images using foldscope coupled
with mobile phone
The specimen slide is inserted into the foldscope attached
with high-resolution mobile phone. The infected tomato leaf
specimen is visualized by adjusting the sample stage and
panning guide of foldscope. While focusing the leaf specimen
by adjusting the focus ramp in the foldscope and zooming of
mobile camera, the presence of the pathogen is identified and
captured on the mobile.
C. Training phase
The training dataset consists of 100 images in which 60
images are typical Alternaria solani pathogen images, and the
remaining 40 images are other pathogen images (non-
Alternaria solani) taken by foldscope. For non-Alternaria
solani case, Septoria lycopersici images are taken. These
images are labeled corresponding to its category. The textural
descriptors such as I con , I e , I corr and I hom o are extracted
from these images using GLCM.
Then the extracted features and their corresponding labels
are tabulated which is the input table to the learning
algorithms for constructing the model using classification
learner in MATLAB (R2017a).
Test image
Feature Extraction
Prediction phase
Trained Classifier
Learning
Algorithms model
(LDA, KNN,
linear SVM
and quadratic
SVM)
Output Label
Output
Pathogen : Alternaria Solani
Disease : Early Blight
 The parameters of learning algorithms are defined as
follows:
m – number of observations = 100 images in the
proposed method
For this m observations, the training set T is defined as
follows:

T  x1 , y1,l , x2 , y 2,l ,........, x j , y j ,l 

  
(1)

where x j is the d dimensional keywords or feature
vectors which is defined as:

x j  {x1 ,........., xd } , d= 4 in the proposed work,
which are I con , I e , I corr and I hom o .
y j ,l is the class labels. In the proposed work, two classes
of labels are used which is defined as:
y j ,l   1,1. If y j ,l is +1, it classifies the pathogen
as Alternaria solani and if y j ,l is -1, it classifies the pathogen
as non-Alternaria solani.
These are the parameters which are the input to the four
learning algorithms. Using these parameters, the trained
model is developed.
Fig.6. Flow chart for the learning algorithms
D. Prediction phase
In the prediction phase, 40 test images were taken to III. SIMULATION RESULTS
predict the class of the each image using the already Computational experiments are carried out to show the
constructed model implementing the above four learning efficacy of the proposed method. The experiments are
algorithms. In these 40 images, 25 images are Alternaria executed on windows 10 processor with an Intel® Core™ i5-
solani and the remaining 15 images are non-Alternaria 6200U laptop with 8GB RAM and 2.4GHz speed. All the
solani. programs are written and compiled on MATLAB (R2017a)
version.
The test images were captured using foldscope attached
with the mobile phone. Feature extraction is done on these The captured images of pathogen using foldscope are
images. These features are tabulated (i.e, each image transferred to the MATLAB (R2017a) workspace.
comprising of contrast, energy, correlation and homogeneity) Preprocessing such as greyscale conversion is done on these
and the table is given to the trained classifier model to predict images, followed by feature extraction. The textural features
the class of pathogen. as described in Table I are extracted from the test pathogen
images. The values of textural descriptors for one of the
E. Classification of test pathogen images example test image is tabulated in Table II.
The trained classifier using LDA, KNN, linear SVM and TABLE II. FEATURES EXTRACTED FROM THE EXAMPLE INPUT TEST IMAGE
quadratic SVM are used to map feature vectors into a higher AND ITS VALUES
dimensional feature space and then separating two classes Texture descriptors Values
based on the GLCM features. The classifier highlights the Contrast,I con 0.040013712
pixels based on the GLCM features which helps to make the
boundaries in an image. The classifier classifies the pathogen Energy, I e
0.289466882
images with the trained model and it predicts the label (i.e, Correlation, I corr
Alternaria solani or non-Alternaria solani). The flow of the 0.98525872
learning algorithms used in the proposed system is shown in Homogeneity, I homo 0.979993311
Fig. 6. The flow of the learning algorithm is described as
follows:
Based on these values (for each test image), the trained
The dataset of training images are initially labelled as one
classifier of four machine learning algorithms predict the
of the class as Alternaria solani or non-Alternaria solani.
label. These descriptors are calculated for the 40 test images
Features extraction is done on these training images. The
in the prediction phase. Then a table is formulated from the
learning parameters such as predictors (textural features) and
obtained feature values of all the 40 images. This table is
responses (two classes) are defined and the training process
given as an input to the already trained classifier model which
is started using four learning algorithms. Then 5-fold cross
predicts the pathogen images along with the specific disease
validation process is applied and the trained model is
types.
obtained. This model is used to predict the new test images in
the prediction phase.
A. Prediction Results Under the ROC Curve (AUC) is 0.97 for the quadratic SVM
The test pathogen images are predicted by all four prediction. The AUC implies the collection of performance
classifier models. They predict the label based on the textural measure across all possible classification thresholds. The
descriptors values. The accuracy given by quadratic SVM in normal range of AUC lies between 0 and 1. The predicted
prediction phase is 89%. Alternaria solani pathogen image from the test images is
shown in Fig. 10 and Fig. 11.
The scatter plot of training dataset images of two
pathogen classes for quadratic SVM is shown in Fig.7. In this
plot, the blue color dots corresponds to the Alternaria solani
pathogen and red color dots scattered are the non-Alternaria
solani. The confusion matrix for the trained model
corresponding to quadratic SVM is shown in Fig.8. The
confusion matrix is the performance measure in which the
number of correct predictions and incorrect predictions are
outlined with count values and marked by each class.

Fig.9. ROC curve for the quadratic SVM trained model

Fig.7. Scatter plot for the quadratic SVM trained model

Prediction results
Pathogen class : Alternaria solani
Disease type : Early blight
Prediction Accuracy : 89% by quadratic SVM

Fig.10. Predicted test result of Alternaria solani image using quadratic SVM

Fig.8. Confusion matrix for the quadratic SVM trained model

From the above confusion matrix, it is inferred that the

trained model by quadratic SVM produced the correct
prediction of Alternaria solani pathogen by the count value
of 58 and incorrect prediction by the count value of 2. In the Prediction results
case of non-Alternaria solani, correct prediction is 33 and Pathogen class : Alternaria solani
incorrect prediction is 7. Fig.9 shows the Receiver Operating Disease type : Early blight
Prediction Accuracy : 85.4% by linear SVM
Characteristic (ROC) curve of the quadratic SVM trained
model. It is plotted between true positive rate and false
Fig.11. Predicted test result of Alternaria solani image using linear SVM
positive rate at different threshold settings. The value of Area
B. Performance evaluation of the proposed method BT/IN/Indo-US/Foldscope/39/2015). The authors would like
One of the metric is used to evaluate the classification to acknowledge Dr. Durga Prasad Awasthi, Assistant
models is accuracy. It is defined as the ratio between number Professor, Department of Plant Pathology, College of
Agriculture, Tripura, for his support.
of correct predictions and total number of predictions. The
accuracy values in percentage for various machine learning
algorithms in both phases (i.e, training and prediction phase)
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