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Identification of Diseases in Rice Plant (Oryza

Sativa) using Back Propagation Artificial Neural
Network
Conference Paper November 2014
DOI: 10.1109/HNICEM.2014.7016248

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7th IEEEInternational Conference Humanoid, Nanotechnology, Information Technology

Communication and Control, Environment and Management (HNICEM)
The Institute of Electrical and Electronics Engineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centro, Puerto Princesa, Palawan, Philippines

Identification of Diseases in Rice Plant (Oryza

Sativa) using Back Propagation Artificial Neural
Network
John William ORILLO#1, Jennifer DELA CRUZ*2, Leobelle AGAPITO#3, Paul Jensen SATIMBRE#4 Ira
VALENZUELA#5
1,2#

Mapua Institute of Technology 2,3,5#Technological University of the Philippines

Manila, Philippines
1

johnwilliamorillo@yahoo.com
jennifer.delacruz@mapua.edu.ph
3
leobelleagapito@gmail.com
4
paulsatimbre@yahoo.com
5
valenzuela.ira12@gmail.com

AbstractIn this study, digital image processing was

incorporated to eliminate the subjectiveness of manual inspection
of diseases in rice plant and accurately identify the three common
diseases to Philippines farmlands: (1) Bacterial leaf blight, (2)
Brown spot, and (3) Rice blast. The image processing section was
built using MATLAB functions and it comprises techniques such
as image enhancement, image segmentation, and feature
extraction, where four features are extracted to analyze the
disease: (1) fraction covered by the disease on the leaf; (2) mean
values for the R, G, and B of the disease; (3) standard deviation
of the R, G, and B of the disease and; (4) mean values of the H, S
and V of the disease. The Backpropagation Neural Network was
used in this project to enhance the accuracy and performance of
the image processing. The database of the network involved 134
images of diseases and 70% of these were used for training the
network, 15% for validation and 15% for testing. After the
processing, the program will give the corresponding strategic
options to consider with the disease detected. Overall, the
program was proven 100% accurate.
IndexTermsRice Plant Diseases, Image Processing, Artificial
Neural Network

I. INTRODUCTION
Agriculture is considered as the primary economic sector
of Philippines, and one of its essential crops is rice or
palay. This country as the worlds 8th top producer and also the
top importer needs to compensate its production to 2% increase
of population annually. Thus, there is a need to increase rice
yield to cope with the countrys growing population.
The task of producing more rice to meet the
increasing demand poses a major challenge. Disease
infection on rice plant are one of the major causes of crop yield
declination. In a study conducted by IRRI [1], it was found
that, on average, farmers lose 37% of their rice yield to pests
and diseases, and that these losses can range between 24% and
41% depending on the production situation.

978-1-4799-4020-2/14/$31.00 2014 IEEE

There are three most common diseases present in the

Philippines: (1) Bacterial leaf blight, (2) Brown spot, and (3)
Rice blast [2]. Brown spots are small, circular, oval spots fairly
scattered on the leaves with graycenter. Rice Blasts are small to
spindle-shaped (typically seen as diamond-shaped) spots with
brown border and graycenter. Bacterial leaf blight (BLB) are
water-soaked stripes that later cover a large area of leaf blade.
In study conducted by Phadikar and Sil (2008) [3], they
developed a software prototype system for rice disease
detection based on the infected images of various rice
plants. The images, captured by digital camera, were
processed using image growing, image segmentation
techniques to detect infected parts of the plants. Then the
infected part of the leaf has been used for the classification
purpose using neural network. Another study which was
conducted by Pugoy, presented a system called ARNELADDE
[4]. The system uses digital image analysis to detect
nutrients deficient and toxic, and diseases present in the
rice leaf. To implement the system, the C++ programming
language is used. It also makes use of ImageLab, which is an
image processing library.
The main goal of this research is to provide more accurate
identification of disease on rice plant by image processing as it
applies a training model called Artificial Neural Network using
BackPropagation Algorithm. It also provides recommendations
which contains immediate remedies and proper strategic
options for the next planting.
II. METHODOLOGY
Image
Acquisition

Image
Enhancement

Image
Segmentation

Back
Propagation

Feature
Extraction

7th IEEEInternational Conference Humanoid, Nanotechnology, Information Technology

Communication and Control, Environment and Management (HNICEM)
The Institute of Electrical and Electronics Engineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centro, Puerto Princesa, Palawan, Philippines

The system is composed of five sections and is shown in

Fig. 1.
Fig. 1. Main Block Diagram

A. Image Acquisition
Images with inoculated diseases were obtained at the
Greenhouse of the International Rice Research Institute located
at Los Banos, Laguna, Philippines. Using a controlled-light
module box, a total of 134 image samples were collected (55
images for Bacterial leaf Blight, 37 images for Brown Spot,
and, 42 images for Rice Blast). Samples of each diseases
collected are shown in the figure below.

cube; however the color components of HSV (hue and

saturation) model are defined with respect to the color triangle
shown in Fig. 3(a) [5]. In Fig.3 (a), hue, H, of color point P is
the angle of the vector shown with respect to the red axis.
Thus, the Hue component describes the color itself in the form
of the angle between [0,360] degrees. 0 degree mean red, 60
degree means yellow, 120 means green, 240 means blue, and
300 as magenta. The saturation, S, of color point P is the
degree to which the color is undiluted by white and is
proportional to the distance from P to the center of the triangle.
The range of S is [0, 1]. The Value range is between [0, 1] and
0 means black, 1 means white. The Value is measured with
respect to a line perpendicular to the triangle and passing
through its center. Top most is white, and the bottom most is
black.

Fig. 2. (a) Rice Leaf infected with Brown Spot (b) Diamond-shaped of leaf
blast caused by fungal pathogen (c) bacterial leaf blight with the
advanced development symptoms

Fig. 3. (a) HSV color triangle (b) HSV color solid

For acquisition of leaf samples, a controlled light module

box is used to control the lighting when the photo is taken. It
consists of a box, camera (attached on the box) and
illumination system inside. The length of the box is measured
to capture the certain length of rice leaf needed of the program.
The height of the box is approximated to get the desired
distance of object from lens with acceptable focus from camera
using macro mode. The width of the box is estimated to
provide enough space for the light to be disseminated inside it
and avoid light reflectance. . Two 3mm white LEDs and two
330 ohms resistors are used as part of the circuit in
illumination. These two LEDs, which are connected in series,
are covered by tracing paper as diffuser and pointing 45
degrees downward to disperse the light evenly to the base of
the box.

The RGB color space image to HSI space conversion

begins by the RGB values normalization. The equation for the
RGB normalization is shown in (1).

B. Image Enhancement
Noise reduction and contrast adjustment will be performed
in image enhancement. It will also include a conversion of the
acquired leaf sample images in RGB color space to HSV (HueSaturation-Value), as well as image intensity adjustment.
The HSV color space is used in the image processing
because it represents colors similarly how the human eye
senses colors. RGB model is defined with respect to a unit

(3)

(1)

The normalized H, S, and V components can be obtained

using equations (2), (3), (4), and (5).
.

cos

0,
(2)

cos

,2

3 min , ,

;
;

0,1

(4)

0,1

(5)

7th IEEEInternational Conference Humanoid, Naanotechnology, Information Technology

Communication and Control, Envvironment and Management (HNICEM)
The Institute of Electrical and Electronics Enggineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centroo, Puerto Princesa, Palawan, Philippines

To convert HSV values to a more connvenient range of

[0,360], [0,100], [0,255], respectively equatioon (6) is used.
;
100;
255
(6)
The RGB matrix of the images of the leaf samples was
obtained using equation (1). Figure 4 shows the RGB image of
one leaf sample with bacterial leaf blight.

Fig. 4. RGB image of a leaf sample with bacterrial leaf blight.

C. Image Segmentation
The main procedure donee here is the thresholding and
masking. After the alterationn of the captured image, the
processed image is converted to
t binary-level image (black and
white image) using the process of thresholding. Figure 7 shows
the result of this process.

Fig. 7. Binary image

i
with noise

The RGB image is converted to HSV color space using

equations (2) to (6) to reduce computattion and increase
efficiency in the image processing. The resultt of the conversion
is shown in Figure 5.

Fig. 5. HSV Conversion of RGB image (V-D

Dimension)

To adjust the intensity of the image forr the segmentation

process, the study employed Otsus method [6]. It is a method
to select a threshold automatically from a graay level histogram
which has been derived from the viewpoinnt of discriminant
analysis. This directly deals with the problem
m of evaluating the
goodness of thresholds. An optimal threeshold (or set of
thresholds) is selected by the discriminant criiterion; namely, by
maximizing the discriminant measure q (oor the measure of
separability of the resultant classes in gray leevels). The method
is characterized by its nonparametric and unnsupervised nature
of threshold selection.
Equation (7) shows how to calculatee,, the criterion
measure to evaluate the goodness (or seeparability) of the
threshold at level k.
(7)
Where: ^2 B(k) = function of thresholdd level k and based
on first-order statistics (class means of the dichotomize
d
pixels
of the image). ^2 = sum of the class variance
v
and class
means of the dichotomize pixels. Equation (8) and (9) shows
these functions.

Fig. 6. Image withh adjusted intensity

Small white pixels (noise) are present after the conversion

to binary-level image. Blob exxtraction is used to remove the
noise from the image. The ricee leaf part of the image will be
considered as the largest blob and
a the other blobs present in the
image are omitted.
The segment leaf image is converted to LAB color space
and the A-color plane is used for extracting the disease. The
processed image is then converrted to binary-level image using
histogram equalization using 2 bins (black and white). The
converted image will serve as the mask to remove the healthy
part of the rice leaf and leavinng the diseased-part of the rice
leaf to be used for extracting thee features.

(
(a)

(b)

(
(c)

(d)

(8)

(9)
In this study, the Value color plane had its intensity
adjusted so that the darker parts of the imagge go darker to aid
the segmentation process. The result is shownn in Fig. 6.

(
(e)
Fig. 8. (a)Noise-cancelled image usinng largest blob extraction (b) Segmented
leaf image (c) LAB conversionn of Image (A-Dimension) (d) Binary
image using histogram equalizattion (e) Diseased-part of the leaf image

7th IEEEInternational Conference Humanoid, Naanotechnology, Information Technology

Communication and Control, Envvironment and Management (HNICEM)
The Institute of Electrical and Electronics Enggineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centroo, Puerto Princesa, Palawan, Philippines

D. Feature Extraction
t disease, which
Four features are extracted to analyse the
includes: (a) fraction covered by the disease on
o the leaf. This is
calculated by dividing the measured area of the disease by the
total mask area (b) arithmetic mean values foor the R, G, and B
color components of the disease (c) the stanndard deviation of
the R, G, and B color components of the diseease, and, (d) mean
values of the H, S, and, V of the disease. These
T
four features
through heuristic analysis had given the opttimal performance
of the back propagation ANN.
E. Back Propagation Neural Network
The neural network will serve as the medium for
identifying the disease manifesting on thee rice leaves. The
basic structure of a neural network is a neuroon, which involves
mathematical equations and processes. The figure
fi
below shows
the components of a neuron.

initialized. The program appliied Otsu's method to select the

threshold level for proper reducction of the graylevel image to a
binary image. The standard gaamma distribution value applied
is 2. Values less than 2, wouldd result to an excessively bright
image, whereas a greater value would produce an unnecessarily
dark image. Parts of the imaage less than 6000 pixels are
considered as noise and are therefore
t
reduced. This process
produces a pure black backgrouund. Afterwards, the healthy part
of the leaf is removed, and feaature extraction begins. The data
obtained are stored in the matriix and fed to the neural network.
The identified disease is prresented in the user interface
window. Moreover, strategic opptions for proper management of
the disease are generated in PDF format.
IV. EXPERIMENTS AND RESULTS
A. Results of Disease Identificaation
RICE PLANT
DISEASES

ACCURAC
CY

30 out of 300
100 %
Fig. 9. Components of neuron

The equation governing the neuron is giveen by:

(10)
i the weight term,
Where Y is the output, X is the input, W is
is the bias term, and is the transfer funcction. The learning
rule used for the neural network is thee backpropagation
algorithm, a gradient-descent algorithm, meaning
m
the error
computed after a forward computation is minnimized after each
iteration. The training will only stop after thhe neural network
has met the stopping criterions: (1) Maxiimum iteration is
reached, (2) Minimum gradient is reached, and
a (3) Maximum
validation checks (number of iterations in which
w
the error has
failed to decrease). If the neural network prroduced satisfying
results after the training, the network can be used now for
disease identification.
NS
III. DESIGN CONSIDERATION

A. Implementation of MATLAB Software for Rice Disease

using Backpropagation Neural Network
fying the disease of
The actual flow of the program in identify
the rice plant is detailed as follows: First, a 10x1 matrix (10
rows represent the features used for disease identification, and
a column corresponds to the number of images needed) is

Brown Spot
(Small,
circular, oval
spots fairly
scattered on the
leaves with
graycenter)

30 out of 300
100 %
Rice Blast
(Small to
spindle-shaped
(typically seen
as diamondshaped) spots
with brown
border and
graycenter)

RECOMMENDATION

Proper management of
fertilizer by using silicon
fertilizers (e.g., calcium
silicate slag) in poor soil
conditions can be used to
reduce disease intensity.
Since the fungus is seed
transmitted, a hot water
seed treatment (53 -54C)
for 10-12 minutes may be
effective before sowing.
This treatment controls
primary infection at the
seedling stage.

Choose tolerant varieties

such as PSB Rc82 and
NSIC Rc170. Before
heading, regularly scout
blast-infected collars.
Excessive use of fertilizer
should be avoided as it
increases the incidence of
blast. Nitrogen should be
applied in small increments
at any time.

7th IEEEInternational Conference Humanoid, Naanotechnology, Information Technology

Communication and Control, Envvironment and Management (HNICEM)
The Institute of Electrical and Electronics Enggineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centroo, Puerto Princesa, Palawan, Philippines

30 out of 30
Bacterial Leaf
Blight
(Water-soaked
stripes that
later cover a
large area of
leaf blade.
Lesions are
grayish white
with wavy light
brown margin
and progresses
downwards)

100 %

Choosee BLB-tolerant
varietiees such as: PSB
Rc82, NS
SIC Rc150, Rc54,
and
Rc170.
Seed treatment
t
with
bleacching powder
(100gg/ml) and zinc
sulfatee (2%) reduce
bactterial blight.

The images were collected from experrimental nurseries

wherein rice plants were inoculated with diseease. Thirty images
per disease were collected and verified by the technicians of
IRRI. The program analysed these images annd identified what
kind of disease is present in the leaf. The same plants were
a compared with
manually inspected by the experts of IRRI and
the output of the program.
B. Disease Identification Confusion, Perform
mance and Train
State Plots
Figure 10 shows the training simulaation for disease
identification. The training has stopped whhen it reached the
minimum required gradient (min_grad = 1ee-12) at epoch 87
with gradient value of 9.7909e-13. The nettwork weights and
biases used for the neural network for diseease identification
occurs at epoch 87 with a validation perform
mance of 6.9643e13.

Fig. 11. Disease Identiification Train State Plot

In Fig. 12 there are fourr (4) matrices shown namely:

Training Confusion Matrix, Vaalidation Confusion Matrix, Test
Confusion Matrix and All Conffusion Matrix.
1) For the Training Confusioon Matrix
Forty one (41) samples in Class
C
1 were correctly classified
as Class 1; twenty eight (28) saamples in Class 2 were correctly
classified as Class 2; and twennty five (25) samples in Class 3
were correctly classified as Class 3.
2) For the Validation Confussion Matrix
Eight (8) samples in Classs 1 were correctly classified as
Class 1; three (3) samples in Class
C
2 were correctly classified
as Class 2; and nine (9) sam
mples in Class 3 were correctly
classified as Class 3.
M
3) For the Test Confusion Matrix
Six (6) samples in Class 1 were
w correctly classified as Class
1; six (6) samples in Class 2 were
w
correctly classified as Class
2; and eight (8) samples in Claass 3 were correctly classified as
Class 3.
4) For the All Confusion Maatrix
Fifty five (55) samples in Class
C
1 were correctly classified
as Class 1; thirty seven (37) saamples in Class 2 were correctly
classified as Class 2; and fortty two (42) samples in Class 3
were correctly classified as Class 3.

Fig. 10. Disease Identification Performannce Plot

Figure 11 shows the trend of the gradieent with respect to

the epoch and the corresponding validation performance
p
state.
The gradient has reached a value of 9.79009e-13 for the 0th
validation check.

Fig. 12. Disease Identificcation Confusion Matrices

7th IEEEInternational Conference Humanoid, Nanotechnology, Information Technology

Communication and Control, Environment and Management (HNICEM)
The Institute of Electrical and Electronics Engineers Inc. (IEEE) Philippine Section
12-16 November 2013 Hotel Centro, Puerto Princesa, Palawan, Philippines

[3] Phadikar, S. &Sil, J. (2008). Rice Disease Identification

using Pattern Recognition Techniques. Paper presented at the
11th International Conference on Computer and Information
Technology, Khulna, Bangladesh.
[4] Pugoy, R. A. and Dr. Mariano, V. (2011). Automated Rice Leaf
Disease Detection Using Shape Image Analysis.
Paper
presented at the 11th Philippine Computing Science Congress,
Naga City, Philippines.
[5] Gonzales and Woods. (1992). Digital Image Processing, 1st ed.
Retrieved from www.imageprocessingbook.com
[6] Nobuyuki Otsu (1980), A Threshold Selection Method from
Gray-Level Histograms, in the IEEE Systems, Man, and
Cybernetics, Vol 9,no.1.
[7] S. G. Wu et al., A leaf recognition algorithm for plant using
probabilistic neural network, in Proc. IEEE ISSPIT, China:
Chinese Academy Science, 2007.
Fig. 13. Graph of the accuracy of the program

The figure shows the accuracy of the program output by

comparing it to the manual visual inspection made by the
experts.
V. CONCLUSION
The development of a program which determines the
diseases present in rice leaf through image processing coupled
with backpropagation neural network was successfully
implemented using MATLAB. Also, typical lesions of the
diseased leaves were successfully identified by having an
accuracy of 100% for the Disease Identification.
The project was successfully done and proven to provide
accurate results; however, the researchers suggest the following
recommendations to further improve the project: (1) add more
type of diseases that can be identified using the program; (2)
consider the severity of the disease and variety of rice (3)
collect more images for the dataset of neural network which
could yield more accurate results.
VI. COPYRIGHT FORMS
ACKNOWLEDGMENT
The authors would like to acknowledge Dr. Roland J.
Buresh, Dr. Adam Sparks, Mr. Joselito Villa and all the staffs
of the International Rice Research Institute for their support
and cooperation in doing this project. Technological University
of the Philippines, Electronics Engineering Department for the
encouragement. And above all, God for His continuous
guidance.
REFERENCES
[1] International Rice Research Institute. (2003). Rice in the
Philippines.
Retrieved
from:
irri.org/ourwork/locations/philippines.
[2] Aragon, M. et al. (2003). FIELD GUIDE on Major
Disorders of the Rice Plant in the Philippines (Diseases and
Nutritional Deficiencies). Nueva Ecija, Philippines: DAPhilRice, 1-32.

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