1

Plant Disease Detection Using

Convolutional Neural Network

Submitted By
- Suman Chatterjee.
Admn No.-15je001400.
UNDER THE GUIDANCE OF

Dr. A.C.S RAO

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

INDIAN INSTITUTE OF TECHNOLOGY(INDIAN SCHOOL OF MINES),

DHANBAD.

DHANBAD-826004.

April, 2019.
 ACKNOWLEDGEMENT

I take this opportunity to express my deep sense of gratitude and respect towards my project
guide, Dr. ACS Rao, Assistant Professor, Department of Computer Science And Engineering,
IIT(ISM) DHANBAD.
I am very much indebted to him for the generosity, expertise and guidance I have received from
him while working on the project.

I wish to express my profound gratitude to Dr. Haider Banka, Head of Department Of

Computer Science And Engineering, IIT(ISM) DHANBAD for his inspiration.

DATE-01/12/2018 NAME-SUMAN CHATTERJEE.

ADMISSION NO.-15JE001400
 Abstract

When plants and crops are affected by pests it affects the agricultural
production of the country. Usually farmers or experts observe the plants
with naked eye for detection and identification of disease. But this
method can be time processing, expensive and inaccurate. Automatic
detection using image processing techniques provide fast and accurate
results. This paper is concerned with a new approach to the
development of plant disease recognition model, based on leaf image
classification, by the use of deep convolutional networks. Advances in
computer vision present an opportunity to expand and enhance the
practice of precise plant protection and extend the market of computer
vision applications in the field of precision agriculture. Novel way of
training and the methodology used facilitate a quick and easy system
implementation in practice. All essential steps required for implementing
this disease recognition model are fully described throughout the paper,
starting from gathering images in order to create a database, assessed
by agricultural experts, a deep learning framework to perform the deep
CNN training. This method paper is a new approach in detecting plant
diseases using the deep convolutional neural network trained and fine-
tuned to fit accurately to the database of a plant’s leaves that was
gathered independently for diverse plant diseases. The advance and
novelty of the developed model lie in its simplicity; healthy leaves and
background images are in line with other classes, enabling the model to
distinguish between diseased leaves and healthy ones or from the
environment by using CNN.
 INTRODUCTION

The problem of efficient plant disease protection is closely related to

the problems of sustainable agriculture Inexperienced pesticide usage
can cause the development of long-term resistance of the pathogens,
severely reducing the ability to fight back. Timely and accurate
diagnosis of plant diseases is one of the pillars of precision agriculture.
It is crucial to prevent unnecessary waste of financial and other
resources, thus achieving healthier production in this changing
environment, appropriate and timely disease identification including
early prevention has never been more important. There are several
ways to detect plant pathologies. Some diseases do not have any
visible symptoms, or the effect becomes noticeable too late to act, and
in those situations, a sophisticated analysis is obligatory. However,
most diseases generate some kind of manifestation in the visible
spectrum, so the naked eye examination of a trained professional is the
prime technique adopted in practice for plant disease detection. In order
to achieve accurate plant disease diagnostics a plant pathologist should
possess good observation skills so that one can identify characteristic
symptoms. Variations in symptoms indicated by diseased plants may
lead to an improper diagnosis since amateur gardeners and hobbyists
could have more difficulties determining it than a professional plant
pathologist. An automated system designed to help identify plant
diseases by the plant’s appearance and visual symptoms could be of
great help to amateurs in the gardening process and also trained
professionals as a verification system in disease diagnostics. Advances
in computer vision present an opportunity to expand and enhance the
practice of precise plant protection and extend the market of computer
vision applications in the field of precision agriculture. Exploiting
common digital image processing techniques such as colour analysis
and thresholding were used with the aim of detection and classification
of plant diseases. In machine learning and cognitive science, ANN is an
information-processing paradigm that was inspired by the way biological
nervous systems, such as the brain, process information. Neural
networks or connectionist systems are a computational approach used
in computer science and other research disciplines, which is based on a
large collection of neural units (artificial neurons), loosely mimicking the
way a biological brain solves problems with large clusters of biological
neurons connected by axons. Each neural unit is connected with many
others, and links can be enforcing or inhibitory in their effect on the
activation state of connected neural units. Each individual neural unit
may have a summation function which combines the values of all its
inputs together. There may be a threshold function or limiting function
on each connection and on the unit itself, such that the signal must
surpass the limit before propagating to other neurons. These systems
are self-learning and trained, rather than explicitly programmed, and
excel in areas where the solution or feature detection is difficult to
express in a traditional computer program. Neural networks typically
consist of multiple layers or a cube design, and the signal path
traverses from front to back. Back propagation is the use of forward
stimulation to reset weights on the "front" neural units and this is
sometimes done in combination with training where the correct result is
known. More modern networks are a bit more free flowing in terms of
stimulation and inhibition with connections interacting in a much more
chaotic and complex fashion. Dynamic neural networks are the most
advanced, in that they dynamically can, based on rules, form new
connections and even new neural units while disabling others.
The goal of the neural network is to solve problems in the same way
that the human brain would, although several neural networks are more
abstract. Modern neural network projects typically work with a few
thousand to a few million neural units and millions of connections, which
are still several orders of magnitude less complex than the human brain
and closer to the computing power of a worm. New brain research often
stimulates new patterns in neural networks. One new approach is using
connections which span much further and link processing layers rather
than always being localized to adjacent neurons. Other research being
explored with the different types of signal over time that axons
propagate, such as Deep Learning, interpolates greater complexity than
a set of Boolean variables being simply on or off. Their inputs can also
take on any value between 0 and 1. Also, the neuron has weights for
each input and an overall bias. The weights are real numbers
expressing importance of the respective inputs to the output. The bias is
used for controlling how easy the neuron is getting to output 1. For a
neuron with really big bias it is easy to output 1, but when the bias is
very negative then it is difficult to output 1.
 Materials and Methods:-

 The Dataset:-
The Dataset was taken from kaggle of PlantVillage dataset
present online as such the code was also written on the online
kernel of Kaggle for better computation and analysis of training
loss and validation.
 Image Preprocessing and Labelling:
Preprocessing images commonly involves removing low-frequency
background noise, normalizing the intensity of the individual particles
images, removing reflections, and masking portions of images. Image
preprocessing is the technique of enhancing data Furthermore,
procedure of image preprocessing involved cropping of all the images
manually, making the square around the leaves, in order to highlight the
region of interest (plant leaves). During the phase of collecting the
images for the dataset, images with smaller resolution and dimension
less than 500 pixels were not considered as valid images for the
dataset. In addition, only the images where the region of interest was in
higher resolution were marked as eligible candidates for the dataset. In
that way, it was ensured that images contain all the needed information
for feature learning. Many resources can be found by searching across
the Internet, but their relevance is often unreliable. In the interest of
confirming the accuracy of classes in the dataset, initially grouped by a
keywords search, agricultural experts examined leaf images and
labeled all the images with appropriate disease acronym. As it is known,
it is important to use accurately classified images for the training and
validation dataset. Only in that way may an appropriate and reliable
detecting model be developed. In this stage, duplicated images that
were left after the initial iteration of gathering and grouping images into
classes were removed from the dataset.
  Neural Network Training :-
Training the deep convolutional neural network for making an image
classification model from a dataset was proposed. Tensor Flow is an
open source software library for numerical computation using data flow
graphs. Nodes in the graph represent mathematical operations, while
the graph edges represent the multidimensional data arrays (tensors)
communicated between them. The flexible architecture allows you to
deploy computation to one or more CPUs or GPUs in a desktop, server,
or mobile device with a single API. Tensor Flow was originally
developed by researchers and engineers working on the Google Brain
Team within Google's Machine Intelligence research organization for
the purposes of conducting machine learning and deep neural networks
research, but the system is general enough to be applicable in a wide
variety of other domains as well. In machine learning, a convolutional
neural network is a type of feed-forward artificial neural network in
which the connectivity pattern between its neurons is inspired by the
organization of the animal visual cortex. Individual cortical neurons
respond to stimuli in a restricted region of space known as the receptive
field. The receptive fields of different neurons partially overlap such that
they tile the visual field. The response of an individual neuron to stimuli
within its receptive field can be approximated mathematically by a
convolution operation. Convolutional networks were inspired by
biological processes and are variations of multilayer perceptron
designed to use minimal amounts of pre-processing. They have wide
applications in image and video recognition, recommender systems and
natural language processing. Convolutional neural networks (CNNs)
consist of multiple layers of receptive fields. These are small neuron
collections which process portions of the input image. The outputs of
these collections are then tiled so that their input regions overlap, to
obtain a higher-resolution representation of the original image; this is
repeated for every such layer. Tiling allows CNNs to tolerate translation
of the input image. Convolutional networks may include local or global
pooling layers, which combine the outputs of neuron clusters. They also
consist of various combinations of convolutional and fully connected
layers, with point wise nonlinearity applied at the end of or after each
layer. A convolution operation on small regions of input is introduced to
reduce the number of free parameters and improve generalization .One
major advantage of convolutional networks is the use of shared weight
in convolutional layers, which means that the same filter (weights bank)
is used for each pixel in the layer; this both reduces memory footprint
and improves performance. The layer’s parameters are comprised of a
set of learnable kernels which possess a small receptive field but
extend through the full depth of the input volume. Rectified Linear Units
(Re LU) are used as substitute for saturating nonlinearities. This
activation function adaptively learns the parameters of rectifiers and
improves accuracy at negligible extra computational cost. In the context
of artificial neural networks, the rectifier is an activation function defined
as:
f (x)=max(0,x)
,where x is the input to a neuron. This is also known as a ramp function
and is analogous to half-wave rectification in electrical engineering. This
activation function was first introduced to a dynamical network by Hahn
loser et al. in a 2000 paper in Nature with strong biological motivations
and mathematical justifications. It has been used in convolutional
networks more effectively than the widely used logistic sigmoid (which is
inspired by probability theory; see logistic regression) and its more
practical counterpart, the hyperbolic tangent. The rectifier is, as of 2015,
the most popular activation function for deep neural networks. Deep
CNN with ReLUs trains several times faster. This method is applied to
the output of every convolutional and fully connected layer. Despite the
output, the input normalization is not required; it is applied after ReLU
nonlinearity after the first and second convolutional layer because it
reduces top-1 and top-5 error rates. In CNN, neurons within a hidden
layer are segmented into “feature maps.” The neurons within a feature
map share the same weight and bias. The neurons within the feature
map search for the same feature. These neurons are unique since they
are connected to different neurons in the lower layer. So for the first
hidden layer, neurons within a feature map will be connected to different
regions of the input image. The hidden layer is segmented into feature
maps where each neuron in a feature map looks for the same feature
but at different positions of the input image. Basically, the feature map is
the result of applying convolution across an image. The convolutional
layer is the core building block of a CNN. The layer's parameters consist
of a set of learnable filters (or kernels), which have a small receptive
field, but extend through the full depth of the input volume. During the
forward pass, each filter is convolved across the width and height of the
input volume, computing the dot product between the entries of the filter
and the input and producing a 2-dimensional activation map of that
filter. As a result, the network learns filters that activate when it detects
some specific type of feature at some spatial position in the input.
Stacking the activation maps for all filters along the depth dimension
forms the full output volume of the convolution layer. Every entry in the
output volume can thus also be interpreted as an output of a neuron
that looks at a small region in the input and shares parameters with
neurons in the same activation map. When dealing with high-
dimensional inputs such as images, it is impractical to connect neurons
to all neurons in the previous volume because such network
architecture does not take the spatial structure of the data into account.
Convolutional networks exploit spatially local correlation by enforcing a
local connectivity pattern between neurons of adjacent layers: each
neuron is connected to only a small region of the input volume. The
extent of this connectivity is a hyper parameter called the receptive field
of the neuron. The connections are local in space (along width and
height), but always extend along the entire depth of the input volume.
Such architecture ensures that the learnt filters produce the strongest
response to a spatially local input pattern. Three hyper parameters
control the size of the output volume of the convolutional layer: the
depth, stride and zero-padding.
1. Depth of the output volume controls the number of neurons in the
layer that connect to the same region of the input volume. All of these
neurons will learn to activate for different features in the input. For
example, if the first Convolutional Layer takes the raw image as input,
then different neurons along the depth dimension may activate in the
presence of various oriented edges, or blobs of color.
2. Stride controls how depth columns around the spatial dimensions
(width and height) are allocated. When the stride is 1, a new depth
column of neurons is allocated to spatial positions only 1 spatial unit
apart. This leads to heavily overlapping receptive fields between the
columns, and also to large output volumes. Conversely, if higher strides
are used then the receptive fields will overlap less and the resulting
output volume will have smaller dimensions spatially.
3. Stride controls how depth columns around the spatial dimensions
(width and height) are allocated. When the stride is 1, a new depth
column of neurons is allocated to spatial positions only 1 spatial unit
apart. This leads to heavily overlapping receptive fields between the
columns, and also to large output volumes. Conversely, if higher strides
are used then the receptive fields will overlap less and the resulting
output volume will have smaller dimensions spatially.

Parameter sharing scheme is used in convolutional layers to control the

number of free parameters. It relies on one reasonable assumption:
That if one patch feature is useful to compute at some spatial position,
then it should also be useful to compute at a different position. In other
words, denoting a single 2-dimensional slice of depth as a depth slice,
we constrain the neurons in each depth slice to use the same weights
and bias. Since all neurons in a single depth slice are sharing the same
parameterization, then the forward pass in each depth slice of the
CONV layer can be computed as a convolution of the neuron's weights
with the input volume (hence the name: convolutional layer). Therefore,
it is common to refer to the sets of weights as a filter (or a kernel), which
is convolved with the input. The result of this convolution is an activation
map, and the set of activation maps for each different filter are stacked
together along the depth dimension to produce the output volume.
Parameter Sharing contributes to the translation invariance of the CNN
architecture. It is important to notice that sometimes the parameter
sharing assumption may not make sense. This is especially the case
when the input images to a CNN have some specific centred structure,
in which we expect completely different features to be learned on
different spatial locations. One practical example is when the input is
faces that have been centred in the image: we might expect different
eye-specific or hair-specific features to be learned in different parts of
the image. In that case it is common to relax the parameter sharing
scheme, and instead simply call the layer a locally connected layer.
Another important layer of CNNs is the pooling layer, which is a form of
nonlinear down sampling.
Pooling operation gives the form of translation invariance; it operates
independently on every depth slice of the input and resizes it spatially.
Overlapping pooling is beneficially applied to lessen over fitting. Also in
favour of reducing over fitting, a dropout layer is used in the first two
fully connected layers. But the shortcoming of dropout is that it
increases training time 2-3 times comparing to a standard neural
network of the exact architecture. Bayesian optimization experiments
also proved that ReLUs and dropout have synergy effects, which means
that it is advantageous when they are used together. The advance of
CNNs refers to their ability to learn rich mid-level image representations
as opposed to hand-designed low-level features used in other image
classification methods.

Results And Conclusion

The Results presented in this section are related to training with the
whole database containing both original and augmented images. As it is
known that convolutional networks are able to learn features when
trained on larger datasets, results achieved when trained with only
original images will not be explored. After fine-tuning the parameters of
the network, an overall accuracy of 96.77% was achieved. Furthermore,
the trained model was tested on each class individually. Test was
performed on every image from the validation set. As suggested by
good practice principles, achieved results should be compared with
some other results. In addition, there are still no commercial solutions
on the market, except those dealing with plant species recognition
based on the leaves images. In this paper, a approach of using deep
learning method was explored in order to automatically classify and
detect plant dise ases from leaf images. The complete procedure
was described, respectively, from collecting the images used for training
and validation to image pre-processing and augmentation and finally the
procedure of training the deep CNN and fine-tuning. Different tests were
performed in order to check the performance of newly created model.
As the presented method has not been exploited, as far as we know, in
the field of plant disease recognition, there was no comparison with
related results, using the exact technique.
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