A

TECHNICAL SEMINAR REPORT

ON
BRAIN TUMOR SEGMENTATION BASED ON HYBRID
CLUSTERING TECHNIQUE

Submitted by

B. NAGA DEVI PRIYA (20W91A0517)

Under the Esteemed Guidance of

Mrs. L.PRIYANKA

To

Jawaharlal Nehru Technological University, Hyderabad

In partial fulfillment of the requirements for award of degree of

BACHELOR OF TECHNOLOGY

IN

COMPUTER SCIENCE AND ENGINEERING

DEPARTMENT OF COMPUTER SCIENCE AND ENGINEERING

MALLA REDDY INSTITUTE OF ENGINEERING AND TECHNOLOGY
(UGC AUTONOMOUS)
(Sponsored by Malla Reddy Educational society)
(Affiliated to JNTU, Hyderabad)
Maisammaguda, Dhulapally post, Secunderabad-500014.
2023-2024
 Department of Computer Science and Engineering

BONAFIDE CERTIFICATE

This is to certify that this is the Bonafide certificate of the Technical Seminar Report

titled “BRAIN TUMOR SEGMENTATION BASED ON HYBRID CLUSTERING

TECHNIQUE” is submitted by B.NAGA DEVI PRIYA (20W91A0517) of B.Tech in

the partial fulfillment of the requirements for the degree of Bachelor of Technology in

Computer Science and Engineering, Malla Reddy Institute of Engineering & Technology.

Internal Guide Sign Head of the Department Sign

 DECLARATION

I hereby declare that the technical seminar report entitled“BRAIN TUMOR

SEGMENTATION BASED ON HYBRID CLUSTERING TECHNIQUE”
submitted to Malla Reddy Institute of Engineering and Technology, affiliated to Jawaharlal
Nehru Technological University Hyderabad (JNTUH), for the award of the degree of
Bachelor of Technology in Computer Science & Engineering.

It is further declared that the seminar report or any part thereof has not been previously
submitted to any University or Institute for the award of degree or diploma.
 ACKNOWLEDGEMENT

First and foremost, I am grateful to the principal DR.SRINIVAS PORANDLA for providing
me with all the resources in the college to make my project a success.I thank him for his
valuable suggestions at the time of seminars which encouraged me to give my best in the
project.
I would like to express my gratitude Dr. MUHAMMAD ASHFAQUL HASSAN, Head of
the Department of Computer Science and Engineering for his support and valuable suggestions
during the dissertation work.
I offer my sincere gratitude to my technical seminar- coordinator Mrs. L. PRIYANKA,
Assistant Professor of Computer Science and Engineering department who has supported me
throughout this technical seminar with their patience and valuable suggestions.

I would also like to thank all the supporting staff of the dept. Of CSE and all other departments
who have been helpful directly or indirectly in making the project a success.

I am extremely grateful to my parents for their blessings and prayers for my completion of
project this gave me strength to do my project.

B.NAGA DEVI PRIYA

20W91A0517
 ABSTRACT

This project describes the detection of cancerous tumor cells in an MRI of the human brain through
the process of image segmentation using clustering. The MRI image segmentation is done by using
“K-means clustering algorithm incorporated with Fuzzy C-means clustering method, trailing intensity
threshold and level set segmentation” steps to precisely detect tumor cells in the brain MRI. The
algorithm gets the profitsof the K-means clustering with respect to minimal execution time in addition
to the benefits of Fuzzy C- means featuring accuracy. The implementation of the algorithm is tested
for various diseases of the brain and the detection of the tumor region is shown in each case.
 TABLE OF CONTENT

Chapter Content PageNo

1 Introduction 1-3

2 Image Processing Overview 4-6

3 Clustering in Image Processing 7-8

4 KIFCM Algorithm 9-11

5 Architecture of Brain Tumor Segmentation 12-13

6 Graphical User Interface 14-15

7 Results 16-19

8 Conclusion & future scope 20

9 References 21-22
 1. INTRODUCTION

Brain tumor is one of the most serious diseases, which often have lethal outcomes. At present,
more and more attention has been paid to the study of brain tumor image. Nowadays, MRI is
especially useful for brain imaging, which can be performed without injecting radioisotopes.
MRI is based on multi parameter imaging,which can form different images by adjusting
different parameters and contains a large amount of information. Figure exemplifies brain
MRI with tumors, and the images were obtained in four different modalities:T1, T1c, T2, and
FLAIR. The FLAIR modalities are usually used for finding the extensions of tumors and
edemas. Here, we use segmentation of FLAIR images in BRATS 2012.

F
IG: Brain MRI images containing tumors in four different modalities

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As shown in above figure MRI images usually have low contrast, and it is difficult to diagnose
lesion areas owing to noise accurately. Therefore, accurate tumor segmentation is essential.
Nowadays, many image segmentation techniques have been widely applied to segmentation
of medical images. Examples include the threshold segmentation algorithm, edge-based
segmentation algorithms and neural network-based segmentation.

The threshold-based segmentation algorithm determines the segmentation threshold

based on certain pixel features. The pixels’ feature values are compared with the segmentation
threshold to determine which parts of the image to categorize the pixels. This method is simple
to implement and execute.

Since the characteristics of the boundary pixels are discontinuous, the pixel features
onboth sides of the boundary will have relatively obvious differences. Therefore, the basic
idea of the edge-based segmentation algorithm is to find the boundaries using some method
and tospecify the directions of the boundary first. Then, the pixels on one side of the boundary
are divided into one sub image, while the pixels on the other side are considered to belong to
another sub image. Although this algorithm is fast, it is sensitive to noise and usually obtains
incomplete information.

In recent years, image segmentation using neural networks has become increasingly
popular. The basic idea in this approach is to train a neural network on a training set and then
modify the architecture and weights of connections between the network’s nodes. New image
data are segmented using a trained neural network.

Convolutional neural networks (CNNs) have been particularly popular among

different neural network methods

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The EM algorithm assumes that data can be described as a mixture of probability
distributions. Then, the algorithm iteratively calculates the posterior probability and estimates
the mean, co-variance and mixture coefficients using the maximal likelihood estimation
approach and clustering criteria However, this clustering algorithm is sensitive to noise.

In order to improve the instability clustering and to alleviate its sensitivity to noise,
an effective clustering segmentation algorithm is proposed in this paper. The main
contributions of this paper are as follows:

(i) A hybrid clustering algorithm based on K-means++ and Gaussian kernel-based fuzzy
C- means (K++GKFCM) is proposed.

(ii) K-means++ algorithm is utilized to initialize the clustering center, which greatly
improvesthe stability of the algorithm.

iii)Gaussian kernel-based fuzzy C-means is proposed, which improves the sensitivity to noise.

(iv)The proposed method is combined with morphological operations for pre-processing and
post-processing, which further improves the accuracy of segmentation.

As a result, the accuracy of image segmentation is significantly improved.

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 2. IMAGE PROCESSING OVERVIEW

Image segmentation:
Image segmentation specifically used for medical purposes plays an important role
since medical images have poor contrast, various kinds of image noise or unclear
boundaries. Brain anatomy can be captures by Magnetic Resonance Imaging (MRI) –
whichis preferable as it does not use any radiation. Often, doctors treat the symptoms
rather than treating the disease, hence making it necessary for early detection of brain
tumor.
Several methods have been developed for image segmentation, the simplest one
being thresholding – a threshold numeric is predefined to convert an image in gray-scale
to a binary format. Another iterative technique which is used in this algorithm is
clustering, along with a few morphological procedures.

Clustering techniques:
As an overview, clustering can be grouped into, but not limited by, two main classes:
hard clustering and soft clustering. For example, the k-means clustering process is put
underhard clustering category and Fuzzy C- means is categorized as soft clustering.

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 In image segmentation, K-means clustering process partitions the total number of
pixels into k number of clusters where every pixel becomes a member to the cluster with
thesmallest average. Pixels contains the number of clusters, the centroid of the cluster and
all the pixels in cluster Ck are defined by ck and Nk.

Similarly, the Fuzzy C-means clustering algorithm is soft clustering with the only
difference is that a pixel can belong to more than one cluster; it can be part of more than one
cluster by acertain degree. Any pixel p has a predefined set of numerical constants providing

the “degreeof being in the kth cluster wk(x)“.As per the C-means algorithm, the centroid of a
cluster is the mathematical average of all the pixels, weighted by the degree of the
individual pixel being a member of the cluster.

KIFCM algorithm:
According to Abdel-Maksoud’s paper, the “K-means algorithm combined with the
FuzzyC-means algorithm” – KIFCM – makes use of the advantages of K-means technique
in terms of speed of execution as well as the precision of Fuzzy C-means algorithm.

Median filter:
A median filter, in image processing, is a nonlinear filtering operation to decrease
Gaussian noise and salt and pepper noise while preserving edges. The procedure is to move
throughout the image pixel by pixel continuously exchanging the value by the median of the
surrounding pixels – called the neighborhood. The segments of neighbors is called the window
which “slides” over the whole image, replacing all the values hence removing the noise while
preserving edges in the image. This median value is computed by arranging all the pixel values
– the number depends on the size of the structuring element (SE) or the window – in order
andreplacing the pixel which is found to be the middle or the median pixel value.
Developed by Math Works with its own proprietary programming language. MATLAB
primarily allows matrix data manipulations, function plotting and data implementation of
algorithms along with user interface creation. Images in MATLAB are
represented by 2D arrays, in which each member stores data about a pixel in the image it
represents digitally.

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MRI:
Magnetic Resonance Imaging (MRI), according to Demarco “is primarily

used in radiology to constitute pictures of the human anatomy and the process of the

human beings in not only health but disease as well. It is a medical imaging

technique where the machine scanners use strong magnetic fields and radio

waves to produce images of organs in the human body.”

With complications of X-rays and CT scans, also generated images of organs,not is

preferred since MRI was invented as they expose the body to harmful radiations, and patients
with medical implants can undergo MRI scanning safely.

With MRI being a richly flexible process, it is widely used in diagnostic medicine and is
also a part of various research. Relative to image processing, different contrasts may be
generated between layers of human tissues and the MRIs are also capable of producing
various chemical and physical data and detailed spatial images, all of which are most suited
for image processing.

FIG:MRI(Magnetic Resonance Imaging.

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 3. CLUSTERING IN IMAGE PROCESSING

With the objective to detect the presence (or absence) of certain objects in a given image,
the logical first step would be to represent the image in attribute-value pairs, suchas the
pixels of the image serving as attributes: 103x 103– the conservative approach. Taking
individual pixels as attributes which is not very efficient as there are lots of pixelsending
up with lots of attributes where each attribute itself is uninformative about whether the
image contains the said object or not.

Another procedure would be the bag-of-words approach, where a unique

distribution of pixels, texture distribution or the orientation of edges in the patch would
begiven a word to represent. This ‘patch’ here represents some part of the image which
requires human intervention. We could then take that patch and make necessary
computations on it, such as a histogram of the patch is more meaningful than the histogram
of the whole image. The patch provides information such as its relative position, pixel
distribution, texture and edge orientation.

FIG:Image Segmentation-Clustering

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Further, all the clustering algorithms initially assume there is one and only one feature
vector for every instance. Here, we have a bunch of feature vectors. Hence, the question
arises whether we have to concatenate them into one long vector. This would only make
sense if the particular pixel appears in the same position in every image, which is not likely
to happen, even with human intelligence.

If a patch or segment of the image is named by an algorithm instead of human intervention,

it accelerates the segmentation process as the algorithm is the one coming up with name
for the patches.

Briefly, the algorithm begins by assigning k pixels as the first step centroids. This is
followed by calculating the distance every centroid and every data point. This process is
repeated using the updated membership of each of the pixels until some predefined
convergence is met.

Template based clustering:

To increase efficiency while grouping the pixels into corresponding clusters, a
template window is used. Here, the template mentioned is chosen depending on the gray-
level intensity of the normal brain tissue and the tumor tissue. In this modification, during
the clustering process – the recurrent cluster formation – after initial k cluster formation,
the updated degree to which a pixel belongs in a cluster is acquired as the measure of
distance from the cluster centroid to the pixel point, until convergence. This is called the
Euclidean distance and it depends on the MRI image features such as the image entropy
and the pixel homogeneity.

Fuzzy C-means algorithm:

Entropy serves as a measure of disorder and can be related to the amount of uncertainty
about a change in pixel value with the given probability distribution of the gray-scale image.
Homogeneity of an image is the measure of the uniformity of gray levels in that image. It is
computed by first calculating the median and subtracting that value from each pixel value in
the image followed by the count of the number of times the pixel value will go up and down
the median. The above-mentioned features were computed using MATLAB in-built function.

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 4.KIFCM ALGORITHM

While many systems use the K-means algorithm to detect cancer cells in an MRI, there is a
major limitation of failing to detect the tumor cells completely, especially if the tumor is
malignant. In contrast, medical systems utilize C-means technique as it is designed to
preserve more data of the original MRI scan to detect malignant tumor cells precisely
relative to the K-means algorithm. But this arrangement suffers from long execution times
and is more prone to noise.

The designed medical image segmentation system has four main steps:pre-processing the
MRI, clustering procedure, extraction of the tumor cluster and contouring the tumor area.
Generally, the pre-processing stage consists of applying noise removal procedures and
improving image qualitybefore actually applying the segmentation algorithms. Basically, it
attempts to improve the low- quality image for the algorithm.

The principal idea behind integrating the two clustering algorithms is to reduce the
runtimeoverhead as well as the number of iterations completed. This is done by
initializing the right cluster centroids –from the K-means – to the Fuzzy C-means
clustering, thereby minimizing the execution time and provide accurate results.

Pre-processing-step: To improve the condition of the image and to remove any noise
present, this phase is implemented using various initial image processing methods. This is
usually done in case of brain images since they are more susceptible to noise than other
anatomic images. This initial phase consists of two sub-stages:

a)Removal of noise: It is observed that most MRIs are spoiled by intrusions like
Poisson and Gaussian noise, which is acceptable since various de-noising algorithms work
on the basis of Gaussian noise. In the KIFCM algorithm, a Median Filter is used for this
purpose. Ieffectiveness in preserving edges while

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 b)Skull Removal:The background of an MRI usually does not contain any useful

information, but it will be processed anyway which causes the execution time to increase.
One solution is to remove the background and obtain only the part of the brain which is
relevant to finding the tumor. In other words, we run an algorithm to erase the skull and
thecomposition that is not in the interest. This kind of algorithm is called the Brain Surface
Extractor algorithm (BSE). Generally used with MRIs, the BSE filters the image to erase
any contortions, preserve edges and conduct morphological operations such as erosion and
image masking which result in isolating the brain region. The program removes the skull
from the brain MRI leaving only area of actual brain tissue. In MATLAB, a morphological
operation call erosion is performed on the boundaries of the image, essentially segmenting
using the dark space between the skull and the brain occupied by the cerebro spinal fluid
(CSF). The final output of pre-processing is a noise free MRI containing only the brain part.

Clustering Step:By eliminating noise in the MRI and erasing the skull, the image now
serves as input to the KIFCM algorithm. First step of the algorithm is initialization by setting
the initial value of clusters, k, the total iterations limit, and the conclusion criterion The
next step, according to, is to “assign each pixel value to the closest cluster focus based on a
base distance by calculating the Euclidian separation between the pixel and the center of the
cluster then re-calculate the new centers. This goes on until a pre-defined convergencerule is
met. While scanning the image, there is a possibility that some pixels scattered and far away
from any of the subsequent cluster centers”.

The additional repetitive step will result in a smaller number of iterations than randomly
selecting values as the beginning centers of the cluster groups were not picked haphazardly,
thereby saving time and manual work. Although, the pixel values were clustered once
again.due to its altered cluster membership value, there is no deduction between pixels in
their groups as there isn’t any significant change done by the reiteration process

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Extraction Step: The extraction stage is done by thresholding segmentation of the
image clusters. Most of the image processing segmentation procedures are categorized as
one of the two features of the image intensity levels: discontinuity and similarity. In the
former, thesegmentation process is based on splitting up the processed image grounded
on variations inintensity values such as boundaries, edges or corners.

Contouring Step: The principle of Active contouring is to begin with the underlying
boundary shapes which are generally shown in the arrangement of an end-to-end
terminating curve, i.e., contours, and running through various iterations modify the said
contours by involving shrinking or expanding operation relative to the given restrictions.
The clustered output image is processed into binary format by implementing inverse
thresholding algorithm with a pre-set number of iterations.

Alternatively, this step can be included in the previous one if the classical Fuzzy C-means
is used where the end-user is provided with the ability to gain admittance to the cluster to
be a threshold otherwise appear in the MRI. Here, user interaction is eliminated, and
proceededby feeding the resultant image with the white cancerous area to the contouring
process.

The contouring covers the cancer area of the resultant tumor extracted in the input MRI.
Output of this phase is the tumor extracted image and the input noise detached MRI
superimposed with the highlighted cancerous area

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5. ARCHITECTURE OF BRAIN TUMOR SEGMENTATION

Fig:Architecture of Brain Tumor Segmentation

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FIG:Proposed techniques works brain tumor segmentation

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 6. GRAPHICAL USER INTERFACE

Graphical User Interface (GUI) implementation in MATLAB is executed through figure

windows with various built-in UI control objects. A user defined program is necessary for
each object to perform the function its was coded to do when the object is activated. These
essential tasks are streamlined in GUIDE – the MATLAB graphical user interface
development environment.

Creating a GUI in MATLAB consists of the following steps:

1.Layout the components of
GUI 2.Programming the call-
back functions

The GUIDE environment is primarily a set of UI layout tools. An M-file is generated that
consists the skeleton code to handle the initialization and launching the GUI, essentially a
framework for implementing step 2 – the call-back function where the code executes to
activate GUI components. As a result, the GUIDE automatically generates two files:

1.FIG file: A. fig extension file consists a complete description of the GUI figure in
the layout and all its components and object properties.

2.M file: A .m extension file consists of the functions the run and control the GUI as
wellas the call-back functions. This file is generally called GUIM-file.

3.M file: A .m extension file consists of the functions the run and control the GUI as
wellas the call-back functions. This file is generally called GUIM-file.

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The GUI consists of the following:

1.A function to load the MRI

2.Output of the KIFCM algorithm

3.Output of the segmented image

4.Approximated Region of the tumor

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 7. RESULTS

In this segment, the results of the KIFCM image segmentation procedure obtained
using brain MRI scan are shown for various cases of brain diseases. This project

was executed using MATLAB 9.5.0 (R2018b). The computations were run on “a

core i7/2.4G Hz computer with 8GB RAM and NVIDIA/4GB VRAM”.

As an overview,the graphical user interface, shows the various phases of the medical
image segmentation system initially from the original MRI, median filtered and smoothed
images, clustered– the “KIFCM technique and segmented output – using thresholding and
Contouring the tumor area by level set algorithm”, according to Abdel-Maksoud’s research.

In the following section, the KIFCM algorithm is tested on various diseases of the brain
and thealgorithm successfully detects the tumor cells in each of the scenario.

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Chronic necrosis:
In Richard Demarco’s paper he believes that “cancer is essentially a disorder of cell

death rather than cell development – a consequence when cells don’t die an apoptotic death
and release a bunch of hazardous molecules when they die by necrosis”.

This is captured in an MRI with a unique intensity compared to the rest of the brain. Chronic
necrosis, commonly known as Stage III cancer, is caused by several factors such as infection,
infarction, toxins and inflammation (commonly labeled Stage I).

In figure 3, the algorithm shows the segmented image along with the highlighted (red)tumor
region indicating the tumor variable to 1. This helps to augment the patient’s life by a considerable
amount while exploring other treatment options – treat the symptoms rather thantreat the tumor

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Metastases:

One of the primary reasons’ cancers is dreaded lethal is its exceptional capability to
metastasize in the human body. Cancer cells can proliferate limited to a by propagating to
surrounding normal healthy tissues. At the point when this occurs, it is termed metastatic
cancer and for most kinds of the disease, it is likewise called Stage IV cancer.

Often, when patients are diagnosed with metastatic malignant growth, doctors are unable
topinpoint the area of origin. This sort of brain disease is called cancer of unknown primary
origin. The algorithm fails to detect the region of origin,nevertheless it detects the active.

Hydrocephalus: Hydrocephalus is the unusual development of liquid like material in

the depressions (ventricles) deep within the human brain. The abundance of fluid builds the
size of the ventricles and puts pressure against the cerebrum. The performance of the
algorithm is shown in figure 5 – dilated lateral ventricles in normal pressure.

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Encephalopathy: Encephalopathy is a general term portraying a malady that impacts
the capacity of structure of the cerebrum. There are many types – permanent and temporary,
either acquired or occurring from birth. The algorithm here, positively, fails to detect the
presence – which is very brain tumor.

Chronic infarct: A cerebral infarction is a region of necrotic tissue in the focal part of
the brain which is caused by a stoppage or acute tapering in the blood vessels supplying
oxygen. The confinedoxygen due to the limited blood supply causes an is chemic stroke that
results in an infraction if the blood stream is not re-established.

A human brain infarct appears in the MRI, with gliosis and cystic formation, as shown in figure 7.
TheKIFCM algorithm correctly detects the major area of tumor cells affecting the brain

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 8.CONCLUSION & FUTURESCOPE

While there are many image segmentation algorithms that are quite efficient, many fail to
precisely find the number of tumor cells in a brain MRI with a short execution time. The
KIFCM algorithm efficiently utilizes the advantages in both clustering algorithms, that is,
the “K-means and Fuzzy C-means clustering, originally individually fail to segment,
therefore detect tumor cells, the MRI distorted by noise”. From the experimental results, this
four-stage framework is proven to detect various types of brain tumors based on the MRI in
a short execution time.

As a future scope, an attempt can be made to rise effectiveness of the image segmentation
procedure, by adaptation of intensity relating to the tumor cells which might permit to improve
the patient outcomes.

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 9.REFERENCES

Eman Abdel-Maksoud, Mohammed Elmogy, Rashid Al-Awadi, “Brain tumor

segmentation based on a hybrid clustering technique”, Egyptian Informatics Journal, vol
16, issue 1, 2015.

S.K. Bandhyopadhyay, T.U. Paul “Automatic segmentation of brain tumour from multiple
images of brain MRI”, Int J Appl Innovat Eng. Manage (IJAIEM), 2 (1) (2013), pp. 240-
248.

Rajeev Kumar, Dr. K. James Mathai, “Brain Tumor Segmentation by Modified K- Mean
with Morphological Operations”, International Journal of Innovative Research in Science,
Engineering and Technology, Vol. 6, Issue 8, August 2017.

Parveen and Amritpal Singh, “Detection of Brain Tumor in MRI Images, using
Combination of Fuzzy C-Means and SVM” 2015 2nd International Conference on
SignalProcessing and Integrated Networks (SPIN) ©2015 IEEE.

Dipali B. Birnale1, S. N. Patil2, “Brain Tumor MRI Image Segmentation using FCM and
SVM Techniques”, International Journal of Engineering Science and Computing,
December2016.

M. Kass, A. Witkin, D. Terzopoulos, Snakes, “active contour model”, Int J Comput Vision,
1 (4) (1988), pp. 321-331.

D. Naik, P. Shah, “A review on image segmentation clustering algorithms”, Int J CompSci

IT, pp 3289-3293, 2014.

Richard A Demarco and Michael T Lotze, “Dying Dangerously: Necrotic Cell Deathand
Chronic Inflammation”, Molecular Medicine Institute - Center for Biotechnology and
Bioengineering, University of Pittsburgh School of Medicine.

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Richard A Demarco and Michael T Lotze, “Dying Dangerously: Necrotic Cell Deathand
Chronic Inflammation”, Molecular Medicine Institute - Center for Biotechnology and
Bioengineering, University of Pittsburgh School of Medicine.

Rasel Ahmmed and Foisal Hossain, “Tumor Detection in Brain MRI Image Using
Template based K-means and Fuzzy C-means Clustering Algorithm”, International
Conference on Computer Communication and Informatics, 2016.

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