1

Table of contents

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 TABLE OF CONTENT

CHAPTER PAGE
TITLE
NO NO
ABSTRACT i
LIST OF FIGURES v
LIST OF ABBREVATION vi
1. INTRODUCTION 1
2. LITERATURE REVIEW 4
2.1 IMAGING TECHNIQUES 4

2.1.1 Electron microscopy 4

2.1.2 Fluoroscopy 5
2.1.3 X Rays 5
2.1.3.1 Projection radiography 5
2.1.3.2 Computer tomography 6
2.1.3.3 Angiogram 8
2.1.4 Mammography 9
2.1.5 Magnetic Resonance Imaging 11
2.1.6 Ultrasonography 12
2.1.7 Thermography 13
2.1.8 Positron Emission Tomography 14
2.1.9 Photo Acoustic Imaging 14
2.1.10 Endoscopic Imaging 15
2.2 SKIN TUMOR AND STAGES 15
2.2.1 Introduction 16
2.2.2 Stages of tumor 17
2.3 CAUSES OF SKIN TUMOR 17
2.3.1 Race 17
2.3.2 Age 17
2.3.3 Family history 18
2.4 SYMPTOMPS OF SKIN ii TUMOR 18
2.4.1 Head ache 18
2.4.2Seizures 18
2.4.3 Nausea and vomiting 19
2.4.4 Behavioural and cognitive Problems 19
2.5 TESTS AND DIAGNOSIS 19
2.5.1 A Neurological exam 19
2.5.2 Imaging test 19
2.5.3 Biopsy 20
2.6 TYPES OF TUMOR 20
2.6.1 Acoustic Neuroma 20

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 2.6.2 Astrocytom 21
2.6.2.1 Pilocytic Astrocytoma 21
2.6.2.2 Low-grade Astrocytoma 21
2.6.2.3 Anaplastic Astrocytoma 22
2.6.2.4 Anaplastic Astrocytoma 22
2.6.3 Glioblastoma multiframe 23
2.6.4 Chordoma 23
2.6.5 CNS Lymphoma 24
2.6.6 Craniopharyngioma 25
2.6.7 Skin stem Glioma 26
2.6.8 Meningioma 27
2.6.9 Schwannoma 29
2.6.10 Ependymoma 29
2.6.11 Rhabdoid tumor 31

3. SEGMENTATION ALGORITHMS 32
3.1 EDGE DETECTION 32
3.1.1 Sobel operator iii 32
3.1.2 Canny operator 35
3.1.3 Prewitt’s operator 36
3.1.4 Robertt’s cross operator 38
3.2 HISTOGRAM EQUALIZATION 40
3.3 THRESHOLDING TECHNIQUES 42
3.4 REGION BASD SEGMENTATION 44
3.5 FUZZY C-MEANS ALGORITHM 45
4. PROJECT DESCRIPTION 50
4.1 BLOCK DIAGRAM 50
4.2 WATERSHED SEGMENTATION 50
4.3 INDEPENDENT COMPONENT ANALYSIS 55
4.3.1 Introduction 55
4.3.1.1 Linear noiseless ICA 56
4.3.2 Need for classification 57
4.3.3 Preprocessing steps in ICA 60
4.3.3.1 Centering 60
4.3.3.2 Whitening 60
4.4 COMPARISION OF PCA AND ICA 62
5. RESULT 63
6. CONCLUSION 65
APPENDIX 66
7. REFERENCE 71

iv
List of figures

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 LIST OF FIGURES

FIGURE
TITLE PAGENO
NO
2.1 Computer Tomography 7
3.1 Original Skin MR Image 34
3.2 Output of Edge Detection by Sobel Operator 34
3.3 Output of Edge Detection by Canny Operator 36
3.4 Output of Edge Detection by Prewitt Operator 38
Output of Edge Detection by Roberts
3.5 40
Operator
3.6 Histogram 41
3.7 Output of Histogram Equalized Image 41
3.8 Output for Various Threshold Values 43
3.9 Output of Region Based Segmentation 45
3.10 Output of FCM Algorithm 49
4.1 Block Diagram 50
4.2 Segmentation using Watershed Algorithm 51
4.3 Original MR Image 53
4.4 Enhanced Image 53
4.5 Boundary Extraction of Reconstructed Image 54
4.6 Boundary Super Imposed on Original Image 54
4.7 Block Diagram of Spatial and Temporal ICA 58
4.8 Plot of ICA and PCA 62

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LIST OF ABBREVATIONS

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 LIST OF ABBREVIATIONS

MRI MAGNETIC RESONANCE IMAGING

CT COMPUTER TOMOGRAPHY
OPT ORTHOPANTOMOGRAPHY
NDE NONDESTRUCTIVE EVALUATION
DSA DIGITAL SUBTRACTION ANGIOGRAPHY
BSE BREAST SELF-EXAMINATION
PEM POSITRON EMISSION MAMMOGRAPHY
NMRI NUCLEAR MAGNETIC RESONANCE IMAGING
OCT OPTICAL COHERENCE TOMOGRAPHY
PNET PRIMITIVE NEUROECTODERMAL TUMOR
FCM FUZZY C-MEANS
SICA SPATIAL INDEPENDENT COMPONENT ANALYSIS
TICA TEMPORAL INDEPENDENT COMPONENT ANALYSIS

vi
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 Chapter-1
Introduction

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 CHAPTER 1

INTRODUCTION

The body is made up of many types of cells. Each type of cell has
special functions. Most cells in the body grow and then divide in an
orderly way to form new cells as they are needed to keep the body
healthy and working properly. When cells lose the ability to control their
growth, they divide too often and without any order. The extra cells form
a mass of tissue called a tumor. Tumors are benign or malignant. The aim
of this work is to design an automated tool for Skin tumor quantification
using MRI image data sets. Magnetic Resonance Imaging (MRI) is the
state of the art medical imaging technology which allows cross sectional
view of the body with unprecedented tissue contrast. MRI plays an
important role in assessing pathological conditions of the ankle, foot and
Skin. It has rapidly evolved into an accepted modality for medical
imaging of disease processes in the musculoskeletal system, especially
the foot and Skin due to the use of non-ionizing radiation.

MRI provides a digital representation of tissue characteristic that

can be obtained in any tissue plane. The images produced by an MRI
scanner are best described as slices through the Skin. MRI has the added
advantage of being able to produce images which slice through the Skin
in both horizontal and vertical planes. This work is a small and modest
part of a quite complex system. The whole system when completed
visualizing the inside of the human body, it makes surgeons able to
perform operations inside a patient without open surgery. More
specifically the aim for this work is to segment a tumor in a Skin. This
will make the surgeon able to see the tumor and then ease the treatment.

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The instruments needed for this could be ultrasound, Computer
Tomography (CT scan) and Magnetic Resonance Imaging (MRI). In this
Paper, the technique used is Magnetic Resonance Imaging (MRI). The
segmentation of Skin tumors in magnetic resonance images (MRI) is a
challenging and difficult task because of the variety of their possible
shapes, locations, image intensities.

Segmentation is an important process to extract information from

complex medical images. Segmentation has wide application in medical
field. The main objective of the image segmentation is to partition an
image into mutually exclusive and exhausted regions such that each
region of interest is spatially contiguous and the pixels within the region
are homogeneous with respect to a predefined criterion. Widely used
homogeneity criteria include values of intensity, texture, color, range,
surface normal and surface curvatures. Here Watershed segmentation
based algorithm has been used for detection of tumor. Watershed
segmentation uses the intensity as a parameter to segment the whole
image data set. Moreover, the additional complexity of estimation
imposed to other algorithms causes a tendency towards density
dependent approaches. Among all possible methods for this purpose,
watershed can be used as a powerful tool which implicitly extracts the
tumor surface. For detection of tumor and its classification in 2D the
software used is MATLAB.

After the segmentation of the detected tumor, the classification is

applied to the segmented surface. The algorithm used here for the
classification is ICA. Independent component analysis (ICA) which has
recently been developed in the area of image processing. ICA is a variant
of principal component analysis (PCA) in which the components are
assumed to be mutually statistically independent instead of merely

11
uncorrelated. The stronger condition allows one to remove the rotational
invariance of PCA, i.e. ICA provides a meaningful unique bilinear
decomposition of two-way data that can be considered as a linear mixture
of a number of independent source signals. On applying the ICA
algorithm to the segmented tumor it is classified that, if the intensity
found is between 248 and 256 , it is found to be ASTROCYTOMA and
for the values between 224 and 228 it is found to be GLIOBLASTOMA.
For the values between 238 and 240 it is found to be LYMPHOMA and
for values between 263 and 290 it is found to be MENINGLOMA.

This report consists of six chapters. The second chapter provides a

brief insight about the medical imaging techniques commercially
available. The third chapter explains about the development of Skin
tumor and its types. The fourth chapter gives a literature survey of
various segmentation algorithms available for Skin MRI image. The fifth
chapter gives a brief description about this project and its corresponding
results and the sixth chapter leads to the conclusion.

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 Chapter-2
Literature review

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 CHAPTER 2

MEDICAL IMAGING TECHNIQUES

2.1.1 ELECTRON MICROSCOPY

An Electron Microscope is a type of microscope that uses a

particle beam of electrons to illuminate a specimen and create a highly-
magnified image. Electron microscopes have much greater resolving
power than light microscopes that use electromagnetic radiation and can
obtain much higher magnifications of up to 2 million times, while the
best light microscopes are limited to magnifications of 2000 times. Both
electron and light microscopes have resolution limitations, imposed by
the wavelength of the radiation they use. The greater resolution and
magnification of the electron microscope is because the wavelength of an
electron; its de Broglie wavelength is much smaller than that of a photon
of visible light.

The electron microscope uses electrostatic and electromagnetic

lenses in forming the image by controlling the electron beam to focus it
at a specific plane relative to the specimen. This manner is similar to how
a light microscope uses glass lenses to focus light on or through a
specimen to form an image.

Types of Electron

a) Transmission Electron Microscope (TEM)

b) Scanning Electron Microscope (SEM)

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 c) Reflection Electron Microscope (REM)

d) Scanning Transmission Electron Microscope (STEM)

2.1.2 FLUOROSCOPY

Fluoroscopy is an imaging technique commonly used by

physicians to obtain real-time moving images of the internal structures of
a patient through the use of a fluoroscope. In its simplest form, a
fluoroscope consists of an x-ray source and fluorescent screen between
which a patient is placed. However, modern fluoroscopes couple the
screen to an x-ray image intensifier and CCD video camera allowing the
images to be recorded and played on a monitor.

The first fluoroscopes consisted of an x-ray source and fluorescent

screen between which the patient would be placed. As the x rays pass
through the patient, they are attenuated by varying amounts as they
interact with the different internal structures of the body, casting a
shadow of the structures on the fluorescent screen. Images on the screen
are produced as the untenanted X rays interact with atoms in the screen
through the photoelectric effect, giving their energy to the electrons.
While much of the energy given to the electrons is dissipated as heat, a
fraction of it is given off as visible light, producing the images. Early
radiologists would adapt their eyes to view the dim fluoroscopic images
by sitting in darkened rooms, or by wearing red adaptation goggles.

2.1.3 X- RAYS

2.1.3.1 PROJECTION RADIOGRAPHY

Radiographs, more commonly known as x-rays, are often used to

determine the type and extent of a fracture as well as for detecting

15
pathological changes in the lungs. With the use of radio-opaque contrast
media, such as barium, they can also be used to visualize the structure of
the stomach and intestines - this can help diagnose ulcers or certain types
of colon cancer.

2.1.3.2 COMPUTED TOMOGRAPHY

Tomography is the method of imaging a single plane, or slice, of

an object resulting in a tomogram. There are several forms of
tomography:

 Linear tomography

 Poly tomography

 Zonography

 Orthopantomography (OPT or OPG)

 Computed Tomography (CT), or Computed Axial Tomography

A basic problem in imaging with x-rays (or other penetrating

radiation) is that a two-dimensional image is obtained of a three-
dimensional object. This means that structures can overlap in the final
image, even though they are completely separate in the object. This is
particularly troublesome in medical diagnosis where there are many
anatomic structures that can interfere with what the physician is trying to
see. During the 1930's, this problem was attacked by moving the x-ray
source and detector in a coordinated motion during image formation.
From the geometry of this motion, a single plane within the patient
remains in focus, while structures outside this plane become blurred. This
is analogous to a camera being focused on an object at 5 feet, while

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objects at a distance of 1 and 50 feet are blurry. These related techniques
based on motion blurring are now collectively called classical
tomography. The word tomography means "a picture of a plane". In spite
of being well developed for more than 50 years, classical tomography is
rarely used. This is because it has a significant limitation: the interfering
objects are not removed from the image, only blurred. The resulting
image quality is usually too poor to be of practical use. The long sought
solution was a system that could create an image representing a 2D slice
through a 3D object with no interference from other structures in the 3D
object. This problem was solved in the early 1970s with the introduction
of a technique called computed tomography (CT). Computed
Tomography (CT) is a powerful nondestructive evaluation (NDE)
technique for producing 2-D and 3-D cross-sectional images of an object
from flat X-ray images. Figure 2.1 shown below is a schematic of a CT
system.

Figure 2.1 Computed Tomography

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 Characteristics of the internal structure of an object such as
dimensions, shape, internal defects, and density are readily available
from CT images. The test component is placed on a turntable stage that is
between a radiation source and an imaging system. The turntable and the
imaging system are connected to a computer so that x-ray images
collected can be correlated to the position of the test component. The
imaging system produces a 2-dimensional shadowgraph image of the
specimen just like a film radiograph.

2.1.3.3 ANGIOGRAPHY

Angiography or Arteriography is a medical imaging technique

used to visualize the inside, or lumen, of blood vessels and organs of the
body, with particular interest in the arteries, veins and the heart chambers.
This is traditionally done by injecting a radio-opaque contrast agent into
the blood vessel and imaging using X-ray based techniques such as
fluoroscopy. The word itself comes from the Greek words angeion,
"vessel", and graphein, "to write or record". The film or image of the
blood vessels is called an angiograph, or more commonly, an angiogram.

Although the term angiography is strictly defined as based on

projectional radiography, the term has been applied to newer vascular
imaging techniques such as CT angiography and MR angiography.
Depending on the type of angiogram, access to the blood vessels is
gained most commonly through the femoral artery, to look at the left side
of the heart and the arterial system or the jugular or femoral vein, to look
at the right side of the heart and the venous system. Using a system of
guide wires and catheters, a type of contrast agent (which shows up by
absorbing the x-rays), is added to the blood to make it visible on the x-
ray images.

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 The X-ray images taken may either be still images, displayed on a
image intensifier or film, or motion images. For all structures except the
heart, the images are usually taken using a technique called digital
subtraction angiography (DSA). Images in this case are usually taken at 2
- 3 frames per second, which allows the radiologist to evaluate the flow
of the blood through a vessel or vessels. This technique "subtracts" the
bones and other organs so only the vessels filled with contrast agent can
be seen. The heart images are taken at 15-30 frames per second, not using
a subtraction technique. Because DSA requires the patient to remain
motionless, it cannot be used on the heart. Both these techniques enable
the radiologist or cardiologist to see stenosis (blockages or narrowings)
inside the vessel which may be inhibiting the flow of blood and causing
pain.

2.1.4 MAMMOGRAPHY

Mammography is the process of using low-dose amplitude-X-rays

(usually around 0.7 mSv) to examine the human breast and is used as a
diagnostic as well as a screening tool. The goal of mammography is the
early detection of breast cancer, typically through detection of
characteristic masses and/or microcalcifications. Mammography is
believed to reduce mortality from breast cancer. No other imaging
technique has been shown to reduce risk, but breast self-examination
(BSE) and physician examination are considered essential parts of
regular breast care.

In many countries routine mammography of older women is

encouraged as a screening method to diagnose early breast cancer. The
United States Preventive Services Task Force recommends screening
mammography, with or without clinical breast examination, every 1-2

19
years for women aged 40 and older. Altogether clinical trials have found
a relative reduction in breast cancer mortality of 20%, but the two
highest-quality trials found no reduction in mortality. Mammograms have
been controversial since 2000, when a paper highlighting the results of
the two highest-quality studies was published. Normally longer
wavelength X-rays are used for taking mammograms. Radiologists then
analyze the image for any abnormal findings.

At this time, mammography along with physical breast

examination is the modality of choice for screening for early breast
cancer. Ultrasound, ductography, positron emission mammography
(PEM), and magnetic resonance imaging are adjuncts to mammography.
Ultrasound is typically used for further evaluation of masses found on
mammography or palpable masses not seen on mammograms.
Ductograms are still used in some institutions for evaluation of bloody
nipple discharge when the mammogram is non-diagnostic. MRI can be
useful for further evaluation of questionable findings as well as for
screening pre-surgical evaluation in patients with known breast cancer to
detect any additional lesions that might change the surgical approach, for
instance from breast-conserving lumpectomy to mastectomy. New
procedures, not yet approved for use in the general public, including
breast tomosynthesis may offer benefits in years to come.

Mammography has a false-negative (missed cancer) rate of at least

10 percent. This is partly due to dense tissues obscuring the cancer and
the fact that the appearance of cancer on mammograms has a large
overlap with the appearance of normal tissues.

2.1.5 MAGNETIC RESONANCE IMAGING (MRI)

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 MRI or nuclear magnetic resonance imaging (NMRI), is primarily
a medical imaging technique most commonly used in radiology to
visualize the internal structure and function of the body. MRI provides
much greater contrast between the different soft tissues of the body than
computed tomography (CT) does, making it especially useful in
neurological (Skin), musculoskeletal, cardiovascular, and oncological
(cancer) imaging. Unlike CT, it uses no ionizing radiation, but uses a
powerful magnetic field to align the nuclear magnetization of (usually)
hydrogen atoms in water in the body. Radio frequency (RF) fields are
used to systematically alter the alignment of this magnetization, causing
the hydrogen nuclei to produce a rotating magnetic field detectable by the
scanner. This signal can be manipulated by additional magnetic fields to
build up enough information to construct an image of the body.

How MRI works

The body is largely composed of water molecules which each

contain two hydrogen nuclei or protons. When a person goes inside the
powerful magnetic field of the scanner, these protons align with the
direction of the field.

A radio frequency electromagnetic field is then briefly turned on,

causing the protons to absorb some of its energy. When this field is
turned off the protons release this energy at a resonance radio frequency
which can be detected by the scanner. The frequency of the emitted signal
depends on the strength of the magnetic field. The position of protons in
the body can be determined by applying additional magnetic fields during
the scan which allows an image of the body to be built up. These are
created by turning gradients coils on and off which creates the knocking
sounds heard during an MR scan.

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 Diseased tissue, such as tumors, can be detected because the
protons in different tissues return to their equilibrium state at different
rates. By changing the parameters on the scanner this effect is used to
create contrast between different types of body tissue. MRI is used to
image every part of the body, and is particularly useful for neurological
conditions, for disorders of the muscles and joints, for evaluating tumors,
and for showing abnormalities in the heart and blood vessels.

2.1.6 ULTRASONOGRAPHY

Medical ultrasonography uses high frequency broadband sound

waves in the megahertz range that are reflected by tissue to varying
degrees to produce (up to 3D) images. This is commonly associated with
imaging the fetus in pregnant women. Uses of ultrasound are much
broader, however. Other important uses include imaging the abdominal
organs, heart, breast, muscles, tendons, arteries and veins. While it may
provide less anatomical detail than techniques such as CT or MRI, it has
several advantages which make it ideal in numerous situations, in
particular that it studies the function of moving structures in real-time,
emits no ionizing radiation, and contains speckle that can be used in
electrograph. It is very safe to use and does not appear to cause any
adverse effects, although information on this is not well documented. It is
also relatively inexpensive and quick to perform. The real time moving
image obtained can be used to guide drainage and biopsy procedures.
Doppler capabilities on modern scanners allow the blood flow in arteries
and veins to be assessed.

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2.1.7 THERMOGRAPHY

Thermal imaging, thermographic imaging, or thermal video, is a

type of infrared imaging science. Thermographic cameras detect radiation
in the infrared range of the electromagnetic spectrum (roughly 900–
14,000 nanometers or 0.9–14 µm) and produce images of that radiation,
called thermograms. Since infrared radiation is emitted by all objects
based on their temperatures, according to the black body radiation law,
thermography makes it possible to "see" one's environment with or
without visible illumination. The amount of radiation emitted by an
object increases with temperature, therefore thermography allows one to
see variations in temperature (hence the name). When viewed by
thermographic camera, warm objects stand out well against cooler
backgrounds; humans and other warm-blooded animals become easily
visible against the environment, day or night.

The use of thermal imaging has increased dramatically with

governments and airports staff using the technology to detect suspected
swine flu cases during the 2009 pandemic. Other uses include,
firefighters use it to see through smoke, find persons, and localize the
base of a fire. With thermal imaging, power lines maintenance
technicians locate overheating joints and parts, a tell-tale sign of their
failure, to eliminate potential hazards. Some physiological activities,
particularly responses, in human beings and other warm-blooded animals
can also be monitored with thermo graphic imaging.

2.1.8 POSITRON EMISSION TOMOGRAPHY

Positron emission tomography (PET) is a nuclear medicine

imaging technique which produces a three-dimensional image or picture

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of functional processes in the body. The system detects pairs of gamma
rays emitted indirectly by a positron-emitting radionuclide (tracer), which
is introduced into the body on a biologically active molecule. Images of
tracer concentration in 3-dimensional space within the body are then
reconstructed by computer analysis. In modern scanners, this
reconstruction is often accomplished with the aid of a CT X-ray scan
performed on the patient during the same session, in the same machine.

If the biologically active molecule chosen for PET is FDG, an

analogue of glucose, the concentrations of tracer imaged then give tissue
metabolic activity, in terms of regional glucose uptake. Although use of
this tracer results in the most common type of PET scan, other tracer
molecules are used in PET to image the tissue concentration of many
other types of molecules of interest.

2.1.9 PHOTO ACOUSTIC IMAGING

Photo acoustic imaging is a recently developed hybrid biomedical

imaging modality based on the photo acoustic effect. It combines the
advantages of optical absorption contrast with ultrasonic spatial
resolution for deep imaging in (optical) diffusive or quasi-diffusive
regime. Recent studies have shown that photo acoustic imaging can be
used in vivo for tumor angiogenesis monitoring, blood oxygenation
mapping, functional Skin imaging, and skin melanoma detection etc.

2.1.10 ENDOSCOPIC IMAGING

Endoscopy is a medical tool at the forefront in the diagnosis and

treatment of human diseases. Endoscopes, inserted through orifices such
as the mouth, nose, anus, and urethra, play an instrumental role in the
management of diseases of the pharynx, esophagus, stomach, small

24
intestine, colon, larynx, bronchial tree, and urinary system. The
fundamental concepts of endoscopy, including the optical and mechanical
components of typical endoscopes are given. The field of endoscopy
continues to evolve with the aid of technological innovations and
development. Early endoscopes consisted of simple rigid tubes that
provided limited views of a few easily accessed organs. Recent
developments have substantially enhanced the capabilities of endoscopes.
For example, fiber optic imaging bundles have allowed for the
development of flexible instruments that may be guided through tortuous
organs to visualize deeply into the body.

Conventional endoscopy is based on the detection of diffusely

reflected white light from tissue surfaces to reveal neoplasm.
Advancements in optical imaging take full advantage of light's properties
such as its spectral content and coherence to improve contrast and
resolution. Ultrasound imaging has been combined with endoscopy to
enable visualization beyond the tissue surface. Novel imaging modalities
such as fluorescence imaging and optical coherence tomography (OCT)
provide even more informative images. Technological improvements that
are enhancing the capability of endoscopes to visualize, diagnose, and
treat human diseases are revolutionizing the practice of medical
endoscopy.

SKIN TUMOR AND ITS STAGES

2.2.1 INTRODUCTION

The Skin tumor is an abnormal growth of cells within the Skin. Skin
tumors can be

1. Benign (Non-cancerous)

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 2. Malignant(Cancerous)

Benign Skin tumors do not contain cancer cells. Usually, benign

tumors can be removed, and they seldom grow back. The border or edge
of a benign Skin tumor can be clearly seen. Cells from benign tumors do
not invade tissues around them or spread to other parts of the body.
However, benign tumors can press on sensitive areas of the Skin and
cause serious health problems. Unlike benign tumors in most other parts
of the body, benign Skin tumors are sometimes life threatening. Very
rarely, a benign Skin tumor may become malignant.

Malignant Skin tumors contain cancer cells. Malignant Skin

tumors are generally more serious and often are lives threatening. They
are likely to grow rapidly and crowd or invade the surrounding healthy
Skin tissue. Very rarely; cancer cells may break away from a malignant
Skin tumor and spread to other parts of the Skin, to the spinal cord, or
even to other parts of the body. The spread of cancer is called metastasis.
Sometimes, a malignant tumor does not extend into healthy tissue. The
tumor may be contained within a layer of tissue or the bones of the skull
or another structure in the head may confine it. This kind of tumor is
called encapsulated.

2.2.2 STAGES OF TUMOR

Different stages of tumors are given as follows:

Stage 0 - A typical cells in a normal anatomical configuration

Stage 1 - Tumor limited to the local anatomical site

Stage 2 - Involvement of ipsilateral regional lymph nodes

Stage 3 - Involvement of contra lateral lymph nodes

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Stage 4 - Involvement of a distant site

The stage together with an assessment of the degree of

differentiation is very important for treatment planning and for
determining cancer prognosis.

2.3 CAUSES OF SKIN TUMOR

2.3.1 RACE

Skin tumors occur more often among white people than among
people of other races.

2.3.2 AGE

Most Skin tumors are detected in people who are 70 years old or
older. However, Skin tumors are the second most common cancer in
children. (Leukemia is the most common childhood cancer.) Skin tumors
are more common in children younger than 8 years old than in older
children.

2.3.3 FAMILY HISTORY

People with family members who have gliomas may be more

likely to develop this disease. Being exposed to radiation or certain
chemicals at work:

 Radiation - Workers in the nuclear industry have an increased risk

of developing a Skin tumor.

 Formaldehyde - Pathologists and embalmers who work with

formaldehyde have an increased risk of developing Skin cancer.
Scientists have not found an increased risk of Skin cancer among
other types of workers exposed to formaldehyde.

27
  Vinyl chloride - Workers who make plastics may be exposed to
vinyl chloride. This chemical may increase the risk of Skin tumors.

 Acrylonitrile - People who make textiles and plastics may be

exposed to acrylonitrile. This exposure may increase the risk of
Skin cancer.

2.4 SYMPTOMS OF SKIN TUMOR

2.4.1 HEADACHES:

This was the most common symptom, with 46% of the patients
reporting having headaches. They described the headaches in many
different ways, with no one pattern being a sure sign of Skin tumor. Many
- perhaps most - people get headaches at some point in their life, so this is
not a definite sign of Skin tumors.

2.4.2 SEIZURES:

This was the second most common symptom reported, with 33%
of the patients reporting a seizure before the diagnosis was made.
Seizures can also be caused by other things, like epilepsy, high fevers,
stroke, trauma, and other disorders. This is a symptom that should never
be ignored, whatever the cause. In a person who never had a seizure
before, it usually indicates something serious and you must get a Skin
scan. A seizure is a sudden, involuntary change in behavior, muscle
control, consciousness, and/or sensation. Symptoms of a seizure can
range from sudden, violent shaking and total loss of consciousness to
muscle twitching or slight shaking of a limb. Staring into space, altered
vision, and difficulty in speaking are some of the other behaviors that a
person may exhibit while having a seizure. Approximately 10% of the
population will experience a single seizure in their lifetime.

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2.4.3 NAUSEA AND VOMITING:

As with headaches, these are non-specific - which means that most

people who have nausea and vomiting do not have a Skin tumor. Twenty-
two percent of the people in our survey reported that they had nausea and
/or vomiting as a symptom.

2.4.4 BEHAVIORAL AND COGNITIVE PROBLEMS:

Many reported behavioral and cognitive changes, such as:

problems with recent memory, inability to concentrate or finding the right
words, acting out - no patience or tolerance, and loss of inhibitions -
saying or doing things that are not appropriate for the situation.

2.5 TESTS AND DIAGNOSIS

2.5.1 A NEUROLOGICAL EXAM.

A neurological exam may include, among other things, checking

your vision, hearing, balance, coordination and reflexes. Difficulty in one
or more areas may provide clues about the part of your Skin that could be
affected by a Skin tumor.

2.5.2 IMAGING TESTS.

Magnetic resonance imaging (MRI) is commonly used to help

diagnose Skin tumors. MRI uses magnetic fields and radio waves to
generate images of the Skin. In some cases a dye may be injected through
a vein in your arm before your MRI. A number of specialized MRI scans
may help your doctor in evaluation and treatment planning, including
functional MRI, perfusion MRI and magnetic resonance spectroscopy.

2.5.3 BIOPSY.

29
 A biopsy can be performed as part of an operation to remove the
Skin tumor, or a biopsy can be performed using a needle. A stereo tactic
needle biopsy may be done for Skin tumors in hard to reach areas or very
sensitive areas within your Skin that might be damaged by a more
extensive operation. A neurosurgeon drills a small hole, called a burr
hole, into the skull. A narrow, thin needle is then inserted through the
hole. Tissue is removed using the needle, which is frequently guided by
computerized tomography (CT) or MRI scanning. The biopsy sample is
then viewed under a microscope to determine if it is cancerous or benign.
This information is helpful in guiding treatment.

2.6 TYPES OF TUMOR

2.6.1 Acoustic Neuroma

An acoustic neuroma is also known as a vestibular schwannoma or

neurilemmoma.

Characteristics

 Grows on the sheath surrounding the eighth cranial nerve in the

inner ear.

 More common in women than men.

Symptoms

 Hearing loss in one ear

 Dizziness or vertigo

 Tinnitus (ringing in the ear)

 Tingling or numbness in the face

 Walking and balance problems

30
  Lack of coordination

2.6.2 Astrocytom

2.6.2.1 Pilocytic Astrocytoma

Also called: Juvenile Pilocytic Astrocytoma (JPA).

Characteristics

 Slow growing, with relatively well-defined borders

 Grows in the cerebrum, optic nerve pathways, Skin stem and

cerebellum

 Occurs most often in children and teens

 Accounts for two percent of all Skin tumors

2.6.2.2 Low-Grade Astrocytoma

An astrocytoma is a type of glioma that develops from star-shaped

cells (astrocytes) that support nerve cells. The WHO classifies a low-
grade astrocytoma as a grade II tumor.

Characteristics

 Slow growing

 Rarely spreads to other parts of the CNS

 Borders not well defined

 Common among men and women in their 20s-50s

2.6.2.3 Anaplastic Astrocytoma

An astrocytoma is a glioma that develops from star-shaped glial

cells (astrocytes) that support nerve cells. An anaplastic astrocytoma is
classified as a grade III tumor.

31
Characteristics

 Grows faster and more aggressively than grade II astrocytomas

 Tumor cells are not uniform in appearance

 Invades neighboring tissue

 Common among men and women in their 30s-50s

 More common in men than women

 Accounts for four percent of all Skin tumors

2.6.2.4 Anaplastic Astrocytoma

An astrocytoma is a glioma that develops from star-shaped glial

cells (astrocytes) that support nerve cells. An anaplastic astrocytoma is
classified as a grade III tumor.

Characteristics

 Grows faster and more aggressively than grade II astrocytomas

 Tumor cells are not uniform in appearance

 Invades neighboring tissue

 Common among men and women in their 30s-50s

 More common in men than women

 Accounts for four percent of all Skin tumors

2.6.3 Glioblastoma Multiforme (GBM)

An astrocytoma is a glioma that develops from star-shaped glial

cells (astrocytes) that support nerve cells. A glioblastoma multiforme is

32
classified as a grade IV astrocytoma. It is also referred to as a
glioblastoma or GBM.

Characteristics

 Most invasive type of glial tumor

 Commonly spreads to nearby tissue

 Grows rapidly

 May be composed of several different kinds of cells (i.e.,

astrocytes, oligodendrocytes)

 May have evolved from a low-grade astrocytoma or an

oligodendroglioma

 Common among men and women in their 50s-70s

 More common in men than women

 Accounts for 23 percent of all primary Skin tumors

2.6.4 Chordoma

Characteristics

 Rare and low grade

 Occurs at the sacrum, near the lower tip of the spine, or at the base
of the skull

 Originates from cells left over from early fetal development

 Invades the bone and soft tissues but rarely the Skin tissue

 Can block the ventricles, causing hydrocephalus

 Can metastasize (spread) or recur

33
Symptoms

 Double vision

 Headaches

2.6.5 CNS Lymphoma

CNS Lymphoma is a type of cancer that develops in the lymphatic

system. The lymphatic system is a network of small organs called lymph
nodes and vessels (similar to blood vessels) that carry a clear, watery
fluid called lymph throughout the body. This fluid supplies cells called
lymphocytes that fight disease and infection. To correctly diagnose
primary CNS Lymphoma, staging must be done. Staging is the process of
using CT scanning to examine many parts of the body. Staging helps to
confirm where the cancer originated and how far it has spread.

Characteristics

 Very aggressive

 Usually involves multiple tumors throughout the central nervous

system (CNS)

 More common in people whose immune systems are compromised

 Often develops in the Skin, commonly in the areas adjacent to the

ventricles

 Can be primary (originating in the Skin) or secondary

 Most common among men and women in their 60s-80s, but

incidence is increasing in young adults

 Twice as common in men as in women

34
  Accounts for three percent of all Skin tumors

Symptoms

 Headaches

 Partial paralysis on one side of the body

 Seizures

 Cognitive or speech disorders

 Vision problems

2.6.6 Craniopharyngioma

Characteristics

 Most common in the parasellar region, an area at the base of the

Skin and near the optic nerves

 Also grows in the regions of the optic nerves and the

hypothalamus, near the pituitary gland

 Tends to be low grade

 Often accompanied by a cyst

 Originates in cells left over from early fetal development

 Occurs in children and men and women in their 50s and 60s

35
Symptoms

 Headaches

 Visual changes

 Weight gain

 Delayed development in children

2.6.7 Skin Stem Glioma

Characteristics

 Named for its location at the base of the Skin

 Can range from low grade to high grade

 Occurs most often in children between three and ten years of age,
but can occur in adults

Symptoms

 Headaches

 Nausea

 Speech or balance abnormalities

 Difficulty swallowing

 Weakness or numbness of the arms and/or legs

 Facial weakness

 Double vision

36
 Symptoms can develop slowly and subtly and may go unnoticed for
months. In other cases, the symptoms may arise abruptly. A sudden onset
of symptoms tends to occur with rapidly growing, high-grade tumors.

2.6.8 Meningioma

These tumors grow from the meninges, the layers of tissue

covering the Skin and spinal cord. As they grow, meningiomas compress
adjacent Skin tissue. Symptoms are often related to this compression of
Skin tissue, which can also affect cranial nerves and blood vessels. In
some cases, meningioma growth can also extend into the bones of the
head and face, which may produce visible changes. Most meningiomas
are considered nonmalignant or low grade tumors. However, unlike
nonmalignant tumors elsewhere in the body, some of these Skin tumors
can cause disability and may sometimes be life threatening. In many
cases, meningiomas grow slowly. Other meningiomas grow more rapidly
or have sudden growth spurts. There is no way to predict the rate of
growth of a meningioma or to know for certain how long a specific tumor
was growing before diagnosis. Meningiomas are graded from low to
high. The lower the grade, the lower the risk of recurrence and aggressive
growth.

The WHO classification divides meningiomas into three grades:

Grade I: Benign Meningioma

Grade II: Atypical Meningioma

Grade III: Malignant (Anaplastic) Meningioma

37
Characteristics

 May arise after previous treatment from ionizing radiation or

excessive x-ray exposure

 Common among women and men in their 40s-50s, but can occur at
any age

 Twice as common in women as in men

 Accounts for over 30 percent of all primary Skin tumors

 In very rare cases, can invade the skull or metastasize to the skin or
lungs

 Women with meningiomas can experience tumor growth during

pregnancy

 In rare cases, multiple meningiomas can develop at the same time

in different parts of the Skin and/or spinal cord

Symptoms

 Seizures

 Headaches

 Nausea and vomiting

 Vision changes

 Behavioral and cognitive changes

 Sometimes no symptoms occur and tumor is detected incidentally

38
2.6.9 Schwannoma

Also known as vestibular schwannoma and acoustic neuroma (see

acoustic neuroma).

Characteristics

 Arises from cells that form a protective sheath around nerve fibers

 Typically grows around the eighth cranial nerve, but can be found
around other cranial or spinal nerves

Symptoms

 Reduced hearing in the ear on the side of the tumor when eighth
cranial nerve is involved Tinnitus (ringing in the ear)

 Balance problems

 Deficits depend on the nerve that is affected

2.6.10 Ependymoma

Ependymal tumors begin in the ependyma, cells that line the

passageways in the Skin where cerebrospinal fluid (CSF) is produced and
stored. Ependymomas are classified as either supratentorial (in the
cerebral hemispheres) or infratentorial (in the back of the Skin).
Variations of this tumor type include subependymoma, subependymal
giant-cell astrocytoma, and malignant ependymoma. Ependymoblastoma,
which occurs in infants and children under three years, is no longer
considered a subtype of ependymoma. For ependymoblastoma, see
primitive neuroectodermal tumor (PNET) in the Non-glial Tumors
section.

39
Characteristics

 Usually localized to one area of the Skin

 Develops from cells that line the hollow cavities at the bottom of
the Skin and the canal containing the spinal cord

 Can be slow growing or fast growing

 May be located in the ventricles (cavities in the center of the Skin)

 May block the ventricles, causing hydrocephalus (water on the

Skin)

 Sometimes extends to the spinal cord

 Common in children, and among men and women in their 40s and
50s

 Occurrence peaks at age five and again at age 34

 Accounts for two percent of all Skin tumors

Symptoms

 Severe headaches

 Nausea and vomiting

 Difficulty walking

 Fatigue and sleepiness

 Problems with coordination

 Neck pain or stiffness

 Visual problems

40
2.6.11 Rhabdoid Tumor

Characteristics

 Rare

 Highly aggressive and tends to spread throughout the CNS

 Often appears in multiple sites in the body, especially the kidneys

 Difficult to classify; may be confused with medulloblastoma or

PNETs

 Occurs most often in young children but can also occur in adults

Symptoms

 Vary depending on location of tumor in the Skin or body

 An orbital tumor may cause the eye to protrude

 Balance problems may occur

41
 Chapter-3
Segmentation algorithms

42
 CHAPTER 3

SEGMENTATION ALGORITHMS

Segmentation refers to the process of partitioning a digital image

into multiple segments (sets of pixels) (Also known as super pixels). The
goal of segmentation is to simplify and/or change the representation of an
image into something that is more meaningful and easier to analyze.
Image segmentation is typically used to locate objects and boundaries
(lines, curves, etc.) in images. More precisely, image segmentation is the
process of assigning a label to every pixel in an image such that pixels
with the same label share certain visual characteristics.

3.1 EDGE DETECTION

An edge is the boundary between two regions with relatively

distinct gray-level properties. Edge detection is a terminology in image
processing and computer vision, particularly in the areas of feature
detection and feature extraction, to refer to algorithms which aim at
identifying points in a digital image at which the image brightness
changes sharply or more formally has discontinuities.

3.1.1 SOBEL OPERATOR

The Sobel operator is used in image processing, particularly within

edge detection algorithms. Technically, it is a discrete differentiation
operator, computing an approximation of the gradient of the image
intensity function. At each point in the image, the result of the Sobel
operator is either the corresponding gradient vector or the norm of this
vector. The Sobel operator is based on convolving the image with a
small, separable, and integer valued filter in horizontal and vertical
direction and is therefore relatively inexpensive in terms of computations.

43
On the other hand, the gradient approximation which it produces is
relatively crude, in particular for high frequency variations in the image.
The operator consists of a pair of 3×3 convolution kernels as shown in
Figure. One kernel is simply the other rotated by 90°.

These kernels are designed to respond maximally to edges running

vertically and horizontally relative to the pixel grid, one kernel for each
of the two perpendicular orientations. The kernels can be applied
separately to the input image, to produce separate measurements of the
gradient component in each orientation (call these Gx and Gy). These can
then be combined together to find the absolute magnitude of the gradient
at each point and the orientation of that gradient. The gradient magnitude
is given by equation 3.1,

(3.1)

Typically, an approximate magnitude is computed using equation 3.2,

(3.2)

which is much faster to compute.

44
The angle of orientation of the edge (relative to the pixel grid) giving rise
to the spatial gradient is given by equation 3.3,

(3.3)

Figure 3.1 Original Skin MR Image

45
 Figure 3.2 Output of Edge Detection by Sobel Operator

3.1.2 CANNY OPERATOR

Canny (1986) considered the mathematical problem of deriving an

optimal smoothing filter given the criteria of detection, localization and
minimizing multiple responses to a single edge. He showed that the
optimal filter given these assumptions is a sum of four exponential terms.
He also showed that this filter can be well approximated by first-order
derivatives of Gaussians. Canny also introduced the notion of non-
maximum suppression, which means that given the presmoothing filters,
edge points are defined as points where the gradient magnitude assumes a
local maximum in the gradient direction.

Although his work was done in the early days of computer vision,
the Canny edge detector (including its variations) is still a state-of-the-art
edge detector. Unless the preconditions are particularly suitable, it is hard
to find an edge detector that performs significantly better than the Canny
edge detector.

The Canny-Deriche detector (Deriche 1987) was derived from

similar mathematical criteria as the Canny edge detector, although
starting from a discrete viewpoint and then leading to a set of recursive
filters for image smoothing instead of exponential filters or Gaussian
filters.

46
 Figure 3.3 Output of Edge Detection by Canny Operator

Fig 3.3 shows the edge detection output by applying the Canny operator.
Canny operator has detected not only the tumor region also detects the
unwanted artifacts.

3.1.3 PREWITT’S OPERATOR

Prewitt is a method of edge detection in image processing which

calculates the maximum response of a set of convolution kernels to find
the local edge orientation for each pixel.Prewitt operator is similar to the
Sobel operator and is used for detecting vertical and horizontal edges in
images.

47
 Various kernels can be used for this operation. The whole set of 8
kernels is produced by taking one of the kernels and rotating its
coefficients circularly. Each of the resulting kernels is sensitive to an
edge orientation ranging from 0° to 315° in steps of 45°, where 0°
corresponds to a vertical edge.

The maximum response for each pixel is the value of the

corresponding pixel in the output magnitude image. The values for the
output orientation image lie between 1 and 8, depending on which of the
8 kernels produced the maximum response.

This edge detection method is also called edge template matching,

because a set of edge templates is matched to the image, each
representing an edge in a certain orientation. The edge magnitude and
orientation of a pixel is then determined by the template that matches the
local area of the pixel the best.

The Prewitt edge detector is an appropriate way to estimate the

magnitude and orientation of an edge. Although differential gradient edge
detection needs a rather time-consuming calculation to estimate the
orientation from the magnitudes in the x- and y-directions, the Prewitt
edge detection obtains the orientation directly from the kernel with the
maximum response. The set of kernels is limited to 8 possible
orientations; however experience shows that most direct orientation
estimates are not much more accurate.

On the other hand, the set of kernels needs 8 convolutions for each
pixel, whereas the set of kernel in gradient method needs only 2, one
kernel being sensitive to edges in the vertical direction and one to the
horizontal direction. The result for the edge magnitude image is very
similar with both methods, provided the same convolving kernel is used.

48
 Figure 3.4 Output of Edge Detection by Prewitt Operator

Fig 3.4 shows the edge detection output by applying the Prewitt
operator. Like the Sobel operator, Prewitt operator detects only the
boundary of object.

3.1.4 ROBERT’S CROSS OPERATOR

The Roberts Cross operator performs a simple, quick to compute,

2-D spatial gradient measurement on an image. Pixel values at each point
in the output represent the estimated absolute magnitude of the spatial
gradient of the input image at that point.

The operator consists of a pair of 2×2 convolution kernels as

shown in Figure. One kernel is simply the other rotated by 90°. This is
very similar to the Sobel operator.

49
 These kernels are designed to respond maximally to edges running
at 45° to the pixel grid, one kernel for each of the two perpendicular
orientations. The kernels can be applied separately to the input image, to
produce separate measurements of the gradient component in each
orientation (call these Gx and Gy). These can then be combined together
to find the absolute magnitude of the gradient at each point and the
orientation of that gradient. The gradient magnitude is given by equation
3.4,

(3.4)

Although typically, an approximate magnitude is computed using

equation 3.5,

(3.5)

which is much faster to compute.

The angle of orientation of the edge giving rise to the spatial gradient
(relative to the pixel grid orientation) is given by:

50
3.2 HISTOGRAM EQUALIZATION

Histogram equalization is a method in image processing of contrast

adjustment using the image's histogram. This method usually increases
the global contrast of many images, especially when the usable data of
the image is represented by close contrast values. Through this
adjustment, the intensities can be better distributed on the histogram. This
allows for areas of lower local contrast to gain a higher contrast without
affecting the global contrast. Histogram equalization accomplishes this
by effectively spreading out the most frequent intensity values.

The method is useful in images with backgrounds and foregrounds

that are both bright or both dark. In particular, the method can lead to
better views of bone structure in x-ray images, and to better detail in
photographs that are over or under-exposed. A key advantage of the
method is that it is a fairly straightforward technique and an invertible
operator. So in theory, if the histogram equalization function is known,
then the original histogram can be recovered. The calculation is not
computationally intensive. A disadvantage of the method is that it is
indiscriminate. It may increase the contrast of background noise, while
decreasing the usable signal.

Figure 3.6 Histogram

51
 Figure 3.7 Output of Histogram equalized image

The spatial domain enhancement technique, histogram equalization

improves contrast of the MR image by reassigning the brightness values
of pixels based on the image histogram. Generally, images have unique
brightness histograms. Even images of different areas of the same
sample, in which the various structures present have consistent brightness
levels wherever they occur, will have different histograms, depending on
the area fraction of each structure. Here the pixel intensities are modified
by a position invariant transformation function. The traditional histogram
equalization method for MR image suffers from the following
drawbacks:

 It lacks of a mechanism to adjust the degree of enhancement.

52
  It often causes unpleasant visual artifacts, such as over
enhancement, level saturation and raised noise level.

 It could dramatically change the character of the image, e.g., the

average luminance (mean) of the image. Changing the overall
illumination of MR image will shifts the peaks in the histogram,
there is a very little scope to improve contrast by global
transformation.

3.3 THRESHOLDING TECHNIQUES

Thresholding is the simplest method of image segmentation. From

a grayscale image, thresholding can be used to create binary images.
During the thresholding process, individual pixels in an image are
marked as “object” pixels if their value is greater than some threshold
value (assuming an object to be brighter than the background) and as
“background” pixels otherwise. This convention is known as threshold
above. Variants include threshold below, which is opposite of threshold
above; threshold inside, where a pixel is labeled "object" if its value is
between two thresholds; and threshold outside, which is the opposite of
threshold inside (Shapiro, et al. 2001:83). Typically, an object pixel is
given a value of “1” while a background pixel is given a value of “0.”
Finally, a binary image is created by coloring each pixel white or black,
depending on a pixel's label.

53
3.4 REGION BASED SEGMENTATION

Region-based segmentation methods attempt to partition or group

regions according to common image properties. These image properties
consist of

1. Intensity values from original images, or computed values based

on an image operator

2. Textures or patterns that are unique to each type of region

3. Spectral profiles that provide multidimensional image data

These can be classified as two main classes

 Merging Algorithms - in which neighboring regions are compared

and merged if they are close enough in some property.

 Splitting Algorithms – in which large non-uniform regions are

broken up into small areas which may be uniform.

These algorithms which are combination of splitting and merging.

In all cases some uniformity criterion must be applied to decide if a
region should be split or two regions should be merged. This criterion is
based on some region property which will be decided by the application
and could be one of the measurable image attributes such as image mean
intensity, color, etc.,

54
 Fig 3.9 Output of region based segmentation

Fig 3.9 shows the segmented image by applying the region based
algorithm. From the output tumor regions are segmented exactly but the
drawback of region based algorithm is it is difficult to identify the seed
points.

3.5 FUZZY C-MEANS ALGORITHM

Fuzzy C-Means Clustering (FCM) is also known as Fuzzy

ISODATA, for clustering technique. The aim of FCM is to find cluster
centers (centroids) that minimize a dissimilarity function. The fuzzified
c-means algorithm (Bezdek in Jang et al., 1997) allows each data point to
belong to a cluster to a degree specified by a membership grade, and thus
each point may belong to several clusters. The FCM employs fuzzy
partitioning such that a data point can belong to all groups with different
membership grades between 0 and 1. FCM is an iterative algorithm and it
is a method of grouping the similar types of pixels in the image.

55
 Fuzzy c-means is different from hard c-means, mainly because it
employs fuzzy partitioning, where a point can belong to several clusters
with degrees of membership.

Clustering of numerical data forms the basis of many segmentation

and system modeling algorithms. The purpose of clustering is to identify
natural groupings of data from a large data set to produce a concise
representation of a system's behavior.

Fuzzy c-means (FCM) is a data clustering technique wherein each

data point belongs to a cluster to some degree that is specified by a
membership grade. This technique was originally introduced by Jim
Bezdek in 1981 [Bez81] as an improvement on earlier clustering
methods. It provides a method that shows how to group data points that
populate some multidimensional space into a specific number of different
clusters.

FCM starts with an initial guess for the cluster centers, which are
intended to mark the mean location of each cluster. The initial guess for
these cluster centers is most likely incorrect. Additionally, FCM assigns
every data point a membership grade for each cluster. By iteratively
updating the cluster centers and the membership grades for each data
point, FCM iteratively moves the cluster centers to the right location
within a data set. This iteration is based on minimizing an objective
function that represents the distance from any given data point to a
cluster center weighted by that data point's membership grade. By using
information returned by FCM to represent the fuzzy qualities of each
cluster.

A new cluster validity index is proposed that determines the

optimal partition and optimal number of clusters for fuzzy partitions

56
obtained from the fuzzy c-means algorithm. The proposed validity index
exploits an overlap measure and a separation measure between clusters.
The overlap measure, which indicates the degree of overlap between
fuzzy clusters, is obtained by computing an inter-cluster overlap. The
separation measure, which indicates the isolation distance between fuzzy
clusters, is obtained by computing a distance between fuzzy clusters.

A good fuzzy partition is expected to have a low degree of overlap

and a larger separation distance. Fuzzy cluster-validity criterion tends to
evaluate the quality of fuzzy c-partitions produced by fuzzy clustering
algorithms. Many functions have been proposed. Some methods use only
the properties of fuzzy membership degrees to evaluate partitions. Others
techniques combine the properties of membership degrees and the
structure of data. Major problems exist in both crisp and fuzzy clustering
algorithms. The fuzzy c-means type of algorithms use weights
determined by a power m of inverse distances that remains fixed over all
iterations and over all clusters, even though smaller clusters should have
a larger.

This method uses a different “distance” for each cluster that changes
over the early iterations to fit the clusters. Clustering refers to the process
of unsupervised partitioning of a data set based on a dissimilarity
measure, which determines the cluster shape. Considering that cluster
shapes may change from one cluster to another, it would be of the utmost
importance to extract the dissimilarity measure directly from the data by
means of a data model.

The fuzzy c-means (FCM) clustering algorithm has been

extensively used for pattern recognition. It has also been used in the
process of generating fuzzy rules from data. It has been used with success

57
in the soft segmentation of MR images and for the estimation of partial
volumes.

FCM partitions a collection of n vector Xi,i=1,2,3,……..,n. into

‘C’ fuzzy groups and finds the cluster center in each group such that a
cost function of dissimilarity measure is minimized. FCM employs fuzzy
partitioning such that a given data point can belong to several groups
with the degree of belongingness specified by membership grades
between 0 and 1.

The FCM algorithm is simply an iterative procedure. In a batch

mode operation FCM determines the cluster centers Ci and the
membership matrix U using following steps.

Step 1: Intialize the cluster centers the membership matrix U with

random values between 0 and 1 such that the following constraints are
satisfied

u
j 1
jk 1

Step 2: Calculate ‘C’ fuzzy cluster centers Ci,i=1,2,……..,C

Step 3: Compute the cost functions

 u 
n c
J m U , Y   E j  xk 
m
jk
k 1 j 1

Where,

Y={yi },is the set of centers of clusters.

Ej(xk), is a dissimilarity measure between the sample xk and the center yj

of a specific cluster j.

58
U=[ujk], is the c x n fuzzy c-partition matrix, containing the membership
values of all samples in all clusters.

m  (1,  ), is a control parameter of fuzziness.

Stop if either Jm below a certain tolerance or it is improved over

previous iteration.

Step 4: Compute a new U and repeat the steps until an optimum result is
obtained.

The performance depends on the initial cluster centers, thereby allowing

to run FCM several times, each starting with a different set of initial
cluster centers.

59
Figure 3.10 Output of FCM Algorithm

60
 Chapter-4
Project description

CHAPTER 4

PROJECT DESCRIPTION

4.1 BLOCK DIAGRAM

61
 Fig 4.1 BLOCK DIAGRAM

4.2 WATERSHED SEGMENTATION

The watershed algorithm is an image processing segmentation

algorithm that splits an image into areas, based on the topology of the
image. The length of the gradients is interpreted as elevation information.
During the successive flooding of the grey value relief, watersheds with
adjacent catchment’s basins are constructed. This flooding process is
performed on the gradient image, i.e. the basins should emerge along the
edges. Normally this will lead to an over-segmentation of the image,
especially for noisy image material, e.g. medical CT data. Either the
image must be pre-processed or the regions must be merged on the basis
of a similarity criterion afterwards.

A hierarchic watershed transformation converts the result into

a graph display (i.e. the neighbor relationships of the segmented regions
are determined) and applies further watershed transformations
recursively. A problem is that the watersheds will increase in width.

62
 The marker based watershed transformation performs
flooding starting from specific marker positions which have been either
explicitly defined by the user or determined with morphological
operators. Interactive watershed transformations allow to determine
include and exclude points to construct artificial watersheds. This can
enhance the result of segmentation.

Fig 4.2 Segmentation using Watershed Algorithm

The image on the left represents the type of result obtained from the
thresholding of classical images where Watershed segmentation is
efficient. This could be a picture of coffee beans, blood cells, sand ...
Concepts of Watershed segmentation is

 The concepts of watersheds and catchment basins are well known

in topography.

 Watershed lines divide individual catchment basins.

 The North American Continental Divide is a textbook example of a

watershed line with catchment basins formed by the Atlantic and
Pacific Oceans.

63
  Working the 2D function presentations, image data may be
interpreted as a topographic surface where the image gray-levels
represent altitudes.

 Thus, region edges correspond to high watersheds and low-

gradient region interiors correspond to catchment basins.

 The goal of region growing segmentation is to create homogeneous

regions.

 In watershed segmentation, catchment basins of the topographic

surface are homogeneous in the sense that all pixels belonging to
the same catchment basin are connected with the basin's region of
minimum altitude (gray-level) by a simple path of pixels that have
monotonically decreasing altitude (gray-level) along the path.

 Such catchment basins then represent the regions of the segmented

image.

One of the important drawbacks of watershed segmentation

algorithm is producing severe oversegmentation due sensitivity of noise.

Fig 4.3 Original MRI image

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 Fig 4.4 Enhanced Image

Fig 4.5 Boundary extraction of reconstructed image using watershed

algorithm

Fig 4.6 Boundary superimposed on original image

4.3 INDEPENDENT COMPONENT ANALYSIS

4.3.1 INTRODUCTION

Independent component analysis (ICA) is a computational method

for separating a multivariate signal into additive subcomponents
supposing the mutual statistical independence of the non-Gaussian source
signals.

65
 A simple application of ICA is the “cocktail party problem”,
where the underlying speech signals are separated from a sample data
consisting of people talking simultaneously in a room. The problem is
simplified by assuming no time delays and echoes. If N number of source
present, at least N observations are needed to get the original signals.
This constitutes the square

J=D
Where,
D = input dimension of the data
J = dimension of the model
There are two cases:
1. If (J < D) is underdetermined
2. If (J>D) is overdetermined

TYPES OF ICA

There are two types of ICA.They are

1 .Non Linear ICA

2. Linear ICA

(a) Linear Noiseless ICA

(b) Linear Noisy ICA

4.3.1.1 LINEAR NOISELESS ICA

The components xi is a random vector are generated as a sum of

the independent components sk, weighted by the mixing weights ai,k.The
generative formula is given by

x = As

X=Mixture; A=Mixing coefficients; S=Sources.

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 This is called ICA MODEL. This is done by adaptively calculating
the w vectors and setting up a cost function which either maximizes the
nongaussianity of the calculated by

sk = (wT * x)

ASSUMPTIONS

1. Linear mixing

2. Independence of sources

3. Non Gaussianity

(A) LINEAR MIXING

Linear mixing based on first and second order stastics are usually
optimal. When the linear transformation takes place it leads to
gaussianty.So limited amount of information can be separated into
independent components. But when this phenomenon takes place with
higher order stastics then it does not miss out extra information which
enhances the image quality.

(B) INDEPENDENCE OF SOURCE

If two random variables x and y are present in an image, they are

said to be independent if the information regarding x does not dependent
on y this is one of the key concept in independent component analysis.

(C) NON GAUSSIANITY

According to central limit theorem sum of non Gaussian variables

is closer to Gaussian original ones. Its non gaussianity will attain the

67
local maximum equal to independent components. This is because, if it
were the mixture of two are more components it would be closer to
Gaussian distribution but this is eliminated by central limit theorem. If
the contained data in an image is non Gaussian then their high order
statistics would contain extra information which makes the process
easier.

4.3.3 NEED FOR CLASSIFICATION

In magnetic resonance imaging (MRI), a set of slices are acquired

over time, and small differences in the intensity of the signal over time
are extracted. The first application of ICA to MRI data used spatial ICA
(SICA). SICA when applying ICA to MRI have several reasons:

The most important is that the spatial dimension is much larger

than the temporal dimension in MRI. By choosing a particular
component is examined through the spatial map using knowledge of Skin
structure and function. A spatial ICA analysis is performed on the data.

The application of SICA to MRI data is typically done in one of

two ways:

Consistently task-related components are then chosen by

correlating their time courses with the predicted waveform. Transiently
task-related components are also extracted by examination of those
components that are correlated, but not as highly correlated as the
consistently task-related component.

CLASSIFICATION OF ICA

1. Spatial Independent Component Analysis (SICA)

2. Temporal Independent Component Analysis (TICA)

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 Fig 4.7 BLOCK DIAGRAM OF SPATIAL AND TEMPORAL ICA

In spatial ICA, suppose X is an N-by-M matrix, where N is the

number of time points and M is the number of voxels. The “signals” are
the M spatial voxels , flattened to a 1-D vector, and there are thus N
different instances of these signals whereas TICA would consider the
signals the N individual time courses of which there are M instances.

The SICA decomposition can then be described as

C = W* X

W= N-by-N estimated linear mixing matrix

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C = N-by-M matrix with N independent components.

Now,

X = Wˆ -1*C

Where the spatially independent components (images) are located in the

rows of C.

In temporal ICA, X is an M-by-N matrix. The decomposition is

C = W* X

W= M-by-M estimated linear mixing matrix

C =M-by-N matrix containing the M independent component

Now, we can write

X = Wˆ -1*C

Where the temporally independent time courses are located in the

rows of C and the associated temporally independent maps (images) are
found in the columns of Wˆ -1.

Spatial independent components suits for MRI application because

number of voxels in MRI is independent of time space so it is
unpredictable. So SICA has good practical feasibility than the Temporal
independent component analysis.

4.3.4 PREPROCESSING STEPS IN ICA

The preprocessing method is used to segment the MR image and it

consists of two types:

1. CENTERING

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 2. WHITENING

4.3.4.1 CENTERING

The most basic and necessary pre-processing is to centre x, subtract its

mean vector m = E{x} where X is a zero-mean variable. This implies that
s is zero-mean as well, as can be seen by taking expectations on both
sides. This pre-processing is made solely to simplify the ICA algorithms.

4.3.4.2 WHITENING

ICA or statistical model is represented as X=AS, Where W= A -1,

this transformation takes place through the observed vector x linearly as
˜x which is white. The covariance matrix of ˜x equals the identity matrix

E{˜x˜xT } = I.

It reduces the number of parameters to be estimated by considering

the original matrix A, there are n2 parameters but we only need to
estimate the new, orthogonal mixing matrix ˜A.

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 Fig 4.8 Orthogonal Mixing Matrix

JOINT DISTRIBUTION OF WHITENED MIXTURES

Because whitening is a very simple and standard procedure, it

reduces the complexity and reduces the dimension of the data. When
considering in PCA it proceeds as follows:

1. Obtain data

2. Subtract the mean

3. Calculate the covariance matrix

4. Calculate the Eigen vector and Eigen value.

Thus the highest Eigen value is obtained as principle and it also

retains the lowest Eigen value which produces noise. But in ICA Eigen
values which are too small are discarded. Thus it enhances in reducing
the noise in an image.

4.4 COMPARISON OF PCA AND ICA

72
 The basis images found by PCA depend only on pair wise
relationships between pixels in the image database. In a task such as Skin
tumor detection, in which important information may be contained in the
high-order relationships among pixel so Independent component analysis
(ICA), a generalization of PCA, is one such method.

Applying PCA on MR Images where pixel location and Skin

images are treated as observation and measures respectively which leads
to maximum variability in pixels so the input does not throw high order
statistics. So, maximum amount of data cannot be separated.

Fig 4.8 PLOT OF ICA AND PCA

73
Chapter-5
Result

74
 CHAPTER 5

RESULT

Chapter-6
Conclusion

75
 CHAPTER 6

CONCLUSION

The results show that Watershed Segmentation can successfully

segment a tumor provided the parameters are set properly. The watershed
method did not require an initialization while the others require an
initialization inside the tumor. The visualization and quantitative
evaluations of the segmentation results demonstrate the effectiveness of
this approach. Watershed Segmentation algorithm performance is better
for the cases where the intensity level difference between the tumor and
non tumor regions is higher. It can also segment non homogenous tumors
providing the non homogeneity is within the tumor region. This paper
proves that methods aimed at general purpose segmentation tools in
medical imaging can be used for automatic segmentation of Skin tumors.

The quality of the segmentation was similar to manual

segmentation and will speed up segmentation in operative imaging.
Among the segmentation methods investigated, the watershed
segmentation is marked out best out of all others. The user interface in
the main application must be extended to allow activation of the
segmentation and to collect initialization points from a pointing device
and transfer them to the segmentation module. Finally the main program

76
must receive the segmented image and present the image as an opaque
volume and the type of the tumor is also detected using ICA Algorithm.

appendix

77
 APPENDIX

clc;

s=input('ENTER THE IMAGE FILE NAME TO

TRAIN::','s');

i=imread(s);

k=trainimage_filtering(i);

figure,imshow(k);

title('FILTERED IMAGE');

n1=imcrop(k);

n2=imcrop(k);

dd=trainimage_segment(n2);

f=ica_training(n1,n2);

78
disp(f);

if(f>248 || f<256)

figure,imshow('tissue1.bmp');

title('ASTROCYTOMA');

disp('detected tumour is astrocytoma'); display disease name

elseif(f>224 || f<228)

figure,imshow('tissue2.bmp');

title(' GLIOBLASTOMA');

disp('detected tumour is glioblastoma'); display disease name

elseif(f>238 || f<240)

figure,imshow('tissue3.bmp');

title(' LYMPHOMA');

disp('detected tumour is lymphoma');

elseif(f>263 || f<290)

figure,imshow('tissue4.bmp');

title(' MENINGLOMA');

disp('detected tumour is meningioma');

else

disp('unknown detected or no tumour found');

79
 end

disp('project completed successfully');

function [k]=trainimage_filtering(i)

d=rgb2gray(i);

c=input('ENTER THE CORRESPONDING VALUE FOR

FILTERING:1-SOBEL,2-PREWITT,3-MEDIAN,4-LAPLACIAN:');

switch (c)

case 1

h=fspecial('sobel');

k=imfilter(d,h);

case 2

h=fspecial('prewitt');

k=imfilter(d,h);

case 3

k= medfilt2(d,[5 5]);

otherwise

h=fspecial('laplacian');

k=imfilter(d,h);

end

80
Explanation for User Defined Function Segmentation:

function [n1]=trainimage_segment(g)

BW = edge(g,'canny',0.2);

[imx,imy]=size(BW);

msk=[0 0 0 0 0;

0 1 1 1 0;

0 1 1 1 0;

0 1 1 1 0;

0 0 0 0 0;];

B=conv2(double(BW),double(msk));

L = bwlabel(B,8);

mx=max(max(L));

[r,c] = find(L==2);

rc = [r c];

[sx sy]=size(rc);

n1=zeros(imx,imy);

for i=1:sx

x1=rc(i,1);

y1=rc(i,2);

81
n1(x1,y1)=255;

end

RGB = label2rgb(B);

figure,imshow(RGB,[]);

title('SEGMENTED IMAGE(AFFECTED REGION');

end

function[hss]=ica_training(v1,v2)

M = 2;

N = 100;

v1=double(v1);

v2=double(v2);

v1=v1(1:N);

v2=v2(1:N);

v=[v1,v2];

A=ones(1,N*2);

x =v.*A;

W = eye(1,N*2);

y = x.*W;

maxiter=100;

82
 eta=1;

/*****************************************************/

CHAPTER 7
References

83
 CHAPTER 7

BIBLIOGRAPHY

1. ICGST-GVIP Journal, ISSN 1687-398X, Volume (9), Issue (III),

June’09

2. L.P. Clarke, R.P.Velthuizen, M.A. Camacho, J.J. Heine, M

Vaidyanathan, L.O. Hall, R.W. Thatcher, and M.L. Silbinger: MRI

Segmentation: Methods and Applications. Magnetic Resonance
Imaging, 1995.

3. Medical image analysis, volume 2, issue 2,march 1998.

4. Information Technology in Biomedicine, IEEE Transactions on sep

2005.

5. Medical Image Computing and Computer-Assisted Intervention

6. MICCAI,2002. Indian Journal of Science and Technology Vol.2

No 2 (Feb. 2009) ISSN: 0974- 6846

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7. Jonathan sachs (1996)”Digital Image Basics”.

8. www.icgst.com

9. www.ieeeexplorer.com

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