AUTOMATIC TUMOR DETECTION AND CLASSIFICATION OF BRAIN IMAGE

A PROJECT REPORT Submitted by

KALIDAS.U KANIMOZHI.K KANIMOZHI.T RAJESH.V

72306106019 72306106020 72306106021 72306106046

In partial fulfillment for the award of the degree of

BACHELOR OF ENGINEERING in ELECTRONICS AND COMMUNICATION ENGINEERING of ANNA UNIVERSITY, CHENNAI 600 025
DEPARTMENT OF ELECTRONICS AND COMMUNICATION ENGINEERING VELALAR COLLEGE OF ENGINEERING AND TECHNOLOGY ERODE-638 012. APRIL 2010

VELALAR COLLEGE OF ENGINEERING AND

TECHNOLOGY, ERODE- 9. DEPARTMENT OF ELECTRONICS AND COMMUNICATION ENGINEERING
1

Certificate

BONAFIDE CERTIFICATE
This is to certify that, the project report titled AUTOMATIC TUMOR DETECTION AND CLASSIFICATION OF BRAIN IMAGE is the bonafide work of

KALIDAS.U KANIMOZHI.K KANIMOZHI.T RAJESH.V

72306106019 72306106020 72306106021 72306106046

Submitted in partial fulfillment of the requirements for the degree of BACHELOR OF ENGINEERING during the year 2006-2010.

Dr.K.VENKATACHALAM, M.Tech., Ph.D.,

Mrs. J.NANDHINI B.E.,

HEAD OF THE DEPARTMENT DEPARTMENT OF ECE

SUPERVISOR & LECTURER DEPARTMENT OF ECE

Submitted for the university examination held on 08.04.2010 & 09.04.2010

INTERNAL EXAMINER

EXTERNAL EXAMINER

Acknowledgement

ACKNOWLEDGEMENT

We are privileged to express our heartfelt thanks to our honorable secretary Mr.S.D.CHANDRASEKAR B.A., who provided all the facilities to build our project. We hereby thank our former Principal and Administrative Director Dr. P. SABAPATHI B.E. (Hons.), M.Sc., (Engg.), Ph.D., and our Principal Dr. K.PALANISWAMY, M.E., Ph.D., who have been a great inspiration not only for this project but also throughout this course of study. We express our profound gratitude to our beloved Head of the Department Dr. K. VENKATACHALAM, M.Tech., (PhD) who laconically brought us to the processor world. We are highly indebted to our gregarious guide

Mrs.J.NANDHINI for her valuable guidance, advice and helps rendered whenever we approached her in times of need. We express our sincere thanks to our project coordinator Dr.T.BALAKUMARAN,M.E., Phd., for their guidance to complete our project successfully. We are also highly thankful to all our indefatigable staff members and non teaching staffs for helping us throughout the completion of the project.

Abstract

AUTOMATIC TUMOR DETECTION AND CLASSIFICATION OF BRAIN IMAGE

ABSTRACT: Segmentation of anatomical regions of the brain is the fundamental problem in medical image analysis. In this paper, a brain tumor segmentation method has been developed and validated segmentation on 2D MRI Data. This method can segment a tumor provided that the desired parameters are set properly. This method does not require any initialization while the others require an initialization inside the tumor. In our segmentation approach watershed segmentation algorithm is used. Watershed uses the intensity as a parameter to segment the whole image data set. The input MRI image is preprocessed and loaded into matlab workspace. In the segmentation process the image is divided into blocks depending on the edge, gray and threshold parameter. The blocks are divided by comparing the intensity value of the image with the parameters as the intensity of the tumor affected area will be higher. Likewise the tumor surface from the MRI image is segmented out. After the detection of the tumor it is then classified using ICA algorithm which gives the type of the tumor for the doctors convenience. Here the threshold limit is applied to each image and the limit is tested on the ICA applied algorithm. According to the intensity, tumor is classified into ASTROCYTOMA, GLIOBLASTOMA, LYMPHOMA, MENINGLOMA

Table of contents

TABLE OF CONTENT CHAPTE R NO ABSTRACT LIST OF FIGURES LIST OF ABBREVATION INTRODUCTION LITERATURE REVIEW 2.1 IMAGING TECHNIQUES 2.1.1 Electron microscopy 2.1.2 Fluoroscopy 2.1.3 X Rays 2.1.3.1 Projection radiography 2.1.3.2 Computer tomography 2.1.3.3 Angiogram 2.1.4 Mammography 2.1.5 Magnetic Resonance Imaging 2.1.6 Ultrasonography 2.1.7 Thermography 2.1.8 Positron Emission Tomography 2.1.9 Photo Acoustic Imaging 2.1.10 Endoscopic Imaging 2.2 BRAIN TUMOR AND STAGES 2.2.1 Introduction 2.2.2 Stages of tumor 2.3 CAUSES OF BRAIN TUMOR 2.3.1 Race 2.3.2 Age 2.3.3 Family history ii 2.4 SYMPTOMPS OF BRAIN TUMOR 2.4.1 Head ache 2.4.2Seizures 2.4.3 Nausea and vomiting 2.4.4 Behavioural and cognitive Problems 2.5 TESTS AND DIAGNOSIS 2.5.1 A Neurological exam 2.5.2 Imaging test 2.5.3 Biopsy
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PAGE TITLE NO i v vi 1 4 4
4

1. 2.

5 5
5

6 8 9 11 12 13 14 14 15 15 16 17 17 17 17 18 18 18 18 19 19 19 19 19 20

2.6 TYPES OF TUMOR 2.6.1 Acoustic Neuroma 2.6.2 Astrocytom 2.6.2.1 Pilocytic Astrocytoma 2.6.2.2 Low-grade Astrocytoma 2.6.2.3 Anaplastic Astrocytoma 2.6.2.4 Anaplastic Astrocytoma 2.6.3 Glioblastoma multiframe 2.6.4 Chordoma 2.6.5 CNS Lymphoma 2.6.6 Craniopharyngioma 2.6.7 Brain stem Glioma 2.6.8 Meningioma 2.6.9 Schwannoma 2.6.10 Ependymoma 2.6.11 Rhabdoid tumor 3. SEGMENTATION ALGORITHMS 3.1 EDGE DETECTION 3.1.1 Sobel operator iii 3.1.2 Canny operator 3.1.3 Prewitts operator 3.1.4 Robertts cross operator 3.2 HISTOGRAM EQUALIZATION 3.3 THRESHOLDING TECHNIQUES 3.4 REGION BASD SEGMENTATION 3.5 FUZZY C-MEANS ALGORITHM PROJECT DESCRIPTION 4.1 BLOCK DIAGRAM 4.2 WATERSHED SEGMENTATION 4.3 INDEPENDENT COMPONENT ANALYSIS 4.3.1 Introduction 4.3.1.1 Linear noiseless ICA 4.3.2 Need for classification 4.3.3 Preprocessing steps in ICA 4.3.3.1 Centering 4.3.3.2 Whitening 4.4 COMPARISION OF PCA AND ICA RESULT CONCLUSION APPENDIX
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20 20 21 21 21 22 22 23 23 24 25 26 27 29 29 31 32 32 32 35 36 38 40 42 44 45 50 50 50 55 55 56 57 60 60 60 62 63 65 66

4.

5. 6.

7.

REFERENCE

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iv

12

List of figures

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LIST OF FIGURES

FIGUR E NO 2.1 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8

TITLE Computer Tomography Original Brain MR Image Output of Edge Detection by Sobel Operator Output of Edge Detection by Canny Operator Output of Edge Detection by Prewitt Operator Output of Edge Detection by Roberts Operator Histogram Output of Histogram Equalized Image Output for Various Threshold Values Output of Region Based Segmentation Output of FCM Algorithm Block Diagram Segmentation using Watershed Algorithm Original MR Image Enhanced Image Boundary Extraction of Reconstructed Image Boundary Super Imposed on Original Image Block Diagram of Spatial and Temporal ICA Plot of ICA and PCA

PAGENO 7 34 34 36 38 40 41 41 43 45 49 50 51 53 53 54 54 58 62

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LIST OF ABBREVATIONS

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

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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 brain 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 brain. It has rapidly evolved into an accepted modality for medical imaging of disease processes in the musculoskeletal system, especially the foot and brain 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 brain. MRI has the added advantage of being able to produce images which slice through the brain 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
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patient without open surgery. More specifically the aim for this work is to segment a tumor in a brain. This will make the surgeon able to see the tumor and then ease the treatment. 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 brain 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. has Here been Watershed used for segmentation based algorithm

detection of tumor. Watershed segmentation uses the intensity as a parameter to segment the whole image data set. Moreover, the additional complexity Among of all estimation imposed to other algorithms causes a tendency towards density dependent approaches. 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.
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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 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 brain tumor and its types. The fourth chapter gives a literature survey of various segmentation algorithms available for brain 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 highlymagnified 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
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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 Transmission Electron Microscope (TEM) Scanning Electron Microscope (SEM) Reflection Electron Microscope (REM) 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
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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 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 threedimensional object. This means that structures can overlap in the final image, even though they are completely separate in the object. This is
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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 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.

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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

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absorbing the x-rays), is added to the blood to make it visible on the xray images. 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
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United States Preventive Services Task Force recommends screening mammography, with or without clinical breast examination, every 1-2 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.

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2.1.5 MAGNETIC RESONANCE IMAGING (MRI) 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 (brain), 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.

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These are created by turning gradients coils on and off which creates the knocking sounds heard during an MR scan. 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 90014,000 nanometers or 0.914 m) 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 brain 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
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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. BRAIN TUMOR AND ITS STAGES 2.2.1 INTRODUCTION The brain tumor is an abnormal growth of cells within the brain. Brain tumors can be
1. Benign (Non-cancerous)

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2. Malignant(Cancerous) Benign brain tumors do not contain cancer cells. Usually, benign tumors can be removed, and they seldom grow back. The border or edge of a benign brain 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 brain and cause serious health problems. Unlike benign tumors in most other parts of the body, benign brain tumors are sometimes life threatening. Very rarely, a benign brain tumor may become malignant. Malignant brain tumors contain cancer cells. Malignant brain tumors are generally more serious and often are lives threatening. They are likely to grow rapidly and crowd or invade the surrounding healthy brain tissue. Very rarely; cancer cells may break away from a malignant brain tumor and spread to other parts of the brain, 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 BRAIN TUMOR 2.3.1 RACE Brain tumors occur more often among white people than among people of other races. 2.3.2 AGE Most brain tumors are detected in people who are 70 years old or older. However, brain tumors are the second most common cancer in children. (Leukemia is the most common childhood cancer.) Brain 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 brain tumor.

Formaldehyde - Pathologists and embalmers who work with

formaldehyde have an increased risk of developing brain cancer. Scientists have not found an increased risk of brain cancer among other types of workers exposed to formaldehyde.
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 Vinyl chloride - Workers who make plastics may be exposed to

vinyl chloride. This chemical may increase the risk of brain tumors.
Acrylonitrile - People who make textiles and plastics may be

exposed to acrylonitrile. This exposure may increase the risk of brain cancer. 2.4 SYMPTOMS OF BRAIN 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 brain tumor. Many - perhaps most - people get headaches at some point in their life, so this is not a definite sign of brain 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 brain 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

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person may exhibit while having a seizure. Approximately 10% of the population will experience a single seizure in their lifetime. 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 brain 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 brain that could be affected by a brain tumor. 2.5.2 IMAGING TESTS. Magnetic resonance imaging (MRI) is commonly used to help diagnose brain tumors. MRI uses magnetic fields and radio waves to generate images of the brain. 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,
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including functional MRI, perfusion MRI and magnetic resonance spectroscopy. 2.5.3 BIOPSY. A biopsy can be performed as part of an operation to remove the brain tumor, or a biopsy can be performed using a needle. A stereo tactic needle biopsy may be done for brain tumors in hard to reach areas or very sensitive areas within your brain 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

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Tinnitus (ringing in the ear) Tingling or numbness in the face Walking and balance problems 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, brain stem and cerebellum

Occurs most often in children and teens Accounts for two percent of all brain 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 lowgrade 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

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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. 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 brain 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 brain tumors

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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 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 brain 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

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Invades the bone and soft tissues but rarely the brain tissue Can block the ventricles, causing hydrocephalus Can metastasize (spread) or recur

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 brain, commonly in the areas adjacent to the ventricles

Can be primary (originating in the brain) or secondary

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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 Accounts for three percent of all brain 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 brain 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

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Symptoms

Headaches Visual changes Weight gain Delayed development in children

2.6.7 Brain Stem Glioma Characteristics

Named for its location at the base of the brain 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

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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 brain and spinal cord. As they grow, meningiomas compress adjacent brain tissue. Symptoms are often related to this compression of brain 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 brain 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

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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 brain 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 brain 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

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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 brain 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 brain). 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.
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Characteristics

Usually localized to one area of the brain Develops from cells that line the hollow cavities at the bottom of the brain 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 brain) May block the ventricles, causing hydrocephalus (water on the brain)

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 brain tumors

Symptoms

Severe headaches Nausea and vomiting Difficulty walking Fatigue and sleepiness Problems with coordination Neck pain or stiffness Visual problems
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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 brain or body An orbital tumor may cause the eye to protrude Balance problems may occur

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Chapter-3 Segmentation algorithms

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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.
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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 33 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.

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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 Brain MR Image

Figure 3.2 Output of Edge Detection by Sobel Operator

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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 nonmaximum 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.

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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 PREWITTS 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.

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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.
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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 ROBERTS 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 22 convolution kernels as shown in Figure. One kernel is simply the other rotated by 90. This is very similar to the Sobel operator.

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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:

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Figure 3.5 Output of Edge Detection by Roberts Operator Fig 3.5 shows the edge detection output by applying the Robert operator. From the above outputs, all operators have failed to detect the tumor location. 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
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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

Figure 3.7 Output of Histogram equalized image

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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. 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
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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.

Thresholding Between 100-200

Thresholding Between 175-200

Thresholding Between 200-225

Thresholding above 240

Figure 3.8 Output for various Threshold values

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Fig 3.8 shows the output images by applying various threshold values. The drawbacks of thresholding includes Threshold selection is not always straightforward. Pixels assigned to a single class need not form coherent regions as the spatial locations of pixels are completely ignored. 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

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and could be one of the measurable image attributes such as image mean intensity, color, etc.,

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
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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. 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.
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A new cluster validity index is proposed that determines the optimal partition and optimal number of clusters for fuzzy partitions 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.

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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 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
J m (U , Y )
k =1 n

( u )
c j =1 jk

E j ( xk )

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

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Ej(xk), is a dissimilarity measure between the sample xk and the center yj of a specific cluster j. 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.

Figure 3.10 Output of FCM Algorithm

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Chapter-4 Project description

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CHAPTER 4 PROJECT DESCRIPTION 4.1 BLOCK DIAGRAM

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 catchments 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
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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. 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.

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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.

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 lowgradient 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.

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Fig 4.3 Original MRI image

Fig 4.4 Enhanced Image

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Fig 4.5 Boundary extraction of reconstructed image using watershed algorithm

Fig 4.6 Boundary superimposed on original image

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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. 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
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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. 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.

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(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 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 brain 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:
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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)

Fig 4.7 BLOCK DIAGRAM OF SPATIAL AND TEMPORAL ICA

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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 C = N-by-M matrix with N independent components. Now, X = W -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 = W -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 W -1.
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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 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{xxT } = 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
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The basis images found by PCA depend only on pair wise relationships between pixels in the image database. In a task such as brain 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 brain 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

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Chapter-5 Result

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CHAPTER 5 RESULT OUTPUT OF CLASSIFIED TUMOR

Tumor Image 1

GLIOBLASTOMA

Tumor Image 2

ASTROCYTOMA

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Tumor Image 3

LYMPHOMA

Tumor Image 4

MENINGLOMA

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Chapter-6 Conclusion

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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 brain 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 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.

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appendix

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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); disp(f); if(f>248 || f<256) figure,imshow('tissue1.bmp'); title('ASTROCYTOMA');

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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'); end disp('project completed successfully'); function [k]=trainimage_filtering(i) d=rgb2gray(i);

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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 Explanation for User Defined Function Segmentation: function [n1]=trainimage_segment(g) BW = edge(g,'canny',0.2); [imx,imy]=size(BW);
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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); n1(x1,y1)=255; end RGB = label2rgb(B); figure,imshow(RGB,[]);

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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; eta=1; /*****************************************************/

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CHAPTER 7 References

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CHAPTER 7 BIBLIOGRAPHY
1. ICGST-GVIP Journal, ISSN 1687-398X, Volume (9), Issue (III),

June09
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

7. Jonathan sachs (1996)Digital Image Basics. 8. www.icgst.com 9. www.ieeeexplorer.com

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