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Medical Image Processing Using MATLAB 2016

Some Aspects of Digital Image Processing


Introduction to Medical Imaging
Medical imaging is the technique and process of creating visual representations of the
interior of a body for clinical analysis and medical intervention. Medical imaging
seeks to reveal internal structures hidden by the skin and bones, as well as to diagnose
and treat disease. Medical imaging also establishes a database of normal anatomy and
physiology to make it possible to identify abnormalities. Although imaging of
removed organs and tissues can be performed for medical reasons, such procedures
are usually considered part of pathology instead of medical imaging.

As a discipline and in its widest sense, it is part of biological imaging and


incorporates radiology which uses the imaging technologies of X-ray Radiography,
Magnetic Resonance Imaging, Medical Ultrasonography or Ultrasound, Endoscopy,
Elastography, Tactile Imaging, Tomography, Medical Photography and Nuclear
Medicine Functional Imaging Techniques as Positron Emission Tomography.

Measurement and recording techniques which are not primarily designed to produce
images, such as electroencephalography (EEG), magneto encephalography (MEG),
electrocardiography (ECG), and others represent other technologies which produce
data susceptible to representation as a parameter graph vs. time or maps which contain
information about the measurement locations. In a limited comparison these
technologies can be considered as forms of medical imaging in another discipline.

Up until 2010, 5 billion medical imaging studies had been conducted worldwide.
Radiation exposure from medical imaging in 2006 made up about 50% of total
ionizing radiation exposure in the United States.

In the clinical context, "invisible light" medical imaging is generally equated to


radiology or "clinical imaging" and the medical practitioner responsible for
interpreting (and sometimes acquiring) the image, is a radiologist. "Visible light"
medical imaging involves digital video or still pictures that can be seen without
special equipment. Dermatology and wound care are two modalities that use visible
light imagery. Diagnostic radiography designates the technical aspects of medical
imaging and in particular the acquisition of medical images. The radiographer or
radiologic technologist is usually responsible for acquiring medical images of
diagnostic quality, although some radiological interventions are performed by
radiologists.

As a field of scientific investigation, medical imaging constitutes a sub-discipline of


biomedical engineering, medical physics or medicine depending on the context:
Research and development in the area of instrumentation, image acquisition (e.g.
radiography), modelling and quantification are usually the preserve of biomedical
engineering, medical physics, and computer science; Research into the application
and interpretation of medical images is usually the preserve of radiology and the
medical sub-discipline relevant to medical condition or area of medical science
(neuroscience, cardiology, psychiatry, psychology, etc.) under investigation. Many of

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Medical Image Processing Using MATLAB 2016

the techniques developed for medical imaging also have scientific and industrial
applications.

Medical imaging is often perceived to designate the set of techniques that


noninvasively produce images of the internal aspect of the body. In this restricted
sense, medical imaging can be seen as the solution of mathematical inverse problems.
This means that cause (the properties of living tissue) is inferred from effect (the
observed signal). In the case of medical ultrasonography, the probe consists of
ultrasonic pressure waves and echoes that go inside the tissue to show the internal
structure. In the case of projectional radiography, the probe uses X-ray radiation,
which is absorbed at different rates by different tissue types such as bone, muscle and
fat.

A CT scan image showing a ruptured abdominal aortic aneurysm

Digital Image Representation


An image may be defined as a two-dimensional function fxy(,), where x and y are
spatial (plane) coordinates, and the amplitude of fat any pair of coordinates is called
the intensity of the image at that point. The term gray level is used often to refer to the
intensity of monochrome images. Colour images are formed by a combination of
individual images. For example, in the RGB colour system a colour image consists of
three individual monochrome images, referred to as the red (R), green (G), and blue
(B) primary (or component) images. For this reason, many of the techniques
developed for monochrome images can be extended to colour images by processing
the three component images individually. An image may be continuous with respect
to the x- and y-coordinates, and also in amplitude. Converting such an image to digital
form requires that the coordinates, as well as the amplitude, be digitized. Digitizing
the coordinate values is called sampling; digitizing the amplitude values is called
quantization. Thus, when x, y, and the amplitude values of f are all finite, discrete
quantities, we call the image a digital image.

Applications of Digital Image Processing


Some of the major fields in which digital image processing is widely used are
mentioned below

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Medical Image Processing Using MATLAB 2016

 Image sharpening and restoration

 Medical field

 Remote sensing

 Transmission and encoding

 Machine/Robot vision

 Colour processing

 Pattern recognition

 Video processing

 Microscopic Imaging

 Others

Applications in Medical Field


The common applications of DIP in the field of medical is

1. Gamma ray imaging


2. PET scan
3. X-Ray Imaging
4. Medical CT
5. UV imaging

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Medical Image Processing Using MATLAB 2016

Images and MATLAB


Introduction
This example introduces some basic image processing concepts. The example starts
by reading an image into the MATLAB workspace. The example then performs some
contrast adjustment on the image. Finally, the example writes the adjusted image to a
file.

Step 1: Read and Display an Image


First, clear the MATLAB workspace of any variables and close open figure windows.

Clear,close all

To read an image, use the imread command. The example reads one of the sample
images included with the toolbox, pout.tif, and stores it in an array named I.

I = imread('pout.tif');

imread infers from the file that the graphics file format is Tagged Image File Format
(TIFF). For the list of supported graphics file formats, see the imread function
reference documentation.

Now display the image. The toolbox includes two image display functions: imshow
and imtool.imshow is the toolbox's fundamental image display function.

imshow(I)

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Medical Image Processing Using MATLAB 2016

Step 2: Check How the Image Appears in the Workspace


To see how the imread function stores the image data in the workspace, check the
Workspace browser in the MATLAB desktop. The Workspace browser displays
information about all the variables you create during a MATLAB session. The
imread function returned the image data in the variable I, which is a 291-by-240
element array of uint8 data. MATLAB can store images as uint8, uint16, or
double arrays.

You can also get information about variables in the workspace by calling the whos
command.

whos

MATLAB responds with

Name Size Bytes Class Attributes

I 291x240 69840 uint8

Step 3: Improve Image Contrast


pout.tif is a somewhat low contrast image. To see the distribution of intensities in
pout.tif, you can create a histogram by calling the imhist function. (Precede the call
to imhist with the figure command so that the histogram does not overwrite the
display of the image I in the current figure window.)

figure, imhist(I)

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Medical Image Processing Using MATLAB 2016

intensity histogram of the original unprocessed image.

Notice how the intensity range is rather narrow. It does not cover the potential range
of [0, 255], and is missing the high and low values that would result in good contrast.

The toolbox provides several ways to improve the contrast in an image. One way is to
call the histeq function to spread the intensity values over the full range of the
image, a process called histogram equalization.

I2 = histeq(I);

Display the new equalized image, I2, in a new figure window.

figure, imshow(I2)

Equalized Version of pout.tif

We call imhist again to create a histogram of the equalized image I2. If you
compare the two histograms, the histogram of I2 is more spread out than the
histogram of I1.

figure, imhist(I2)

Step 4: Write the Image to a Disk File


To write the newly adjusted image I2 to a disk file, use the imwrite function. If
you include the filename extension '.png', the imwrite function writes the image
to a file in Portable Network Graphics (PNG) format, but you can specify other
formats.

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imwrite (I2, 'pout2.png');

Step 5: Check the Contents of the Newly Written File


To see what imwrite wrote to the disk file, use the imfinfo function.

imfinfo('pout2.png')

The imfinfo function returns information about the image in the file, such as its
format, size, width, and height. See Getting Information about a Graphics File for
more information about using imfinfo.

ans =

Filename: 'pout2.png'

FileModDate: '29-Dec-2005 09:34:39'

FileSize: 36938

Format: 'png'

FormatVersion: []

Width: 240

Height: 291

BitDepth: 8

ColorType: 'grayscale'

The above example is a preliminary image processing task that can be handled by the
MATLAB. We can do a lot more things like image analysis, element counting,
sharpening of the image, modifying blurred images, adding or subtracting images etc
by MATLAB. Some image examples are processed through MATLAB in the section.

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Medical Image Processing Using MATLAB 2016

Introduction to MATLAB
What is MATLAB?
MATLAB is widely used in all areas of applied mathematics, in education and
research at universities, and in the industry. MATLAB stands for MATrixLABoratory
and the software is built up around vectors and matrices. This makes the software
particularly useful for linear algebra but MATLAB is also a great tool for solving
algebraic and differential equations and for numerical integration. MATLAB has
powerful graphic tools and can produce nice pictures in both 2D and 3D. It is also a
programming language, and is one of the easiest programming languages for writing
mathematical programs. MATLAB also has some tool boxes useful for signal
processing, image processing, optimization, etc.

How to start MATLAB


Mac: Double-click on the icon for MATLAB.

PC: Choose the submenu "Programs" from the "Start" menu. From the "Programs"
menu, open the "MATLAB" submenu. From the "MATLAB" submenu, choose
"MATLAB".

Unix: At the prompt, type matlab

You can quit MATLAB by typing exit in the command window.

The MATLAB environment


The MATLAB environment (on most computer systems) consists of menus, buttons
and a writing area similar to an ordinary word processor. There are plenty of help
functions that you are encouraged to use. The writing area that you will see when you
start MATLAB, it is called the command window. In this window you give the
commands to MATLAB. For example, when you want to run a program you have
written for MATLAB you start the program in the command window by typing its
name at the prompt. The command window is also useful if you just want to use
MATLAB as a scientific calculator or as a graphing tool. If you write longer
programs, you will find it more convenient to write the program code in a separate
window, and then run it in the command window.

In the command window you will see a prompt that looks like >>. You type your
commands immediately after this prompt. Once you have typed the command you
wish MATLAB to perform, press <enter>. If you want to interrupt a
command that MATLAB is running, type <ctrl> + <c>.

The commands you type in the command window are stored by MATLAB and can be
viewed in the Command History window. To repeat a command you have already
used, you can simply double-click on the command in the history window, or use the

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Medical Image Processing Using MATLAB 2016

<up arrow> at the command prompt to iterate through the commands you have used
until you reach the command you desire to repeat.

Useful functions and operations in MATLAB


Using MATLAB as a calculator is easy.

Example: Compute. 5*sin(2.5^(3-pi))+1/75

In MATLAB this is done by simply typing

>> 5*sin(2.5^(3-pi))+1/75

ans =

3.8617

Note that MATLAB is case sensitive. This means that MATLAB knows a difference
between letters written as lower and upper case letters. For example, MATLAB will
understand sin(2) but will not understand Sin(2).

Here is a table of useful operations, functions and constants in MATLAB.

MATLAB
Operation, function or constant
command
+ (addition) +
- (subtraction) -
× (multiplication) *
/ (division) /
|x| (absolute value of x) abs(x)
square root of x sqrt(x)
ex exp(x)
ln x (natural log) log(x)
log10 x (base 10 log) log10(x)
sin x sin(x)
cos x cos(x)
tan x tan(x)
cot x cot(x)
arcsin x asin(x)
arccos x acos(x)

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Medical Image Processing Using MATLAB 2016

arctan x atan(x)
arccot x acot(x)
n! (n factorial) gamma(n+1)
e (2.71828...) exp(1)
(3.14159265...) Pi
i (imaginary unit, sqrt(-1)) I

Obtaining Help on MATLAB commands


To obtain help on any of the MATLAB commands, you simply need to type

>> help <command>at the command prompt.

For example, to obtain help on the gamma function, we type at the command prompt:

>> help gamma

Try this now. You may also get help about commands using the "Help Desk", which
can be accessed by selecting the MATLAB Help option under the Help menu.

Note that the description MATLAB returns about the command you requested help on
contains the command name in ALL CAPS. This does not mean that you use this
command by typing it in ALL CAPS. In MATLAB, you almost always use all lower
case letters when using a command.

Variables in MATLAB
We can easily define our own variables in MATLAB. Let's say we need to use the
value of 3.5 sin (2.9) repeatedly. Instead of typing 3.5*sin (2.9)over and
over again, we can denote this variable as x by typing the following:

>> x=3.5*sin (2.9)

x =

0.8374

Now type:

>> x+1

ans =

1.8374

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Medical Image Processing Using MATLAB 2016

Note that we did not need to declare x as a variable that is supposed to hold a
floating point number as we would need to do in most programming languages.

Often, we may not want to have the result of a calculation printed-out to the command
window. To supress this output, we put a semi-colon at the end of the command;
MATLAB still performs the command in "the background". If you defined x as
above, now type

>> y=2*x;

>> y

y =

1.6747.

In many cases we want to know what variables we have declared. We can do this by
typing whos. Alternatively, we can view the values by opening the "Workspace"
window. This is done by selecting the Workspace option from the View menu. If you
want to erase all variables from the MATLAB memory, type clear. For erase a
specific variable, say x, type clear x. To clear two specific variables, say x and y,
type clear x y, that is separate the different variables with a space. Variables can also
be cleared by selecting them in the Workspace window and selecting the delete
option.

Vectors and matrices in MATLAB


We create a vector in MATLAB by putting the elements within [] brackets.

Example: x= [1 2 3 4 5 6 7 8 9 10]

We can also create this vector by typing


x=1:10
the vector (1 1.1 1.2 1.3 1.4 1.5) can be created by typing
>> x = [1 1.1 1.2 1.3 1.4 1.5]

Or by typing

>> x=1:0.1:1.5

Matrices can be created according to the following example. The matrix


1 2 3
A= [4 5 6] is created by typing
7 8 9

>> A = [1 2 3; 4 5 6; 7 8 9];

A =

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Medical Image Processing Using MATLAB 2016

1 2 3

4 5 6

7 8 9

i.e., rows are separated with semi-colons. If we want to use a specific element in a
vector or a matrix, study the following example:

Example:

>> x (2)

ans =

20

>> A (3, 1)

ans =

Here we extracted the second element of the vector by typing the variable and the
position within parentheses. The same principle holds for matrices; the first number
specifies the row of the matrix, and the second number specifies the column of the
matrix.

Note that in MATLAB the first index of a vector or matrix starts at 1, not 0 as is
common with other programming languages.

If the matrices (or vectors which are special cases of a matrices) are of the same
dimensions then matrix addition, matrix subtraction and scalar multiplication works
just like we are used to.

Example: Type

>> X = [1 2 3]

>> y = [4 5 6]

>> a=2

>> x+y

ans =

4.8374 5.8374 6.8374

>> x-y

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ans =

-3.1626 -4.1626 -5.1626

>> a*x

ans =

1.6747

If want to apply an operation such as squaring each element in a matrix we have to


use a dot (.) before the operation we wish to apply. Type the following commands in
MATLAB.

>> x=1:10

x =

1 2 3 4 5 6 7 8 9
10

>> x.^2

ans =

1 4 9 16 25 36 49 64 81
100

>> A = [1 2 3; 4 5 6; 7 8 9]

A =

1 2 3

4 5 6

7 8 9

>> A.^2

ans =

1 4 9

16 25 36

49 64 81

>> A^2

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ans =

30 36 42

66 81 96

102 126 150

The dot allows us to do operations element wise. All built-in functions such as sin,
cos, exp and so on automatically act elementwise on a matrix.

Type

>> y = [0 1/4 1/2 3/4 1

y=

0 0.2500 0.5000 0.7500 1.0000

>> y = pi*y

y=

0 0.7854 1.5708 2.3562 3.1416

>> sin (y)

ans =

0 0.7071 1.0000 0.7071 0.0000

How to plot with MATLAB


There are different ways of plotting in MATLAB. The following two techniques,
illustrated by examples, are probably the most useful ones.

Example 1: Plot sin(x2) on the interval [-5, 5]. To do this, type the following:

>> x=-5:0.01:5;

>> y=sin(x.^2);

>> plot(x,y)

Example 3: Plot x5/2 for x = 10-5 to 105.

To do this, type the following:

>> x=logspace(-5,5,101);

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>> y=x.^(5/2);

>> plot(x,y)

The plots are shown below:

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The following commands are useful when plotting:

Graphing functions MATLAB command

Label the horizontal axis. xlabel('text')

Label the vertical axis. ylabel('text')

Attach a title to the plot. title('text')

Change the limits on the x and y axis. axis([xminxmaxyminymax])

"Keep plotting in the same window." hold on

Turn off the "keep-plotting-in-the-same-


hold off
window-command".

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Medical image processing through MATLAB


Image Processing of a Male Leg X-Ray
For the processing of Leg X-Ray of male following steps are involved:

Step 1:- Opening MATLAB.

Step 2:- Using the command ‘clear, close all’, we make the work space
bar empty for fresh processing of images.

>> clear, close all

Step 3:- Leg X-Ray of male is stored in jpg format. The important task is to import
this X-Ray image from the memory of the compute r to the MATLAB environment.
We write in the command window

>> I= imread (‘nits.jpg’);

Imread is a MATLAB’s function to read images from the computer into its
environment. But there is a word of caution. If we don’t change the current directory’s
name, the MATLAB will not be able to read the image. But there is another way of
overcoming to this problem. We can make the MATLAB to read the desired image by
giving the exact location and file name details. For instance if an image is on the
desktop, we can use

>> I=imread ('C:\Users\VAIBHAV\Desktop\nits.jpg');

Step 4:- After reading the image, to know the dimension of the image use size (
) command. This results as shown below:

>> size(I)

ans =

1275 1650

The result shows that the image named ‘nits.jpg’ which is being processed is an
array of 1275 and1650, where there are 1275 rows and 1650 columns. Each element
of this array is an image point or pixels. So the total numbers of the pixels in this
image is 2103750 i.e. it is approximately 2.00 Mega pixel image.

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Step 5:- To get additional information about the image use whos as
>> whos

Name Size Bytes Class


Attributes

I 1275x1650 2103750 uint8

ans 1x2 16 double

nits 1275x1650 2103750 uint8

Grand total is 2103750 elements using 2103750 bytes.

Step 6:- (Image Display)


Now to see the image how it has been read by MATLAB. Use imshow function as:

>> imshow (I)

The image is shown in a different window as

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Step 7:- To add the title and other labels we use title command. In this case, X-ray
image is named as ‘A Male Leg X-Ray’ as follows:

>> title('A Male Leg X-Ray')

>> xlabel('Processed and Modified by Vaibhav Tripathi')

Step 8:- (Histogram Equalization)


The X-ray image which is being processed is biased towards the dark end of the grey
scale. The low dynamic range is evident from the fact that the histogram is narrow
with respect to entire grey scale. To show the histogram of the leg X-ray image, we
write:

>> figure, imhist (I)

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Now we want that the intensity level of pixels should spread or take on all possible
values on the scale. So, to solve the problem of low dynamic range of pictures we
equalize the intensity histogram. MATLAB provides an important function histeq
( ) for this purpose.

>> I2 = histeq (I);

>> figure, imhist(I2)

And the histogram equalised image is shown below along with its histogram.

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Step 9:- (Spatial Resolution)

Spatial resolution is the density of pixels over the image: the greater the spatial
resolution, the more pixels are used to display the image. We can experiment with
spatial resolution with MATLAB's imresize function. By changing the parameters of
imresize, we can change the effective resolution of the image to smaller amounts:
The command imresize(I,1/2);

We get the resized image as:

Step 10:- (Arithmetic Operations)


An elegant way to use the MATLAB function imadd which is designed precisely to
do addition.

>> b1=imadd(I,128);
Subtraction is similar; we can transform out matrix in and out of double, or use the
imsubtract function:
>> b2=imsubtract (I,128);

Similarly command for the multiplication and division is given as

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Medical Image Processing Using MATLAB 2016

>> b3=immultiply(I,5);

>> b4=imdivide(I,2)

The multiplication by 5 is shown in following figure as:

Step 11:- (Complement)


The complement of a greyscale image is its photographic negative. If the image is of
type uint8, the best approach is the imcomplement function.

The command is:

>> bc=imcomplement(I);
>> imshow(bc)

The complement i.e. of the X-ray is figured below:

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Medical Image Processing Using MATLAB 2016

Step 12:- (Thresholding)


Thresholding is a vital part of image segmentation, where we wish to isolate objects
from the
background. Thresholding can be done very simply in MATLAB. Suppose we have
an 8 bit image, stored as the variable X. Then the command X>T will perform the
thresholding.

The command is given as:

>> imshow(I), figure, imshow(I>50)

Step 13:- (Noise and their Reduction)


We may define noise to be any degradation in the image signal, caused by external
disturbance. Cleaning an image corrupted by noise is thus an important area of image
restoration.
Salt and pepper noise
It is also called impulse noise, shot noise, or binary noise. This degradation can be
caused by sharp, sudden disturbances in the image signal; its appearance is randomly
scattered white or black (or both) pixels over the image.
To add salt and pepper noise, we use the command as:
>> t_sp=imnoise(I,'salt & pepper');
>> imshow(t_sp)

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Medical Image Processing Using MATLAB 2016

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Medical Image Processing Using MATLAB 2016

Gaussian noise
Gaussian noise is an idealized form of white noise, which is caused by random
fluctuations in the signal. We can observe white noise by watching a television which
is slightly mistuned to a particular channel. Gaussian noise is white noise which is
normally distributed. If the image is represented as I and the Gaussian noise by N,
then we can model a noisy image by simply adding the two: I+N
The effect can again be demonstrated by the imnoise function:
>> t_ga=inoise(t,'gaussian');
The noisy figure by Guassian noise is shown below:

Median filtering of salt and pepper noise


Median filtering seems almost tailor-made for removal of salt and pepper noise. In
MATLAB, median filtering is implemented by the medfilt2 function:
>> t_sp_m3=medfilt2(t_sp);
>> imshow(t_ga)

Wiener filtering of Guassian noise


Suppose we take the noisy image and attempt to clean this image with Wiener
filtering. We will use the wiener2 function as
>> t1=wiener2(t_ga);
>> imshow(t1)

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Step 14:- (Getting a Binary Image)


The X-ray image is of grey scale nature but if we want to convert it into a binary
image where all the pixels whose luminescence value is less than 1 are shown black
and all the pixels having luminescence value greater than 1 are represented as white.

>>bw= im2bw(I);

>> imshow (bw)

The output binary image is as follows;

Step 15:- (Pseudo-Colouring)


This means assigning colours to a grey-scale image in order to make certain aspects of
the image more amenable for visual interpretation for example, i.e. medical images.
This is way to highlight some parts or whole of the image, using different colours for
showing image details. For example, in the image processing of the X-ray image
which is actually a grey scale image is pseudo-coloured using the following
command.
>> X= grayslice (I,16);

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Medical Image Processing Using MATLAB 2016

>> figure, imshow(X,jet(16));


The output figure window is shown below:

A bad choice of colourmap can ruin an image, then we apply the vga colourmap.
This is done with the grayslice function:
>> b16=grayslice(I,16);
>> figure,imshow(b16,colormap(vga))
We can easily create our own colourmap: it must by a matrix with 3 columns, and
each row
consists of RGB values between 0.0 and 1.0. Suppose we wish to create a blue,
magenta, green, red colourmap as shown in table using the RGB values:

Colour Red Blue Green


Blue 0 0 1
Magenta 1 0 1
Green 0 1 0
Red 1 0 0

We can create our colourmap with:


>> mycolourmap=[0 0 1;1 0 1;0 1 0;1 0 0];
>> b4=grayslice(b,4);
>> imshow(b4,mycolourmap)

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Analysis and Conclusion


From the analysis of the X-ray of a Male Leg, it is clear that after processing using
MATLAB the X-ray images can be enhanced and pseudo colouring may be utilized to
get finer details about the affected bone. Hairline fracture which may be there can be
easily detected which may not be clear in X-ray Image taken using ordinary X-ray
machine. Thus we can say that medical image processing may emerge as an important
tool for editing, modifying and enhancing different types of medical images. The field
of medical imaging is not just confined to the processing of the X-rays, other types of
images using different diagnostic techniques like MRI, CT Scans etc are also
processed with these techniques. The MATLAB is very versatile software proves its
worth in the medical field, through the true power of MATLAB is to be realized in
this field. Developing new algorithms, we can not only make the image processing
more insight giving, but also can enrich the library of image processing tools of
MATLAB.

Main Advantages of Medical Image Processing


1. It saves the cost of taking the medical image again of the patient organ if the
X-Ray, CT scan or any other type of medical image is blurred or noisy due to
some reasons.
2. It gives more details about the patient which is not however possible by mere
inspection of unprocessed image.
3. A new way to provide better diagnostic services at low cost.
4. No major setup is needed for medical image processing.
5. Images generated by medical image processing can be utilized for the study of
anatomy of human body.

Main features of Medical Image Processing


1. Brightness enhancement.
2. Editing and labelling of the medical image.
3. Getting true image from noisy and blurred image.
4. Pseudo colouring for highlighting different parts, tissues, bones etc. of the
body.
5. Complementing the image i.e.; generating the negative of a medical image.
6. Filtering, contrast enhancement and smoothing.
7. Methods of medical image processing are applicable to both B/W as well as
colour medical images.

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