Laboratory Report 1 - ALYA NAJIHAH ZULKUFLI 141151620 PDF

ENT 413
BIOMEDICAL IMAGING
Laboratory Module 1: Medical Image Manipulation

and Processing Using Imagej Part
NAME: ALYA NAJIHAH BINTI ZULKUFLI
MATRIC NO: 141151620
BIOMEDICAL ELECTRONIC ENGINEERING PROGRAMME

SCHOOL OF MECHATRONIC ENGINEERING
UNIVERSITI MALAYSIA PERLIS
SLIP SUBMISSION REPORT
..........................................................
PLV SIGNATURE
DATE:
*****please cut this area and KEEP

THE CUTTING SLIP
1.0 OBJECTIVES:
1. To expose student in real clinical principles of practice of radiography x-ray.

2. To study the noise in image processing. To study type of filters and find out the most
suitable filters that can reduce the noise.
2.0 INTRODUCTION
ImageJ is a public domain, Java-based image processing program developed at the National
Institutes of Health. ImageJ was designed with an open architecture that provides
extensibility via Java plugins and recordable macros. Custom acquisition, analysis and
processing plugins can be developed using ImageJ's built-in editor and a Java compiler. User-
written plugins make it possible to solve many image processing and analysis problems,
from three-dimensional live-cell imaging, to radiological image processing, multiple imaging
system data comparisons to automated hematology systems.
After starting the computer and booting Windows you can start ImageJ by double-clicking
the ImageJ Symbol on the desktop. The program will start with the ImageJ main window
(Fig.1):
Figure 1: ImageJ Main Window
ImageJ can display, edit, analyze, process, save and print images of various formats including
TIFF, GIF, JPEG, BMP, DICOM. It supports standard image processing functions such as
contrast manipulation, filtering (i.e. sharpening, smoothing), edge detection and others. It
can calculate area and pixel value statistics of a user-defined region of interest (ROI).
Measurements of distances and angles are possible. It can create density histograms and
line profile plots. It does geometric transformations such as scaling, rotation, flips and
zooming. Spatial calibration (in units such as millimeters) as well as density or grey scale
calibration are available. The program supports any number of images (display in separate
windows) simultaneously.
3.0 RESULT AND DISCUSSION
TASK A: IMAGE TYPE
i) Medical Image type conversion
Figure 1: Original medical image
Figure 2: 8bit greyscale Figure 3: GRB Green
Figure 4: RGB Blue Figure 5: RGB Red

ii) Discussion on image result
Grayscale images are also call bi-level or binary images that distinct from one-
bit bi-tonal black-and-white images. A particular weighted combination of
frequencies by measure the intensity of light at each pixel will result in grayscale
images. All image processing requires some form of collapsing data because
processing raw images might be impossible even using a modern computer. Grayscale
image can help us identify important edges or other extra features in image processing
rather than a colour information image. Therefore the image is convert to 8bit
greyscale before proceed to RGB.
This can be proven by the figure 1 above where the grayscale images make a
clearer image for our vision and visualize all the other features in the images.
As the human vision is trichromatic hence most colour model represent

colours by three colours. RGB images also call true colour images that reflect colour
values directly rather than through a colourmap. Each pixel is specified by three
values which is red, green and blue.
For example, the green colour in an RGB image above reflects the green
colour in the specimen which is darker than blue and red of RGB image. Hence, we
can see the white blood cell with the segmentation clearer. The red colour in RGB
images are less darker than the green images. Whereas, the blue colour in the RGB
image are brighter than the other two which means the original image doesnt have a
pixel with more colour of blue.
TASK B: IMAGE EHANCEMENT
i) Medical Image enhancement result
Type of noise : Gaussian Noise
Type of Filter:
Mean Median
Gaussian
Type of noise : Gaussian Noise(25s.d)
Type of Filter:
Mean Median
Gaussian
Type of noise: Salt and Pepper
Type of Filter:
Mean Median
Gaussian
ii) Discussion on image result
Image noise is random variation of brightness or color information in images, and is

usually an aspect of electronic noise. Noise is an unwanted signal. Hence, it needs to filter to
give the actual subjects in the image. There are several types of filtering which is Gaussian,
Median and Mean.
Gaussian filter is smoothing filter in the 2D convolution operation that is used to

remove noise and blur from image. Mean filter is simple-linear filter where. It smooths the
current image by replacing each pixel with the neighborhood mean. Mean filter usually used
to remove the impulse noise. Median filter is a non-linear filter where reduces the amount of
intensity variation between one pixel and the other pixel. Median filter replaces each pixel
value with the median value that reduces the noise in the active image.
Based on the result above, the image with a Gaussian noise become clearer and
blurring is reduces when using a Gaussian filter compared to median filter that doesnt give
any change of the images. However, when using a mean filter, it also gives a good result
compared to median filter.
For image with a Gaussian noise (25 standard deviation), it also give the same result
which median filter doesnt work well to reduce the noise. Gaussian filtering is highly
effective in removing Gaussian noise from the image. The resulting effect is that Gaussian
filters tend to blur edges, which is undesirable.
Meanwhile, with image of Salt and Pepper noise, median filter gives a better
resolution of the images. This is because the noisy pixel is most likely an outlier, median will
choose the middle distribution of neighbour. However with mean filter it does not work well
because the outlier is included in the mean.
4.0 CONCLUSION
Image processing gives an impact to medical field which help the doctor to diagnose
and increase the quality of life of the patient. This has been proven especially in medical
imaging that enable the radiologist to detect the position of the fracture, differentiate between
cancerous cell and normal cell and give an actual condition of the patient health. Therefore,
image enhancement and image segmentation usually used in medical imaging where can
reduce the blurring from patient motion by using filtering.
5.0 REFERENCES
1. Article, R. (2013). Available Online at www.jgrcs.info A BRIEF STUDY OF VARIOUS NOISE

MODEL AND FILTERING TECHNIQUES, 4(4).
2. Dasgupta, P. B. (2014). Analytical Comparison of Noise Reduction Filters for Image

Restoration Using SNR Estimation, 17(3), 121124.
3. Filtering and Enhancing Images. (n.d.), (1).
4. ImageJ User Guide User Guide ImageJ. (n.d.).
5. Processing, I., & February, B. (2012). Image Noise and Filtering Types of Image Noise.
6. Resonance, M., Magnetic, N., & Imaging, R. (n.d.). Importance of Image Processing, 5
8. https://doi.org/10.1007/978-981-287-624-9
7. Stanchev, P. (1994). Medical image conversion, 1994(196 203).

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ENT 413

Laboratory Module 1: Medical Image Manipulation

BIOMEDICAL ELECTRONIC ENGINEERING PROGRAMME

SLIP SUBMISSION REPORT

*****please cut this area and KEEP

1. To expose student in real clinical principles of practice of radiography x-ray.

Figure 1: ImageJ Main Window

TASK A: IMAGE TYPE

i) Medical Image type conversion

Figure 1: Original medical image

Figure 2: 8bit greyscale Figure 3: GRB Green

Figure 4: RGB Blue Figure 5: RGB Red

As the human vision is trichromatic hence most colour model represent

Image noise is random variation of brightness or color information in images, and is

Gaussian filter is smoothing filter in the 2D convolution operation that is used to

1. Article, R. (2013). Available Online at www.jgrcs.info A BRIEF STUDY OF VARIOUS NOISE

2. Dasgupta, P. B. (2014). Analytical Comparison of Noise Reduction Filters for Image

3. Filtering and Enhancing Images. (n.d.), (1).

4. ImageJ User Guide User Guide ImageJ. (n.d.).

7. Stanchev, P. (1994). Medical image conversion, 1994(196 203).

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