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Procedia Computer Science 113 (2017) 531–538

The 4th International Symposium on Emerging Information, Communication and Networks

The 4th International Symposium on Emerging Information, Communication and Networks
(EICN 2017)
(EICN 2017)
Enhanced 3D segmentation techniques for reconstructed 3D medical
Enhanced 3D segmentation techniques for reconstructed 3D medical
volumes: Robust and Accurate Intelligent System
volumes: Robust and Accurate Intelligent System
Shadi Al-Zu’biaa* , Mahmoud Al-Ayyoubbb, Yaser Jararwehbb, Mohammed A.
Shadi Al-Zu’bi * , Mahmoud Al-Ayyoub , Yaser Jararweh , Mohammed A.
Shehabbb
a
Shehab
Computer Science Department, School of science and information technology, Zaytoonah University of Jordan Amman, Jordan
a a
Computer
Computer Science
Science Department,
Department, School
School of science
of science and information
and information technology,
technology, Zaytoonah
Jordan University
University of Scienceofand
Jordan Amman,Irbid,
Technology JordanJordan
a
Computer Science Department, School of science and information technology, Jordan University of Science and Technology Irbid, Jordan

Abstract
Abstract
Medical images play an important role in treating a large number of ailments as they are integral and even indispensable to the
Medical
diagnosisimages
processplay an important
of such ailments.role in treating
Medical a large
images comenumber of ailments
from different as they are
acquisition integral
systems (suchandaseven
PET,indispensable
CT, MRI) and, to the
in
diagnosis
many processautomated
situations, of such ailments.
processing Medical
of theseimages
imagescome from different
can greatly acquisition
aid physicians systems
and make (such
their jobs as PET,InCT,
easier. MRI)imaging
medical and, in
manyitssituations,
and automated
applications, processing (with
2D segmentation of these
itsimages canapproaches
different greatly aidsuch
physicians
as FCM,andk-means,
make their jobs easier.
MRFM and NN)In medical imaging
is the first step
and itsisapplications,
which 2DROI.
used to extract segmentation
This helps(with its different
in extracting ROI approaches
in each slicesuch
(2D as FCM,image)
medical k-means, MRFMregardless
separately and NN) of is its
therelation
first step
to
which
the nextis used
and to
theextract ROI.slices.
previous This helps in extracting
In this paper, a 3DROImodel
in eachofslice
FCM (2Dsegmentation
medical image) separately
techniques is regardless
proposed ofto its relationthe
enhance to
the next and process
segmentation the previous slices.
and take In this
in mind paper, 3D-Volume
the overall a 3D modelasof oneFCM segmentation
testing data. techniques is proposed to enhance the
segmentation process and take in mind the overall 3D-Volume as one testing data.
© 2017 The Authors. Published by Elsevier B.V.
©
© 2017
2017 The
The Authors.
Authors. Published
Published byby Elsevier B.V.
Peer-review
Peer-review under
under responsibility
responsibility of Elsevier
of the
B.V. Program Chairs.
the Conference
Conference Program Chairs.
Peer-review under responsibility of the Conference Program Chairs.
Keywords: Medical imaging; 3D image Processing; Fuzzy C-Means; Volume Reconstruction;
Keywords: Medical imaging; 3D image Processing; Fuzzy C-Means; Volume Reconstruction;

1. Introduction
1. Introduction
Health care is one of the major sectors in our lives. A huge number of health-related problems and challenges are
Health
tackled care day
every is one
byofthe
theresearchers
major sectors
in in ourarea.
this lives.New
A huge
and number of health-related
emerging problems
technologies can and challenges
be assumed here as are
an
tackled every day by the researchers in this area. New and emerging technologies can be assumed here as an

* Corresponding author. Tel.: +962799100034;

* E-mail
Corresponding
address:author. Tel.: +962799100034;
smalzubi@zuj.edu.jo
E-mail address: smalzubi@zuj.edu.jo
1877-0509 © 2017 The Authors. Published by Elsevier B.V.
1877-0509 ©under
Peer-review 2017responsibility
The Authors. of
Published by Elsevier
the Conference B.V. Chairs.
Program
Peer-review under responsibility of the Conference Program Chairs.

1877-0509 © 2017 The Authors. Published by Elsevier B.V.

Peer-review under responsibility of the Conference Program Chairs.
10.1016/j.procs.2017.08.318
532 Shadi Al-Zu’bi et al. / Procedia Computer Science 113 (2017) 531–538
2 Author name / Procedia Computer Science 00 (2015) 000–000

advantage to the researchers to address these challenges. One of the most important aspects of health care that
benefits from technological advances is the diagnosis process.
Computer-aided diagnosis (CAD) systems aim at improving the diagnosis process using computerized techniques
to. Such systems would allow for high speed processing of large amounts of data of possibly different sources (such
as lab tests, medical images, physical examination, etc.) in order to help the physician reach a quick and accurate
diagnosis 1. Medical image processing has played an important role in this research, which justifies the great interest
in all methods related to medical images including capturing, storing, processing, etc 33.
Due to their importance, many researchers (from both academia and industry) have proposed various CAD
systems designed for various ailments. Many of these systems are based on image processing. Examples include
bone fractures 2,3, osteoporosis 4, disc herniation 5,6, brain hemorrhage 7,8, brain tumor 9,10, breast cancer 11,12, lung
cancer 13, liver cancer 14, colon cancer 15, myocardial infarction 16-18, diabetic retinopathy 19, etc 33. Effective and
efficient processing of medical imaging processing is at the core of CAD systems 20.
The sources of medical images are acquisition systems. Many new technologies are used for producing medical
images such as X-ray, Computed Tomography (CT), Magnetic Resonance Tomography (MRT) and Magnetic
Resonance Imaging (MRI). Many of these technologies use magnetic radio waves and crystal sensors to capture an
identical structure of the human bodies as medical images 21,22.
The 2D matrices produced from these acquisition systems as very complex. Computerized image processing
operations are used here to facilitate the radiologist’s job in diagnosing ailments including: de-noising, segmentation,
interpolation, registration, etc. 23-25. In many medical image processing applications, segmentation is one of the early
processing steps to be executed after acquiring images from medical scanners. Image segmentation is the process of
segmenting or partitioning a digital image into a set of classes or regions, which is a vital step for many computer
vision tasks 26. In medical images, it is typically used as a pre-processing step to separate the different regions
representing different types of tissues. This can be a useful beginning in extracting the Region of Interest (ROI),
which helps in directing the physician's attention to any abnormalities in the body tissues such as tumors 27. In fact,
extracting the ROI in order to study it independently is the basis of many CAD systems 28. In order to enhance the
result of the segmentation process, many methods, such as morphological operations and region growing techniques,
can be applied 29, 30,33.
The work presented in this paper is concerned with the automatic and unsupervised segmentation algorithms
based on Fuzzy C-Means (FCM) clustering algorithm to be applied on both 2D images and 3D volumes.
Specifically, in this paper, a system that uses both 2D FCM clustering and 3D FCM clustering algorithms to extract
ROI for object in 3D volumes has been presented. The input files for this system are DICOM files extracted from a
CT scanner 33.
This paper is organized as follows. The second section illustrates important concepts about 2D images and 3D
volumes, especially in the medical domain. Then, Section 3 discusses the related works on the segmentation
operation using FCM with other applications. Section 4 comprises the illustration of the proposed segmentation
algorithm with two different implementations: the 2D version and the 3D version. Section 5 explains the
experiments used to evaluate the proposed work and results discussion. Finally, this work is concluded in Section 6.

2. 2D images and 3D volumes in medical applications 33

For medical images, the standard output of many acquisition systems (medical scanners) is a DICOM file. Such files
include in details the image data, which consist of medical data. The image data from DICOM files (which is the
focus of this work) is extracted by using DICOM reader from the Fellow Oak DICOM 2.0.2 library.† 2D images are
the most widely used type in medical imaging and most of the image processing operations are designed for such
images 27. In this works, we also consider 3D volume, where the X, Y and Z axes are the width, the height and the
number of slices in the image, respectively. This is shown in Fig. 1. The type of medical image we consider is CT.
So, the image is a grey-scale image. This reduces the data size in the proposed system.

†
https://www.nuget.org/packages/fo-dicom/
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Fig. 1. 3D image model.

Fig. 2. Flowchart of extracting data.

Fig. 2 illustrates the steps applied to extract data from DICOM files and use them to build 3D models. The
loading process begins by extracting DICOM files in an ascending order by their names. Each DICOM file has
detailed image data. The DICOM reader retrieves image pixels and represents them as 2D plane. The second image
will be located behind the first image and so on till the rest of the DICOM files. A 3D model is built from all those
slices using image reconstructing process.
Image reconstructing is an image processing technique that folds many 2D images into a single 3D volume of a
single rigid volume from different angles. The image position is read from the DICOM file. ‡ After that, the DICOM
reader checks the pixels format if they are CT Image Storage by checking one of the Service-Object Pairs (SOPs).§
All these processes are done by files from the Medical Image Visualization Using WPF project.**
The Marching Cubes algorithm builds the 3D model. It was introduced in 1987 by Lorensen and Cline 31 and it
became popular with Volume Rendering and for game design. Each pixel in this algorithm is represented as a cube
with vertex indexes ranging from 0 to 7, while each edge also has indexes ranging from 0 to 11 as shown in Fig. 3. A
divide and conquer technique is used to check the shape of the cube as presented in Figure 4 31.
The cube that represents the pixel unit in 2D system gets one of 15 cases. These cases depend on the pixel
location and state. Many cases of cube can be drawn as 3D unit for each pixel in 2D (illustrated in Fig. 5). From Fig.
6, the resolution of the image is set by the grid size. The result is a 3D model as represented in Fig. 7, which is input
into the FCM algorithm.

‡
http://www.sno.phy.queensu.ca/~phil/exiftool/TagNames/DICOM.html
§
http://www.dicomlibrary.com/dicom/sop/
**
http://www.codeproject.com/Articles/466955/Medical-image-visualization-using-WPF
4 Author name / Procedia Computer Science 00 (2015) 000–000

534 Shadi Al-Zu’bi et al. / Procedia Computer Science 113 (2017) 531–538

Fig. 3. The cube structure used in the Marching Cube algorithm.

Fig. 4. Adjacent pixels and cube shape

Fig. 5. Cube shape cases

Fig. 6. The effect of grid size with 3D model resolution.

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Fig. 7. The final result of applying the Marching Cube algorithm.

3. Fuzzy C-Means for segmentation 33

Fuzzy C-Means (FCM) is a clustering technique used to separate data into a number of groups. Each group has a
number of data points and each point has a membership value to each group; however, the strongest membership
determines the best group for this point. This membership characteristic is calculated by the Euclidean distance 32.
FCM works in three main steps. The first step is to initialize random numbers to be the cluster centroids. Those
centroids are updated on each iteration according to the following equation 27.

where m is the fuzziness factor, N is the number of points and v j is the center of cluster j. Secondly, memberships
for each data point are calculated by using the following equation.

where C is the number of clusters and xi is an object point. In this step, each data point will have a percentage of
correlation with all clusters. At this stage, each data point cannot determine to which cluster it belongs. This
situation is called the fuzzification state, where any data point is related to more than single cluster. Furthermore, the
total sum of all membership values for a single data point is equal to one and the range of each membership value is
[0-1] 32. The third step of FCM is to calculate the objective function which can be calculated by the following
equation:

Using this function, FCM can take a decision to stop at a specific point. A termination condition is assumed in
each iteration of FCM based on the comparison between current and the previous objective function value. A
threshold value is used in the comparison as a termination condition to stop the FCM algorithm. At this point, the
segmented data will be generated and each pixel (point) in the medical image must belong to one class (segmented
cluster). This is also named the defuzzification state, which can be done by choosing the maximum membership
value for each data point from all of its membership values to all clusters 32. FCM algorithm follow the steps in the
following pseudocode.
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4. 3D Segmentation technique

The main idea behind 3D FCM is considering more neighbors with any pixel before deciding the class (group or
cluster) to which it belongs. In 2D FCM, each pixel is compared with the 8 neighbors as illustrated in Fig. 8.
Calculations are made to the pixel value taking in mind the all eight neighbors values to come up with a modified
value leads to the exact group (cluster) to belong into. In the other hand, in 3D FCM, the number of neighbors is
increased. Two more images (medical slices) are effecting on the new value of corresponding pixel: a slice before
and a slice after the image containing the corresponding pixel. Fig. 9 and Fig. 10 show all these neighbors.

Fig. 8. Pixel neighbors in 2D FCM.

5. Conclusion

In this paper, we focused on the automatic and unsupervised segmentation algorithms based on FCM clustering
algorithm and to be applied on both 2D images and 3D volumes. Specifically, we presented a system that uses both
2D FCM clustering and 3D FCM clustering algorithms to extract ROI for object in 3D volumes. The input files for
this system are medical DICOM files extracted from a CT scanner. In the future, we plan on extensively testing our
system on various modalities. We are also considering expanding it to cover other segmentation algorithms as well
as pre-processing and post-processing steps typically applied to medical image analysis.
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Fig. 9. Pixel neighbors in 3D FCM.

Fig. 10. the new Pixel neighbors in 3D FCM.

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