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Efficient ReconfigurableArchitectures for 3-D Medical
A thesis submitted for the degree of
Doctor of Philosophy
Dr Abbes Amira
Department Electronic and Computer Engineering
School of Engineering and Design
Brunel University, West London
Recently, the more widespread use of three-dimensional (3-D) imaging modalities,
such as magnetic resonance imaging (MRI), computed tomography (CT), positron
emission tomography (PET), and ultrasound (US) have generated a massive amount
of volumetric data. These have provided an impetus to the development of other
applications, in particular telemedicine and teleradiology. In these fields, medical
image compression is important since both efficient storage and transmission of data
through high-bandwidth digital communication lines are of crucial importance.
Despite their advantages, most 3-D medical imaging algorithms are
computationally intensive with matrix transformation as the most fundamental
operation involved in the transform-based methods. Therefore, there is a real
need for high-performance systems, whilst keeping architectures flexible to allow
for quick upgradeability with real-time applications. Moreover, in order to obtain
efficient solutions for large medical volumes data, an efficient implementation of
these operations is of significant importance. Reconfigurable hardware, in the form
of field programmable gate arrays (FPGAs) has been proposed as viable system
building block in the construction of high-performance systems at an economical price.
Consequently, FPGAs seem an ideal candidate to harness and exploit their inherent
advantages such as massive parallelism capabilities, multimillion gate counts, and
special low-power packages.
The key achievements of the work presented in this thesis are summarised
as follows. Two architectures for 3-D Haar wavelet transform (HWT) have been
proposed based on transpose-based computation and partial reconfiguration suitable
for 3-D medical imaging applications. These applications require continuous hardware
servicing, and as a result dynamic partial reconfiguration (DPR) has been introduced.
Comparative study for both non-partial and partial reconfiguration implementation
has shown that DPR offers many advantages and leads to a compelling solution
for implementing computationally intensive applications such as 3-D medical image
compression. Using DPR, several large systems are mapped to small hardware
resources, and the area, power consumption as well as maximum frequency are
optimised and improved.
Moreover, an FPGA-based architecture of the finite Radon transform (FRAT)
with three design strategies has been proposed: direct implementation of pseudo-code
with a sequential or pipelined description, and block random access memory (BRAM)-
based method. An analysis with various medical imaging modalities has been carried
out. Results obtained for image de-noising implementation using FRAT exhibits
promising results in reducing Gaussian white noise in medical images. In terms of
hardware implementation, promising trade-offs on maximum frequency, throughput
and area are also achieved.
Furthermore, a novel hardware implementation of 3-D medical image
compression system with context-based adaptive variable length coding (CAVLC)
has been proposed. An evaluation of the 3-D integer transform (IT) and the discrete
wavelet transform (DWT) with lifting scheme (LS) for transform blocks reveal that
3-D IT demonstrates better computational complexity than the 3-D DWT, whilst
the 3-D DWT with LS exhibits a lossless compression that is significantly useful for
medical image compression. Additionally, an architecture of CAVLC that is capable
of compressing high-definition (HD) images in real-time without any buffer between
the quantiser and the entropy coder is proposed. Through a judicious parallelisation,
promising results have been obtained with limited resources.
In summary, this research is tackling the issues of massive 3-D medical volumes
data that requires compression as well as hardware implementation to accelerate the
slowest operations in the system. Results obtained also reveal a significant achievement
in terms of the architecture efficiency and applications performance.
Certificate of Originality
I hereby certify that the work presented in this thesis is my original research and has
not been presented for a higher degree at any other university or institute.
(Afandi Ahmad 0729168)
23 July 2010
To everyone who supports me, it just begins...
I gratefully acknowledge who has supported me throughout my PhD work and finally
the preparation of this thesis. In particular, I would like to thank my supervisor,
Dr Abbes Amira, for accepting me as a student, whilst I am in a dark tunnel. Abbes,
many thanks for your relentless commitment you have shown along this journey. You
could have taken the short cut, but you stood by me. I will always remember and look
to you as an example of how to work hard! I would also like to thank Dr Hassan Rabah,
Dr Yves Berviller and Dr David Smith for insightful guidance of my research studies.
All your effort shows me the real meaning of sincerity!
I would like to thank all the great friends I have had at Brunel, Ulster and
Nancy over the years: Ben, Abdallah, Michael, Hairol, Thian, Linda, Khalid, Shafinar
and Aida. Thank you all for providing many happy memories and truly friendship
colours. I wish to thank my sponsors, Ministry of Higher Education Malaysia (MOHE),
Universiti Tun Hussein Onn Malaysia (UTHM) and the British Council. I must also
thank to Faculty of Electrical and Electronic Engineering, especially to colleagues in
Department of Computer Engineering for their support.
I would achieve nothing without the encouragement and compassion I received
from my understanding wife, parents and all of my families. This thesis is dedicated
to them. Their love and support kept me going. I owe you!
Journal Papers Accepted
1. A. Ahmad, B. Krill, A. Amira, and H. Rabah, Efficient Architectures for
3-D HWT using Dynamic Partial Reconfiguration, Elsevier Journal of System
Architecture - Special Issue on Hardware/Software Co-Design, ISSN 1383-7621,
Volume 56, Issue 8, pp. 305316, August 2010.
2. B. Krill, A. Ahmad, A. Amira, and H. Rabah, An Efficient FPGA-based
Dynamic Partial Reconfiguration Framework for Image and Signal Processing
IP Cores, Elsevier Journal of Signal Processing: Image Communication -
Special Issue on Breakthrough Architectures for Image and Video Systems, ISSN
0923-5965, Volume 25, Issue 5, pp. 377387, May 2010.
3. P. Nicholl, A. Ahmad, and A. Amira, A Novel Feature Vectors Construction
Approach for Face Recognition, Springer Transactions on Computational
Science (TCS) - Special Issue on Security in Computing.
Journal Papers In Revision
1. M. Guarisco, A. Ahmad, H. Rabah, A. Amira, and Y. Berviller, 3-D Medical
Image Compression System using CAVLC, IEEE Transactions on Medical
Journal Papers Under Review
1. M. Guarisco, A. Ahmad, H. Rabah, A. Amira, and Y. Berviller, FPGA-based
Implementation of a CAVLC for 3-D Medical Compression, IEEE Transactions
on Consumer Electronics.
2. A. Ahmad, A. Amira, and M. Jiang , Reconfigurable Architectures for 3-D
Medical Image Processing: Design Issue and Challenges, ACM Computing
3. A. Ahmad, A. Amira, H. Rabah, and Y. Berviller, An Efficient FPGA-based
Architecture of Finite Radon Transform for Medical Imaging Application,
IEEE Transactions on Medical Imaging.
xConference Papers Accepted
1. A. Ahmad, A. Amira, M. Guarisco, H. Rabah and Y. Berviller, Efficient
Implementation of a 3-D Medical Imaging Compression System using CAVLC,
The 2010 International Conference on Image Processing (ICIP), September
26th - 29th 2010, Hong Kong.
2. A. Ahmad, B. Krill, A. Amira, and H. Rabah, 3-D Haar Wavelet Transform
with Dynamic Partial Reconfiguration for 3-D Medical Image Compression,
The IEEE Biomedical Circuits and Systems Conferences (BIOCAS), November
26th - 28th 2009, Beijing, China, pp. 137140.
3. A. Ahmad and A. Amira, Efficient Reconfigurable Architectures for 3-D
Medical Image Compression, The 2009 International Conference on Field-
Programmable Technology (FPT), December 9th - 11th 2009, Sydney, Australia,
4. H. Taha, A. Sazish, A. Ahmad, M. Sharif, and A. Amira, Efficient
FPGA Implementation of a Wireless Communication System using Bluetooth
Connectivity, The 2010 IEEE International Symposium on Circuits and
Systems (ISCAS), May 30th - June 2nd 2010, Paris, France, pp. 17671770.
5. A. Ahmad, A. Amira, Y. Berviller, and H. Rabah, Rapid Prototyping of
Finite Radon Transform (FRAT) for Medical Imaging Applications, The 2nd
European Workshop On Visual Information Processing (EUVIP), July 5th - 7th
2010, Paris, France.
6. B. Krill, A. Ahmad, A. Amira and H. Rabah, New FPGA-Bas