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  • Efficient ReconfigurableArchitectures for 3-D Medical

    Image Compression

    A thesis submitted for the degree of

    Doctor of Philosophy

    by

    Afandi Ahmad

    Supervisor

    Dr Abbes Amira

    Department Electronic and Computer Engineering

    School of Engineering and Design

    Brunel University, West London

    July 2010

  • A

  • Abstract

    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

  • iv

    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)

    Afandi.Ahmad@brunel.ac.uk

    23 July 2010

    v

  • To everyone who supports me, it just begins...

    vi

  • Acknowledgements

    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!

    vii

  • Authors Publications

    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

    Imaging.

    viii

  • ix

    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

    Surveys.

    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,

    pp. 472474.

    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