AN EFFICIENT FPGA IMPLEMENTATION OF MRI IMAGE FILTERING AND TUMOUR CHARACTERIZATION USING XILINX SYSTEM GENERATOR

International Journal of VLSI design & Communication Systems (VLSICS) Vol.2, No.4, December 2011
DOI : 10.5121/vlsic.2011.2409 95
AN EFFICIENT FPGA IMPLEMENTATION OF MRI
IMAGE FILTERING AND TUMOUR
CHARACTERIZATION USING XILINX SYSTEM
GENERATOR
Mrs. S. Allin Christe1
, Mr.M.Vignesh2
, Dr.A.Kandaswamy3
1,2
Department of Electronics & Communication Engineering , PSG College of
Technology, Coimbatore,India
sac@ece.psgtech.ac.in , vigneshhh@gmail.com
3
Department of Biomedical Engineering, PSG College of Technology, Coimbatore,India
hod@bme.psgtech.ac.in
ABSTRACT
This paper presents an efficient architecture for various image filtering algorithms and tumor
characterization using Xilinx System Generator (XSG). This architecture offers an alternative through a
graphical user interface that combines MATLAB, Simulink and XSG and explores important aspects
concerned to hardware implementation. Performance of this architecture implemented in SPARTAN-3E
Starter kit (XC3S500E-FG320) exceeds those of similar or greater resources architectures. The proposed
architecture reduces the resources available on target device by 50%.
KEYWORDS
MRI, Matlab, Xilinx System Generator, FPGA, Edge Detection
1. INTRODUCTION
The handling of digital images has become a subject of widespread interest in different areas
such as medical, technological applications and many others. There are lots of examples where
image processing helps to analyze, infer and make decisions. The main objective of image
processing is to improve the quality of the images for human interpretation, or the perception of
the machines independently. This paper focuses on processing an image pixel by pixel and in
modification of pixel neighbourhoods and the transformation that can be applied to the whole
image or only a partial region. The need to process the image in real time, which is time
consuming, leads to this implementation in hardware level, which offers parallelism, and thus
significantly reduces the processing time. FPGAs are increasingly used in modern imaging
applications image filtering[1,2], medical imaging[3,4], image compression[5-7], wireless
communication[8,9].The drawback of most of the methods are that they use a high level language
for coding. This objective lead to the use of Xilinx System Generator, a tool with a high- level
graphical interface under the Matlab, Simulink based blocks which makes it very easy to handle
with respect to other software for hardware description [10]. The various applications where
image filtering operations applied are noise removal, enhancing edges and contours, blurring and
so on. This paper presents an architecture of filtering images for edge detection using System
Generator, which is an extension of Simulink and consists of a models called "XILINX

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BLOCKS", which are mapped into architectures, entities, signs, ports and attributes, which
Scripts file to produce synthesis in FPGAs, HDL simulation and developments tools. The tool
retains the hierarchy of Simulink when it is converted into VHDL/Verilog. There are many
research works related to image processing and its real time implementation using XSG which
uses high end hardware similar to the one used in paper [11] by Sami Hasan, Alex Yakovlev and
Said Boussakta et al, complicated design used in paper [12] by Zhang Shanshan et al, but the
proposed design in this work eliminates the design complexity, takes least resource usage and
also implemented in low cost basic FPGA device (Spartan 3E).
2. XILINX SYSTEM GENERATOR
Xilinx System Generator (XSG) [12,13] is an integrated design Environment (IDE) for FPGAs
within the ISE 11.3 development suite, which uses Simulink[14], as a development environment
and is presented in the form of model based design. It has an integrated design flow, to move
directly to the Bit stream file (*. bit) from Simulink design environment which is necessary for
programming the FPGA.
One of the most important features of XSG is that it possesses abstraction arithmetic that is
working with representation in fixed point with a precision arbitrary, including quantization and
overflow. XSG can only perform simulations as a fixed point double precision type. XSG
automatically generates VHDL/Verilog code and a draft of the ISE model being developed. It
also generates hierarchical VHDL/Verilog synthesis, floor plan and mapping hardware. In
addition to this it also generates a user constraint file (UCF), simulation and testbech and test
vectors.
XSG was created primarily to deal with complex Digital Signal Processing (DSP) applications,
but it also deals with implementation of many images processing application. The blocks in XSG
operate with Boolean values or arbitrary values in fixed point type, for a better approach in
hardware implementation. In contrast Simulink works with numbers of double-precision floating
point. The connection between XSG blocks and Simulink blocks are the gateway blocks. The
Fig.1 shows the broad flow design of XSG.
As previously mentioned, XSG is configured to program the FPGA. The synthesis and
implementation of the program are done subsequently. In real time implementation of edge
detection on FPGA by Sudeep K C et al [15], is done with Spartan3A DSP board but in present
work Spartan3E starter kit is used to implement the design with least resource usage. The
architecture implemented in this paper is versatile for any edge detection operator unlike the
paper [11] by Sami Hasan et al, which only deals with Sobel operators. Compared to vehicle
image edge detection algorithm hardware implementation on FPGA by Zhang Shanshan et al
[12], the resource usage by the proposed architechture is reduced by 50%.
Fig 1: XSG Design Flow

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3.EDGE DETECTION
Edge detection [16] is one of the most commonly used operations in image analysis, and there are
probably more algorithms in literature for enhancing and detecting edges. An edge is point of
sharp change in an image, a region where pixel locations have abrupt luminance change i.e. a
discontinuity in gray level values. In other words, an edge is the boundary between an object and
the background. The shape of edges in images depends on many parameters like the depth
discontinuity, surface orientation discontinuity, reflectance discontinuity, illumination
discontinuity, and noise level in the images.
The main steps in edge detection are:
1) Filtering which is gradient computation based on intensity values of two points which are
susceptible to noise. Filtering reduces noise but there is a trade-off between edge strength and
noise reduction.
2) Enhancement is done in order to facilitate the detection of edges, it is essential to determine
intensity changes in the neighbourhood of a pixel in an improved manner. Enhancement
emphasizes pixels where there is a significant change in local intensity values and is usually
performed by computing the gradient magnitude.
3) Detection is done because many points in an image have a nonzero value for the gradient, but
not all these points can be considered to be edges. Therefore, some method should be used to
determine which points are edge points. Frequently, threshold provides the criterion for detection.
4)Localize/analyze mainly rejects spurious edges include weak but justified edges.
Measuring the relative brightness of pixels in a neighbourhood is mathematically analogous to
calculating the derivative of brightness. Brightness values are discrete, not continuous, so we
approximate the derivative function. Different edge detection methods use different discrete
approximations of the derivative function. The design flow of edge detection using XSG is shown
in Fig 2.
Fig: 2 Design Flow of XSG for image edge detection
The edge detection operators used in this paper is based on the behavioural study of edges with
respect to the following two categories:
• Gradient edge detectors (first derivative or classical)
• Zero Crossing or Laplacian (second derivative)
From the first order derivative the Roberts, Prewitt, Sobel and Scharr operators, and from the

98
second order derivative the Laplacian of Gaussian (LoG) operator, also known as the Marr-
Hildreth operator and some additional filtering operations has been utilized in this work which is
discussed below:
3.1. Fist Order Derivative
The Roberts' Cross operator[16] is one of the first edge detectors initially proposed by Lawrence
Roberts in 1963 used in image processing and computer vision for edge detection. It a differential
operator that approximates the gradient of an image through discrete differentiation which is
achieved by computing the sum of the squares of the differences between diagonally adjacent
pixels implemented by two 2x2 mask shown in equation (1). These filters have shortest support
and more vulnerable to output noise.
(1)
Where Gx is the gradient along x-axis, Gy is the gradient along y-axis. Total Gradient magnitude G
and direction can be obtained by using equation (2),
The Prewitt operator [16] is based on the idea of central difference and is much better than
Roberts’s operator. It is based on convolving the image with a small, separable, and integer
valued filter in horizontal and vertical direction as shown in equation (3). Prewitt’s operator has
longer support and is less vulnerable to noise.
The Sobel operator is also a central difference with more weights to the central pixels where
averaging as given by equation (4). It has an improved noise suppression than Prewitt’s operator.
The Sobel operator, while reducing artifacts associated with a pure central differences operator,
does not have perfect rotational symmetry.
Scharr operator [17] looked into optimizing this property. Scharr operators’ results from an
optimization of weighted mean squared angular error in Fourier domain which is done under the
condition that resulting filters are numerically consistent. Therefore they really are derivative
kernels with symmetry constraints which are shown in equation (5).

99
3.2. Second Order Derivative:
The Laplacian [16] is a 2-D isotropic measure of the second order spatial derivative of an image.
The Laplacian of an image highlights regions of rapid intensity change using zero crossing. The
LoG is often applied to an image that has first been smoothed with a Gaussian smoothing filter to
reduce its sensitivity to noise followed by Laplacian operator. The operator normally takes a
single gray level image as input and produces another gray level image as output. The 3x3 kernel
approximations to the Laplacian filter is given in equation (6)
3.3. Additional Filtering Operations
Gaussian blur is usually applied to smoothen the image by reducing the noise in the image.
Gaussian 3x3 kernel used is shown in equation (7)
Edge sharpening is usually done to strengthen the output image, this leads to connecting the edges
to get a sharp output image. 3x3 filter mask applied for edge sharpening is given in equation (8).
Thresholding is the simplest method of image segmentation. From a gray scale image,
thresholding can be used to create binary images.
4. PROPOSED DESIGN
The entire operation of edge detection proposed using Simulink and Xilinx blocks goes through 3
phases,
• Image pre-processing blocks.
• Edge detection using XSG.
• Image post-processing blocks
For the design of filters to meet hardware requirements, it is a must to pre-process the image prior
to the main hardware architecture. In the software level simulation using Simulink blocksets
alone, where the image is used as a two-dimensional(2D) arrangement such as M x N, there is no
need for any image pre-processing, but at hardware level this matrix must be an array of one
dimension(1D), namely a vector, where it requires image pre-processing.
4.1 Image Pre-processing Blocksets
The model based design used for image pre-processing is shown in Fig.3, the blocks utilized here
are discussed below. Input images which could be color or grayscale are provided as input to the
File block. A color space conversion block converts RGB to grayscale image and this data which
is in 2D is to be converted to 1D for further processing. Frame conversion block sets output signal

100
to frame based data and provided to unbuffer block which converts this frame to scalar samples
output at a higher sampling rate.
Fig 3: Image Pre-Processing
4.2 Edge detection using XSG Blocksets
The model based design [12] using Xilinx blocksets for processing the input image for edge
detection is shown in Fig.4,
Fig 4: Edge Detection Using XSG
Xilinx fixed point type conversion is made possible by Gateway In block. To perform the edge
detection a convolution operation of the input image with a filter mask is to be performed for
which a n-tap MAC FIR filter block is used provided with nine programmable coefficients. This
is followed by certain arithmetic blocks to merge all the processed data’s.
4.3 Image post-processing Blocksets
The image post-processing blocks which are used to convert the image output back to floating
point type is shown in Fig.5,
Fig 5: Image Post-Processing

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For post-processing it uses a Buffer block which converts scalar samples to frame output at lower
sampling rate, followed by a 1D to 2D (matrix) format signal block, finally a sink is used to
display the output image back in the monitor, utilizing the Simulink blocksets.
This proposed design architecture has also been utilized in an application oriented design by
adding appropriate image post processing blocks as shown in Fig.6 with added features like
region of interest (ROI) section which defines the shape and position of ROI and statistical
feature extraction for different tissue analysis. The different textural statistics that can
differentiate the tissues like mean, variance and standard deviation are computed using equation
(9-11)
( 9)
(10)
(11)
These parameter are measured for a abnormal region and normal region for 3 different cases of
tumours, where M x N is 2D data It could seen from the Table 1 and graphs as shown in Fig
18- Fig 20 there is a clear variation in the properties of 3 cases of tumours considered. This
analysis can be extended to further statistical based differentiation among the tumours by
considering larger data sets.
Fig 6: ROI Extraction and Statistical Analysis
5.HARDWARE IMPLEMENTATION
The architecture explained above deals only with software simulation level. For implementing
this design in a FPGA board the entire module should be converted to FPGA synthesizable one.
For that purpose main module for edge detection is converted for JTAG hardware co-simulation,
this is done with the help of System generator block which is shown in Fig 7. This block is
configured according to the target platform and a bit stream (*.bit) file is generated.

102
Fig: 7 System Generator Block
After the bit stream file is generated, hardware co-simulation target is selected and in this work,
Spartan 3E starter kit (XC3S500E-FG320) is used for board level implementation. The complete
design with the edge detection, gaussian blur, thresholding & edge sharpening operations is
shown in Fig 8. The entire architecture with the hardware and software co-simulation design is
shown in Fig 9.
Fig: 8 Complete Design with edge detection, blur, thresholding, & sharpening operation

103
Fig 9: Complete Hardware/Software Co-simulation Design
6.RESULTS
The different edge detection operators implemented in this paper are given below along with their
corresponding hardware outputs obtained except for Roberts house image which was not clear.
The input image utilized for edge detection and outputs of various operators is shown in Fig.10.
(a): Input Images
(b) Roberts’ Cross Operator Output
(c) Prewitt Edge Detection Output

104
(d) Sobel Edge Detection Output
(e) Scharr Operator Output
(f) LoG Operator Output
(g) Gaussian Blur Output
(h) Threshold operation Output

105
(i) Edge sharpen Output
Fig 10.(a)Input Images of resolution 256 x 256, Edge output using (b)Roberts (c)Prewitt
(d)Sobel (e)Scharr (f)LoG (g) Gaussian Blur (h) Threshold (i) Edge Sharpening
The device resource usage is also estimated for this proposed design which is literally reduced by
50% compared vehicle image edge detection algorithm hardware implementation on FPGA by
ZhangShanshan and WangXiaohong et Al [12].
FPGA Board Selected: XC3S500E-4 FG320
Clock Frequency: 50 MHz
Table 1 Resources utilized
Resource Used Available
Device
Usage by
proposed
design
Device
Usage by
Zhang [11]
Flip Flop 163 9312 2 % 4%
Slices 116 4656 2.5 % 5%
LUTs 130 9312 1.5 % 3%
IOBs 49 232 21 % 16%
The VHDL code automatically generated by using XSG has got 4547 lines of VHDL coding from
this it’s clear, that DSP application are more complex and tedious if coded and moreover these
DSP application are not logic based, they involve lot of floating/fixed point operation which are
hard to be determined. Hence it’s clear that by using XSG, program developing & debugging can
avoided thereby the design development time is minimized.
The ROI extracted output image is shown in Fig 11, which clearly shows in the MRI-Brain
image, with the tumour (ROI) part alone extracted.
Fig 11: ROI Extracted Output Image

106
The various textural statistical parameters like mean, variance and standard deviation for
different class of tumour (ROI) images are tabulated in Table 2 and its graphical
representation is also shown in Fig. 12-14.
Table 2 Textural statistical Parameter estimation of MRI tissues
case IMAGE ROI TYPE MEAN VARIANCE STANDARD
DEVIATION
I
Normal 3.18 e-1
3.08 e-3
5.55 e-2
Abnormal 2.29 e-1
4.37 e-3
6.61 e-2
I
Normal 3.23e-1
2.02e-3
4.49e-2
Abnormal 2.25e-1
5.17e-3
7.19e-2
II
Normal 4.10e-1
4.05e-3
6.36e-2
Abnormal 5.13e-1
2.48e-2
1.57e-1
II
Normal 4.20e-1
3.40e-3
5.83e-2
Abnormal 5.13e-1
1.60e-2
1.26e-1
III
Normal 3.91e-1
3.15e-3
5.62e-2
Abnormal 8.94e-1
2.80e-2
1.67e-1
III
Normal 2.38e-1
3.30e-3
5.76e-2
Abnormal 6.17e-1
4.90e-2
2.21e-1

107
Fig 12. Mean Analysis
Fig 13. Variance Analysis
Fig 14. Standard Deviation Analysis

108
7. CONCLUSION
The Xilinx System Generator tool is a new application in image processing, and offers a model
based design for processing. The filters are designed by blocks and it even supports Matlab codes
through user customizable blocks. It also offers an ease of designing with GUI environment. This
tool support software simulation, but most importantly it generates necessary files for
implementation in all Xilinx FPGAs, with the parallelism, robust, speed and automatic area
minimization. These features are essentials in real time image processing. The design architecture
used in this paper can be used for all Xilinx FPGA Kit with proper user configuration in System
generator block and could be extended to real time image processing.
REFERENCES
[1] “Implementation and Evaluation of Image Processing Algorithms on Reconfigurable Architecture
using C-based Hardware Descriptive Languages” Daggu Venkateshwar Rao, Shruti Patil, Naveen
Anne Babu and V Muthukumar , International Journal of Theoretical and Applied Computer
Sciences,Volume 1 Number 1 (2006) pp. 9–34
[2] “Implementation of Image Processing Algorithms on FPGA hardware” by Anthony Edward Nelson
,MS thesis, May 2000.
[3] “FPGA Implementation of an Efficient Partial Volume Interpolation for Medical Image Registration”,
C. John Moses, Dr. D. Selvathi, S.Sajitha Rani, ICCCCT-10, 2010 IEEE
[4] “An Overview of MRI Brain Classification using FPGA Implementation” Dr Mohd Fauzi Bin
Othman , Norarmalina Abdullah, Nur Aizudin Bin Ahmad Rusli,IEEE Symposium on Industrial
electronics & Applications (ISIEA) Oct 2010,Malaysia.
[5] “JPEG Image Compression Using an FPGA”, by James Rosenthal , MS thesis, Dec 2006
[6] “FPGA Implementation of Subband Image Encoder Using Discrete Wavelet Transform”, by Youn-
Hong Kim , Kyong-il Jun, Kang-Hyeon Rhee, 1999 IEEE TENCON
[7] “FPGA Implementation of Image Compression using bottom- up approach of Quad tree technique”
by Satish K.Shah, Rakesh K.Soni,,Brijesh Shah, IETE Journal of research , Vol 57, Issue 2, Mar-Apr
2011.
[8] “Efficient FPGA Implementation of a WirelessCommunication System Using Bluetooth
Connectivity”,Hasan Taha, Abdul N. Sazish, Afandi Ahmad, Mhd Saeed Sharif, and Abbes Amira,
IEEE, 2010
[9] “Efficient hardware co-simulation of down converters for wireless communication systems”Rajesh
Mehra and Swapna Devi, International journal of VLSI design & Communication Systems
( VLSICS ), Vol.1, No.2, June 2010
[10] “Modeling and Implementation of DSP FPGA Solutions",Robert D. Turney, Chris Dick1, David B.
Parlour, and James Hwang , Xilinx Inc
[11] “Performance Efficient FPGA Implementation of Parallel 2-D MRI Image Filtering Algorithms using
Xilinx System Generator” by Sami Hasan, Alex Yakovlev and Said Boussakta, CSNDSP IEEE ,2010
.
[12] Vehicle Image Edge Detection Algorithm Hardware Implementation on FPGA by ZhangShanshan
and WangXiaohong, International Conference on Computer Application and System Modeling
,ICCASM 2010.

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[13] Xilinx System Generator User’s Guide,2010, downloadable from;http:// www. Xilinx.com.
[14] Xilinx Inc., “Xilinx Foundation Series”, http://www.xilinx.com/products/found.html.
[15] Mathworks Inc., “Simulink 3.0”, http://www.mathworks.com/products/simulink/.
[16] The Mathworks Inc., “Matlab 7.1”, http://www.mathworks.com/products/matlab/
[17] “A Novel Architecture for Real Time Implementation of Edge Detectors on FPGA” by Sudeep K C
and Dr. Jharna Majumdar, IJCSI International Journal of Computer Science Issues, Vol. 8, Issue 1,
January 2011,pp 193-202
[18] “Digital Image Processing” by Rafael C. Gonzalez , Richard E. Woods,2nd Edn,Prentice Hall,2002
[19] “Optimal Operators in Digital Image Processing” by Scharr, Hanno, PhD thesis , 2000.
Authors
S.Allin Christe is working as an Assistant Professor (S.Gr) in the Department of
Electronics & Communication Engineering of PSG College of Technology,
Coimbatore, India. She is pursuing her Ph.D degree from Anna University, Chennai,
India. Her research interests include Image Processing, VLSI Design and Soft
computing.
Vignesh M graduated from PSG College of Technology in 2011 from Dept. of
Electronics and Communication. His areas of interests include Sytem On Chip, ASIC
Design and Image Processing. His research areas include implementation of image
processing algorithms on Embedded and Reconfigurable [FPGA] hardware.He was a
post graduate student in Dept. of Electronics and Communication in PSG College of
Technology between 2009-2011.
Dr.Kandaswamy Arumugam is Professor and Head , Department of Biomedical
Engineering, PSG College of Technology, Coimbatore, India. He has 38 years of
teaching experience. He has published more than 80 papers in national and
international journals and conference proceedings. His fields of interest are Image
Processing Applications in Medicine and wireless communication systems.

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