Proceedings of International Conference on Computing Sciences

WILKES100 ICCS 2013

ISBN: 978-93-5107-172-3
Mixed noise reductions in microarray images using wavelet
thresholds
Lakshmana Phaneendra Maguluri
1*
, SK Salma Begum
2
, Dr. G V S N R V Prasad
3
,
P Avinash
4
, V Trinadh Babu
5

and M Siva Naga Srikanth
6
1, 2, 3 ,4, 5
Department of CSE, Gudlavalleru Engineering College, Gudlavalleru, AP, India.
6
PG Student (CSE) in L P University
Abstract
Nowadays programming knowledge has become very essential for engineering professionals as well as scientist and
researchers to develop simulation models, performing analysis, optimization and decision-making. So they require some
neutral software tool like MATLAB to take input from Software, perform computations and output the results to another
software package. In these days processing microarray image leads to unsatisfactory results. Segmenting the image into
homogeneous is one of the important tasks in image analysis and is widely used in a variety of consumer electronics
applications such as Object recognition geographical imaging robot vision and medical imaging. While processing the
microarray images, we facing some of the problems like dead centers, trapped centers and some portions of images contain
mixed noise. Here for noise reductions, dead centers problems we are move towards OKMBEMD. In BEMD process which
segments the image into high and low residual IMFs. Neutralize these results we proposing Wavelet models.
2013 Elsevier Science. All rights reserved.
Keywords: OKM, BEMD, MATLAB, Microarray Images Mixed Noise, DWT.
1. Introduction
Availability of computational resources and the demand for faster production lead to a greater emphasis on
virtual engineering in which many problems need to be solved using a computer. This kind of computational
research or problem solving requires a strong background in mathematical methods, computational skills and
knowledge of at least one scientific computing tool. MALAB is a software tool, which provides the numerical
computing environment and fits the bill, perfectly. It allows the users to solve variety of engineering problems
and also analyze the data with a lot of visualization, plotting, printing, and manipulating of engineering data as
well as performing various engineering computations. Though it is primarily for numerical computing, there are a
lot of additional facilities called toolboxes for genetic algorithms, optimization, neural networks, simulations
(Simulink) etc.
Microarray is an innovative tool in biomedical research, which enables researchers to analyze genes, proteins
and other biological molecules. A microarray is a collection of spots containing DNA deposited on the solid
surface of glass slide. Each of the spot contains multiple copies of single DNA sequence [2]. Microarray
expression technology helps in testing and extracting the expression of large number of genes in parallel and its
applications can vary from cancer diagnosis to human identification.
While pre-processing microarray image is mainly to improve its defects including noise and poorly expressed
spots. The processing of cDNA Microarray Images constitutes of following steps: Gridding, Segmentation and
*
Corresponding author. Lakshmana Phaneendra Maguluri
238 Elsevier Publications, 2013
Lakshmana Phaneendra Maguluri et al.
Intensity Extraction. In order to identify where exactly the spots are located, gridding is critical step in microarray
image processing and it is a process in which segments the microarray image into compartments Segmentation is
the process of dividing each compartment into spots and image background. In Intensity extraction, this
calculates the foreground and background intensity pairs.
In this Article we propose a new method for segmenting microarray images by using OKMBEMD. But after
segmenting the images at some places we are identifying mixed noises. In these aspects to overcome noisy
images we are shifting to wavelets models. For De-noising the microarray images we are going to use peak signal
to noise ratio. The flow diagram of the proposed method is shown in following Fig1, Table1.
2. Proposed Optimized K-means Algorithm
In this paper, the OKM algorithm has been introduced as them modified version of the conventional Kmeans
(KM) algorithm. The OKM algorithm fully concentrates on differentiating between the dead centers and cluster
with similar intensity pixels. The pixel with the same Euclidian distance to two or more adjacent clusters is
initially assigned to the dead centre and in upcoming next iteration it is assigned to the cluster with lower
variance cluster, till up to no dead centre could be encountered. OKM Algorithm designed to ensure both types of
centres or clusters are continuously updated for every iteration till up to the pixels assigned to the fitting clusters.
From the mentioned description, the implementation of the OKM clustering algorithm could be outlined as
follows:
Initialize the all the cluster centre value and , and let iteration t =0. (Note: is the constant and its value
within range 0<1).
Based on Euclidean distance, assigning all pixels to the nearby clusters.
For starting cluster we have measure Mean Square Error value from the following equation (Note: this step is
only implemented for iteration t =0).

)
Where p
i
(x, y) is the i
th
pixel with the coordinate (x, y) to be segmented and c
j
is the j
th
centre or cluster and n
is the no of pixels in the image.
For all the clusters we have to calculate fitness value based on following equation we have to find cluster with
high fitness value.

For the pixels having the same Euclidean distance to two or three adjacent clusters, sort the grey intensity of
these pixels in the ascending order according to their distance from cl and denote the sorting array as Er,
where r = 1,2, 3 (K1). Find the empty cluster as
1. If cluster without members is found
1.1. Sot all clusters in the ascending order according to their fitness values and name the sorting array as Fq,
where q =1, 2, 3 k.
1.2. For all clusters obtained in step 6.i) (a), sort these clusters in ascending order according to the number
of pixels or members in the clusters and denote the sorting array as Hw, where w = 1, 2, 3.z (z is the total
number of empty and zero variance clusters)
1.3. Begin with assign the pixels with grey intensity of Eb to Hb where b=1and continue until the value of b
in Hb equals to z or the value of b in Eb equals to (k-1).
2. If cluster with member is found
2.1. We begin to assign the pixels with grey intensity E
b
to the clusters with the lowest fitness value among
their adjacent clusters, where b =r = 1, 2..k1
3. Increase iteration by t = t + 1, and update the centre positions, and measure the Mean Square Error value
using following Equations
239 Elsevier Publications, 2013
Mixed Noise Reductions in Microarray Images Using Wavelet Thresholds

Where, n j is the number of pixels in the j
th
cluster.
3. Wavelet Transformations
Wavelet theory is an alternative approach to the short-time Fourier transforms (STFT) and extension of
Fourier theory. A wavelet as its name implies is a small wave that grows and decays essentially in a limited time
period. In Fourier theory, the signal is decomposed into sins and cosines but while coming to wavelets the signal
is projected on a set of wavelet functions. Fourier transform would provide good resolution in frequency domain
and wavelet would provide good resolution in both time and frequency domains.
Wavelet analysis the signal is decomposed into scaled and shifted versions of the chosen mother wavelet.
Wavelets have been extensively used in image processing that provides a multi-resolution decomposition of an
image. Wavelet transform provides better spatial and spectral information of image formation because it
provides a non-redundant image representation. The wavelet transform decomposes the image into low-high,
high-low, high-high spatial frequency bands at different scales and the low-low band at the coarsest scale. DWT
allows thresholding, clipping and shrinking to separate signals or remove noise. Wavelet transform has been
greatly used in many areas, such as texture analysis, data compression, feature detection, and image fusion.
De-noising of microarray images affected by Gaussian noise using wavelet thresholding is very effective
approach because its ability to capture the energy of signal into a few energy transforms values. De-noising the
microarray image using wavelet threshold is as follows:
1. For noisy microarray image apply wavelet transformation to obtain noisy wavelet coefficients.
2. At each level we have to choose appropriate threshold limit is chosen to overcome noise. Here soft
thresholding approaches are used for removal of noise microarray images.
3. Perform Inverse wavelet transformation to obtain De-noising image.
While wavelet threshold is explained as decomposition of image wavelet coefficients, which contains energy,
transform values and comparing coefficient values with given detailed threshold values. The image f is corrupted
Gaussian noise with independent and identically distributed mean and standard deviation. Then the noisy image
received is g
ij
=f
ij
+sn
ij
.
They are basically two types of thresholdings are there 1) Hard Thresholding and 2) Soft Thresholding. Where
Hard Thresholding is discontinuous and also input is kept if it is greater than threshold T, otherwise it is kept as
Zero. Where as in soft thresholdings it will degrades all other coefficients that trend to blur the images. We can
see that soft thresholding approach is better and yields good resultant images.
4. Proposed methodology BEMD Using Filter
The filtering process using BEMD is summarized as follows:
The noisy image is firstly decomposed into IMFs and residue components using BEMD. After decomposition,
the first few IMFs contain the large amount of noise (High Frequency Components).
The wavelet transform is applied to filter these first few IMFs, to improve the visual quality of the image. To
reduce noise, we just reject all values lower than a specified threshold in the extrema points of the IMFs.
Thereafter wavelet reconstruction algorithm is applied to obtain the IMF image.
240 Elsevier Publications, 2013
Lakshmana Phaneendra Maguluri, SK Salma Begum, Dr. G J S N R J Prasad, P Avinash, J Trinadh Babu and M Siva Naga Srikanth
Fig. 1. De-noising using wavelet transformation filtering
Fig. 2. Proposed BEMD with Filtering Method
Finally the BEMD reconstruction (combination of Low frequency components and wavelet filtered high
frequency components) gives the de-noised image.
Thresholding is one of the most important approaches in image segmentation. In this approach pixels are alike
are grouped together. Often a image histogram is used to best setting for threshold together we are combining
four types of thresholding techniques Universal Threshold SURE Shrink, Bayes Shrink and Normal Shrink. The
proposed methods perform significantly better in terms of noise suppression and detail preservation of microarray
images.
LW (IMF) HF (IMF)
Input
DWT
Wavelet
Threshold
IDWT
Output
Noisy Microarray
Image
BENB with Filteiing
De-noising Microarray
Image
Wavelet
Thresholdings
241 Elsevier Publications, 2013
Mixed Noise Reductions in Microarray Images Using Wavelet Thresholds
5. Experimental Results
Noise removal steps of the microarray image are performed on a 48 blocks, each block consisting of 110
spots. A sample block has been chosen and 108 spots of the block have been cropped for simplicity. The sample
image is a 154*200 pixel image that consists of a total of 30800 pixels. The microarray image have been
converted to grayscale image to specify a single intensity value that varies from the darkest (0) to the brightest
(255) for each pixel shown in figure 4 We used the image quality metric, peak signal-to-noise ratio (PSNR), to
measure the quality of the restored image. The PSNR measure is defined as
PSNR=2u.log1u

Where MSE is the mean squared error between the original noise-free image and the restored images.

Microarray Image White Gaussian Noise Image
Wavelet Thresholds Filtered using thresholding
Fig. 3. Experimental Results.
Table 1. PNSR Values for filtering Method
Method =0.015 =0.025 =0.036
Wavelets (Universal Shrink) 24.02 18.98 16.49
Wavelets (Sure Shrink) 22.9 17.11 14.76
Wavelets (Bayes Shrink) 21.08 16.72 12.91
Wavelets (Normal Shrink) 21.98 16.63 11.91
BEMD+Wavelets (UniversalThreshold) 32.11 29.87 23.86
BEMD+Wavelets (Sure Shrink) 31.89 28.74 22.11
BEMD+Wavelets (Bayes Shrink) 32.26 25.78 19.43
BEMD+Wavelets (Normal Shrink) 38.91 30.24 24.22
242 Elsevier Publications, 2013
Fig. 4. PNSR Values for filtering method.
6. Conclusion
The BEMD decomposes the image into IMFs and residual component. Then, the selected high frequency
IMFs are de-noised with wavelet model by using different thresholds and finally the BEMD reconstruction gives
the de-noised image. The experimental results show the proposed algorithm can perform significantly better in
terms of noise suppression and detail preservation in microarray images.
References
[1] M.Schena, D.Shalon, Ronald W.davis and Patrick O.Brown,Quantitative Monitoring of gene expression patterns with a complementary
DNA microarray, Science, 270,199,pp:467-470.
[2] Wei-Bang Chen, Chengcui Zhang and Wen-Lin Liu, An Automated Gridding and Segmentation method for cDNAMicroarray Image
Analysis, 19th IEEE Symposium on Computer-Based Medical Systems.
[3] Tsung-Han Tsai Chein-Po Yang, Wei-ChiTsai, Pin-Hua Chen, Error Reduction on Automatic Segmentation in MicroarrayImage, IEEE
2007.
[4] Eleni Zacharia and Dimitirs Maroulis, Microarray Image Analysis based on an Evolutionary Approach 2008 IEEE.
[5] Nor Ashidi Mat Isa, Cluster-based Adaptive Fuzzy switching median filter for removal of universal impulse noiseIEEE Transactions
on customer electronics vol.56.no.4.November 2010.
[6] S.Satheesh, Dr.KVSVR Prasad, Medical Image Denoising using Adaptive Threshold based on Contourlet Transform, Advanced
Computing: An International J ournal ( ACIJ ), Vol.2, No.2,P.52-58, 2011.
[7] Geoffrine J udith.M.C1 and N.Kumarasabapathy, Study and Analysis of Impulse Noise Reduction Filters, Signal & Image Processing :
An International J ournal(SIPIJ ) Vol.2, No.1,P. 82-92, 2011.
[8] Rastislav Lukac_, Bogdan Smoka, Application of the Adaptive CenterWeighted Vector Median Framework for the Enhancement of
CDNA Microarray Images, Int. J . Appl. Math. Comput. Sci., Vol. 13, No. 3, 369383, 2003.
[9] Amir Beck, Marc Teboulle, A Fast Iterative Shrinkage-Thresholding Algorithm with Application to Wavelet-based Image Deblurring,
IEEE conference, ICASSP 2009,P.693-696,2009.
[10] Gnanambal Ilango and R. Marudhachalam, New Hybrid Filtering Techniques for Removal of Gaussian Noise From Medical Images,
ARPN J ournal of Engineering and Applied Sciences, VOL. 6, NO. 2, P.8-12, 2011.
[11] Naga Sravanthi Kota, G.Umamaheswara Reddy , Fusion Based Gaussian noise Removal in the Images Using Curve lets and Wavelets
With Gaussian Filter, International J ournal of Image Processing (IJ IP), Vol.5, No.4 ,P.456-468, 2011.
[12] D.Rama Krishna Noise Removal using Empirical Mode Decomposition and Wavelet Transform in Microarray ImagesProceedings of
the National Conference on Emerging Trends in Information Technology NCETIT-2013.
[13] Agarwal, R. Bit plane average filtering to remove Gaussiannoise from high contrast images, ICCCI 2012
u
1u
2u
Su
4u
Su
s=o.o1S s=u.u2S s=u.uS6
Wavelets
(0niveisal
Thiesholu)
Wavelets (Suie
Shiink)
243 Elsevier Publications, 2013
Lakshmana Phaneendra Maguluri, SK Salma Begum, Dr. G J S N R J Prasad, P Avinash, J Trinadh Babu and M Siva Naga Srikanth
Index

A
Arabidopsis thaliana, 233235

M
miRNA in arabidopsis thaliana and oryza sativa, 232
materials and methods, 233
nucleotide position wise AUGC, 235236
results and disscusion, 233235

O
Oryza sativa, 233235