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IOSR Journal of Computer Engineering (IOSR-JCE)
e-ISSN: 2278-0661, p- ISSN: 2278-8727Volume 11, Issue 5 (May. - Jun. 2013), PP 79-83
www.iosrjournals.org
www.iosrjournals.org 79 | Page
A Hierarchical Clustering Algorithm Based Computer Aided
Molecular Modeling with Haematoxylin & Eosin Images of Colon
Cancer
K. Satish Reddy1
, Shaik Basha2
, B. Prashanth3
, K. Sridhar Reddy4
1,2,3,4
Department of ECE, Vardhaman College of Engineering, Hyderabad 501218 , India.
Abstract: Color Image segmentation plays a crucial role in many medical imaging applications. In this paper
we present a novel algorithm for computer aided molecular modeling in MATLAB R2012, a real time simulation
environment. This manuscript presents a novel algorithm for color image segmentation of Haematoxilin and
Eosin images of colon cancer. With help of this algorithm we can classify the differences between benign and
malignant tumor cells.
Keywords: - Color segmentation, Hierarchical Clustering, Real Time Simulation Environment, Molecular
Modeling.
I. INTRODUCTION
In this manuscript we compare the existing k-means clustering based Computer Aided Molecular
Modeling approach of H & E (Haematoxilin & Eosin) images of Colon Cancer as illustrated in [1] with the
current hierarchical clustering based approach. Ideally image segmentation is defined as the separation of an
image into non-overlapping, constituent regions which are homogeneous with respect to some characteristics
such as intensity or texture [2]. In present research work, we developed computer image-processing techniques
for classifying colon cancer and non-malignant tissue in digital histological images acquired from tissue sections
captured using scanning electronic microscope (SEM) acquired with high resolution charged coupled device
(CCD) camera from regions of interest (ROI) marked by pathologists on colon tissue sections [5].
II. DESIGN OF ALGORITHM
The different steps involved in the design of algorithm are explained as follows:
a. The input color image will be coarsely represented using 25 bins.
b. Coarse representation uses the spatial information from a Histogram based windowing process.
c. Hierarchical clustering is used to cluster the coarse image data.
d. Parameters Used
Input Color Image
Number of bins for coarse representation
Window size for histogram processing
Number of classes
Output segmented image
The coding part is illustrated as shown in the below code snippet, this coding part is done in MATLAB
R2012 - a real time simulation environment [6].
%Clear Memory & Command Window
clc;
clear all;
close all;
%Parameters for the Segmentation
nBins=5;
winSize=7;
nClass=6;
%Read Input Image
x = imread('DSS.PNG');
figure;imshow(x);title('Input Image');
%Segmentation
outImg = colImgSeg(x, nBins,winSize,nClass);
%Displaying Output
A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin
www.iosrjournals.org 80 | Page
figure;imshow(outImg);title('Image labled by cluster index');
%colormap('default');
%Image segmentation using Hierarchical clustering algorithm
xr = x(:, :, 1);
xg = x(:, :, 2);
xb = x(:, :, 3);
figure , imshow(xr, [ ]);title('objects in cluster1');
figure ,imshow(xg, [ ]);title('objects in cluster2');
figure ,imshow(xb, [ ]);title('objects in cluster3');
se = strel('disk', 3);
f = imopen(xg, se);
%figure ,imshow(f, [ ]);
xgd = im2double(f);
w = fspecial('average');
xgd2 = imfilter(xgd, w, 'replicate');
%figure ,imshow(xgd2, [ ]);
wg = fspecial('gaussian',[9 9], 1.8);
xgd3 = imfilter(xgd2, wg,'conv', 'replicate');
%figure ,imshow(xgd3, [ ]);
wm = fspecial('average',[69 69]);
xgb = imfilter(xgd3,wm, 'replicate');
%figure ,imshow(xgb, [ ]);
d = 255*xgd3-255*xgb;
%figure ,imshow(d, [ ]);
dmat = mat2gray(d);
isc = im2uint8(dmat);
%figure ,imshow(isc, [ ]);
ginmax = max(max(isc));
[m, n] = size(isc);
giimax = max(isc);
for i = 1:m
for j = 1:n
g = double(isc(i,j))+128-ginmax;
if g<0
ih(i,j) = 0;
elseif g>255
ih(i,j) = 255;
else
ih(i,j) = g;
end
end
end
figure ,imshow(ih, [ ]);
title('blue nuclei');
Modeling steps involved are from reading the image to segmentation of the nuclei into a separate image [3].
Further there are also intermediate steps that are involved between reading the image and segmenting the nuclei
into a separate image in MATLAB real-time simulation environment [4].
A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin
www.iosrjournals.org 81 | Page
Flow chart is designed as follows
A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin
www.iosrjournals.org 82 | Page
III. RESULTS AND DISCUSSIONS
The resulting output flow diagram as shown in Figure 1 is derived from the algorithm based on the above steps.
Figure 1: Output Results
IV. CONCLUSIONS
We have proposed a novel algorithm for color segmentation based on hierarchical clustering. Our
algorithm improves the color segmentation accuracy more significantly than previous approaches. One
distinctive advantage of our approach is that our algorithm also provides an explicit feature for ROI which can
be used for classification and recognition of benign and malignant tissues.
A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin
www.iosrjournals.org 83 | Page
REFERENCES
[1] Venkata Subbaiah Kotakadi, Gaddam Susmila Aparna, Prashanth B. U. V. and Sai D. V. R. Gopal. Article: Computer Aided
Molecular modeling approach of H & E (Haemotoxylin & Eosin) images of Colon Cancer. International Journal of Computer
Applications 44(9):5-8, April 2012. Published by Foundation of Computer Science, New York, USA.
[2] Otsu Nobuyuki, “A Threshold Selection Method from gray level Histograms”, vol. SMC-9, no.1, January 1979.
[3] G.Deng, L. W. Cahill and G.R. Tobin, “The Study of Logarithmic Image Processing Model and Its Application to Image
Enhancement”.
[4] Joongho Chang, Gunhee Han, Hose M. Valverde, Norman C. Grisworld, J. Francisco Duque-Carillo, Edgar anchez-Sinencio,(
1997) “Cork Quality Classification System using a Unified Image Processing and Fuzzy-Neural Network Methodology”, vol. 8, no.
4, July.
[5] Crabb D.P., Edgar D.F., Fitzke F.W., Mcnaught A.I. & Wynn H.P. (1995). New Approach to Estimating Variability in Visual-Field
Data Using An Image-Processing Technique. British Journal of Ophthalmology 79:213-217.
[6] R.C Gonzalez and R.E Woods , “ Digital Image Processing using MATLAB”, Addison Wesley/ Pearson education,2nd Education,
2002.

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A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin & Eosin Images of Colon Cancer

  • 1. IOSR Journal of Computer Engineering (IOSR-JCE) e-ISSN: 2278-0661, p- ISSN: 2278-8727Volume 11, Issue 5 (May. - Jun. 2013), PP 79-83 www.iosrjournals.org www.iosrjournals.org 79 | Page A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin & Eosin Images of Colon Cancer K. Satish Reddy1 , Shaik Basha2 , B. Prashanth3 , K. Sridhar Reddy4 1,2,3,4 Department of ECE, Vardhaman College of Engineering, Hyderabad 501218 , India. Abstract: Color Image segmentation plays a crucial role in many medical imaging applications. In this paper we present a novel algorithm for computer aided molecular modeling in MATLAB R2012, a real time simulation environment. This manuscript presents a novel algorithm for color image segmentation of Haematoxilin and Eosin images of colon cancer. With help of this algorithm we can classify the differences between benign and malignant tumor cells. Keywords: - Color segmentation, Hierarchical Clustering, Real Time Simulation Environment, Molecular Modeling. I. INTRODUCTION In this manuscript we compare the existing k-means clustering based Computer Aided Molecular Modeling approach of H & E (Haematoxilin & Eosin) images of Colon Cancer as illustrated in [1] with the current hierarchical clustering based approach. Ideally image segmentation is defined as the separation of an image into non-overlapping, constituent regions which are homogeneous with respect to some characteristics such as intensity or texture [2]. In present research work, we developed computer image-processing techniques for classifying colon cancer and non-malignant tissue in digital histological images acquired from tissue sections captured using scanning electronic microscope (SEM) acquired with high resolution charged coupled device (CCD) camera from regions of interest (ROI) marked by pathologists on colon tissue sections [5]. II. DESIGN OF ALGORITHM The different steps involved in the design of algorithm are explained as follows: a. The input color image will be coarsely represented using 25 bins. b. Coarse representation uses the spatial information from a Histogram based windowing process. c. Hierarchical clustering is used to cluster the coarse image data. d. Parameters Used Input Color Image Number of bins for coarse representation Window size for histogram processing Number of classes Output segmented image The coding part is illustrated as shown in the below code snippet, this coding part is done in MATLAB R2012 - a real time simulation environment [6]. %Clear Memory & Command Window clc; clear all; close all; %Parameters for the Segmentation nBins=5; winSize=7; nClass=6; %Read Input Image x = imread('DSS.PNG'); figure;imshow(x);title('Input Image'); %Segmentation outImg = colImgSeg(x, nBins,winSize,nClass); %Displaying Output
  • 2. A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin www.iosrjournals.org 80 | Page figure;imshow(outImg);title('Image labled by cluster index'); %colormap('default'); %Image segmentation using Hierarchical clustering algorithm xr = x(:, :, 1); xg = x(:, :, 2); xb = x(:, :, 3); figure , imshow(xr, [ ]);title('objects in cluster1'); figure ,imshow(xg, [ ]);title('objects in cluster2'); figure ,imshow(xb, [ ]);title('objects in cluster3'); se = strel('disk', 3); f = imopen(xg, se); %figure ,imshow(f, [ ]); xgd = im2double(f); w = fspecial('average'); xgd2 = imfilter(xgd, w, 'replicate'); %figure ,imshow(xgd2, [ ]); wg = fspecial('gaussian',[9 9], 1.8); xgd3 = imfilter(xgd2, wg,'conv', 'replicate'); %figure ,imshow(xgd3, [ ]); wm = fspecial('average',[69 69]); xgb = imfilter(xgd3,wm, 'replicate'); %figure ,imshow(xgb, [ ]); d = 255*xgd3-255*xgb; %figure ,imshow(d, [ ]); dmat = mat2gray(d); isc = im2uint8(dmat); %figure ,imshow(isc, [ ]); ginmax = max(max(isc)); [m, n] = size(isc); giimax = max(isc); for i = 1:m for j = 1:n g = double(isc(i,j))+128-ginmax; if g<0 ih(i,j) = 0; elseif g>255 ih(i,j) = 255; else ih(i,j) = g; end end end figure ,imshow(ih, [ ]); title('blue nuclei'); Modeling steps involved are from reading the image to segmentation of the nuclei into a separate image [3]. Further there are also intermediate steps that are involved between reading the image and segmenting the nuclei into a separate image in MATLAB real-time simulation environment [4].
  • 3. A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin www.iosrjournals.org 81 | Page Flow chart is designed as follows
  • 4. A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin www.iosrjournals.org 82 | Page III. RESULTS AND DISCUSSIONS The resulting output flow diagram as shown in Figure 1 is derived from the algorithm based on the above steps. Figure 1: Output Results IV. CONCLUSIONS We have proposed a novel algorithm for color segmentation based on hierarchical clustering. Our algorithm improves the color segmentation accuracy more significantly than previous approaches. One distinctive advantage of our approach is that our algorithm also provides an explicit feature for ROI which can be used for classification and recognition of benign and malignant tissues.
  • 5. A Hierarchical Clustering Algorithm Based Computer Aided Molecular Modeling with Haematoxylin www.iosrjournals.org 83 | Page REFERENCES [1] Venkata Subbaiah Kotakadi, Gaddam Susmila Aparna, Prashanth B. U. V. and Sai D. V. R. Gopal. Article: Computer Aided Molecular modeling approach of H & E (Haemotoxylin & Eosin) images of Colon Cancer. International Journal of Computer Applications 44(9):5-8, April 2012. Published by Foundation of Computer Science, New York, USA. [2] Otsu Nobuyuki, “A Threshold Selection Method from gray level Histograms”, vol. SMC-9, no.1, January 1979. [3] G.Deng, L. W. Cahill and G.R. Tobin, “The Study of Logarithmic Image Processing Model and Its Application to Image Enhancement”. [4] Joongho Chang, Gunhee Han, Hose M. Valverde, Norman C. Grisworld, J. Francisco Duque-Carillo, Edgar anchez-Sinencio,( 1997) “Cork Quality Classification System using a Unified Image Processing and Fuzzy-Neural Network Methodology”, vol. 8, no. 4, July. [5] Crabb D.P., Edgar D.F., Fitzke F.W., Mcnaught A.I. & Wynn H.P. (1995). New Approach to Estimating Variability in Visual-Field Data Using An Image-Processing Technique. British Journal of Ophthalmology 79:213-217. [6] R.C Gonzalez and R.E Woods , “ Digital Image Processing using MATLAB”, Addison Wesley/ Pearson education,2nd Education, 2002.