PULMONARY AIRWAY TISSUE EXTRACTION FOR LESION DETECTION USING HRCT IMAGES

Ms. A. ARUL SELVI

Department Of Computer Science And Engineering Anna University, Chennai

Abstract:

Lung diseases are one of the biggest killers in the world. Improved survival rate could be obtained

if the diseases can be detected at early stages. Accurate extraction of lung texture is very important for detection and diagnosis of Lung diseases such as bronchitis, asthma and other small airway diseases. The Computer Aided Diagnosis (CAD) is automated for detection of lung lesions through various techniques. Unfortunately, existing methods do not necessarily extract sufficient information for diagnosing. In this work, a method for diagnosing airway diseases, through reconstruction of airway tree is proposed. The method has two stages: segmentation of bronchus and detection of suspicious structures through extraction of lung texture. Firstly, preprocess the image using Gaussian filter which reduce image noise, detect the bronchus trees through Mathematical Morphological approach to process geometrical structures, automatically deduct the airway tree branch by branch through adaptive region growing approach. Secondly, from the segmented bronchus, extract the diseased lung tissue accurately and calculate the area of lung tissue for quantitative data analysis through Region of interest. Features are extracted from the selected regions by Grayscale Co-occurrence Matrix method and Relational features of the pathological area. The image is processed on low level clusters like color, intensity, location etc., by K-means clustering iterative technique for partitioning the image into K clusters, while the Bayesian classifier trains the selected image through the features extracted based on probability models that incorporate strong independence assumptions. Prior knowledge of the radiologists combined with observed data helps in identifying the efficiency of the work. The performance measures are analyzed based on the results and the evaluated accuracy of the detected lesions is 83.1%. Thus the work helps the radiologists in identifying the lesions in the airway tree. Keywords: Gaussian Filter, Mathematical Morphological approach, region growing, region of interest, feature extraction, K-Means Clustering, Bayesian Classification, Gray level Co-Occurrence Matrix.

I. INTRODUCTION
Lung airway diseases are the most common threat to human health, and a large number of medical imaging systems are used for diagnosis. One of these systems is High Resolution X-ray Computed Tomography (HRCT), which provides fine details of lung anatomy, but it causes a massive increase of the amount of data. Thus, computer-aided diagnosis (CAD) system serves as an aid to doctors for reducing the probable risk of neglecting early potential symptoms. In lung CAD system, analyzing of bronchus using CT image, where the airway is the treelike lumen filled with air and separated from the pulmonary parenchyma by a thin bronchial wall. Accurate airway tree segmentation is the basis for subsequent processes such as registration, quantitative analysis, lesion detecting and staging.

Airway tree segmentation methods build up a tree by propagating some form of locally adaptive region growing along candidate search directions in an effort to detect and stem leakages. Segmentation leakage is detected when the front splits too rapidly or exhibits an irregular or spongy texture. When leakage is detected, a locally adaptive algorithm typically switches to a more conservative set of parameters and reruns the segmentation. Such methods can be overly conservative, as the decision to stop the segmentation at a particular location is usually made without the benefit of global information he detection of various forms of small airways disease has undergone a renaissance as a result of increased understanding of the high-resolution computed tomography (HRCT) appearances of the various pathological subtypes of small airways disease. While conceptually convenient, the reality of anatomical continuity between the small and large airways, and the presence of coexisting parenchymal abnormalities in many diseases, has been starkly revealed in the detailed images of HRCT. Abnormalities on HRCT that reflect small airways disease can be broadly categorized into indirect and direct signs: widespread scarring and obliteration of the bronchioles results in the indirect sign of patchy density differences of the lung parenchyma. The pathological lung tissue is extracted accurately and the area of lung tissue of the diseased pixel is calculated for quantitative data analysis. The features are extracted for each of the regions, extracted from the lung airway. The features may include pixel level, region level and image level measures in the form of shape, texture and relations among objects. The effectiveness of various shape features and selected features, that optimize classifications, are explored. There are classification methods which are used to maximize identification of lesions in the bronchus. This technique was favorable compared to other methods such as decision trees. The K-Means clustering technique is used to discover cluster centers based on the relative distances to the clusters. The lower level clusters like intensity, color, location etc. are taken as clusters in this technique. The assumptions of class independence allows the Naive Bayes classifier to better estimate the parameters required for accurate classification while using less training data than many other classifiers. This makes it particularly effective for datasets containing many predictors or features. The rest of the paper is organized as follows: Literature survey is presented in Section II. System architecture is discussed in Section III. Experimental results are presented in Section IV and analysed. Conclusion and future work is briefed in Section V.

II. Literature Survey

M.Ceresa . Et al (2010) presented an algorithm for robust airway segmentation that attains both high sensitivity and accuracy, but the major pitfall is in the connectivity based methods, is that the detection of disconnected branches, due to tumors or diseases. Mamatha Rudrapatnal Et al. [2006] proposed an automatic detection of tram tracks on HRCT images for diagnosing bronchiectasis using Shapes based features and K-Means clustering algorithm to characterize the appearance of tram tracks through image analysis techniques on HRCT images. The difficulty was in measuring tapering due to small size of the regions and also due to the bias towards retaining potential positive findings. Danilo Babin Et al. [2010], proposes a novel method for segmenting low-contrast 3-D CTA images of airways in lungs for disease diagnosing, Execution time for a 3-D data set with dimensions 500_512_512 on a 2.4 GHz processor is approximately one hour. Mithun Prasad Et al. [2008] describes BV_pairs, a system capable of detecting abnormal bronchovascular pairs in high-resolution CT scans with sparse datasets, but the small-sized bronchi appear faint and discontinuous, making the task of segmentation difficult. CAO Tainuri Et al. [2010], introduced texture feature extraction into the HRCT images through segmentation based on tolerance granular space model and region

growing method, which can be used for further diagnosis of lung diseases. Adrien Depeursinge Et al. [2007], describe a texture classification system that identifies lung tissue patterns from HRCT images of patients affected with interstitial lung diseases (ILD). The main weaknesses of the presented technique are the lack of resolution in scales with the DWF decomposition, along with required feature weighting while merging features from different origins. Soo Chang Kim Et al. [2007], propose a scheme for texture classification and segmentation, which involves extraction of energy as a texture feature using incomplete tree structured wavelet packet decomposition . Since not every feature extracted it can be unified with Gaussian mixture model to improve the performance. A. Tolouee Et al. [2008], proposes segmentation using two sets of wavelet filters, namely discrete wavelet frames (DWF) and rotated wavelet frames (RWF), but yet to increase the robustness of the algorithm against image noise and variabilities in imaging parameters. Comparing with the works discussed in the literature, the proposed system applies preprocessing for denoising using Gaussian Filter with morphological operations for determination of airway locations. Adaptive region growing is applied to connect the regions evaluated on basis of threshold value, having the upper and lower limit. Further, global thresholding is used to segment the bronchus and ROIs to extract the pathological pixel. A set of textural features are extracted from ROIs by constructing a gray level co-occurrence matrix of the ROI. The extracted feature vectors are used to classify whether the bronchus region is diseased. The results were shown to an experienced radiologist and the system performance was based on his findings.

III. SYSTEM ARCHITECTURE

This architecture gives the processing of input image to reconstruct the airway tree using the various methods of the medical imaging techniques of image processing. It segments the input image through preprocessing with morphological filtering to extract the bronchus followed by adaptive region for connecting the regions. The segmented image undergoes global thresholding to extract the features of the selected region for disease diagnosis using classification methods. Fig. 1: Architecture of System
Image Acquisition

Segmentation of region

Preprocessing Denoising to Segmentation check leakages of Tree

Global Thresholding

ROI Extraction Morphological Filtering To extract well defined airway bronchus

Adaptive Region Growing To connect the regions

Disease Diagnosis
Feature Extraction Classification Subsystem

Lung Image with Bronchus Tree Resultant Diagnosis

A. Image Denoise:
Pre-processing is done to remove the noise present in the CT images. To remove the high intensity noise, Gaussian filter is used which gives an estimate of the original uncorrupted image with minimum mean square error. This filtration is used to mitigate the leakage problem before the process of region growing. hg (n1, n2) hg (n1, n2) = hg n1 n2

(n12 + n2 2) / (22)

hg (n1, n2) = e

Fig. 2. The Input image smoothened using Gaussian Filter B.Morphological Filtering: To extract the main branches and the secondary branches the 2-D cross section, morphological filtering is done for determination of candidate airway locations. The method first scans all 2-D sections of the original image in the transverse, sagittal, and coronal directions, to locate candidate 2-D airway cross-section. First, for each intensity threshold t [-1000, - 600], locate all 2-D cross sections Ai in I (. z1) and their boundaries were Ai, where Ai = connected voxels (x, y, z1) where I(x, y, z1) <= t Ai = voxels Ai f (Ai) = min I(x,y,z1) (X, y, z) Ai - (1 / |Ai|) I(x,y,z1) (x, y, z) Ai

c. Region Growing: The region is iteratively grown by comparing all unallocated neighboring pixels to the region. The difference between a pixel's intensity value and the region's mean is used as a measure of similarity. The pixel with the

smallest difference measured this way is allocated to the respective region. This process stops when the intensity difference between region mean and new pixel become larger than a certain threshold (t). The adaptive process requires two runs of region growing: In the first run, parameters are estimated, and they are applied, using the same seed point, in second run for extracting the region. Lower and upper thresholds are computed for determining region membership: Tupper= mgv (n ) [ud (n ) . w+ c(n )] and Tlower= mgv (n ) [ld (n ) . w+ c(n )]

Fig.3 Segmented Image through Region Growing d. Image Enhancement The contrast limited adaptive histogram equalization (CLAHE) enhances the contrast of the grayscale image I by transforming the values. CLAHE operates on small regions in the image, called tiles, rather than the entire image. Each tile's contrast is enhanced, so that the histogram of the output region approximately matches the histogram specified by the 'Distribution' parameter. e. Global Thresholding Global thresholding consists of setting an intensity value (threshold) such that all voxels having intensity value below the threshold belong to one phase, the remainder belong to the other. Global thresholding is as good as the degree of intensity separation between the two peaks in the image. The global thresholding procedure is straightforward. Let a Rx be the source image and [h,k] be a given threshold range. The thresholded image b {0, 1}X 1 b(x) = 0 is given by for all x X. f. Region of Interest A region of interest (ROI) is a portion of an image that you want to filter or perform some other operation on. ROI can be defined by creating a binary mask, which is a binary image that is the same size as the image you want to process with pixels that define the ROI set to 1 and all other pixels set to 0. The regions can be geographic in nature, such as polygons that encompass contiguous pixels, or they can be defined by a range of intensities. In the latter case, the pixels are not necessarily contiguous. There are several strategies for selecting a ROI: otherwise, if h<=a(x) <= K

- based on the actual activation (select region based on the voxels above some threshold) -drawing a sphere around some peak in the activation - based on anatomical labeling

Fig. 4. ROI sampled from the segmented image g. Feature Extraction Features can be extracted from the co-occurrence matrix to reduce feature space dimensionality. The Gray Level Co-occurrence Matrix (GLCM) method is a way of extracting second order statistical texture features. A GLCM is a matrix where the number of rows and columns is equal to the number of gray levels, G, in the image. The matrix element P (i, j | x, y) is the relative frequency with which two pixels, separated by a pixel distance (x, y), occur within a given neighborhood, one with intensity i and the other with intensity j. One may also say that the matrix element P (i, j | d, ) contains the second order statistical probability values for changes between gray levels i and j at a particular displacement distance d and at a particular angle ( ). Given an MN neighborhood of an input image containing G gray levels from 0 to G 1, let f (m, n) be the intensity at sample m, line n of the neighborhood. Then P (i,j | x, y) = WQ(i,j | x, y) where 1 w= (M x)(N y)

Q (i, j | x, y) =

N y n=1

M x m=1

and A= 1 if f (m, n) = i and f (m + x, n + y) = j 0 elsewhere

The features are defined and the following formulas are used to calculate the Haralick texture features [17]: Angular Second Moment (ASM) ASM is defined as a measure of homogeneity of the image. ASM = i Entropy Inhomogeneous scenes have low first order entropy, while a homogeneous scene has high entropy. Entropy G-1 G-1 =- P (i, j) log (P (i, j)) i=0 j=0 j {P (i, j)} 2

Contrast This measure of contrast or local intensity variation will favour contributions from P (i, j) away from the diagonal. Contrast = Nq-1 Nq Nq n2 P (i, j) n=0 i= 1 j=1 | i j |= n

Correlation Correlation is a measure of gray level linear dependence between the pixels at the specied positions relative to each other. Ng Ng ( i j) P (i, j) - col row i=1 j=1 . col row

Correlation =

Inverse Difference Moment ( IDM ) IDM is also influenced by the homogeneity of the image which result is a low IDM value for inhomogeneous images, and a relatively higher value for homogeneous images. IDM = G-1 G-1 - i=0 j=0 1 P ( i, j) 1 + (i j) 2

Cluster Shade Cluster Shade is a measure of the skewness of the matrix and represents the lack of symmetry in an image. Cluster Shade = G-1 G-1 i=0 j=0 {i + j - x - y} 3 x P (i, j)

Cluster Prominence Cluster Prominence is a measure of the skewness of the matrix. G-1 G-1

Cluster Prominence = Sum of Squares, Variance

i=0

{i + j - x - y} 4 x P (i, j) j=0

This feature puts relatively high weights on the elements that differ from the average value of P( i, j ). Sum of Squares, Variance= Where G is the number of gray levels used. is the mean value of P. x, y, x
th

G-1 G-1 (i )2 P(i, j) i=0 j=0

and

are the means and standard deviations of PX and Py.

Px (i) is the i entry in the marginal-probability matrix obtained by summing the rows of P (i, j) The relations that our system can detect on the basis of shape of the lesions or the sampled regions are the following: Proximity between bronchus and vessel Circularity of bronchus and vessel: Thickness of wall surrounding the bronchus Location of object in the image Aspect Ratio between bronchus and vessels h. CLASSIFICATION METHODS: Classification Methods are used for data analysis and the data classification undergoes two step process which involves Learning step and Training step and it also helps to improve the accuracy, efficiency and scalability. In the proposed system, the statistical classifiers used are Bayesian classification and K-Means Clustering. The K-means algorithm is an iterative technique that is used to partition an image into K clusters. The basic algorithm is:

1.
2. 3. 4.

Pick K cluster centers, either randomly or based on some heuristic Assign each pixel in the image to the cluster that minimizes the distance between the pixel and the cluster center Re-compute the cluster centers by averaging all of the pixels in the cluster Repeat steps 2 and 3 until convergence is attained (e.g. no pixels change clusters) K-means clustering specifies the number of clusters to be partitioned and a distance metric to quantify

how close two objects are to each other. Given a set of observations (x1, x2, , xn), where each observation is a ddimensional real vector, k-means clustering aims to partition the n observations into k sets (k n) S = {S1, S2, , Sk} so as to minimize the within-cluster sum of squares (WCSS):

Where i is the mean of points in Si.

Fig. 5. K-means Clustering based on intensity and the graph for the intensity clustersr A Naive Bayes classifier is a simple probabilistic classifier based on applying Bayes' theorem (from Bayesian statistics) with strong (naive) independence assumptions. Each training example can incrementally increase/decrease the probability that a hypothesis is correct. Prior knowledge can be combined with observed data. Using Bayes' theorem, we write

i. Performance Evaluation The performance measures are used to obtain a high level of true positives detection rate even for small cells and a low number of false positives. Based on the feedback of a radiologist on the detection of the pathological regions by the system, the number of True Positives (TP), True Negatives (TN), False Positives (FP) and False Negatives (FN) were counted. IV EXPERIMENTAL RESULTS AND ANALYSIS Experiments were performed using 20 subjects with 240 slices, randomly chosen from a database. The subjects were scanned at a thickness of 1.25mm slices, and images were obtained on a GE (General Electronics) 64 slice CT Volume Computer Tomography machine. Manual labeling of bronchiectasis was performed by a radiologist specialized in diagnostic radiology. Our experiments were carried out on HRCT images with different feature extraction basis using the samples obtained through the ROIs which are shown in Fig. 6.1. The sampled image through ROI is used to extract the Harlick features and shape based features using GLCM concept. The Clustered image performance is evaluated on basis of specificity, accuracy, completeness and correctness using the TP, TN, FP, and FN values extracted using the Confusion matrix. The performance measures were evaluated using the 10 subjects diseased images and compared with the normal images. Specificity is the

number of correctly diagnosed negative diseased out of all negative diseased area. Specificity = __ TN__ TN + FP Accuracy is the number of correctly diagnosed diseased out of the total number of diseased. Accuracy = __ TP+TN_____

TP + FN +TN + FP Precision also known as completeness is the number of correctly classified diseased out of the number of positive diseased area. Completeness = ____TP_____ TP + FP Recall also the correctness is the number of correctly classified positive diseased out of all positive diseased area. Correctness = ____TP_____ TP + FN The values were compared with the radiologists output and the experimented values. The Table.shows the performance measures that are done using K Means clustering.

Performance Measures Specificity Accuracy Completeness Correctness

K-Means Clustering 83.1 % 83.1 % 78.5 % 78.5 %

The classification is processed using the features extracted from the sampled ROI images. The Bayesian Classification evaluates the probability values from the selected ROI image through the 18 Harlick features [17] extracted. The evaluated value predicts the region selected is diseased or non diseased. If the Bayesian classification value is less than 4 then the area is non diseased, if greater than 4, then its the diseased area. And the severity is also evaluated by examining the values; depending on the classified value the probability of the severity is examined. The value thus extracted is shown in the Table.

Bayesian Classification 5.97 1.02 9.95 1.01 8.43 6.8 5.42

Disease Presence Minor Non-Diseased Major Non Diseased Major Minor Minor

V. CONCLUSION: The proposed method is computationally efficient, requiring less than 3 min on average to complete and has essentially no parameter values to select. Algorithms for locating the bronchus and detecting the lesions are novel. Experiments indicate that the method robustly identifies the airways, extracts the features by sampling the image through ROI and the diseases are detected by clustering the lower levels like color, intensity, location etc., by K-Means clustering and then the diseases are classified from the featured trained sample by Bayesian classification using the probability based on the hypothesis. Also the severity of the diseased area is identified based on the values that are evaluated through the probability of the independence on the ROI image. Each training example can incrementally increase/decrease the probability that a hypothesis is correct. Prior knowledge of the radiologists are combined with observed data and estimation is done for checking the efficiency. The performance measures are analyzed based on the results and the evaluated accuracy of the detected lesions is 83.1%. It demonstrates the improvement, effectiveness, and efficiency achieved by the work. Furthermore work can be carried by evaluating the algorithms on more datasets. And also the classification can be improved by using Fuzzy Bayesian Classification and K Means clustering. The lesion detection can also be carried out on specified diseases using the above algorithms to maximize the performance.

REFERENCES
1. Michael W. Graham, Jason D. Gibbs, Duane C. Cornish, And William E. Higgins*, Robust 3-D Airway Tree Segmentation For Image-Guided Peripheral Bronchoscopy, IEEE Transactions On Medical Imaging, Vol. 29, No. 4, April 2010 2. M. W. Graham, J. D. Gibbs, And W. E. Higgins, J. P. W. Pluim And J.M. Reinhardt, Eds., A Robust System For Human Airway Tree Segmentation, In Proc. SPIE Medical Imaging. 2008, Image Process, Vol. 6914, Pp. 69 141J-1 69 141J-18. 3. J. Tschirren, E. A. Hoffman, G. Mclennan, And M. Sonka, Intrathoracic Airway Trees: Segmentation And Airway Morphology Analysis From Low-Dose CT Scans, IEEE Transactions Medical Imaging, Vol. 24, No. 12, Pp. 1529 1539, Dec. 2005. . 4. C. Fetita, F. Preteux, C. Beigelman-Aubry, And P. Grenier, Pulmonary Airways: 3-D Reconstruction From Multislice CT And Clinical Investigation, IEEE Transactions Medical Imaging, Vol. 23, No. 11, Pp. 13531364, Nov. 2004. 5. D. Aykac, E. A. Hoffman, G. Mclennan, And J. M. Reinhardt, Segmentation And Analysis Of The Human Airway Tree From Three-Dimensional X-Ray CT Images, IEEE Trans. Medical Imaging, Vol. 22, No. 8, Pp. 940950, Aug. 2003. 6. Tong TONG, Yufeng Huang, Xingjia Wang, Huanqing Feng, Chuanfu Li, Automatic Exraction Of Three Dimensional Lung Texture Tree From HRCT Images, International Conference On Bioinformatics And Biomedical Technology, IEEE., Pp 198 202, 2010. 7. 8. Mamatha Rudrapatnal, Prinith Amaratungal, Mithun Prasad l, Arcot Sowmya and Peter Wilson, Automatic Detection Of Tram Tracks On HRCT Mages, IEEE Transactions on Medical Imaging, pp.885-888, 2006. D. Aykac, E. Hoffman, G. McLennan and J. Reinhardt, "Segmentation and Analysis of the Human Airway Tree from Three-Dimensional X-Ray CT Images", IEEE Transactions on Medical Imaging, 22(8), 940 - 950, 2003.

9.

Danilo Babin, Ewout Vansteenkiste, Aleksandra Pizurica and Wilfried Philips, Segmentation of airways in lungs using projections in 3-D CT angiography images, International Conference of the IEEE- EMBS pp.3162-3165, 2010.

10. Sata Busayarat1 and Tatjana Zrimec Detection of Bronchopulmonary Segments on High-Resolution CT
Preliminary Results, IEEE Computer Society, International Symposium on Computer-Based Medical Systems, 2007.

11. Mithun Prasad, Arcot Sowmya, and Peter Wilson, Automatic Detection of

Bronchial Dilatation in HRCT Lung Images Journal of Digital Imaging, Vol 21, Suppl 1, pp S148-S163, 2008.

12. CAO Tianuri, XIE Gang, Wang Fang, Yan Chengdong, Texture Features Extraction of Chest HRCT Image, IEEE International conference on Tolerance Granular computing, pp.648 651, 2010.

13. Adrien Depeursinge, Daniel Sage, Asmaa Hidki, Alexandra Platon, Pierre Alexandre Poletti, Michael Unser
and Henning Muller, Lung Tissue classification Using Wavelet Frames, Conference of the IEEE EMBS, pp. 6259 6262, 2007.

14. Soo

Chang Kim, Tae Jin Kang, Texture Classification and Segmentation Using Incomplete Tree Structured Wavelet Packet Frame and Gaussian Mixture Model, International Workshop on Imaging Systems and Techniques, IEEE IST, pp.46 51, 2005. Michael Barnathan, Jingjing Zhang, Erickson Miranda, Vasileios Megalooijonomou, A Texture Based Methodology for Identifying Tissue Type in Magnetic Resonance Images, IEEE Transactions, pp. 464 467, 2008. A. Tolouee, H. Abrishami-Moghaddam1, R. Garnavi2, M. Forouzanfar1, M. Git Texture Analysis in lung HRCT images, IEEE Computer Society, pp.305 311, 2008.

15.

16.

17. R. M. Haralick, K.Shanmugam and I.H.Dinstein, Textural features for image classification, IEEE Transactions on Systems, Man and Cybernatics,Vol. 3, No.6, Pp. 610621, Nov. 1973.