Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Segmentation of Colon Tissue in CT Colonography Using Adaptive Level Sets Method

Dongqing Chen1 , Hossam Abdelmunim1 , Aly A. Farag1 , Robert Falk2 and Gerald Dryden3
Computer Vision & Image Processing (CVIP) Laboratory University of Louisville, Louisville, Kentucky, 40292. {dqchen,farag}@cvip.louisville.edu Department of Medical imaging, Jewish Hospital, Louisville, Kentucky, 40202. 3 Division of Gastroenterology/Hepatology, Department of Medicine University of Louisville, Louisville, KY, 40292.
1

Abstract. In this paper, we introduce an adaptive level set method for segmenting a colon lled with air and opacied uid in CT colonography. We rst use simple thresholding method to remove most of the opacied liquid. Then, closed contours with manual seed initialization are propagated toward the region boundaries through the iterative evolution of an adaptive implicit function. During each iteration, information in each region is considered by estimating the parameters of probability density function (PDF). Finally, we evaluate accuracy of the proposed method by computing the overlaps between the manually segmented colon and the algorithm segmented results. The proposed method has been tested on 10 real CT colonography datasets, and the accuracy achieved is 96.06%.

Introduction

Colorectal cancer is the second leading cause of death among cancers and the third most common form of cancer in the United States [1]. Computer tomographic colonoscopy (CTC) is a minimally invasive technique and rapidly evolving diagnostic tool for the location, detection and identication of benign polyps before their malignant transformation. The computer aided dectection/diagnosis (CAD) system for colorectal cancer as shown in Figure 1, mainly includes: 1) colon segmentation, 2) 3D colon object reconstruction, 3) 3D centerline extraction for navigation, 4) colonic polyp detection, 5) color coding for polyp candidates visualization, 6) polyp features extraction, and 7) benign or malignant polyp classication. Accurate and reliable segmentation of the colon is important for 3D reconstruction, automatic colonic polyp detection and classication [26]. There are several sophisticated image segmentation procedures introduced in literature. They were mainly based on two concepts: thresholding and connectivity [7]. In tagged CT colonography, the opacied liquid is generated when iodine and barium

Hossam Abdelmunim is now with the Department of Computer Science, University of Houston, Houston, TX.

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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

nally enters colon and tags residual uid, both of which are contained in oral contrast agents given to the patients for CT in clinic. Electronic cleaning [8, 9] was a very useful technique to balance CT values in uid-lled lumen parts and others lled with air, and to remove the contrast uid. However, some artifacts were generated which affected image interpretation. Yoshida and N appi [10] designed a CAD framework to detect and classify the colonic polyps by using shape index and curvedness. The rst stage of their CAD system was colon segmentation. It mainly consisted of two major steps: 1) anatomy based extraction and 2) colon based analysis. Recently, Summers et al. [7] proposed an entire framework for hybrid segmentation of colon tissue in CT colonoscopy. While it achieved good accuracy for the segmentation results with eight different steps, 1) modied region growing, 2) individual air/uid pockets extraction, 3) airCuid boundaries identication, 4) the pocket tree construction, 5) tree pruning, 6) fuzzy connectivity, 7) gaps and holes lling, and 8) level set segmentation. Hence, it was complicated to implement. In this paper, we introduce a simple framework for colon segmentation. The proposed framework consists of two steps: 1) threshold for rough removal of the opacied liquid, and 2) adaptive level sets method with manual initialization for colon segmentation. In our work, we classify the colon tissue as the foreground and all others as the background. In this bi-model system, the segmentation partitions the image into different regions, and each region belongs to a certain class.

Methods

2.1 Basic Level Sets Given a curve , it can be embedded into a higher dimension function as = {X : (X) = 0}. Then the curve is dened as the zero level of the implicit function. If we add time t to the function, curves (fronts) evolution function is changed to = (X, t). The basic level sets function is given as follows. t + VN || = 0 where, VN is the velocity component along normal direction. Under discrete case, the level sets evolution is governed by Equation 2. (t + t) = (t) t || (2) (1)

where, = VN , and || is the norm of gradient of curve . If > 0, the original curve shrinks, while it expands when < 0. And the curve will keep unchanged, if = 0. Normally, = 1 , where, is the curvature, and is the parameter controlling the bending of the curve.
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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Fig. 1. Colorectal cancer CAD system

2.2 Adaptive Level Sets Technique A segmented image consists of homogeneous regions characterized by some statistical properties. For the bi-model system, we use Gaussian distributions for the colon part (foreground) and other tissue parts (background). 2 For each class i(i = 1, 2), the mean i , variance i , and the prior probability i are updated during each iteration as follows. i = H (i )I (x)dx H (i )dx (3)

2 i =

H (i )(i I (x))2 dx H (i )dx H (i )dx

2

(4)

i =

(5)

H (i )dx
i=1

where, H () is the Heaviside step function as a smoothed differentiable version of the

2

unit step function. I(x) is the input image.

i=1

i = 1.

Finally, the classication decision at pixel x is based on the Bayesian criteria as follows. i (x) = arg (maxi=1,2 (i pi (I (x)))) (6) For further details, please refer the previous work from our lab in [11].
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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Results and Discussion

In this section, we validate the proposed method on 10 CTC datasets. One has been provided by the 3DR Inc., Louisville, KY, and the rest 9 CTC data have been received from the Virtual Colonoscopy Center, Walter Reed Army Medical Center, Washington, DC. The patients underwent standard 24-hour colonic preparation by oral administration of 90 ml of sodium phosphate and 10 mg of bisacodyl; then consumed 500 ml of barium (2.1 percent by weight) for solid-stool tagging and 120 ml of Gastrogran to opacify luminal uid [12]. A four-channel or eight-channel CT scanner (GE LightSpeed or LightSpeed Ultra) was used. The CT protocol included 1.25 mm to 2.5 mm collimation, 15 mm/second table speed, and 100 mAs and 120 kVp scanner settings. Each dataset contains 400 500 slices. The spatial resolution for each dataset is 1.0 1.0 1.0 mm3 . An original CTC slice typically consists of colon lumen including opacied liquidlled part and air-lled part, small intestine, and some other tissues, for example: bones having the similar image intensity with liquid part. Firstly, we aim to remove the opacied liquid by using simple thresholding method and equalize image intensity inside colon as shown in Figure 2(b). We nd that most opacied liquid is roughly removed, and some tissues such as bones on the same slice are removed as well, since they have the similar image intensities. However, it does not effect the colon segmentation at all, since we manually select the initial seeds totally inside the colon region, which guarantees the segmentation results. The initial seeds, the results after 10 and 30 iterations of level sets evolutions are shown in Figure 2 (b), (c) and (d), respectively. The nal results of zero level sets convergence to the lumen-air boundaries is shown in (e). During the iterations, every candidate pixel is automatically classied to either colon part or background based on its PDFs by using Bayesian decision criteria. After each iteration, the average values and variances for both foreground and background are estimated by using the Maximum Likelihood (ML) method respectively. The iteration procedure will stop when level sets curve converges to the lumen-air boundaries. Figure 3 shows the results of opacied liquid removal on the rst row and colon segmentation on the second row using the proposed method, respectively. In order to evaluate the segmentation accuracy, we manually segment one CTC dataset containing 461 slices under the guidance of an experienced radiologist, who has been working on colon cancer diagnosis and treatment for more than 10 years in the

(a)

(b)

(c)

(d)

(e)

Fig. 2. Segmentation results of colon in tagged CTC data. (a) original CTC slice with oral contrast agent, (b) manual seed initialization inside colon after thresholding, intermediate results after (c) 10, (d) 30 iterations, and (e) nal result
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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Fig. 3. Results of opacied liquid removal and segmentation by the proposed adaptive level sets method

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Fig. 4. The 1st15th comparison results by manual(upper) and algorithm segmentation (lower)

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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

(16)

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Fig. 5. The 16th30th comparison results by manual (upper) and algorithm segmentation (lower)

local hospital. Then, the accuracy is calculated by computing the overlap between the results by manual and algorithm segmentations in Equation 7. = Sa Sm Sa Sm (7)

where, Sa and Sm denote the results by manual and algorithm segmentation, respectively. Due to the space limitation, we just list 30 examples in Figures 4 and 5. The manual segmentation results are shown on the upper part, while the results segmented by the proposed algorithm are listed on the lower part, respectively. From the comparison, we nd that the proposed method works well on these CTC slices. This is further veried by the blue accuracy curve as shown in Figure 6, which shows the overlap ranging from 94.5% up to almost 97%. The maximum and minimum overlaps are given in Table 1. The average accuracy of the total 461 slices in the CTC
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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Fig. 6. Accuracy curve of calculating overlaps of the segmentation results as shown in Figure 4 and Figure 5.

dataset have achieved 96.06% 0.56%. All the iso-surfaces are reconstructed by using Marching Cubes algorithm [13], and they are shown in Figure 7.
Table 1. Average Overlap and its standard deviation (STD) maximum minimum average std overlap 96.99% 94.48% 96.06% 0.56%

Conclusions

In this paper, a framework has been proposed for colon segmentation for CTC data. In the bi-model, an adaptive and iterative level sets function is applied for the colon segmentation. Total 10 real CTC datasets have been used to test the accuracy of the proposed segmentation framework, and high accuracy of 96.06% on average has been achieved.
Acknowledgments. We would like to thank Dr. J. Richard Choi at Walter Reed Army Medical Center, Washington, DC for providing CT colonography datasets.

References
1. Abbruzzese, J., Pollock, R.: Gastrointestinal cancer. (2004) 2. Paik, D., Beaulieu, C., Rubin, G., Acar, B., Jeffery, R., Yee, J., Dey, J., Napel, S.: Surface normal overlap: A computer-aided detection algorithm with application to colonic polyps and lung nodules in helical ct. IEEE Transaction on Medical Imaging 23 (2004) 661675

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Proc MICCAI 2008 Workshop: Computational and Visualization Challenges in the New Era of Virtual Colonoscopy

Fig. 7. 3D colon surfaces reconstructed from the segmented colon datasets by searching isosurfaces using Marching Cubes algorithm [13].

3. Chen, D., Hassouna, M., Farag, A., Falk, R., Dryden, G.: Geometric features based framework for colonic polyp detection using a new color coding scheme. Volume 5., (Proceeding of IEEE Conference on Image Processing (ICIP07)) 2132 4. Chen, D., Hassouna, M., Farag, A., Falk, R., Dryden, G.: Curvature ow based 3d surface evolution models for polyp detection and visualization in ct colonography. Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems (2008) 5. Summers, R., Beaulieu, C., Pusanik, L., Malley, J., Jeffrey, R., Glazer, D., Napel, S.: Automated polyp detector for ct colonography: Feasibility study. Radiology 216 (2000) 284290 6. Yao, J., Miller, M., Franazek, M., Summers, R.: Colonic polyp segmetattion in CT colonography-based on fuzzy clustering and deformable models. IEEE Transactions on Medical Imaging 23 (2004) 13441352 7. Franazek, M., Summers, R., Pickhardt, P., Choi, J.: Hybrid segmentation of colon lled with air and opacied uid for ct colonography. IEEE Transactions on Medical Imaging 25 (2006) 358368 8. Zalis, M., Perumpillichira, J., Hahn, P.: Digital subtraction bowel cleaning for ct colonography using morphological and linear lteration methods. IEEE Transactions on Medical Imaging 23 (2004) 13351443 9. Chen, D., Liang, Z., Wax, M., Li, L., Li, B., Kaufman, A.: A novel approach to extract colon lumen from ct images for virtual colonoscopy. IEEE Transactions on Medical Imaging 19 (2000) 12201226 10. Yoshida, H., N appi, J.: Three-dimensional computer-aided diagnosis scheme for detection of colonic polyps. IEEE Transactions on Medical Imaging 20 (2001) 12611274 11. Farag, A., AbdElMunim, H.: Adaptive segmentation of multi-modal 3d data using robust level set techniques, (MICCAI 2004) 143150 12. Pickhardt, P.J., Choi, J.R., Hwang, I., Butler, J.A., Puckett, M.L., Hildebrandt, H.A., Wong, R.K., Nugent, P.A., Mysliwiec, P.A., Schindler, W.R.: Computed tomographic virtual colonoscopy to screen for colorectal neoplasia in asymptomatic adults. The New England Journal of Medicine 349 (2003) 21912200 13. Lorensen, W., Cline, H.E.: Marching cubes: A high resolution 3d surface construction algorithm. Computer Graphics (SIGGRAPH 87 Proceedings) 21 (1997) 163170

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