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Improved Watershed Algorithm for Cell Image Segmentation

1

Department of Electronics and Information Engineering, Huazhong University of Science and

Technology, Wuhan, China

a

zhangyu4013@smail.hust.edu.cn, bxudq@mail.hust.edu.cn

Transformation, Segmentation.

which can determine the boundary of connected section efficiently and effectively. But the

traditional watershed algorithm is sensitive to noise. To overcome the weakness of classical

watershed, this paper presents an improved watershed algorithm based on gradient transform, open-

close reconstruction and distance transform. The experiment result shows that application of this

improved watershed algorithm in cell image segmentation has a good performance.

Introduction

Watershed is an image segmentation algorithm based on mathematical morphology [1]. But the

classical watershed algorithm is sensitive to noise, which can cause serious over-segmentation [2].

Basing on gradient transform, open-close reconstruction and distance transform, this paper proposes

an improved watershed algorithm, which inherits the advantage of classical watershed algorithm

and improves the noise immunity of classical watershed algorithm. This algorithm not only

overcome the over-segmentation, but also has an apparently better performance than the approach

of employing watershed simply based on open-close operation and distance transformation [3].

Image segmentation is one of the fundamental and important tasks in medical image analysis

since only on the basis of a successful segmentation can meaningful cell feature be extracted. The

cell has a round shape which is fit for distance transformation and watershed transformation. And

considering the high speed and accuracy of Watershed Algorithm in solving connected region

segmentation, we apply our improved watershed algorithm in cell image segmentation to solve the

adhesion cell segmentation [4].

Fundamentals

A. Morphological Reconstruction

Morphological reconstruction can be thought of conceptually as repeated dilations of an image,

called the marker image, until the contour of the marker image fits under a second image, called the

mask image. In morphological reconstruction, the peaks in the marker image "spread out," or dilate

[5].

Figure 1 Processing of Reconstruction in 1-Dimension

Fig 1 illustrates this processing in 1-Dimension. Each successive dilation is constrained to lie

underneath the mask. When further dilation ceases to change the image, the processing stops. The

final dilation is the reconstructed image. The figure shows the successive dilations of the marker.

B. Gradient Transform

To simplify the discussion follows, we use the notation in fig 2 to denote image points in a 3x3

region. For example,

the center point z5 denotes f(x,y), and z1 denotes f(x-1,y-1). Denote the cross differences [6]:

C. OTSU Method

Otsu method is firstly proposed by Nobuyuki Otsu [7] in 1979, which is an adaptive method of

determining the threshold. Divide the image into background and objective by its gray scale feature.

The greater the between-class variance between background and objective, the greater difference

between the two parts of the image will have. When some of the objectives are classified wrong into

background or some of the background is classified wrong into objectives, the difference between

these two parts will decrease. Thus, the Otsu method can make the probability of wrong division the

least.

D. Distance Transform

Assume the input image is BW, and the output image is D. Gradient Transform computes the

Euclidean distance transform of the binary image BW. For each pixel in BW, the distance transform

assigns a number that is the distance between that pixel and the nearest nonzero pixel of BW. BW

can have any dimension. D is the same size as BW [8].

E. Median Filter

Median filter replaces the value of a pixel by the median of the gray levels in the neighborhood

of that pixel (the original value of the pixel is included in the computation of the median). Median

filters are particularly effective in the presence of impulse noise, also called salt-and- pepper noise

because of its appearance as white and black dots superimposed on an image [9].

Assume the input matrix is A, and the dimension of its neighborhood is m-by-n. In this paper, we

performs median filtering of the matrix A in two dimensions. Each output pixel contains the median

value in the m-by-n neighborhood around the corresponding pixel in the input image. This paper

pads the image with 0s on the edges, so the median values for the points within [m n]/2 of the edges

might appear distorted.

Suppose that a hole is punched in each regional minimum and that the entire topography is

flooded from below by letting water rise through the holes at a uniform rate. When the rising water

in distinct catchment basins is about to merge, a dam is built to prevent the merging. The flooding

will eventually reach a stage when only the tops of the dams are visible above the water line. These

dam boundaries correspond to the divide lines of the watersheds. Therefore, they are the continuous

boundaries extracted by a watershed segmentation algorithm.

We use the improved watershed algorithm to segment cell image, and this algorithm follows these

steps:

Step 1: Apply open-reconstruction and close-reconstruction to the gray scale cell image

Through applying the open-reconstruction and close-reconstruction filtering to gray scale cell

image, we eliminate the burrs in the cell, isolate the small adhesions between cells, fill the small

holes in cells and smooth the cell boundaries, meanwhile, do not change the size and shape of the

cell images. This pretreatment makes it easier to segment the cell image.

Step 2: Calculate the gradient image of the filtered image

Apply the gradient transform to the image got in step 1. In the gradient image, the gradients of the

boundaries between cells and background in original cell image are much larger than that of region

in cells.

Step 3: Use the OTSU algorithm to get the binary image of the gradient image

Transform the gradient image got in step 2 to binary image using OTSU algorithm. OTSU

algorithm is an adaptive algorithm which can find the best binary threshold. The threshold

determined by OTSU is objective and reasonable, which can lead to a good binarization performance.

After binarization, the boundaries between cells and background can be detected.

Step 4: Fill the cell areas

After detecting the cell boundaries, we fill the cell areas to accomplish the extraction of the cells

in image [11]. Then we segment the adhesion cells.

Step 5: Apply open operation to the filled cell image

Open operation can eliminate the region smaller than structure element and cut off slender

connection. In order to prevent from segmenting non-existent cells, use the open operation to

eliminate the small false cell areas.

Step 6: Apply the distance transform to filled cell image

Apply distance transform to the image got in step 5 to get a gray scale image. Get the complement

image as a new distance image and use median filter method to eliminate the noise in image. In the

new distance image, the values of pixel increase from the inner cell to outer cell. The value of

innermost pixel in cell is the smallest, and the value of outermost pixel in cell is the largest. And the

value of the background pixel is 255.

Step 7: Apply Watershed Transform to gray scale distance image

Find the local minimum point in each cell in the distance image, which is the center of each cell.

We use the minimum points to mark each cell area and use the pixel of value 255 to mark the

background. Then apply the watershed algorithm to the distance image to segment the adhesion cells

and mark the cell regions with different colors.

Step 8: Add the segmentation result to the original image

Add the segmentation result to the original image to show the final result.

We use the staining liquid based cell microscopic image as sample image to test the performance

of the presented algorithm. And the results of each step are shown in Figure 3.

Fig 3(a) is the original cell image. The algorithm is illustrated from fig 3(b) to fig 3(i), where fig(b)

is the image after open-reconstruction filtering, fig(c) is the image after close-reconstruction filtering,

fig(d) is the distance transformed image of (d), fig(e) is the binary image of (d), fig(f) is the filled

image of (e), fig(g) is the image after open operation filtering, fig(h) is the distance transformed

image of (g) and fig(i) is the watershed transformed image of (h). Fig 3(j) is the final segmentation

result.

From fig 3(j), we can find that the result is satisfactory and precisely divide the cell and

background in this image with no over-segmentation.

Conclusions

This paper presents an improved watershed algorithm based on open-close reconstruction,

gradient transformation, median filter and distance transformation. This improved watershed

algorithm overcomes the weakness of classical watershed while inherits the advantage of classical

watershed. Through the experiment, we can conclude that this algorithm has a good performance in

cell image segmentation. The experiment result is satisfactory and successfully segments the

adhesion cells, providing convenience for the further medical processing.

Acknowledgment

This work is supported by Hubei Provincial Natural Science Foundation of China under Grant No.

2009CDB296 and National University Innovative Foundation of China under Grant No. 091048709.

References

[1] Luc Vincent and Pierre soille, “Watersheds in digital spaces: an efficient algorithm based on

immersion simulations,” IEEE Transactions on Pattern Analysis and Machine Intelligence,

1991, Vol.13, No.6, pp.583-598.

[2] Huang Qi-kun and Zhou Yun-cai, “A method based on watershed algorithm for core particles

image segmentation,” Computer Science and Information Technology (ICCSIT), 2010 3rd

IEEE International Conference on, 2010, vol.3, pp.408-410.

[3] Yuqian Zhao, Jianxin Liu, Huifen Li and Guiyuan Li, “Improved watershed algorithm for

dowels image segmentation,” Proceedings of the 7th world congress on intelligent control and

automation, June 25-27, 2008, Chongqing, China, pp.7644-7648

[4] Yu Zhang and Duanquan Xu, “Improvement on Watershed algorithm of OpenCV and its

application in cell image segmentation,” unpublished.

[5] Vincent, L., "Morphological Grayscale Reconstruction in Image Analysis: Applications and

Efficient Algorithms," IEEE Transactions on Image Processing, Vol. 2, No. 2, April, 1993, pp.

176-201.

[6] Rafael C. Gonzalez and Richard E. Woods, Digital Image Processing, 2nd ed, Prentice Hall,

2002, pp.134-137.

[7] Otsu, N., "A Threshold Selection Method from Gray-Level Histograms," IEEE Transactions on

Systems, Man, and Cybernetics, Vol. 9, No. 1, 1979, pp. 62-66.

[8] Maurer, Calvin, Rensheng Qi, and Vijay Raghavan, "A Linear Time Algorithm for Computing

Exact Euclidean Distance Transforms of Binary Images in Arbitrary Dimensions," IEEE

Transactions on Pattern Analysis and Machine Intelligence, Vol. 25, No. 2, February 2003, pp.

265-270.

[9] Rafael C. Gonzalez and Richard E. Woods, Digital Image Processing, 2nd ed, Prentice Hall,

2002, pp.123-124.

[10] Meyer, Fernand, "Topographic distance and watershed lines," Signal Processing , Vol. 38, July

1994, pp. 113-125.

[11] Soille, P., Morphological Image Analysis: Principles and Applications, Springer-Verlag, 1999,

pp. 173-174.

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