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A Watershed Method for MR Renography Segmentation

1
Chun-yan Yu,
Institute of Information and Science Technology
Dalian Maritime university
Dalian, China
yuchunyan1997@126.com
2*
Ying Li
Environmental Information Institute
Dalian Maritime University
Dalian, China
yldmu@126.com

Abstract—MR renography has emerged as a promising
radiological measure of renal function. The MRR image
segmentation has been the important technology in kidney
image processing and analysis. Due to the rapid calculation
speed, watershed transform is developed rapidly in image
segmentation field in recent years. But it has an inevitable
over-segmentation problem in the application. In this paper,
a new watershed method for MR renography image
segmentation has been proposed. To achieve smoothing and
enhancing the contrast in image preprocessing, the total
variation model is used as nonlinear filter. The results of
experiments performed on real medical MRI kidney images
show that the new approach solves the over-segmentation
problem effectively, and it can identify the kidney regions
clearly.
Keywords-MR renography;image segmentation;TV model;
watershed transform
I. INTRODUCTION
Medical image segmentation is an important process
for most medical image analysis tasks. Assessment of
renal function with MR renography(MRR)[1] is based on
visualizing the passage of gadolinium contrast through
the kidney and subsequent analysis of the contrast
concentration in renal tissues. The main task of
segmentation [2] is suggested to identify the kidney
regions in the MR images, and it is the most important
basic pre-processing in different phases.
Watershed transform [3] based on mathematical
morphology is a popular segmentation method. The main
advantages of the watershed method over other
previously developed segmentation methods are [4]: the
resulting boundaries form closed and connected regions,
the boundaries of the resulting regions always correspond
to contours which appear in the image as obvious
contours of objects. However the main limitation is the
over-segmentation in the results of the algorithm.
Recently a lot of researchers do many works in this field.
Paul R. Hill et al. [4] developed a novel marker based
solution that basins are flooded from selected sources
rather than minima, and it was more efficient for image
region characterization for content based retrieval. H.P.
Ng et al. [5] proposed a new algorithm by performing
threshold method on the gradient magnitude image and
performing post-segmentation merging on the initial
segmentation map. Pousse A et al. [6] presented a method
combining a wavelet filtering method with watershed
determination, both leading to hot nodule enhancement,
results showed it can detect more than 97% of modules
on phantoms. Cha et al. [7] proposed a watershed
algorithm based on multi-resolution image, use low
resolution to reduce the burden of computer, and a new
function to merge regions, experiments showed that the
method balances calculated efficiency and segmentation
accuracy. Recently Partial differential equations (PDEs)
[8] [9] have led to an entire new field in image processing
and computer vision [10], it has been widely applied in
image smoothing, edge detection, image segmentation el.
The total variation [11] image processing model has been
generalized and extended in many ways, and has received
a lot of attention in last decade. Because the method uses
the partial differential equation of the anisotropic
diffusion equation for image denoising, it can preserve
edges and solve the restoration of the image details.
In the paper, we proposed a new watershed
segmentation method for MR renography image based on
TV model. To solve the over-segmentation problem of
watershed transformation, we use TV denoising model to
process the original image before the gradient image
composing, use mathematical morphology reconstruction
and a threshold method used to extract marker. The
results of experiments performed on real medical MRI
kidney images, it showed that the new approach reduces
the over-segmentation number greatly, the segmentation
result is effective, and it is practical in real medical MRR
image segmentation. The remainder of the paper is
organized as follows. In Section2 Total Variation Model
is introduced. Section 3 presents the approaches of
watershed method for MRR image, experimental results
are presented in Section 4 and conclusions are drawn in
Section 5.
II. TOTAL VARIATION IMAGE DENOSING
MODEL
The total variation model was first proposed by Rudin
and Osher [11] [12], the TV of function has emerged as a
very successful regularizer for image denoising and
image restored. The main advantages of the resulting
denoising method lie on the fact that it allows the
preservation of the edges in the image, and its numerical
stability and uniqueness property have been shown to be
particularly useful in enhancing the effectiveness of the
image [13]. The original TV (ROF) model [11] was
proposed by Rudin, Osher and Fatemi. Let u be the
original image, f be the noised image,
0
u be the additive
noise image.
So
0
( , ) ( , ) ( , ) f x y u x y u x y = +
Based on total variation of the image noise reduction
can be the solution of the following minimization
problem:
2012 International Conference on Biomedical Engineering and Biotechnology
978-0-7695-4706-0/12 $26.00 © 2012 IEEE
DOI 10.1109/iCBEB.2012.45
700



2 2
min | | min
u u
u d dxdy
x y
Ω Ω
| | ∂ ∂ | |
∇ Ω = +
| |
∂ ∂
\ . \ .
} }
(1)
Where Ω is the image domain, u ∇ denotes the
gradient of image u,
[0, ) u ∇ ∈ ∞

Subject to the two constraints as follow:
udxdy fdxdy
Ω Ω
=
} }
(2)

2 2
1
( ) , 0
2
u f dxdy σ σ

− = >
}
(3)
Where σ is the standard deviation of the noise
image
0
u .Using Lagrange multiplier method to (2) yields
the following TV penalized minimization problem:
2
min | | ( )
2
u dxdy u f dxdy
λ
Ω Ω
∇ + −
} }
(4)
Where λ is a Lagrange multiplier, and it is a
parameter to balance the relationship between the two
terms. The first term is regularization parameter to
smooth the image, and the second term acts as functional
fidelity measuring parameter to control the difference
between u and f.
The Euler-Lagrange equation of (4) is given as
follow:
Let
2
( , ) ( ) | |
2
F u u u f u
λ
∇ = − + ∇
Then
( )
F
u f
u
λ

= −


Let
| |
u
u
F
u


=

then
( )
| |
u
u
F
u

| | ∇
∇ = ∇
|

\ .


and
( , )
( ) 0
u
F u u F
F
u u

∂ ∇ ∂
= −∇ =
∂ ∂

So the Euler-Lagrange equation of (4) is

( ) 0
| |
u
u f
u
λ
| | ∇
−∇ + − =
|

\ .

(5)
With boundary condition
1
0
| |
u
u n

=
∇ ∂

Where () ∇ is the divergence operator, and when
u ∇ →∞ where diffusion is weak on edges, when
0 u ∇ → where diffusion is strong in smooth region, and
in this way it can eliminate noise. In order to avoid
ill-condition when | | 0 u ∇ = , in practical Calculation,
usually use
2 2
| | | | u u
ε
ε ∇ = ∇ + instead of
| | u ∇
, where
ε is a small positive number and it is a regularization
parameter, the corresponding Euler-Lagrange equation (5)
becomes:
2 2
( ) 0
| |
u
u f
u
λ
ε
| |

| −∇ + − =
|
∇ +
\ .

(6)
III. WATERSHED SEGMENTATION PROCEDURES
A. Watershed algorithm
The watershed transform is the method of choice for
image segmentation in the field of mathematical
morphology. In grey scale mathematical morphology the
watershed transform improved by Beucher[14] and L.
Vincent [15].The watershed transform can be classified as
a region-based segmentation approach. In practice, the
watershed is applied to the image gradient and the
watershed lines separate regions with desired
segmentation result. The intuitive idea underlying this
method comes from geography: it is that of a landscape,
watersheds being the divide lines of the domains of
attraction of rain falling over the region [16]. An
algorithmic definition of the watershed transform by
simulated immersion was given by Vincent and Soille [15]
for the binary case). Let
: f D N →
be a digital grey value
image, with
min
h
and t
max
h he minimum and maximum
value of
f
. Define a recursion with the grey level
h

increasing from
min
h
to
max
h
, in which the basins
associated with the minima of
f
are successively
expanded. Let
h
X
. Denote the union of the set of basins
computed at level h . A connected component of the
threshold set
1 h
T
+
at level 1 h + can be either a new
minimum, or an extension of a basin in
h
X
: in the latter
case one computes the geodesic influence zone of
h
X
within
1 h
T
+
, resulting in an update
1 h
X
+
. Let
h
MIN

denote the union of all regional minima at altitudeh .
Definition1. (Watershed by immersion) Define the
following recursion:
{ }
min min
1
min
1 1 min max
( )
( ), [ , )
h
h h
h h T h
X p D f p h T
X MIN IZ X h h h
+
+ +
¦ = ∈ = =
¦
´
= ∈
¦
¹

(7)
The watershed ( ) Wshed f of
f
is the complement
of
max
h
X
in
D
:
max
( ) \
h
Wshed f D X =

The lower slope LS (p) of f at a pixel p, is defined as
the maximal slope linking p to any of its neighbors of
lower altitude. Formally,

( ) ( )
( ) ( )
( , ) { }
f p f q
LS p MAX
d p q q N p
G

=

(8)
Where N
G
(p) is the set of neighbors of pixel p on the
grid G = (V;E), and d(p; q) is the distance associated to
edge (p; q) (for q = p the expression following the
max-operator in equation (8) is defined to be zero). Note
that for pixels whose neighbors are all of higher grey
value, the lower slope is zero. The cost for walking from
pixel p to a neighboring pixel q is defined as
( ) ( , ) ( ) ( )
cos ( , ) ( ) ( , ) ( ) ( )
1
( ( ) ( )) ( , ) ( ) ( )
2
LS p d p q if f p f q
t p q LS p d p q if f p f q
LS p LS q d p q if f p f q
¦
¦
>
¦
= <
´
¦
¦ + =
¹

701


B. Watershed transform procedure
Due to the rapid calculation speed, the watershed
transformation [17] [18] is developed rapidly in image
segmentation field in recent years. It results in regions
with good located closed contours, but produces an
excessive over-segmentation problem and it is sensitive
to noise. Generally there are two categories to reduce the
problem [16]: image pre-processing and image
post-processing. Image preprocessing mainly includes the
noise removal of gradient image because the noise signal
can affect the number of minima of the image. And the
post-processing refers to merging some of the basins in a
proper way by removing irrelevant watershed lines. In
this paper we use image preprocessing to overcome the
problem of over-segmentation. Because noise in the
gradient image results in over-segmentation, we
use TV denoising model for nonlinear filter, the new
model accomplishes the effect of blurring possible noises
while enhancing edges .It also used maker-extracted
method and distance function in this method. The
watershed segmentation in this article follows these steps:
Step1. Use TV model to filter original image.
Step2. Calculate the image gradient.
Step3. Use threshold method for marker image.
Step4. Compute the distance function.
Step5. Watershed transform on the modified gradient
image.






















Figure1. The Morphological Watershed Segmentation on MRR image
IV. EXPERIMENTAL RESULTS
We use our proposed method to segment real MRR
images to illustrate the effectiveness of our proposed
method. In Figure 2, it is easy to see that there is extreme
over-segmentation problem in traditional morphological
gradient image, after TV model denoising for the original
image, the watershed transform result on the modified
gradient image decreased a lot of segmentation region,
but still there are many over-segmentation regions. After
TV model denoising for the original image, the watershed
transform result is very good. The experiment images of
the proposed method are showed in Figure 3. It is easy to
see that the proposed method is effectively solved the
over-segmentation problem, and finally to identify the
region of only two kidneys (ROI), we extracted the
regions of interested, it is seen that the kidneys region is
clearly contoured by red color line in image in Figure 4.
The new method in this article provides a complete
division of the MRR image with a continuous, closed
boundary. We compute the number of different watershed
transformation, and the results showed in Table 1. We
evaluated the performance of our proposed method by
comparing other segmentation algorithms. And Table2
showed that our method is more efficient compared with
FCM and KFCM algorithms. It can be observed that the
new approach in this article reduces the
over-segmentation number greatly, the segmentation
result is effective, and it is practical in real medical MRR
image.


















Figure2. The comparison of different Watershed transformations
(a) original watershed method (b) multi-scale morphological method (c)
the method proposed in this article




















Figure3. Experiment images (a)Original MRR image, (b) TV model
filtering image(n=20) ,(c) TV model filtering image(n=200), (d)

(a) (b)

(c)

(a) (b)

(c) (d)
702


Watershed transformation segmentation image






Figure4. Result image
TABLE I. NUMBER OF DIFFERENT WATERSHED
TRANSFORMATIONS OF IMAGE (A) IN FIGURE 3[19]
Method
Original
watershed
transformation
Multi-scale
morphological
gradient image
Proposed
in this
article
Numbers of
segmentation
4656 2428 4
TABLE II. THE PERFORMANCE OF DIFFERENT MEDICAL
SEGMENTATION ALGORITHMS[19]
Segmentation
algorithms
FCM(clusters :4) KFCM(clusters :4)
Watershed
method in
this article
Runtime(sec) 61.573 186.77 27.935

V. CONCLUSION
MR renography are playing increasingly important
roles in clinics.. In this paper, to solve the
over-segmentation problem of watershed original
segmentation algorithm, we proposed a new watershed
method for MRR image segmentation, because MRR is
sensitivity to noise, we use TV model as anisotropic
diffusion filter for image smoothing, it enhance the image
contrast, to contour the kidney regions of MRR image, it
also uses the extracted-marker and distance function to
overcome the over-segmentation problem. The
experimental results have shown that our proposed
watershed process for MRR segmentation can reduced the
amount of over-segmentation of watershed transform
greatly and it can get the kidney regions concisely. To
obtain higher speed of TV model filer for MRR image,
how to modify TV iterative regularization is still an
important issue. We will attempt to address this issue and
improve the higher segmentation accuracy in the near
future.
VI. ACKNOWLEDGMENT
This work has been partially supported by the
National Natural Science Foundation of China (Grant No.
41171329 and 41071260), Program of Educational
Commission of Liaoning Province of China (Grant No.
2009T010)
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