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(2.4)
where ( ) s , (s) specify the elasticity and stiffness of the contour snake.
The purpose of the internal energy E
internal
is to force a shape on the deformable snake and ensure
that a constant distance is maintained between nodes in the contour. With this in mind, the first
order term adjusts the elasticity of the snake and the second-order curvature is responsible for
making an active contour shrink or grow. Visually, if there are no other influences acting, the
continuity energy term pushes an open contour into a straight line and a closed contour into a
circle.
int .
( ) (( ) ) ( )
snake ernal external image
E ds E v ds E v ds E v ds = + +
16
A variety of functionals (or metrics) can be used to attract the snake to different artefacts in the
image. Let us take for example a line functional and an edge functional. As described by Kass et
al. in [32] a line functional can be expressed as simply as:
( , )
line
E f x y =
(2.5)
where x,y are coordinates in an image I and f(x,y) is a function which denotes the gray levels at
the location (x,y). The most simple useful image functional based on this is image intensity
where f is substituted for I. In this case, the snake will either attempt to align itself with the
lightest or darkest nearby contour.
An edge-based functional would attract the contour to areas with strong edges and can be
expressed as:
( )
2
( , )
edge
E grad f x y = (2.6)
(a) (b) (c)
Figure 2.5: An Active Contour attracted to edges. (a) An illustration of the target area. Here the
shape of the snake contour between the edges in the illusion is completely determined by a spline
smoothness term [32] (b) A termination snake attracted to the edges and lines in equilibrium on
the subjective contour (extended from Kass et al.)[32][24] (c) An initialization of the ACM.
17
The Active Contour Model uses minimisation of the energy function as a means to achieving
edge detection of objects. The final snake (a contour of the object of interest) is however highly
dependent on its initial starting position and starts from a path close to the solution and converge
to a local minimum of the energy, ideally as close to the expected object boundaries as possible.
There are several possibilities for where a convergence may occur as can be seen above in Figure
2.13 (c). Here, the curve a is outside the object, the curve b overlaps and the curve c is
perpendicular to it.
2.7 Level-set methods
Osher and Sethian [33] proposed a new concept for implementing active contours known as the
Level set theory . Level set methods, rather than following an interface take an original curve and
build it into an isosurface of a function. The produced evolution is then mapped into an evolution
of the level set function itself. Using [33], Osher and Sethian were able to harness the power of a
two-dimensional Lipschitz function, (x,y) : in order to represent a contour implicitly.
The term (x,y) is referred to as a level set function. On the zero level of this function the level
set function is defined as a contour c such that:
{ }
( , ) : ( , ) 0 ( , ) C x y x y x y = =
(2.7)
where denotes the complete image plane. As the level set function increases from its initial
stage the correlated set of contours C propagate towards the outside. Based on this definition, the
contour evolution is equal to the evolution of the level set function.
( , ) C d x y
t dt
=
(2.8)
The primary advantage of using the zero level is that a contour may be expressed as the
boundary or border that lies between a positive area and a negative area, such that the contours
may be explicitly identified by simply checking the sign value of the level set function (x,y).
Contour deformation is typically represented in the form of a PDE. Osher and Sethian
originally proposed a formulation of contour evolution which used the magnitude of the level set
gradient given by:
Here,
the level set function
Figure 2.6
For a contour C
0
(x,y)
When applying level sets to image segmentation, we seek
the image we wish to segment. This is achieved by initializing an interface at a position in the
image and then changing it by allowing appropriate forces to act on it until the correct
boundaries in the image are f
as they make use of an implicit representation of the interface.
because many complications such as breaking and merging are easily handled by the method
with support for both two
Contour deformation is typically represented in the form of a PDE. Osher and Sethian
originally proposed a formulation of contour evolution which used the magnitude of the level set
gradient given by:
Here, v signifies a constant speed to deform the contour and
the level set function
Figure 2.6: An
For a contour C
(x,y) = 0, (x,y)=
When applying level sets to image segmentation, we seek
the image we wish to segment. This is achieved by initializing an interface at a position in the
image and then changing it by allowing appropriate forces to act on it until the correct
boundaries in the image are f
as they make use of an implicit representation of the interface.
because many complications such as breaking and merging are easily handled by the method
ith support for both two
Contour deformation is typically represented in the form of a PDE. Osher and Sethian
originally proposed a formulation of contour evolution which used the magnitude of the level set
gradient given by:
signifies a constant speed to deform the contour and
the level set function (x,y)
An example of the
For a contour C
0
, the initial level set function
(x,y)= C
0.
When applying level sets to image segmentation, we seek
the image we wish to segment. This is achieved by initializing an interface at a position in the
image and then changing it by allowing appropriate forces to act on it until the correct
boundaries in the image are f
as they make use of an implicit representation of the interface.
because many complications such as breaking and merging are easily handled by the method
ith support for both two
Contour deformation is typically represented in the form of a PDE. Osher and Sethian
originally proposed a formulation of contour evolution which used the magnitude of the level set
( , ) d x y
dt
1
p
g I
I
=
+
(2.10)
20
Where
I is a smoothed version of the image I computed using Gaussian filtering and p=1 or 2.
For an ideal edge,
| |
|
=
|
\
(2.13)
Where R is a parametized version of the partition boundaries in planar form, the density
function
c
p measures the likelihood of a given pixel being at the boundaries and g is a positive,
decreasing function with minimal values at the locations in the image containing ones desired
features. The Visual properties of the classes (
a
h ,
b
h ) are additional cues for performing
segmentation with the overall aim being to discover a consistent frame partition between the
observed data, associated hypothesis and the expected properties of these hypotheses.
As the active region model considers both boundary and region forces at the same time, we can
also consider an equivalent region problem being the creation of a consistent partition between
two terms the observed data, the associated hypotheses and also their expected properties. This
particular partition may be viewed as the problem of optimising the posterior frame partition
probability which in respect to partitions P(R) would be represented by a density function as
follows:
( | ( ))
( ( ) | ) ( ( ))
( )
s
p I P R
p P R I p P R
p I
=
(2.14)
where I is the source image, p(I) is the probability of I being in the set of all possible images,
p(P(R)) is P(R)'s probability in the set of all possible partitions and p
s
(I |P(R)) is the posterior
frame partition density function (ie. the posterior segmentation probability for I, given P(R)). The
minimal form of this representation after constants and other redundant terms have been
removed [57] is the posterior segmentation probability for a partition P(R) such that:
( ( ) | ) ( ( )) ( ( ))
A B
s S R A S R B
p P R I p I s p I s
=
(2.15)
24
Where
A
p and
B
p are region probabilities which measure the overall likelihood of a pixel
preserving its expected region properties and ( ( ) | )
s
P P R I is the posterior segmentation
probability for the image I, when given the partition ( ) P R .
The level-set equations which drive the curve propagation for the GARM may then be expressed
as:
{ }
{ }
( )
0
1
, ( ( )
log
, ( ( )
( ) ( ) )
( )
(1 ) ( ( ) ( ) ( ( ).
( )
k
R j
j
j
R j
B B
p t j I u
p t j I u
u u
t
u
g p u u g p u
u
=
( | |
( |
+
| (
\
= (
(
| |
+ (
|
|
(
\
(2.16)
Here:
u = (x,y) and is a point on the initial curve in either region
0
R or
k
R
I
j
(u) specifies the jth band of the Image I(u)
{ } , ( ( )
Rn j
p t j I u represents the regional probability denoting the probability that a pixel
I
j
(u) is a member of the sub-region
n
R
( )
B
p u specifies the probabilistic edge detection operator expressing the probability that a
boundary pixel y found at u
g(p
e
) represents a positive and decreasing function of this probability. The regional
probability is then calculated from each band and added.
When provided with an initial curve, the PDA in equation 2.19 creates a partition of the image -
which is determined by a curve which attracts the region boundaries - where the exterior curve
region corresponds to the background pattern in the image and the interior corresponds to the
other patterns. Although this equation could have been implemented using a Larangian
approach, that decision would have greatly limit it's capabilities as it would be unable to deal
with changes in topology of the moving front. Instead, by harnessing the work of Osher and
Sethian [22], Paragios and Deriche [49] were able to represent the moving front as the zero-level
set of a function , making the representation topology free . The minimization of the GARM's
25
objective function is essentially then the steady-state solution of the above equation where
geometric properties are estimated directly from the level set frame.
Building on from this, one of the problems with the original Geodesic Active Contour approach
[32] was it was not originally defined for the problem of texture segmentation. This was
addressed by the GARM [50] which was extended to solve texture-based segmentation through
greater support for changes in topology (as discussed above) and consideration of both boundary
and region information. The GARMs approach to the problem of texture segmentation is to
implement Gabor features which have the power to discriminate textured surfaces based on their
orientation, scale or the mean of the magnitude. Although this results in a highly capable texture
segmentation approach, Gabor filters introduce quite a lot of redundancy and in-turn, feature
channels. This is an area where significant improvement to the model is possible and work such
as [51] demonstrates that it is possible to reduce the number of feature channels by selecting a
small set of descriptive features using the structure tensor and non-linear diffusion.
There have been some other interesting developments in this area such as [52] which offered a
modified Mumford-Shah function with an alternative cartoon limit facilitating the integration of
statistical prior on the shape of the propagating contour. Consequently, the contour is limited to a
subspace of familiar shapes whilst remaining free to transform, scale or rotate. This concept of a
shape prior greatly improves the power of the segmentation technique on noisy or obscure
backgrounds. Other noteworthy extensions to Paragios and Deriche's active region model are
[53] where the optimized energy terms also take account of the number of regions and also the
idea of multiple-region segmentations, generalising the original active region model [46] to a
multi-phase model for improved results.
2.10 Summary
In this chapter a number of different approaches for image segmentation are reviewed. These
methods include snakes [29], contour-based segmentation [33][36], The Active Contour Model
(ACM) [12][32], The Geodesic Active Region Model (GARM)[49] and Hybrid segmentation
techniques [30][31]. Snake-based segmentation is a basic, well established mode of segmenting
images using the DMT (deformable model theory) [39], whilst contour-based segmentation
evolves this approach, providing methods whereby curve points are influenced by an energy
26
function (parametric active contour models) [38] or where one embeds a snake as a zero-level set
and solves the related equation of motion (geometric active contour model) [37]. The ACM
further improves the accuracy offered by these methods considering internal and external energy
parameters where sets of nodes lying on object edges may locate contours through the process of
energy minimization [32]. It is however unable to segment textured images well, an issue
addressed by the GARM [49]. The GARM introduces an increased level of segmentation
accuracy by extending a contour-based segmentation approach to consider both boundary and
region-based forces [49] - as it is one of the most accurate segmentation approaches available at
the time of writing this thesis, our focus in the next chapter will be exploring the integration of
wavelet-packet based feature data into the GARM.
27
Chapter 3
Wavelet-based Geodesic Active Region Model (WB-GARM)
Introduction
Different medical imaging methods expose different characteristics and with each method, the
differences in image quality, structure and visibility can vary considerably [54]. This poses a
particular problem when it comes to the task of segmentation, where a clinician may wish to
separate a particular region of interest (ROI) from the rest of the image for further analysis or
even operation [55]. The quality of a medical image is determined by several factors. These
include, but are not limited to: the type of equipment used, the imaging method employed and
the imaging configuration selected by the device operator [56]. The quality of the image
produced by an imaging method may be affected by six characteristics [54][57]: noise,
resolution, blurring, contrast, distortion and artefacts. These factors will be looked at in greater
detail in the next section.
There is however a finite amount of work which can be done to improve the segmentation
models used in these instances, and at some point, the question must be posed as to whether there
exists a method to improve the underlying texture data being fed into such an algorithm, in
addition to optimizing the model as well. From a segmentation perspective, the most important
artefacts in an image are the boundaries surrounding the ROIs. These image areas can be
particularly difficult to isolate, especially when dealing with medical images containing any of
the quality-affecting issues previously mentioned. One logical view of how to improve a
segmentation technique's ability to separate the foreground and background of an image is to
improve its visibility of the region-of-interest (ROI) boundaries. There are several methods by
which this boundary sharpening may be achieved with some techniques being more effective
than others.
28
3.1 Texture Descriptors
A critical aspect of texture analysis is the extraction of textural features which can be used as
input during the modelling phase [63]. This is a key step as the ability to select the most
representative features is directly related to the performance and discrimination power of a
texture description model.
In filtering based segmentation linear and non-linear operators are applied to input images which
create a multi-dimensional vector of responses (usually referred to as the feature vector). The
operators used are best selected if the feature vector describes a variety of different textural
properties. A significant body of work exists in the area of optimal filter selection such as [64],
where the output Gabor filter is modelled as a Rician Distribution and [65], where selected filter
parameters using an immune genetic algorithm are applied in order to maximise discrimination
between the multi-textured regions.
The three filters employed by the Geodesic Active Region Model are displayed below in
Equations (3.4) (3.6).
The Gaussian operator g(x,y):
2 2
2
2
1
( , )
2
x y
g x y e
+
=
(3.1)
The isotropic center-surround operator (Laplacian of Gaussian filter) l(x,y) is:
2 2
2
( )
2 2
2
2
( , ) (1 )
2
x y
x y
l x y S e
| |
+
|
|
\
+
= i
(3.2)
Where S is a scale factor and denotes the Gaussian standard deviation.
29
The two-dimensional Gabor operators analyze the image simultaneously in both space [], and
frequency domains [, ].
( ) 2 ( )
( , | , , ) ( , | )
j x y
G
g x y g x y e
+
=
(3.3)
We can decompose the above Gabor function into two primary components the real part gR(x,
y | , , ) and the imaginary part gI (x, y | , , ). The texture features in the GARM are
captured by the spectrum analyser {s(, , )} of the two components. The concept behind a
spectrum analyser is to pass a signal of interest through a set of parallel narrow-band-pass filters.
The outputs of these filters are a measure of the signal's strength within the filter bandwidth.
When the filter is narrower, the power spectrum will have a higher frequency resolution.
Paragios and Deriche [66] opted for a large and general filter bank composed of isotropic and
anisotropic filters for use in their texture segmentation model. These filters provide good filter
responses for images with non-texturally complex backgrounds, however, based on our
experiments these filters are unable to assist in achieving desirable segmentations for detailed
medical images of poor quality or low contrast. The Isotropic, Anisotropic and Gabor filters
were also unable to assist in generating filter responses capable of accurately describing the
edges around certain textured real-world objects.
Although the GARM's standard filter bank provides the capability to help achieve
segmentations of desirable quality, there are many cases where an image may possess
properties which demand a more robust solution. These include images where there are
low-levels of contrast difference across separate regions, images containing areas of
similar texture which belong to different classes and images containing objects which
occupy a very small region of pixels. Two examples of work that can be improved,
from the material presented by Paragios and Deriche in [49] are the animal's legs and
upper body which have been misclassified as belonging to the wrong class.
30
3.2 The Wavelet transform
The wavelet transform is a transform which localises a function in both space and frequency and
replaces the Fourier transforms sinusoidal waves by a family generated by dilations of a window
referred to as a wavelet. The transform can be visualised as a series of filter banks where each
bank is composed of a series of low-pass and high-pass filters. The number of scales an image
can be filtered to depends on its width - if the total length and width of the image is equal to 2
N
,then N layers are possible. A 2-level discrete Wavelet transform of Lena may be viewed in
Figure 3.1.
Figure 3.1 Wavelet transform of the well-known Lena image
There exist many widely used wavelet algorithms which include Dauchechies and the
Biorthogonal wavelet. These approaches have a powerful advantage in that they provide a better
resolution for a n alternating series of data than more simpler approaches (such as the Haar
wavelet) currently offer. The above also have the notable disadvantage of being more
computationally expensive to calculate than Haar. In some cases the higher resolution offered by
the other wavelet types cannot be justified (depending on the type of data in question) which is
why in some cases, the Haar wavelet is chosen instead. The Haar wavelet has several advantages
including its conceptual simplicity, it's speed and it's efficiency - for example. Haar may be
calculated in memory without the need for a temporary data array. Haar isn't however without it's
limitations. When generating each set of averages and coefficients for the next scale, Haar
31
performs an average and a difference on a pair of values. The approach then shifts by two values
and calculated another average and difference on the next pair. Another issue is that all high
frequency changes should be reflected in the high frequency coefficient spectrum, whilst a Haar
window is only two elements wide. Essentially, if a large change occurs from an even value to an
odd value, this change will not be visible in the high frequency coefficients. Haar wavelets are
employed in a wide range of applications, primarily due to specific advantages it offers over
other methods. These are: (1) It is very fast, (2) it is simple and easy to understand, (3) It has low
memory requirements and is efficient as it can be calculated without the use of arrays and (4) It
can be accurately reversed without encountering visible artefacts such as with other transforms.
In spite of having a wide range of benefits, the Haar transform also comes with certain
limitations [67][68][69].
3.3 The Inverse Wavelet transform
The inverse wavelet transform allows the original data set to be recovered from a forward
wavelet transform by integration over all scales and locations this is known as reconstruction.
For the inverse transform, one may make use of the original wavelet function as opposed to its
conjugate which is found in the forward transform. By limiting the integration operation over a
range of scales, instead of all scales, it is possible to perform basic filtering of the original data
set. The inverse wavelet transform reconstructs the original set of wavelet coefficients where the
elements involved are the scaled and translated wavelets. From a mathematical perspective, the
duals of the wavelet transform elements are considered the complex conjugates of said elements
- this however is only true for the continuous transform [70].
(a) Original image (b) Forward WT (c) Inverse WT
Figure 3.2 - Daubechies reconstruction of the Nat-2B image
32
Wavelets may be considered an extension of Fourier analysis which partition an image into a
series of multi-resolution components which capture fine and coarse resolution features based on
the scale used. Images are partitioned with respect to spatial frequency - which refers to the
frequency with which the image intensity values change. Partitioning is achieved by filtering the
signal with two dyadic orthogonal filters which are referred to as a quadrature mirror filter or
QMF. The two components of the QMF are called a "father" and "mother" wavelet. Whilst the
father wavelet captures an approximate or blurry version of the signal at consecutive resolutions,
the mother wavelet provides the detail at each resolution. Applying the WT to a two-
dimensional signal will return a matrix of coefficients which map the spatial relationships at
multiple scales across the vertical, horizontal and diagonal directions.
3.4 Wavelet Packets
Wavelet packets (WP), another class of the general discrete wavelet transform, offer far more
flexibility for the detection of oscillatory behaviour. The wavelet packet transform provides a
level-by-level decomposition of a signal whereby rather than dividing only the approximation
("father") spaces to construct detail spaces and wavelet bases, WP's split the details ("mother"
wavelets) as well as the approximations. WP's generate multi-scale texture feature data which
include detailed information about the ROI boundaries. These images can be used to aid in image
processing applications as they can simplify the task of describing key artefacts without
requiring computationally expensive routines. This makes them an ideal candidate for usage in
one of the key components of a supervised textu$re segmentation model - the texture descriptors.
Object boundary features (such as those typically found in the foreground) are captured well by
edge-detection methods and are expressed using high-intensity pixels. The boundaries of a gland
are one example of a relevant foreground objects edges. Objects of a lower luminance (such as
background features) maintain a much lower-intensity. In order to generate an image with edge-
data at intensities required by the approach defined in this thesis, thresholding is applied to the
multi-scale WP's to allow only pixels of high-intensity to be preserved. Why These may be
referred to as layer 1 images. If the original source image is called layer 2, a new set of
boundary-emphasized images may be produced by individually overlapping each layer 1 on layer
2 by means of an addition operation.
33
3.5 The Forward Wavelet-packet transform
A wavelet packet transform is formed using a number of wavelet transforms. The standard
wavelet transform separates a signal space
i
S into an approximation space
1 i
S
+
and a detail
space
1 i
D
+
by dividing the orthogonal basis into two new orthogonal bases The Wavelet transform
calculates a low pass result using a scaling function and a high pass result through a wavelet
function where the low pass result is a smoothened version of the original signal. The low pass
result becomes the input to the next wavelet step, which generates another low and high pass
result until there is only a single low pass result to be calculated.One may view the Wavelet
Packet Transform as a tree - this is one the most commonly used analogies used to visualize it
and most certainly an intuitive one. Consider the root of this tree as the original image. The very
next level of this tree is the resulting output of one step of the WT. The other subsequent levels
are generated by recursively applying the WT to both the low pass and high pass filter results of
the previous step [63].
Figure 3.3 Decomposition of a Wavelet packet tree.
From an implementation perspective, the Wavelet Packet Tree [Figure 3.3] is composed of two
key stages - the first involves filtering the source image I and sub-sampling it into four new
34
images which represent the spatial frequency sub-bands. Each of these sub-bands are further
filtered and sub-sampled into another four images - a process which one repeats until reaching a
certain pre-defined level. By maintaining the components in every sub-band at each level, the
Wavelet Packet Tree can obtain a complete hierarchy of segmentation in image frequency and is
thus a redundant expansion of the image. If desired, it is possible to improve this result for a
specific problem by selecting a best basis to represent the texture by cutting off branches of the
tree controlled by a cost function applied on a node and its children.
3.6 Cost functions
The decomposition of a signal into a wavelet packet allows one to obtain the representation of
the signal in an overly complete collection of sub-bands. This table can contain much
redundancy and so it is of benefit to have an algorithm which describes the whole data-set and is
able to find a basis which can provide the most desired representation of the data relative to a
particular cost function.
Cost functions may be chosen to fit particular applications - eg. in a compression scheme the cost
function may be considered the number of bits required to represent the final result [70]. When a
Wavelet packet tree is constructed, all of its leaves are marked with a flag. The Best Basis
calculation is performed from the leaves of the tree toward the root.
It is of note that in certain cases the Best Basis may be the same set yielded by a standard
Wavelet transform. There are other cases where the Best Basis may not yield a result which is
different from the original data set (suggesting that the original set is already the most minimal
representation available, according to the cost function).
35
Figure 3.4 A cost function applied to the Wavelet Packet transform from Figure 3.3
In order to calculate the best basis the above tree is traversed and each node is marked with its
value of the cost function. When constructing the wavelet packet tree, every leaf is marked with
a flag which is modified when calculating the best basic set. This calculation is performed from
the bottom of the tree (ie from the leaves) towards the top (the root). Nodes at the bottom of the
tree (called leaves) return their cost value. As one recurses upwards to the root of the tree, the
cost of parent nodes is compared to the total cost values of its children.C2 is then considered the
sum of all the cost values for the children of the node. If C1 <= C2, the node is marked as part of
the best basis set. If C1 > C2, one replaces the cost value of the node with C2. On occasion, the
best basis set may be the same result obtained by the Wavelet Transform and in other cases, the
best basis may not obtain a result which differs from the original data set (ie. One may already
have the most minimal representation of the data relative to the cost function being used).
3.7 Weaknesses of the GARM
The GARM [49] was first introduced as a novel approach for segmenting textured images by
unifying boundary and region-based sources, where boundary information was determined
through the use of a probabilistic edge detector and region information through Gaussian
components of a mixture model. It was shown to be a more effective means of segmenting two-
class image problems involving a background and foreground than the widely-used Active
Contour Model (ACM) [32].
36
The GARM, although an effective segmentation algorithm, does however suffer from partial
misclassifications when applied to images containing what may be referred to as complex
textures. A complex texture may be found in texture descriptors containing detailed patterns such
as gradients, grids, dots and deformed lines of variable intensity. Exemplary and widely
published cases of this phenomenon may be viewed in [63] whereby segmentations of (1) the
cheetah and (2) the zebra do not segment along the correct ROI boundaries. Whilst this
observation does not remove from the GARMs ability to provide useful segmentations, it does
call into question the level of accuracy it is capable of supplying applications.
In support of further evaluation of the GARMs limitations, further segmentation results have
been generated to demonstrate particular aspects of segmentation accuracy which could be
improved upon.
(a) A zebra in a field (b) A wolf (c) Microscopic cells
(d) A cheetah in grass (e) A Brodatz image
Figure 3.5 Examples of texture segmentations output by our own implementation of the
Geodesic Active Region model
37
The images in Figures 3.5 (a)-(e) were sampled from a random distribution of real-world and
medical images with easily distinguishable foreground and background classes. The
segmentation results were obtained using the GARM supervised with 3 texture samples of each
class. As ascertainable from the above, these segmentations could be more accurate.
Figures 3.5 (a), (b) and (d) conducted on real world textured images demonstrate that the GARM
is capable of approximately segmenting the background and foreground in these samples,
however this distinction of separate classes could be greatly improved upon. For example, in
Figure 3.5 (a), the contour stops a distance from the object's true boundary. In Figure (b), a
similar scenario is observed and in Figure 3.5 (d), a slightly more texturally complex problem
due to the skin spots, the algorithm fails to form a contour around the edge of the main object but
also misclassifies part of the animals head as belonging to the background.
Figure 3.5 (c) is an enlarged group of cells which have also been segmented by the GARM. As
noted from the figure to the left, this result also suffers from quite a few misclassifications :
firstly, the curve does not segment the background areas inside clusters of cells (see the large
square nearest the right). Secondly, as can be observed from area lower down and also the area
to the left of the image the contour does not lie as close to the object's edge as it would were
the image accurately segmented The bottom-left corner of the image also suffers from an
inaccurate segmentation as even open ended areas containing cells have not been well classified.
Figure 3.5(e) is a synthetically generated Brodatz image containing five distinct textures. On
allowing the GARM to proceed with a segmentation through 120 iterations, this is the result that
was obtained; to the base of the image can be observed where the algorithm fails to attract the
contour around the circular ROI in the foreground, instead resulting in misclassification contours
within the objects boundaries. Such contours are also prevalent near the top of the image.
Overall, the quality of this segmentation could not be considered poor, however , as with the
previous figures there is space for improvement.
3.8 Improving the GARM
In recent years areas of computer vision such as medical imaging, where strong edge information
may not always be prevalent across the boundaries of an object to be segmented, has seen the
38
overall performance of purely contour based methodologies prove unreliable. This has led to a
class of region based segmentation models becoming increasingly important with additional
metrics such as image statistics being taken into account to provide more accurate results. Work
of note includes [75], [63], [76], [77], [78].
The region-based segmentation approach being examined by this thesis is the GARM, which
combines region and boundary based segmentation information to generate results of a
reasonably quality across real world, textured and medical images. Although efforts have been
previously made to improve on the current level of accuracy offered by the GARM, [78][79],
there has not been a great deal of emphasis placed on revisiting the problem of improving the
capture accuracy of its texture descriptors. This is a vital precursor to segmentation and any
enhancement of the quality of underlying data provided to a segmentation approach could have
large implications in terms of how much more clearly an objects boundaries and separate classes
are represented.
Improving this stage of the GARM is of great importance as many if not all modern approaches
instead opt to tweak aspects of the region and boundary based segmentation paradigm. As
segmentation seeks to separate one part (or class) of an image from another, such optimisations
would focus around enhancing the visibility of ROI boundaries, thus easing the classification
problem of the GARM and possibly other segmentation approaches as well. As mentioned earlier
in this chapter, an approach whereby the object boundaries of an input image could be enhanced
such that this optimisation could yield improved segmentation results using a reliable, well tested
model (such as the GARM) would offer a non-complex path to enhancing the performance of
many supervised segmentation approaches. Wavelet packets have been suggested as a means to
achieving this goal, where the challenge lies in discovering how multi-scale wavelet packet
features be integrated into a model like the GARM to effectively (and consistently) provide
improved segmentation results.
3.9 A Wavelet-packet texture descriptor
The first step in integrating a family of wavelet packet features into a segmentation model (such
as the GARM) is to consider the texture descriptors as a paradigm independent of the supervised
segmentation algorithm. This allows ROI boundary optimization of the image. In a traditionally
39
defined implementation of the GARM, anisotropic and isotropic filters are integrated as part of a
Gabor filter bank in order to accurately capture texture features from a set of pre-defined texture
samples. These features provide the supervised learning data necessary to train the algorithm
such that an image segmentation with n iterations will provide a segmented image result of
reasonable accuracy.
Although algorithms such as the GARM do perform adequately with certain groups of synthetic
and real-world imaging problems, in many cases they are unable to achieve high-rates of
accuracy in images of particularly low-contrast difference, such as clinical biopsies in the field of
medicine as shown in Chapter 5. The core problem being addressed by any enhancement
technique is thus to increase segmentation accuracy of a two-class image problem in cases where
suboptimal results are obtained using what may be considered sufficient training data of
acceptable quality. In reflection of methods previously discussed regarding the GARM, the
primary equation of interest to this research stems from the Gabor Spectrum Filter, used for the
generation of histograms in the Paragious & Deriche algorithm. This equation may be formally
defined as follows:
Computation of the Power Spectrum
( * , * )
i n i n
S Sv tx R tx I =
(3.4)
Where
i
tx
is the current texture sample being processed;
n
R
and
n
I are the current real and
imaginary Gabor kernels and Sv is a function calculating the sum of squares for both sets of
terms. This thesis aims to examine the benefits of harnessing a multi-scale approach for
boundary enhancement. A multi-scale paradigm (such as the Wavelet packet transform) offers an
efficient characterisation of textural regions in terms of spatial frequencies making it an ideal
candidate for the extraction of additional boundary information.
40
3.10 A Pseudo-code description of the WB-GARM texture
descriptor enhancement technique
The primary steps involved in the texture extraction routine being examined are to:
1. CREATE an array of multi-scale wavelet packet sub-bands at a scale k
2. SELECT the sub-bands containing the most boundary information
3. ISOLATE the coefficients for each sub-band selected individually
4. CALCULATE the inverse wavelet packet transform of each band resulting in a feature
image
i
I
5. FILTER
i
I to isolate the edge data from the rest of the image
6. SUM the pixels generated by each texture
i
t with each ( )
n
F I to generate a final set of
boundary-enhanced texture samples
7. IPUT these samples to a contour-based segmentation algorithm to produce an improved
texture segmentation.
3.11 Generating Multi-Scale Wavelet Packet Texture
Features
The process of generating a Forward Wavelet Packet Transform (FWPT) at scale j results in the
creation of
2
2
j
sub-band images containing a variety of texture based feature information. These
sub-bands are visually presented in grid-form and contain information from a pool of coefficients
for each sub-band.
41
Figure 3.6 Forward Wavelet Packet decomposition. As displayed above, the Forward Wavelet
packet transform may be visually viewed in the form of a tree. At the root of this tree is the
original data set. The next level of the tree after this is the result of the one step of the wavelet
transform. All subsequent levels in the tree are created by recursively applying the Wavelet
transform step to both the low and high pass filter results of the previous wavelet transform step.
Figure 3.7 IWPT Recomposition. In this figure, the Inverse Wavelet packet transforms works
up the levels of the tree, performing convolutions on each of the data arrays and reconstructing
the higher resolution data on each level. Each level of the tree is traversed in a similar way to the
FWPT in Figure 3.7. Destination arrays appear on the next higher level and are selected by
dividing the index by two. At the highest level, the destination array is the output data array.
When each convolution operation completes, the length of data is doubled in order to monitor the
interpolation operation during the convolution.
The Inverse Wavelet Packet transform of th
above packets should result in an image similar to the original, as
Figure
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
selected sub
The Inverse Wavelet Packet transform of th
above packets should result in an image similar to the original, as
(a)
Figure 3.9 Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
selected sub-bands. In order to focus on the coefficients of only one selected sub
The Inverse Wavelet Packet transform of th
above packets should result in an image similar to the original, as
(a) Original image
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
resulting reconstruct
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub
Figure 3
The Inverse Wavelet Packet transform of th
above packets should result in an image similar to the original, as
Original image
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
resulting reconstruct
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub
42
3.8 FWPT of the
The Inverse Wavelet Packet transform of the well known Lena image reconstructed from the
above packets should result in an image similar to the original, as
Original image
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
resulting reconstruction can be
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub
42
of the Lena image
e well known Lena image reconstructed from the
above packets should result in an image similar to the original, as
Original image (b) IWPT Reco
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
ion can be viewed in Figure 3.9
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub
Lena image
e well known Lena image reconstructed from the
above packets should result in an image similar to the original, as Figure 3.
IWPT Reco
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure
viewed in Figure 3.9
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub
e well known Lena image reconstructed from the
Figure 3.10 (b) does
IWPT Reconstruction
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
energy, we are able to create a perfect reconstruction of the image in Figure 3.10
viewed in Figure 3.9 (b).
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
bands. In order to focus on the coefficients of only one selected sub-band, the
e well known Lena image reconstructed from the
does.
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
3.10(a). The
In order to generate the IWPT feature data , it is necessary to only retain the coefficients of
band, the
Using the 16 largest wavelet packet coefficients, which contain 98.6% of the signal
The
43
coefficients of all other sub-bands are set to zero, resulting in an inverse feature image once the
IWPT is applied.
(a) Isolating Wavelet packet sub-band 2 (b) IWPT of sub-band 2
Figure 3.10 Generating IWPT Feature data. For the purposes of demonstration, the second
sub-band across in Figure 3.10 (a) at Scale 3 is selected for use with the coefficients of all
remaining sub-bands being set to zero. Figure 3.10 (b) is the feature image generated using this
data after the IWPT has been applied.
Once a sub-band has been selected and all the others successfully discarded, the Inverse Wavelet
Packet transform is then applied to the wp coefficients in the feature frame shown in Figure 3.10
(b). The first observation that may be yielded on examining this result is that the IWPT is highly
pixelated. Edge-data of high pixilation is a problem which may be addressed by means of
convolution filters such as simple smoothing or a Gaussian of window size 3x3 to 6x6.
Although an available option, this particular approach to solving pixilation problems has been
previously attempted by [80] and later criticised for its use of smoothing operations on texture
descriptors [81]. One logical argument for avoiding the usage of more than 2 levels of WPT is
that as a result of their unacceptably low visual-resolution, the deeper levels are unable to assist
in boundary edge-enhancement - instead, noticeably reducing the clarity of boundaries when
integrated as part of a segmentation algorithm. At the first two scales, inverse WP feature images
are of a much higher resolution and are therefore more capable of aiding in the enhancement of
object boundaries due to their edges being more accurately defined.
44
Figure 3.11 - IWPT of sub-band 2 at Scale 2 with greater detail.
In Figure 3.11 we may see a summary of the steps required to create an inverse wavelet feature
image from a chosen sub-band. Collections of feature images may be generated from a selection
of specific sub-bands, an entire scale, or multiple scales (as is the case with the approach outlined
in this thesis).
Figure 3.12 Creating Feature Images
45
3.12 Preparing WPF feature images for usage
As is the case with many contour-based supervised segmentation algorithms, the GARM utilises
two sets of texture samples as its primary source of training data. These texture samples (
s
T ) are
extracted from the original source and typically represent specific areas (or patches) of the
image.
In contrast, WP feature images represent the entire area of a picture and must therefore have
equivalent patches extracted if they are to be used in subsequent processes in place of
s
T . To
facilitate this step, the implementation of wavelet packets used by this thesis allows GARM
texture samples to be defined as sets of coordinates. This renders the task of extracting wavelet-
based texture samples from the IWP frames a trivial procedure.
(a) (b)
Figure 3.13 - Figure 3.13. In this figure we can see a synthetic Brodatz image (3.13(a) and a
Wavelet packet feature image of the same 3.13(b). Brodatz images have become a de facto
standard in texture processing literature and provide a good set of homogeneous textures which
can also be used to testing the effectiveness of segmentation algorithms. In the above WPF
image we can see that a number of strong edge artefacts have been captured by the Wavelet
packet transform. Integrating this additional edge information into a filter bank (such as that
found in the GARM) can have a positive impact on segmentation quality as the algorithm has
more information about the image's topology.
Figure 3.1
can see the Wavelet packet transform of the Brodat
wavelet packets have been rescaled to offer a clearer image in print medium.
group of se
2,3,5,7 and 9. These sub
edge features. It may be observed in
that Wavelet packet feature images can
These are (i) a
Despite many of the edges in these
done to further emphasize these artefacts through simple adjustment in contrast.
3.13
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
contrast difference, rendering it more d
belong to a foreground class or a background class. This fact can affect the
Figure 3.14 Wavelet packet featur
can see the Wavelet packet transform of the Brodat
wavelet packets have been rescaled to offer a clearer image in print medium.
group of selected
2,3,5,7 and 9. These sub
edge features. It may be observed in
that Wavelet packet feature images can
These are (i) areas of mid
Despite many of the edges in these
done to further emphasize these artefacts through simple adjustment in contrast.
13 Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
contrast difference, rendering it more d
belong to a foreground class or a background class. This fact can affect the
(a)
Wavelet packet featur
can see the Wavelet packet transform of the Brodat
wavelet packets have been rescaled to offer a clearer image in print medium.
lected sub-bands taken from Figure 3.14
2,3,5,7 and 9. These sub-bands are selected
edge features. It may be observed in
that Wavelet packet feature images can
reas of mid-
Despite many of the edges in these
done to further emphasize these artefacts through simple adjustment in contrast.
Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
contrast difference, rendering it more d
belong to a foreground class or a background class. This fact can affect the
Wavelet packet features of the well
can see the Wavelet packet transform of the Brodat
wavelet packets have been rescaled to offer a clearer image in print medium.
bands taken from Figure 3.14
bands are selected
edge features. It may be observed in these samples taken f
that Wavelet packet feature images can
-intensity, (ii) areas of low
Despite many of the edges in these images being visible, there is a great deal of detail that
done to further emphasize these artefacts through simple adjustment in contrast.
Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
contrast difference, rendering it more d
belong to a foreground class or a background class. This fact can affect the
46
es of the well
can see the Wavelet packet transform of the Brodat
wavelet packets have been rescaled to offer a clearer image in print medium.
bands taken from Figure 3.14
bands are selected for demonstration
these samples taken f
that Wavelet packet feature images can contain three main types of variation in pi
intensity, (ii) areas of low
images being visible, there is a great deal of detail that
done to further emphasize these artefacts through simple adjustment in contrast.
Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
contrast difference, rendering it more difficult to easily distinguish whether an area
belong to a foreground class or a background class. This fact can affect the
46
es of the well-known Brodatz image.
can see the Wavelet packet transform of the Brodatz image presented in Figure 3.13
wavelet packets have been rescaled to offer a clearer image in print medium.
bands taken from Figure 3.14(a) indexed from across these are sub
for demonstration
these samples taken from the sub
contain three main types of variation in pi
intensity, (ii) areas of low-intensity and (iii) edges of high
images being visible, there is a great deal of detail that
done to further emphasize these artefacts through simple adjustment in contrast.
Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
ifficult to easily distinguish whether an area
belong to a foreground class or a background class. This fact can affect the
known Brodatz image.
z image presented in Figure 3.13
wavelet packets have been rescaled to offer a clearer image in print medium.
indexed from across these are sub
for demonstration as they contain strong, interesting
rom the sub-ban
contain three main types of variation in pi
intensity and (iii) edges of high
images being visible, there is a great deal of detail that
done to further emphasize these artefacts through simple adjustment in contrast.
Contrast adjustment of WPF images
Contrast is a measure of the sensitivity of our human visual system which manifests to us as the
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
ifficult to easily distinguish whether an area
belong to a foreground class or a background class. This fact can affect the
(b)
(c)
known Brodatz image.In Figure 3.14
z image presented in Figure 3.13
wavelet packets have been rescaled to offer a clearer image in print medium. Figure
indexed from across these are sub
as they contain strong, interesting
bands in Figure 3.14
contain three main types of variation in pixel intensities.
intensity and (iii) edges of high
images being visible, there is a great deal of detail that
done to further emphasize these artefacts through simple adjustment in contrast.
which manifests to us as the
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
ifficult to easily distinguish whether an area
belong to a foreground class or a background class. This fact can affect the accuracy
(c)
n Figure 3.14(a),
z image presented in Figure 3.13. The
Figure 3.14(b) -
indexed from across these are sub-bands
as they contain strong, interesting
ds in Figure 3.14(b)
xel intensities.
intensity and (iii) edges of high-intensity.
images being visible, there is a great deal of detail that can be
which manifests to us as the
difference in brightness between the light and dark areas of an image. A large problem with
certain histopathological images is that they may contain multiple regions with low levels of
ifficult to easily distinguish whether an area should
accuracy of
(c)
we
a
bands
as they contain strong, interesting
(b)
xel intensities.
intensity.
can be
which manifests to us as the
(c)
47
segmentation algorithms as well as interfering with thresholding techniques which rely on small
differences between regions being present. For example, if a supervised segmentation approach
is supplied with two texture samples - one from the foreground A and another from the
background B, each of which have low levels of contrast difference and similar pixel intensities
as a result of this, the algorithm can get confused as to whether a window it is currently looking
at should be classified as belonging to A or B. There is however a solution to this problem. As we
are dealing with images within a specific domain, we can analyze the variation in pixel
intensities of regions with similar levels of low-contrast, and thus adjust the contrast levels of
pixels which fall into particular ranges in order to create a more optimal image for the
segmentation algorithm to process. This is applied to the Wavelet packet feature images
using an algorithm known as the Michelson Contrast [84]. This is commonly used in image
processing applications when dealing with images containing an equivalent distribution of pixels
containing low and high intensities. In combination with appropriate rescaling, the contrast
adjustment algorithm offers a fast, computationally cheap method of further emphasising edges
and may be calculated using the following equation:
max min
max min
( )
C
i
i
L L
I I
L L
=
+
(3.5)
Where
C
i
I is the contrast-adjusted texture image,
max
L and
min
L are the highest and lowest intensity
values for luminance and
i
I
is the current wavelet packet feature image being processed. In
order to dim the background and increase the edge-intensities of object outlines, a standard
brightness filter is also applied in this step as a precursor to the rescaling stage.
Brightness is represented as an extension of the Michelson algorithm as follows:
max min
max min
( [( )])
C
i
i
L L
I I pc br
L L
= +
+
(3.6)
where pc is the colour components of each pixel and br denotes the increase in channel
brightness. This is the equation implemented as part of the solution presented with this thesis.
3.14
The above figures
descriptors and the contrast adjusted Wavelet
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
range
thesis, clinical histopathology images) without significant loss of feature representation.
Figure 3.15
gener
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely conve
requirement is enforced to minimis
kept to a bare minimum
interior can easily resu
being independent to their parent objects.
14 Rescaling pixel values
The above figures
descriptors and the contrast adjusted Wavelet
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
range to another, allowing them to fit
thesis, clinical histopathology images) without significant loss of feature representation.
Figure 3.15 (a) and (b)
generating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely conve
quirement is enforced to minimis
kept to a bare minimum
interior can easily resu
being independent to their parent objects.
Rescaling pixel values
(a) Standard WPF
Figure 3.
The above figures display the average range of pixel intensities for standard Gabor filter texture
descriptors and the contrast adjusted Wavelet
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
to another, allowing them to fit
thesis, clinical histopathology images) without significant loss of feature representation.
(a) and (b) show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely conve
quirement is enforced to minimis
kept to a bare minimum - attempting to segment objects containing such solid lines on their
interior can easily result in misclassification as contour
being independent to their parent objects.
Rescaling pixel values
(a) Standard WPF
Figure 3.15
display the average range of pixel intensities for standard Gabor filter texture
descriptors and the contrast adjusted Wavelet
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
to another, allowing them to fit
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely conve
quirement is enforced to minimise the loss of texture data surrounding object boundaries
attempting to segment objects containing such solid lines on their
lt in misclassification as contour
being independent to their parent objects.
48
Rescaling pixel values
(a) Standard WPF (b) Contrast adjusted WPF
An analysis of pixel value ranges
display the average range of pixel intensities for standard Gabor filter texture
descriptors and the contrast adjusted Wavelet-Gabor
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
to another, allowing them to fit a particular computer vision application (in the case of this
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely conve
e the loss of texture data surrounding object boundaries
attempting to segment objects containing such solid lines on their
lt in misclassification as contour
being independent to their parent objects.
48
(b) Contrast adjusted WPF
An analysis of pixel value ranges
display the average range of pixel intensities for standard Gabor filter texture
Gabor packet texture descr
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixe
a particular computer vision application (in the case of this
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
be observed in such images find that they lie between 0 and 110
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
be high enough to ensure edges are not merely converted to solid black lines or curves. This
e the loss of texture data surrounding object boundaries
attempting to segment objects containing such solid lines on their
lt in misclassification as contour-based approaches may consider them as
(b) Contrast adjusted WPF
An analysis of pixel value ranges
display the average range of pixel intensities for standard Gabor filter texture
packet texture descr
of pixel values allows the scaling of pixel values such that they fall within a certain desired
range. The benefits of this are that the intensities of prominent pixels ca
a particular computer vision application (in the case of this
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge
0 and 110 respectiv
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge
rted to solid black lines or curves. This
e the loss of texture data surrounding object boundaries
attempting to segment objects containing such solid lines on their
based approaches may consider them as
(b) Contrast adjusted WPF
An analysis of pixel value ranges
display the average range of pixel intensities for standard Gabor filter texture
packet texture descriptors. Linear rescaling
of pixel values allows the scaling of pixel values such that they fall within a certain desired
ls can be moved from one
a particular computer vision application (in the case of this
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
been performed. Analysis of the average maximum and minimum edge-intensity values that may
respectively.
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
possible in order to generate clearer boundary outlines from existing edge-data. Values must also
rted to solid black lines or curves. This
e the loss of texture data surrounding object boundaries
attempting to segment objects containing such solid lines on their
based approaches may consider them as
display the average range of pixel intensities for standard Gabor filter texture
iptors. Linear rescaling
of pixel values allows the scaling of pixel values such that they fall within a certain desired
n be moved from one
a particular computer vision application (in the case of this
thesis, clinical histopathology images) without significant loss of feature representation.
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
intensity values that may
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
data. Values must also
rted to solid black lines or curves. This
e the loss of texture data surrounding object boundaries and is
attempting to segment objects containing such solid lines on their
based approaches may consider them as
display the average range of pixel intensities for standard Gabor filter texture
iptors. Linear rescaling
n be moved from one
a particular computer vision application (in the case of this
show (i) the range of pixel intensity values that may be observed when
ating WPF feature images and (ii) the range of vales obtained after contrast adjustment has
intensity values that may
Pixel rescaling must be intense enough to lower the overall intensity values to as close to zero as
data. Values must also
and is
based approaches may consider them as
49
Pixel rescaling is not performed on the uniform vector of pixels representing a WPF image.
Instead, rescaling is performed only on those pixels whose values fall outside of a range, R
which is close to zero for the reasons stated in the previous paragraph. Rescaling is performed
based on increment steps defined by a value M, within a range N+M where N is any pixel value
greater or equal to zero. If a pixel p falls within this range, its intensity is lowered by q.
Where p is a selected pixel, M is a range increment, is a starting point,
min
R is the start of a
range and
max
R is the end of a range.
min max
(( ), ( ( )), ( ), ( )) if p p M R R
p p q
>= <= + > <
=
Figure 3.16 Equation for threshold-based pixel rescaling
Where p= 70, M = 20,
min
R = 30 ,
max
R = 150 and = (40 + M)
(( 70), ( (90), (70 30), ( 150))
70 20 50
if p p p
p p
>= <= > <
= =
Figure 3.17 Example of applied pixel rescaling
The application of this approach successfully results in the generation of a set of WP feature
images containing edge and boundary object information of low-intensity and high-contrast
which retain much of their texture detail around each edge.
Sub-bands selected from the set of Wavelet packet features for use in the new texture descriptors
are chosen based on the "usefulness" of the information they contain - certain sub-bands such as
those found at scale 2 {6,8,10 and 11}contain very strong edge and textural features which can
greatly assist in improving
Other sub
be of great
resolution with the optimal sub
1 contains too few sub
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
bands
information
(Above)
adjustment has been applied.
of pixel values.
now be summed with standard texture samples to create t
boundary information.
3.1
There exist two sources of texture data which may be harnessed for use with supervised texture
segmentation
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process o
greatly assist in improving
Other sub-bands at
be of great advantage. Sub
resolution with the optimal sub
1 contains too few sub
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
bands from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
information can
(Above) Figure 3.
adjustment has been applied.
of pixel values.
now be summed with standard texture samples to create t
boundary information.
.15 Pixel Addition
There exist two sources of texture data which may be harnessed for use with supervised texture
segmentation through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process o
greatly assist in improving
bands at this scale are dis
advantage. Sub
resolution with the optimal sub
1 contains too few sub-bands to obtain
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
can be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
Figure 3.1
ure 3.18 (a)
adjustment has been applied.
of pixel values. These images, which are the final wavelet packet feature ima
now be summed with standard texture samples to create t
boundary information.
Pixel Addition
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process o
greatly assist in improving the Gabor filter bank currently used in the Active Region Model.
this scale are discarded as they do not contain suffici
advantage. Sub-bands for the texture descriptors are also chosen based on their
resolution with the optimal sub-bands for this particular application being found at scale 2
bands to obtain
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
18 The effect of contrast
A WPF texture sample.
adjustment has been applied. Figure 3.1
These images, which are the final wavelet packet feature ima
now be summed with standard texture samples to create t
Pixel Addition
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process o
50
the Gabor filter bank currently used in the Active Region Model.
arded as they do not contain suffici
bands for the texture descriptors are also chosen based on their
bands for this particular application being found at scale 2
bands to obtain a sufficiently large breadth of edge information and scales
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
The effect of contrast
WPF texture sample.
Figure 3.18 (c) the sample after contrast adjustment and rescaling
These images, which are the final wavelet packet feature ima
now be summed with standard texture samples to create t
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process o
50
the Gabor filter bank currently used in the Active Region Model.
arded as they do not contain suffici
bands for the texture descriptors are also chosen based on their
bands for this particular application being found at scale 2
a sufficiently large breadth of edge information and scales
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
The effect of contrast-adjustment on WPF samples
WPF texture sample. Figure 3.1
the sample after contrast adjustment and rescaling
These images, which are the final wavelet packet feature ima
now be summed with standard texture samples to create texture descriptors with emphasis
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
these two different image sets together through a process of arithmetic pixel addition, it is
the Gabor filter bank currently used in the Active Region Model.
arded as they do not contain suffici
bands for the texture descriptors are also chosen based on their
bands for this particular application being found at scale 2
a sufficiently large breadth of edge information and scales
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
adjustment on WPF samples
Figure 3.18 (b) the sample after contrast
the sample after contrast adjustment and rescaling
These images, which are the final wavelet packet feature ima
exture descriptors with emphasis
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
f arithmetic pixel addition, it is
the Gabor filter bank currently used in the Active Region Model.
arded as they do not contain sufficient edge information to
bands for the texture descriptors are also chosen based on their
bands for this particular application being found at scale 2
a sufficiently large breadth of edge information and scales
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
(a) (b) (c)
adjustment on WPF samples
the sample after contrast
the sample after contrast adjustment and rescaling
These images, which are the final wavelet packet feature images (WPF) may
exture descriptors with emphasis
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images ca
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
f arithmetic pixel addition, it is
the Gabor filter bank currently used in the Active Region Model.
ent edge information to
bands for the texture descriptors are also chosen based on their
bands for this particular application being found at scale 2 - scale
a sufficiently large breadth of edge information and scales
3 and above have a resolution which is too low to be helpful. By using between 4 and 5 sub-
from scale 2 in conjunction with the GARM's filter banks, a greater set of texture
be supplied to help improve the descriptive powers of the texture descriptors.
the sample after contrast
the sample after contrast adjustment and rescaling
ges (WPF) may
exture descriptors with emphasised
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
Wavelet packet feature images generated using wavelet packets. The Gabor images capture basic
information about the image's textures and the WPF images capture a wide range of useful edge
information about the image taken from different subbands at a chosen scale. By combining
f arithmetic pixel addition, it is
ent edge information to
scale
a sufficiently large breadth of edge information and scales
be supplied to help improve the descriptive powers of the texture descriptors.
the sample after contrast adjustment and rescaling
There exist two sources of texture data which may be harnessed for use with supervised texture
through the Geodesic Active Region model. These are the original set of Gabor
texture feature images which are generated as part of the GARM's filter bank and the new set of
pture basic
information about the image's textures and the WPF images capture a wide range of useful edge
51
possible to generate a third set of texture data which contains both good texture information and
strong edge data. This representation (as will be demonstrated) can have a positive effect on
segmentation quality.
Addition operation :
1 2
( , ) min[ ( , ) ( , ); I ]
image image max
I x y I x y I x y = +
(3.7)
As the range of pixel values across any colour channel is limited by I 0
min
= and I 255
max
= ,
arithmetic pixel addition holds the possibility of value overflow which can result in a clipping of
the pixel intensity. Clipping is a side-effect whereby if the new pixel's intensity is higher than I
max
,
its value will be set to I
max
.The effects of this may however be avoided or reduced through pixels
rescaling prior to the arithmetic addition operation. In order to rescale correctly, an analysis of both
input images may be performed to estimate the maximum and minimum summed intensity values
1 2 max
( ) I I + and
1 2 min
( ) I I + .
(a) Original colon histopathology image (b) WPF image
52
(c) Original + Rescaled image (d) Emphasised boundaries
(e) GARM using texture Gabor texture samples (f) GARM using WPF texture samples
.
Figure 3.19- Visual walkthrough of proposed algorithm with a histopathological colon biopsy
image.
The first step in segmenting an image using the new Wavelet packet texture feature descriptors is
to input a set of texture samples from the image in Figure 3.19 (a) from both the foreground and
background. These are taken in as a set of coordinates from the original image and are referred to
as "standard" texture samples for the algorithm. A set of Wavelet packet feature (WPF) images
(3.19 (b)) is then generated for the image 3.19 (a). WPF based texture samples are then extracted
53
from these images using the coordinates previously provided for the "standard" texture samples.
A final set of texture samples are then generated by combining both Wavelet and "standard"
texture samples through a pixel addition operation - this allows the creation of a texture
descriptor which captures both strong edge features and strong texture information. A
demonstration of how this appears as a whole image may be seen in 3.19 (c). As may be
observed in Figure 3.19 (d), visible improvements have been made to the thickness and
continuity of object boundaries in the original image due to the addition of the Wavelet packet
features. In Figure 3.19 (e), an un-enhanced segmentation, it may be observed that the GARM
segments the foreground regions of interest a distance within the glands, misclassifying the
position of the objects boundaries in the process something that is considerably less prevalent
in 3.19 (f). This result of pixel addition has meant that the GARM segmentation algorithm is
now able to better gauge where the glandular objects boundaries lie and is thus more capable of
attracting an accurate contour around the foreground regions of interest in the original image.
3.16 Adjustments for improved results in Medical
Applications
Although the new proposed method generates improved results across many image domains, one
area of particular interest is in medical image processing. In certain medical applications, such as
the application of texture segmentation to colon biopsy samples, a poor distribution of contrast
and gray levels can reduce the overall visible disparity between cells and can pose a serious
problem to the visual separation of glandular regions and objects that lie near its boundaries.
Contrast adjustment to an input-source in the pre-processing stages can lead to artefacts with
higher luminance, typically objects in the foreground class, to be further distinguishable from
areas of darker pixel intensity which may not be apparent from first glances.
Other types of images that suffer a similar contrast problem to colon biopsy samples are captured
bipolar cells in the retina, a problem addressed in [88] and Computer Tomography (CT images)
[89]. Fahey et al. [88] achieved some interesting results using contrast flashes of positive and
negative polarity applied to the central object of interest. Their results concluded in a 15-20%
increase in contrast on cells in front of a darker background. Computer Tomography is an area
where quite a lot of work into contrast adjustment has been done and methods previously
54
researched include adaptive histogram equalization (AHE) - which maps pixels of a source
image to the resulting image such that the histogram of the resulting image shows a uniform
distribution. [90]. A drawback to this method is noise over-enhancement addressed with more
recent work such as the interpolated AHE [91].
3.17 Summary
As presented in this chapter, enhancement of object boundaries through the use of wavelet
packet features (WPF) using pixel addition is an effective procedure for increasing the
probability of a contour-based segmentation model forming contours with a higher level of
accuracy around objects of interest. The process used harnesses the power of a set of multi-scale
wavelet packet decompositions, combing them with a set of pre-selected texture samples in a
low-cost computational step that may provide supervised segmentations far closer to a ground-
truth than a conventional segmentation model without such enhancement applied.
This improvement in accuracy is achieved by increasing the clarity of the boundaries belonging
to prominent objects in the image by utilizing additional data found in the WPF images to
describe their texture and emphasize where their boundaries end; in turn, heightening the Gabor
kernels ability to correctly capture texture patterns and thus represent the boundaries between the
foreground and background of the image being segmented. Due to the split between these
regions being much more clearly defined, the task of wrapping a contour more closely to the
object's true boundaries becomes more likely.
Although this thesis has focused on the application of this technique to the Geodesic Active
Region Model (GARM), a similar process may be applied to other contour-based segmentation
algorithms as either a pre-processing stage; whereby the boundaries and of a source image are
enhanced prior to segmentation; or as a dynamic process which extracts enhanced patches based
on specific texture samples being supplied to the segmentation model.
55
Chapter 4
Evaluation
Introduction
In order to evaluate the improved segmentation performance of the GARM with the new wavelet
packet texture descriptors presented in this thesis, experiments were conducted on a selection of
both real-world and medical images. Assessment of segmentation quality is a relatively complex
task for which there are currently standard solutions presently available, however a point-by-
point reference comparison along the curves generated were found to be an adequate
performance measure. This involves the usage of a ground truth image with specific points of
curvature through which a segmented curve must pass through in order to be counted as being
successfully segmented.
For the purposes of comparison, segmentation results from the WP-GARM will be compared
against those of the GARM for real world images and the GARM as well as the Active Contour
Model for histology images, as both have been extensively used in the field of image processing
with differing levels of success. As discussed in [49], one of the problems the original GARM
encountered with real-world images was an inability to consistently segment objects in the
foreground accurately. This trait also applies to particular types of medical images, as will be
explored in greater detail shortly. First, the results of Wavelet packet texture descriptors on a set
of real-world images will be presented
4.1 Results on a real-world data set
4.1.1 Data
Our data-set consists of 30 real-world images selected based on the quantity of primary textures
observed in them using the human visual system. Of these, a selection of the 3 best results are
presented based on their ability to demonstrate the strengths of the newly proposed algorithm.
Images presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patt
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
perceptive syste
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
several real
shoot photography. Three images of differing complexity were chosen from the above set to
compare the segmentation quality of the
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
texture descriptors which when comb
better segment the foreground based on its improved knowledge of object boundaries.
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patt
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
perceptive syste
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
several real-world applications including improvements to aut
shoot photography. Three images of differing complexity were chosen from the above set to
compare the segmentation quality of the
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
texture descriptors which when comb
better segment the foreground based on its improved knowledge of object boundaries.
(a) Elephant
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patt
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
perceptive system.
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
world applications including improvements to aut
shoot photography. Three images of differing complexity were chosen from the above set to
compare the segmentation quality of the
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
texture descriptors which when comb
better segment the foreground based on its improved knowledge of object boundaries.
Elephant
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patt
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
world applications including improvements to aut
shoot photography. Three images of differing complexity were chosen from the above set to
compare the segmentation quality of the
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
texture descriptors which when comb
better segment the foreground based on its improved knowledge of object boundaries.
Elephant
Figure 4.1
56
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patt
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
world applications including improvements to aut
shoot photography. Three images of differing complexity were chosen from the above set to
compare the segmentation quality of the GARM and the WB
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
texture descriptors which when combined with the standard sample assists the Gabor kernels to
better segment the foreground based on its improved knowledge of object boundaries.
Elephant (b) Cheetah 1
Figure 4.1 ARM segmentation results
56
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
characteristics such as dots, spots, skin or stone patterns were found to be an invaluable source of
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
world applications including improvements to aut
shoot photography. Three images of differing complexity were chosen from the above set to
GARM and the WB
Any particular image may be segmented by first selecting a
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
ined with the standard sample assists the Gabor kernels to
better segment the foreground based on its improved knowledge of object boundaries.
Cheetah 1
ARM segmentation results
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
erns were found to be an invaluable source of
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can o
world applications including improvements to automatic area detection in point
shoot photography. Three images of differing complexity were chosen from the above set to
GARM and the WB-GARM model.
Any particular image may be segmented by first selecting a set of foreground and background
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
ined with the standard sample assists the Gabor kernels to
better segment the foreground based on its improved knowledge of object boundaries.
Cheetah 1
ARM segmentation results
mages presented were of resolution measuring 256x256 with a single channel of colour
greyscale. In particular, images featuring wildlife or buildings with distinct texture
erns were found to be an invaluable source of
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
the ability for computational process to segment objects in such images can open up the door to
omatic area detection in point
shoot photography. Three images of differing complexity were chosen from the above set to
model.
set of foreground and background
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
ined with the standard sample assists the Gabor kernels to
better segment the foreground based on its improved knowledge of object boundaries.
Cheetah 1 (c) Cheetah 2
mages presented were of resolution measuring 256x256 with a single channel of colour -
greyscale. In particular, images featuring wildlife or buildings with distinct texture
erns were found to be an invaluable source of
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
pen up the door to
omatic area detection in point-and
shoot photography. Three images of differing complexity were chosen from the above set to
set of foreground and background
texture samples and storing the positions of these samples as coordinates relative to the source
image. The algorithm takes these samples and then creates a separate set of Wavelet packet
ined with the standard sample assists the Gabor kernels to
better segment the foreground based on its improved knowledge of object boundaries.
ah 2
erns were found to be an invaluable source of
interesting data for segmentation tests. In certain cases these featured obvious visual differences
along the boundary to the foreground and background whilst others presented challenges to the
Images such as these are an example of why accurate segmentation algorithms are a necessity
pen up the door to
and-
shoot photography. Three images of differing complexity were chosen from the above set to
set of foreground and background
texture samples and storing the positions of these samples as coordinates relative to the source
ined with the standard sample assists the Gabor kernels to
Table
Ground truths of the images in Figures
(a) Elephant
(a) Elephant
Table 4.1
Ground truths of the images in Figures
20
40
60
80
100
120
140
160
180
Elephant
Elephant
Figure 4.3
Comparison of the
Ground truths of the images in Figures
0
20
40
60
80
100
120
140
160
180
(a)
Elephant
Figure 4.2
Elephant
Figure 4.3 Ground truth image
Comparison of the segmentation quality between the GARM, WB
Ground truths of the images in Figures
(a)
57
Elephant (b) Cheetah 1
Figure 4.2 -WBGARM
(b) Cheetah 1
Ground truth image
segmentation quality between the GARM, WB
Ground truths of the images in Figures 4.1-4.3 based on the points of curvature in each ground
truth image.
(b)
57
Cheetah 1
ARM segmentation results
Cheetah 1
Ground truth images featuring points of curvature
segmentation quality between the GARM, WB
4.3 based on the points of curvature in each ground
truth image.
Cheetah 1 (c)
segmentation results
Cheetah 1 (c)
s featuring points of curvature
segmentation quality between the GARM, WB
4.3 based on the points of curvature in each ground
(c)
(c) Cheetah 2
segmentation results
(c) Cheetah 2
s featuring points of curvature
segmentation quality between the GARM, WB-
4.3 based on the points of curvature in each ground
GARM
WB-GARM
Ground-truth
Cheetah 2
Cheetah 2
-GARM and
4.3 based on the points of curvature in each ground
truth
GARM and
4.3 based on the points of curvature in each ground
58
4.1.2 Analysis of real-world results
Figures 4.2 (a)-(c) demonstrate the ability of the Wavelet Packet texture descriptors to improve
the accuracy of a final curve propagation. As the Gabor kernels have been supplied with Wavelet
Packet texture descriptors containing enhanced boundary information the contour wraps around
the true object boundaries significantly more tightly than the un-enhanced standard GARM in
Figures 4.1 (a)-(c). Each of the images in this test set are processed for a number of iterations n -
the steps required for the segmenting contour to reach convergence around the regions of
interest in the image. Figure 4.2(a) displays an elephant whose final segmentation after 150 of
these such iterations has improved from that of Figure 4.1(a) the curve has been attracted to the
actual object boundaries. As the foreground texture samples used for both enhanced and
unenhanced tests include the shaded area behind the elephants ear, a more complete
segmentation of the elephant as a whole is possible.
Figure 4.2 (b) (also after 150 iterations) presents improvements to how close the GARM has
been able to successfully segment the cheetah from its background. In comparison to Figure 4.1
(b) where the segmentation stops short of the objects correct boundaries at almost all key points,
this is another example of where the WB-GARM wavelet packet texture descriptors offer a better
quality of result for real world images. Figure 4.2 (c) (after 200 iterations) is a difficult image to
conventionally segment due to the low differences in pixel intensity between the cheetah and the
grass behind it. The GARM segments most of the animal but does not exclude strands of grass
which overlap the cheetahs head, nor does it correctly segment the cheetahs tail. This is a third
example of wavelet-packets being an excellent source of additional image information which
may be harnessed to assist in achieving more accurate textured image segmentations using
existing models.
In many of the cases tested, the WB-GARM resulted in an improved segmentation with more
correctly classified ground-truth curve points than the GARM . Although the GARM correctly
classifies some of the regions, it fails to form contours on the exact object boundaries and
misclassifies the majority of the elephants trunk and a majority of its back as belonging to the
background. The WB-GARM prevented certain aspects of these misclassifications as has been
demonstrated above.
59
4.2 Glandular segmentation of histology images
Introduction
Validation of the improvements offered by Wavelet packet texture descriptors to the supervised
segmentation of medical images will be applied to the specific problem of Glandular
segmentation. Glandular segmentation is a challenge which spans across many areas of medical
histopathology including colonoscopy and the study of prostate images. In several cases, the
isolation of a particular area of a slide for further study, such as for the detection of Colon
cancer, is of pivotal importance in making an early diagnosis of the disease. As with many areas
of medicine, in histopathology, there is a significant amount of inter and intra-observational
variation between clinicians judgements of specimens which can lead to inaccurate manual
segmentations of ROIs. The absence of a single accurate observation to pathologists is the
motivation for assistance using computer analysis.
Many studies have looked at the problem of classifying histopathological images used in the
diagnosis of colorectal cancer [92][8] whilst other classification efforts have shown interest in
the segmentation of glands from biopsy slides [93][94]. The need for a computationally reliant
alternative to manual glandular segmentation stems from tedious steps required for current
colonoscopy analysis which can often include electronic cleansing techniques combining bowel
preparation, oral contrast agents before finally using image segmentation to extract lumen from
CT images of the colon [95][8]. Glandular segmentation can be thought of as a boundary
detection problem. Possibly the most essential element of glandular segmentation in conjunction
with region-analysis is the accurate segmentation of lumen (the interior part of the cell) from the
darker nuclei on their boundaries. Unfortunately, computational estimation of the lumen
boundaries can sometimes be a difficult task due to the low contrast difference between
attenuation values of the lumen and artefacts surrounding the outer walls of the gland which
occasionally share similar intensity values.
The WP-GARM achieves promising results in glandular segmentation. The performance of our
algorithm in histopathological applications was conducted on a set of five greyscale biopsy
samples with complex textures. For textural features, due to the inter-gland variance in lumen
surface texture, foreground samples and two background samples were chosen as priori. High
segmentation accuracy was achieved with the majority of tests with only minor error contours
60
being formed from misclassification. An optional source filtering technique to help remove
blood cells and other speckled content is applied in a pre-processing stage as this was found to
help avoid a majority of such misclassifications.
4.2.1 Background information on Colon Cancer
Colon cancer is amongst the leading types of cancer affecting the population of Great Britain
today, with high rates of incidence in England (36, 100 cases in 2002), Scotland (1014 cases) and
Northern Ireland (307 cases) [108][109]. On average there are 100 new cases reported every day
and as a result of increases in life expectancy, the frequency of it's occurrence is rising in the
ageing population. With regular screening, the disease can often be detected in its early stages
and treated quite effectively. It is here where a need for improved quantitative analysis of
histopathological images can aid in decreasing the time and work required to obtain a reliable
diagnosis. [96]. The vast majority of colorectal cancers are removed in a very advanced stage,
making the prognosis of the disease dependent on the depth of growth and spread of the tumour.
More than 85% of colon cancer arises from dysplastic polyps (growths on the lining of the colon
with abnormal cells) which may be present in a patient for 5-10 years before malignant
transformation takes place [97]. The type of cell that is responsible for forming the polyp varies
and is important in determining its potential for developing into a cancer. In order for screening
to be effective, the earliest phases of cancer need to predict certain features which may indicate a
rapid progression.
(a) (b) (c)
Figure 4.4 Three colon biopsy specimens featuring variations of glandular size, texture and
intensity.
61
The key feature of interest in diagnosing biopsy samples is one of size. Polyps longer than 1cm
in diameter are generally more likely to experience malignant transformation than those of
smaller size. The risk of developing carcinoma from a polyp is proportionally related to this
metric - typically 0% risk if the polyp is smaller than 5mm, a 1% risk if wider than 5 to 10 mm
and a 10% risk with sizes of 10-20mm [98].
4.2.2 Prior work in Glandular Segmentation
In previous classification approaches, which like image segmentation, share the goal of
distinguishing different classes inside an image, it has been shown that although advancements
such as the 2DPCA perform well on biopsy specimens, a high computational complexity and a
large dimensionality of features can lead to methods being inefficient. It is here that researchers
in classification have discovered that the use of local texture features can aid in minimizing the
size of a feature vector whilst maintaining a good level of accuracy [94][102].
Principal component analysis (PCA) is the study of multivariate data - it can be explained using a
simple analogy. One may imagine a painting that is drawn using a palette of n different mixtures
of paint where each of these was composed of different amount of a common set of pigments.
One may also imagine that spectral noise is present and that each point of the painting that could
be drawn was done so using only a single paint mixture. Principal component analysis may be
used to find the linear combination of pure pigments which was used to make each mixture. Each
of these mixtures is known as a principal component. The PCA is widely used in computer vision
problems requiring facial recognition and image modelling. The two-dimensional principal
component analysis (2DPCA) is based on 2D matrices instead of the standard PCA based on 1D
vectors. It is capable of obtaining a higher recognition accuracy than the standard PCA.
Medical image segmentation approaches have taken into account a wide variety of different
image features such as contrast, correlation, colour and inverse difference moment to
discriminate between benign and cancerous samples [103][104]. Unfortunately, due to the
complexity and quality of the biopsy images often being used (many suffer from irregular
shapes, sizes and poor contrast) as well as the sometimes sporadic nature of cancerous samples,
these approaches have been unable to yield reliable results in this area of medical image
processing.
Figure 4.5
example of a
Figure 4.6
colon biopsy specimen featuring
boundary of
Figure 4.5 - Regions of interest in a
example of a
in (b)
Figure 4.6 A visual analysis of
colon biopsy specimen featuring
boundary of the lumen. (b
Regions of interest in a
highlighted colon gland featuring an area of lumen surrounded by a boundary and
in (b) we see
(a)
(c) (d)
A visual analysis of
colon biopsy specimen featuring
the lumen. (b) An
(a) (b)
Regions of interest in a
highlighted colon gland featuring an area of lumen surrounded by a boundary and
we see the focused area of lumen which we wish to segment.
(a)
(c) (d)
A visual analysis of the difficulties encountered
colon biopsy specimen featuring dark speckles of similar intensity to the nuclei around the
) An absolute binary threshold of (a
62
(a) (b)
Regions of interest in a manually segmented
highlighted colon gland featuring an area of lumen surrounded by a boundary and
the focused area of lumen which we wish to segment.
(a)
(c) (d)
difficulties encountered
dark speckles of similar intensity to the nuclei around the
absolute binary threshold of (a
62
(a) (b)
manually segmented colon biopsy sample. In (a)
highlighted colon gland featuring an area of lumen surrounded by a boundary and
the focused area of lumen which we wish to segment.
(b)
(c) (d)
difficulties encountered
dark speckles of similar intensity to the nuclei around the
absolute binary threshold of (a
(a) (b)
colon biopsy sample. In (a)
highlighted colon gland featuring an area of lumen surrounded by a boundary and
the focused area of lumen which we wish to segment.
(b)
(c) (d)
difficulties encountered in glandular segmentation: (a
dark speckles of similar intensity to the nuclei around the
absolute binary threshold of (a) which maintains large black
colon biopsy sample. In (a)
highlighted colon gland featuring an area of lumen surrounded by a boundary and
the focused area of lumen which we wish to segment.
in glandular segmentation: (a
dark speckles of similar intensity to the nuclei around the
) which maintains large black
colon biopsy sample. In (a) we see an
highlighted colon gland featuring an area of lumen surrounded by a boundary and
the focused area of lumen which we wish to segment.
in glandular segmentation: (a) A
dark speckles of similar intensity to the nuclei around the
) which maintains large black
e see an
highlighted colon gland featuring an area of lumen surrounded by a boundary and
) A
63
regions signifying areas of interest and speckles which interfere with segmentation at this
resolution. (c) A colour-map of the lumen (Ln) in the foreground class and in red and black are
the speckle artefacts we do not wish to include in our input to the WB-GARM (d) A processed
biopsy specimen which has had speckle artefacts selectively thresholded out. This leaves a
simpler two class classification and segmentation problem where the algorithm must separate the
boundary from the lumen.
Prior studies have performed lumen segmentation using a threshold region growing method
[105] harnessing the difference in intensity values between air and colon wall tissue to enable the
use of threshold methods to distinguish between the two different regions during segmentation.
Use of a threshold Level Set Method has also been attempted in studies of Colon-wall based
segmentation for increased accuracy [106] using a modified Active Contour model to attract a
level set to the object's boundary.
Although these methods are theoretically sound for very basic colon biopsy samples, more
complex samples which are either of low-intensity or featuring contorted lumen regions fail to
clearly segment using either of these algorithms. The above warrants further investigation into
contour based approaches for glandular segmentation and is an ideal candidate application for
the WB-GARM model . As our approach benefits from both boundary and region forces as well
as optimised wavelet feature vectors for improved texture segmentation, there is a possibility of
it being more discriminant than some of the prior methodologies outlined.
(a) (b)
64
(c) (d)
Figure 4.7 A close-up of artefacts surrounding : (a) a sampling of the pixels found on the
boundary of the lumen (nuclei). In (b) we can see a similar sample of the cell speckles found in
the fluid surrounding the glands. As demonstrated by the histograms of both (c) An intensity
analysis of the boundary nuclei and (d) an analysis of the fluid speckles, the similarity in pixel
intensity between both samples can present a challenge when segmenting biopsy slides as both
texture samples have the fluid as a
boundary
and similar contrast properties.
4.2.3 Application of WB-GARM to Glandular segmentation
Our procedure for segmenting lumen from a biopsy specimen is as follows:
1. As the intensity levels of both the black nuclei found on the boundary of the gland and those
of the speckles in the fluid surrounding it are very similar, a process to remove these artefacts
is performed upon the image. The process which completes this is very simple and takes into
consideration properties such as height, width and the shape of the speckles - generally
circular in nature. By estimating whether a region found fits this profile, one may remove the
area of pixels containing it and thus decrease the number of speckles the segmentation
algorithm needs to handle. The product of applying cell speckle removal to an image I is
referred to as S(I).
65
2. A vector of Wavelet Packet feature images (WP) are generated at levels 1 and 2 using (S1) as
their input and saved to a local cache.
3. The WB-GARM is supplied with two list of co-ordinates F and B which represent the texture
samples to be extracted from SI for supervised learning. WP is also loaded into the workspace
at this stage and is used to create the texture descriptors.
4. Next, the original untouched source image I is loaded into the segmentation algorithm along
with SI (the version with cell speckles removed) SI is the image input directly into the
segmentation approach. Here the segmenting contour is attracted to the boundaries of the
foreground objects in SI resulting in a segmented image which utilizes both Gabor and Wavelet
packet features to achieve its segmentation. As a final step, the pixels defining the segmentation
contours for SI are copied from the output of the WB-GARM and overlaid on I so that a cell
biopsy containing all original artefacts (including cell speckles) is generated for physicians to
use.
4.2.4 Results on Glandular Segmentation
The WB-GARM achieved promising results in this area. The experiments with histopathology
images were conducted on a set of five greyscale biopsy samples measuring 256x256 pixels on a
Pentium 1.6 GHz dual-core PC system. For textural features, due to the inter-gland variance in
lumen surface texture, a set of five samples was used for supervised segmentation; three from the
foreground class F and two from the background class B. Correct segmentation accuracy was
achieved with the majority of tests with only minor error contours being formed from
misclassification. Here, the form of supervised segmentation used is the same as that used in
Geodesic Active Region Model (GARM). The GARM requires priori texture samples from both
the foreground and background of an image that one wishes to segment. The added step of
removing cell "speckles" which appear in some of the histopahological images demonstrated in
this thesis can also help improve segmentation quality by lowering the quantity of regions which
could be misclassified as belonging to the foreground. One of the biggest challenges which
pathologists face when selecting a computational segmentation approach is finding one that can
appropriately handle the low levels of contrast difference between glands, cells and other regions
of the cell biopsy images. As our experiments demonstrate, Wavelet Packet texture descriptors
66
provide adequate feature vectors for this problem which can transform the Geodesic Active
Region model into a more robust tool for texture segmentation in medical imaging. The average
processing time using GDI+ and .NET in our C++ implementation to generate the necessary
wavelet packet feature images from levels one and two, based on a distribution of 12 tests, is
approximately 7 seconds. Sub-bands selected from the set of Wavelet packet features for use in
the new texture descriptors are chosen based on the "usefulness" of the information they contain
- certain sub-bands such as those found at scale 2 {6,8,10 and 11}contain very strong edge and
textural features which can greatly assist in improving the Gabor filter bank currently used in the
Active Region Model. Other sub-bands at this scale are discarded as they do not contain
sufficient edge information to be of great advantage. Sub-bands for the texture descriptors are
also chosen based on their resolution with the optimal sub-bands for this particular application
being found at scale 2 - scale 1 contains too few sub-bands to obtain a sufficiently large breadth
of edge information and scales 3 and above have a resolution which is too low to be helpful.
As discussed, selective sub-band use from multiple-scales was investigated, and although initial
experiments displayed a variety of improvements in certain tests, it is certainly an area that could
be researched more in the future. WB-GARM lab a C# evolution of our implementation of the
Geodesic Active Region experienced processing times of between 8 and 15 minutes on biopsy
slides with a median segmentation time of 10 minutes. This was based on several factors: (1)
Image complexity, (2) the number of iterations to be conducted and (3) available system
memory. WB-GARM Lab typically required 120MB of system RAM during core processing
with an upper limit of 180MB and a lower limit of 90MB based on the test being conducted.
Similar quantitative measures for establishing the quality of segmentation results such as those
previously used in this thesis will allow an accurate evaluation of our algorithm against both the
Active Contour Model [32] and the Geodesic Active Region Model [67]. These approaches were
selected for two primary reasons. Firstly, they are both based on the deformation a contour model
through slightly differing methods - one is based on the concept of evolving a snake using a local
minimization of energy whilst the other deforms its final contour based on region and boundary
forces. The second reason these approaches were chosen is that their results will offer an
evolutionary view of texture segmentation as a problem domain. ie. The GARM evolved from
the ACM, and the WB-GARM is an evolution of the GARM. The performance of these methods
will offer an insight into the proposed approach.
67
The results of this from the ACM, the GARM and the WB-GARM will be presented below. The
setup and configuration information for each model's implementation are also listed for reference
purposes.
4.3 Segmentation Setup
4.3.1 Data
The human colon tissue samples used for testing purposes in Glandular segmentation were
acquired by colleagues from Yale University School of Medicine from archival hematoxylin and
Eosin stained micro-array tissue sections. The original images used were of size 1080x1024 with
no additional sub-sampling or compression applied to the input. A window size of 60x60 was
employed here.
4.3.2 Texture
For each directional window (Wn) of size 96x96 being examined, texture sampling focused on
extracting the largest possible regions from Wn for each distinct texture and typically measured
[20x20], [32x32], [48x48],[64x64] or [96x96]. Good results were achieved by opting for three
lumen surface textures for the foreground class and three background class samples composed of
one boundary (dark gray-black) area and two fluid areas containing black coloured cells. Texture
samples of sizes less than [14x14] (typically fluid cells) were found to be ineffective in assisting
the description of texture in this application which is one of the basis for integration of a
dedicated thresholding step for the reduction or removal of miniature artefacts prior to
initialisation of the texture segmentation model.
This has proved quite effective as can be seen by the experimental results presented later in this
Chapter. The requirement for a thresholding step does not limit the discrimination abilities of the
model as can be observed by the marked improvements over the GARM in contrast tests, which
are free of initial thresholding.
68
4.3.3 Ground truth generation
Manual image segmentations are created by human observers (such as physicians) who plot a
line around the main objects of interest in an image. Once this process has been completed, an
average of all the manually segmented images available is made in a computational step that
creates the Ground truth image that is used for comparison with computer-based segmentation of
the same photograph.
When one is creating a manual segmentation, indentations, corners and curves are drawn around
the boundaries of objects of interest. On a computer, these are visually created using tools (such
as a Bezier) which allow one to draw a parametric curve based on a series of points - one for
each change in direction the line being drawn takes. For the purposes of evaluating the contour
curves generated through manual segmentation and those generated using computational
methods, we devised a method for segmentation comparison based on this concept.
Using the digital Ground truth image, we trace around the manually segmented boundaries of the
objects of interest using parametric curves via a freeform curve tool. This can be done in any
popular Image Editing suite and allows the generation of a point-based bezier curve along the
same path of pixels which define the segmented boundaries. There is no loss of accuracy
incurred. The same approach is applied to the image output by the segmentation approach being
tested which results in two groups of bezier-points which may be compared by overlaying one
over the other.
The number of bezier-points in the algorithmic-segmentation which pass through the same points
as the Ground truth points allow one to compare how close the segmentation was to what we
would ideally desire. This is called the pass-through rate. A 100% pass-through rate (
points
groundtruth
/points
algorithm
* 100) would indicate that the algorithmic-segmentation correctly
segmented all the boundaries of the objects of interest whilst a lower pass-through rate would
suggest that certain areas of the image's foreground or background may have been incorrectly
classified.
69
SETUP IFORMATIO
Active Contour Model (ACM)
(the scale parameter in the Gaussian kernel for smoothing) = 1.5, timestep = 5, (the
coefficient of the internal energy term = 0.04, (the coefficient of the weighted length term
Lg( )= 5 , (the coefficient of the weighted area term Ag ( ) = 1.5 and the average value of n
(the number of iterations) = 400. Average processing time = 3-4 minutes.
Geodesic Active Region Model (GARM)
Number of foreground textures used = 3, number of background textures used = 3, size of Gabor
range = 100, number Gabor kernels used = 4 per component, average number of iterations to
stable final contour = 150, implementation specific average processing time = 9-12 minutes.
Wavelet-based Geodesic Active Region Model (WB-GARM)
Initial threshold processing applied to each source image. Number of foreground textures used =
3, number of background textures used = 3, size of Gabor range = 50, number of Gabor kernels
used = 4-20 per component (based on no. wavelet packets used), wavelet packet sub-bands used:
all sub-bands from levels 1 and 2 (4+16 =20), average number of iterations to stable final
contour = 140, implementation specific average processing time = 10-15 minutes.
4.4 Results on images without the thresholding of
lymphocytes
In this set of images, minor contrast adjustment was applied to the original sources to enhance
the luminosity of areas that fall inside the nuclei boundaries. Such morphological filtering of the
input is not necessary when the lymphocytes (speckles found outside the lumen boundaries) are
thresh
presented shortly.
Figure 4
boundary edges
to the left of the image
points between the foreground and background classes as indicated by the boundaries in an
image's ground truth.
traced) line points of
boundaries in the image's ground truth. As discussed, a deformable point
of a contour may be manu
freeform Bezier tool.
truth is 70
curvature and below as this suggests that at least half the areas segmented did not capture the
correct object boundaries.
are
correctly
texture samples, a perfect segmentation is not achievable.
interesting of the
intensity than in either of the previous figures,
demonstrating that if a sample from this class of image does have a balanced variance in
thresholded to reduce their visibility in the image. The results of lymphocyte thresholding
presented shortly.
(a) (b) (c)
Figure 4.
Figure 4.8 (a):
boundary edges
to the left of the image
points between the foreground and background classes as indicated by the boundaries in an
image's ground truth.
traced) line points of
boundaries in the image's ground truth. As discussed, a deformable point
of a contour may be manu
freeform Bezier tool.
truth is 70-80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
correct object boundaries.
made, but there are still points of curvature tha
correctly - due to low
texture samples, a perfect segmentation is not achievable.
interesting of the
intensity than in either of the previous figures,
demonstrating that if a sample from this class of image does have a balanced variance in
olded to reduce their visibility in the image. The results of lymphocyte thresholding
presented shortly.
(a) (b) (c)
Figure 4.8 - Glandular segmentation results without
Encouragingly, at many points the contour has been attracted to the desired
boundary edges, but minor misclassifications have been made around some of t
to the left of the image. The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
image's ground truth. A good segmentation is defined
traced) line points of curvature for a segmentation overlay
boundaries in the image's ground truth. As discussed, a deformable point
of a contour may be manu
freeform Bezier tool. A typical quality threshold for points that
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
correct object boundaries.
made, but there are still points of curvature tha
due to low contrast difference
texture samples, a perfect segmentation is not achievable.
interesting of the three specimens in this group. As the colon lumen contain a more uniform
intensity than in either of the previous figures,
demonstrating that if a sample from this class of image does have a balanced variance in
olded to reduce their visibility in the image. The results of lymphocyte thresholding
(a) (b) (c)
Glandular segmentation results without
Encouragingly, at many points the contour has been attracted to the desired
, but minor misclassifications have been made around some of t
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
A good segmentation is defined
curvature for a segmentation overlay
boundaries in the image's ground truth. As discussed, a deformable point
of a contour may be manually generated by tracing over a segmented images boundaries using a
A typical quality threshold for points that
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
Figure 4.8
made, but there are still points of curvature tha
contrast difference
texture samples, a perfect segmentation is not achievable.
three specimens in this group. As the colon lumen contain a more uniform
intensity than in either of the previous figures,
demonstrating that if a sample from this class of image does have a balanced variance in
70
olded to reduce their visibility in the image. The results of lymphocyte thresholding
(a) (b) (c)
Glandular segmentation results without
Encouragingly, at many points the contour has been attracted to the desired
, but minor misclassifications have been made around some of t
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
A good segmentation is defined
curvature for a segmentation overlay
boundaries in the image's ground truth. As discussed, a deformable point
ally generated by tracing over a segmented images boundaries using a
A typical quality threshold for points that
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
(b): In this result, correct segmentation of the lumen areas
made, but there are still points of curvature tha
contrast difference between the boundary texture samples and the speckle
texture samples, a perfect segmentation is not achievable.
three specimens in this group. As the colon lumen contain a more uniform
intensity than in either of the previous figures, segmentation become relatively easier,
demonstrating that if a sample from this class of image does have a balanced variance in
70
olded to reduce their visibility in the image. The results of lymphocyte thresholding
(a) (b) (c)
Glandular segmentation results without
Encouragingly, at many points the contour has been attracted to the desired
, but minor misclassifications have been made around some of t
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
A good segmentation is defined as one where the majority of (Bezier
curvature for a segmentation overlay the same points as those defining the
boundaries in the image's ground truth. As discussed, a deformable point
ally generated by tracing over a segmented images boundaries using a
A typical quality threshold for points that
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
In this result, correct segmentation of the lumen areas
made, but there are still points of curvature that the segmentation does not pass through
between the boundary texture samples and the speckle
texture samples, a perfect segmentation is not achievable. Figure 4.
three specimens in this group. As the colon lumen contain a more uniform
segmentation become relatively easier,
demonstrating that if a sample from this class of image does have a balanced variance in
olded to reduce their visibility in the image. The results of lymphocyte thresholding
(a) (b) (c)
Glandular segmentation results without lymphocyte
Encouragingly, at many points the contour has been attracted to the desired
, but minor misclassifications have been made around some of t
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
as one where the majority of (Bezier
the same points as those defining the
boundaries in the image's ground truth. As discussed, a deformable point
ally generated by tracing over a segmented images boundaries using a
A typical quality threshold for points that successfully overlap the ground
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
In this result, correct segmentation of the lumen areas
t the segmentation does not pass through
between the boundary texture samples and the speckle
Figure 4.8 (c):
three specimens in this group. As the colon lumen contain a more uniform
segmentation become relatively easier,
demonstrating that if a sample from this class of image does have a balanced variance in
olded to reduce their visibility in the image. The results of lymphocyte thresholding
(a) (b) (c)
lymphocyte-thresholding
Encouragingly, at many points the contour has been attracted to the desired
, but minor misclassifications have been made around some of the lymphocytes
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
as one where the majority of (Bezier
the same points as those defining the
boundaries in the image's ground truth. As discussed, a deformable point-by-point Bezier version
ally generated by tracing over a segmented images boundaries using a
successfully overlap the ground
80%. A poor segmentation would have less than or equal to 50% of the true po
curvature and below as this suggests that at least half the areas segmented did not capture the
In this result, correct segmentation of the lumen areas
t the segmentation does not pass through
between the boundary texture samples and the speckle
(c): This is perhaps the most
three specimens in this group. As the colon lumen contain a more uniform
segmentation become relatively easier,
demonstrating that if a sample from this class of image does have a balanced variance in
olded to reduce their visibility in the image. The results of lymphocyte thresholding will be
thresholding.
Encouragingly, at many points the contour has been attracted to the desired
he lymphocytes
The desired boundary edges in an image are the line of distinguishable
points between the foreground and background classes as indicated by the boundaries in an
as one where the majority of (Bezier-
the same points as those defining the
point Bezier version
ally generated by tracing over a segmented images boundaries using a
successfully overlap the ground
80%. A poor segmentation would have less than or equal to 50% of the true points of
curvature and below as this suggests that at least half the areas segmented did not capture the
In this result, correct segmentation of the lumen areas
t the segmentation does not pass through
between the boundary texture samples and the speckle
This is perhaps the most
three specimens in this group. As the colon lumen contain a more uniform
segmentation become relatively easier,
demonstrating that if a sample from this class of image does have a balanced variance in
will be
he lymphocytes
The desired boundary edges in an image are the line of distinguishable
the same points as those defining the
point Bezier version
ally generated by tracing over a segmented images boundaries using a
successfully overlap the ground
ints of
curvature and below as this suggests that at least half the areas segmented did not capture the
In this result, correct segmentation of the lumen areas
between the boundary texture samples and the speckle
This is perhaps the most
71
contrast, more accurate segmentations are possible. In reference to With histopathology images
of this nature there can appear certain artefacts in test images with texture features similar to the
glands we wish to segment. These are typically cells which are round, small and speckled in
nature. In an ideal segmentation these cells would be classified as part of the background. In
some cases however, due to the similarities in topology, they can get misclassified as belonging
to the foreground class. Here, contours which are formed around them erroneously are known as
error contours and shall be addressed shortly.
4.5 Results on images using lymphocyte thresholding
In this section we will compare the results of four colon biopsy slides whose lymphocytes have
been segmented using the same distribution of texture samples as the previous result set using an
additional pre-processing step to aid the segmentation.
White blood cells help the human body to fight against diseases and infections. Lymphocytes are
a type of small white blood cell, usually 7-8 micrometers in length, which are present in the
blood. Their purpose is to help provide a specific response to dangerous micro-organisms when
they have infiltrated the body's main defence systems. Lymphocytes also help to protect the body
from tumours - tissues which grow at an accelerated rate than normal. Physicians involved in the
area of histopathology may be required to distinguish lymphocytes from other cells in a biopsy
slide. The center of a lymphocyte consists of large groups of thin threads called chromatin. When
stained with a stain known as Wright's stain [ref], the nucleus of a lymphocyte appears dark
purple. It is usually round in shape surrounded by a small quantity of blue cytoplasm (a part of a
cell enclosed by a plasma membrane) but can also appear indented.
One of the major problems in segmenting lymphocytes in histopathology images is that
segmentation models such as the GARM may incorrectly classify speckles surrounding these
objects as being part of the image foreground due to the small size of the area occupied by each
speckle. To overcome this problem, a pre-processing step applies a Gaussian filter of size 7x7 to
the source image. A segmentation of this image is then made using purely the enlarged
lymphocytes as the foreground ROIs. The resulting output is an image containing a range of
contours (and pixel positions) which may be ignored when outputting the contours for our main
segmentation on the source using the selected segmentation approach.
4.5.1
Figure 4.9
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
truth image (or Gold standard) which may
algorithms.
4.5.1 Specimen 1
Figure 4.9: Hand Labelling
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
truth image (or Gold standard) which may
algorithms.
Specimen 1
(a) Original Image (b) Observer #1 manual contours
(c) Observer #2 Contour
Hand Labelling
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
truth image (or Gold standard) which may
Specimen 1
Original Image (b) Observer #1 manual contours
(c) Observer #2 Contour
Hand Labelling. Based on the
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
truth image (or Gold standard) which may
72
Original Image (b) Observer #1 manual contours
(c) Observer #2 Contour
Based on the manually drawn contours as shown in Figure
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
truth image (or Gold standard) which may be used to compare to the outputs from existing
72
Original Image (b) Observer #1 manual contours
manually drawn contours as shown in Figure
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
be used to compare to the outputs from existing
Original Image (b) Observer #1 manual contours
(d) Observer #3 Contour
manually drawn contours as shown in Figure
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
be used to compare to the outputs from existing
Original Image (b) Observer #1 manual contours
Observer #3 Contour
manually drawn contours as shown in Figure
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
be used to compare to the outputs from existing
Original Image (b) Observer #1 manual contours
Observer #3 Contour
manually drawn contours as shown in Figure 4.9 (b)
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
be used to compare to the outputs from existing
(b)-
(d), a sampling of points is taken from each curve and averaged in order to produce a ground
(a)
Figure 4.10
) ACM at 560 iteration
(c) ARM
Figure 4.10 A segmentation comparison between the ACM, ARM and WB
at 560 iterations (b
A segmentation comparison between the ACM, ARM and WB
73
s (b
A segmentation comparison between the ACM, ARM and WB
73
s (b) Average Inter
A segmentation comparison between the ACM, ARM and WB
) Average Inter-observer manual segmentation
(d) WB-
A segmentation comparison between the ACM, ARM and WB
observer manual segmentation
-GARM
A segmentation comparison between the ACM, ARM and WB
observer manual segmentation
A segmentation comparison between the ACM, ARM and WB-GARM
observer manual segmentation
74
4.5.1.1 Statistical analysis of results for specimen 1
(a) 195 boundary points in the ground truth (b) Boundary point comparison
Figure 4.11 Boundary point comparison for Specimen 1. Figure 4.11(a) A display of the
number of unique boundary points found in each curve of the source images ground truth.
Boundary points are estimated and plotted based on the following rule: where the curves path
changes direction, a boundary point is plotted. A straight line only has two points (the beginning
and end) but a curve may have many points where the path of the curves line changes. Figure
4.11 (b) A comparison of the number of the number of a segmentations curve points tht correctly
pass through those of the ground truth (ie. The number of boundary points correctly
segmentated).
Table 4.2 Table of Algorithmic comparisons
Algorithm % points on correct
Boundaries
% points outside correct
Boundaries
% of these. points within
3 pixels of boundaries
ACM 7 93 11.8
GARM 21.5 78.5 14.1
WB-GARM 92.3 7.7 40.3
Comparison of results
0
20
40
60
80
100
120
140
160
180
14
42
180
195
ACM
GARM
WBGARM
Gold
Standard
75
As may be observed above, the ACM performed the least well on this specimen. This comes as
no surprise as the algorithm was not designed for use in complex texture segmentation
applications. GARM, which has been shown to work reasonably well with synthetic texture
images performed a little better, however neither of these were able to achieve a segmentation as
close to the average of the intra-observer contours as the WB-GARM model. A combination of
application-specific thresholding and sharp mixed-model texture descriptors helped it achieve a
92% closeness to the gold standard.
4.5.1.2 The effects of contrast-adjustment on segmentation
quality
It has been shown that certain medical images including both colonoscopy [107] and colposcopy
[108] categories can benefit from using contrast and brightness adjustment to improve the
visibility of images prior to using them in computational processing. While this has been touched
upon through in-class contrast adjustment and optional source-adjustment (unsharp masks), the
results from experiments on the medical-image dataset were done independent of further contrast
changes as this allowed the presentation of additional benefits of using the WB-GARM with
other morphological image enhancement techniques.
Our experiments with texture descriptors in the GARM have concluded that applying contrast
adjustments to a histopathological image as part of a pre-processing stage may enhance the
quality of some segmentation results. For this reason, contrast adjustments comparing (1) The
GARM, (2) The WB-GARM and (3) the ground truth of an original image with contrast applied
will also be presented. The first example of contrast adjusted presented below will demonstrate a
case where contrast adjustment does not offer a large improvement with all subsequent examples
featuring contrast adjustment demonstrating the benefits of this adjustment.
76
(a) GARM after 200 iterations (w/Contrast) (b) WBGARM after 200 iterations (w/Contrast)
(c) Contrast adjusted ground Truth (190 pts) (d) Correct boundary-point comparison
Figure 4.12 Comparison of results after contrast adjustment. As can be observed, the
results in Figure 4.12(a) and Figure 4.12 (b) appear at first glances to be quite similar. Although
the WB-GARM offers very minor improvements, this example does not contain a lot of low-
level contrast differences and thus does not hugely benefit from the adjustment.This version of
the implementation does not include an additional threshold filter for artefacts surrounding the
glands a feature which offers some further improvements and is presented visually shortly.
`
Comparison of results
0
20
40
60
80
100
120
140
160
180
63
102
190
GARM
WBGARM
(wi thout
threshol d-
i ng)
Gol d
Standard
Table 4.
Algorithm
GARM
WB
4.5.2
Table 4.3 Comparison table
Algorithm
ARM
WB-GARM
4.5.2 Specimen 2
(a) Original Image
(c)
Comparison table
% of points passing
through correct
boundaries
33.1
53.6
Specimen 2
Original Image
(c) ACM
Comparison table for segmentation results after contrast adjustment
oints passing
through correct
boundaries
Specimen 2
Original Image
77
for segmentation results after contrast adjustment
oints passing % of points outside
correct boundaries
66.9
46.4
77
for segmentation results after contrast adjustment
% of points outside
correct boundaries
for segmentation results after contrast adjustment
% of points outside
correct boundaries
% of points that are within
3 pixels of the boundaries
13.6
19.4
(b)
(d)
for segmentation results after contrast adjustment
% of points that are within
3 pixels of the boundaries
13.6
19.4
Ground truth
(d) GARM
% of points that are within
3 pixels of the boundaries
Ground truth
% of points that are within
3 pixels of the boundaries
78
(e) WBGARM
Figure 4.13 Segmentation comparison
4.5.2.1 Statistical analysis of results for specimen 2
(a) 132 boundary points in the ground truth (b) Correctly segmented points
Figure 4.14 Boundary point comparison
Algorithmic Comparison
0
20
40
60
80
100
120
11
24
71
132
ACM
GARM
WBGARM
Gol d
Standard
Table 4.
Algorithm
ACM
GARM
WB
In a simila
areas of interest in the foreground
a large quantity of erroneous segmentations in the lower half
GARM
the
used.
4.5.2.2
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
low
emphasize the borders and
Table 4.4 Table of Algorithmic Comparisons
Algorithm
ACM
ARM
WB-GARM
In a similar case to the first specimen, the ACM was unable to form contours around the key
areas of interest in the foreground
a large quantity of erroneous segmentations in the lower half
GARM was successfully able to segment the lumen with a reasonable level of accuracy whilst
the GARM only formed contours around lumen within a short proximity of the texture samples
used.
4.5.2.2 Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
low-intensity areas of the image were further enhanced by applying
emphasize the borders and
(a) GARM after 150 iterations (b) WB
Table of Algorithmic Comparisons
% points on correct
Boundaries
8.3
18.1
53.8
r case to the first specimen, the ACM was unable to form contours around the key
areas of interest in the foreground
a large quantity of erroneous segmentations in the lower half
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
intensity areas of the image were further enhanced by applying
emphasize the borders and
(a) GARM after 150 iterations (b) WB
Table of Algorithmic Comparisons
% points on correct
oundaries
r case to the first specimen, the ACM was unable to form contours around the key
areas of interest in the foreground (ie. t
a large quantity of erroneous segmentations in the lower half
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
intensity areas of the image were further enhanced by applying
emphasize the borders and lymphocytes
(a) GARM after 150 iterations (b) WB
79
Table of Algorithmic Comparisons
% points on correct % points outside correct
Boundaries
92.7
81.9
46.2
r case to the first specimen, the ACM was unable to form contours around the key
(ie. the lumen). Both the GARM and the WB
a large quantity of erroneous segmentations in the lower half
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
intensity areas of the image were further enhanced by applying
lymphocytes around each area of lumen.
(a) GARM after 150 iterations (b) WB
79
% points outside correct
Boundaries
r case to the first specimen, the ACM was unable to form contours around the key
n). Both the GARM and the WB
a large quantity of erroneous segmentations in the lower half
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
intensity areas of the image were further enhanced by applying
around each area of lumen.
(a) GARM after 150 iterations (b) WB
% points outside correct
r case to the first specimen, the ACM was unable to form contours around the key
n). Both the GARM and the WB
a large quantity of erroneous segmentations in the lower half of the image, however
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
intensity areas of the image were further enhanced by applying a darkening filter to
around each area of lumen.
(a) GARM after 150 iterations (b) WB-GARM after 150 iterations
% of these. points within 3
pixels of boundaries
3.3
16.8
21.6
r case to the first specimen, the ACM was unable to form contours around the key
n). Both the GARM and the WB-GARM
of the image, however
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
a darkening filter to
GARM after 150 iterations
% of these. points within 3
pixels of boundaries
r case to the first specimen, the ACM was unable to form contours around the key
GARM formed
of the image, however the WB-
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
a darkening filter to
GARM after 150 iterations
% of these. points within 3
r case to the first specimen, the ACM was unable to form contours around the key
formed
was successfully able to segment the lumen with a reasonable level of accuracy whilst
ARM only formed contours around lumen within a short proximity of the texture samples
Improvements obtained through contrast adjustment
The morphological operations applied to the sample for this experiment include the following: A
40% increase in contrast was applied to the specimen with a 20% increase in brightness. The
80
(c) 135 ground-truth boundary points (d) WBGARM after 150 iterations
Figure 4.15 - Comparison of results after contrast adjustment
Table 4.5 Comparison table after contrast adjustment
Algorithm % of points passing
through correct
boundaries
% of points outside
correct boundaries
% of these points that are
within 3 pixels of the
boundaries
GARM 5.1 95.9 10.9
WB-GARM 69.6 30.4 14.6
The contrast adjusted Specimen 2 offers more insights into the GARM's pre-processing
dependence in order to be effective on this application's distribution of images. The GARM on
its own is unfortunately insufficient for segmenting this type of medical image without further
assistance. In retrospect, the WB-GARM (while forming many incorrect segmentations), did
manage to form perfect contours in some cases with 87 more points falling on the boundary than
with the GARM.
Comparison of results
0
20
40
60
80
100
120
7
94
135
GARM
WBGARM
(without
thresholding)
Gold
Standard
81
4.5.3 Specimen 3
(a) Original Image (b) Ground truth
(c) Active Contour Model (d) Active Region Model
(e) WB-GARM
Figure 4.16 Segmentation comparison
82
4.5.3.1 Statistical analysis of results for Specimen 3
(a) 222 boundary points in ground truth (b) Boundary point comparison
Figure 4.17 Boundary point comparison
Table 4.6 Table of Algorithmic Comparisons
Algorithm % points on correct
Boundaries
% points outside correct
boundaries
% of these. points within
3 pixels of boundaries
ACM 9 91 4
GARM 29.2 70.8 10.1
WB-GARM 72.9 27.1 20.8
With more points on the boundaries than any of the previous specimens, this could be considered
the most texturally complex slide tested so far. From a lumen-segmentation perspective, the
Active Region model performed quite poorly, incorrectly capturing parts of the background after
150 iterations. In comparison to the ACM and GARM the WB-GARM performs quite well,
creating reasonably promising contours around the main areas of lumen. There is however some
room for improvement here as a desirable percentage of correct boundary points segmented
would be closer to that of Specimen 1.
Comparison of results
0
50
100
150
200
20
65
162
222
ACM
GARM
WBGARM
Gol d
Standard
4.5.3.2
4.5.3.2 Improvements obtained through contrast adjustment
(a) G
(c) Ground truth
Improvements obtained through contrast adjustment
GARM results
nd truth of contrast adjusted source
Figure 4.1
Improvements obtained through contrast adjustment
ARM results after contrast adjustment (b
of contrast adjusted source
Figure 4.18 - Comparison of results after contrast adjustment
83
Improvements obtained through contrast adjustment
er contrast adjustment (b
of contrast adjusted source 229 points
Comparison of results after contrast adjustment
83
Improvements obtained through contrast adjustment
er contrast adjustment (b) WB
229 points
Comparison of results after contrast adjustment
0
50
100
150
200
Improvements obtained through contrast adjustment
) WB-GARM results on contrast
229 points (d) Boundary
Comparison of results after contrast adjustment
Comparison of results
12
Improvements obtained through contrast adjustment
results on contrast
Boundary- comparison
Comparison of results after contrast adjustment
Comparison of results
138
229
Improvements obtained through contrast adjustment
results on contrast adjustment
comparison
GARM
WBGARM
(without
thresholding)
Gold
Standard
Improvements obtained through contrast adjustment
adjustment
WBGARM
thresholding)
Table
Algorithm
GARM
WB
This set of results requires ana
segments contour points falling on the majority of th
model creates a reasonable result with fewer e
WB
segmenting lumen than it's counterpart
forms far fewe
more free of i
4.5.4
Table 4.7 Comparison table for segmentati
Algorithm
ARM
WB-GARM
This set of results requires ana
segments contour points falling on the majority of th
model creates a reasonable result with fewer e
WB-GARM model (with 138 corre
segmenting lumen than it's counterpart
forms far fewer error contours than the WB
more free of incorrect segmentation artefacts.
4.5.4 Specimen 4
Comparison table for segmentati
% of points passing
through correct
boundaries
5.2
60
This set of results requires ana
segments contour points falling on the majority of th
model creates a reasonable result with fewer e
model (with 138 corre
segmenting lumen than it's counterpart
r error contours than the WB
ncorrect segmentation artefacts.
Specimen 4
(a) Original Image
Comparison table for segmentati
of points passing
through correct
boundaries
This set of results requires analysis from two perspectives: (a)
segments contour points falling on the majority of th
model creates a reasonable result with fewer e
model (with 138 correct boundary points) performs a significantly better job of
segmenting lumen than it's counterpart
r error contours than the WB
ncorrect segmentation artefacts.
Specimen 4
(a) Original Image
84
Comparison table for segmentation results after contrast adjust
of points passing % of points outside
correct boundaries
97.5
40
lysis from two perspectives: (a)
segments contour points falling on the majority of th
model creates a reasonable result with fewer error contours. In respect to (a) it is clear that the
ct boundary points) performs a significantly better job of
segmenting lumen than it's counterpart however, with respect to the second point, the
r error contours than the WB-GARM
ncorrect segmentation artefacts.
84
on results after contrast adjust
% of points outside
correct boundaries
lysis from two perspectives: (a)
segments contour points falling on the majority of the lumen
rror contours. In respect to (a) it is clear that the
ct boundary points) performs a significantly better job of
however, with respect to the second point, the
GARM creating a reasonable result that is much
on results after contrast adjust
% of points outside
correct boundaries
% of these points that are
within 3 pixels of the
boundaries
8.2
12.3
lysis from two perspectives: (a) which algorithm
e lumen-nuclei boundaries and (b)
rror contours. In respect to (a) it is clear that the
ct boundary points) performs a significantly better job of
however, with respect to the second point, the
creating a reasonable result that is much
(b) Ground truth
on results after contrast adjustment
% of these points that are
within 3 pixels of the
boundaries
8.2
12.3
algorithm more correctly
nuclei boundaries and (b)
rror contours. In respect to (a) it is clear that the
ct boundary points) performs a significantly better job of
however, with respect to the second point, the
creating a reasonable result that is much
Ground truth
% of these points that are
within 3 pixels of the
more correctly
nuclei boundaries and (b) which
rror contours. In respect to (a) it is clear that the
ct boundary points) performs a significantly better job of
however, with respect to the second point, the GARM
creating a reasonable result that is much
% of these points that are
more correctly
which
rror contours. In respect to (a) it is clear that the
ARM
(c) ACM
Figure 4.1
85
(c) ACM
(e) WB-
Figure 4.19 Segmentation comparison
85
-GARM
Segmentation comparison
Segmentation comparison
(d) GARM GARM
86
4.5.4.1 Statistical analysis of results on Specimen 4
(a) 312 boundary points in ground truth (b) Boundary point comparison
Figure 4.20 Boundary point comparison
Table 4.8 Table of Algorithmic Comparisons
Algorithm % points on correct
Boundaries
% points outside correct
Boundaries
% of these. points within
3 pixels of boundaries
ACM 7 93 5
GARM 29.1 70.9 13.76
WB-GARM 85.8 14.2 68.18
Due to the widespread occurrence of indentations along the borders of lumen in Specimen 4,
there was an increase in the number of points required to define the ground truth boundaries.
This raised the quality level required by any segmentation algorithm as there was a tightened
restriction on how deviated a contour could be and still fall within a reasonable number of
boundary points to be considered promising. The quality of the GARMs result becomes a little
more clear and despite creating contours of average quality around the main areas of interest,
their sporadic nature and discontinuous properties fail to make them an adequate model for use
in medical applications. Once again, the ACM demonstrates that although it is a worthy tool in
Comparison of results
0
50
100
150
200
250
300
22
91
268
312
ACM
GARM
WBGARM
Gol d
Standard
87
simple segmentation tasks, this is not an area where they can excel without alteration. Unlike the
other two models, the WB-GARM manages to create an acceptable result with only a small
quantity of uncaptured areas. Its contours pass through 85.8% of the stringent points laid down
by the vertices and could be used in real-world applications with minor improvements.
4.5.4.2 Improvements obtained through contrast adjustment
(a) GARM Contrast Result (b) WB-GARM result after contrast adjustment
(c) 245 Boundary points in ground truth (d) Boundary comparison
Figure 4.21 Comparison of results after contrast adjustment
Comparison of results
0
50
100
150
200
117
153
245
GARM
WBGARM
(without
thresholding)
Gold
Standard
88
Table 4.9 Comparison table of segmentation results after contrast adjustment
Algorithm % of points passing
through correct
boundaries
% of points outside
correct boundaries
% of these points that are
within 3 pixels of the
boundaries
GARM 47.7 52.3 13.26
WB-GARM 62.4 37.6 16.9
4.5.5 Specimen 5
(a) Original Image (b) Ground truth
89
(c) ACM (d) GARM
(e) WB-GARM
Figure 4.22 Segmentation comparison
90
4.5.5.1 Statistical analysis of results for Specimen 5
(a) 398 boundary points in ground truth (b) Boundary comparison
Figure 4.23 Boundary comparison
Table 4.10 Table of Comparative Results
Algorithm % points on correct
boundaries
% points outside correct
boundaries
% of these. points within
3 pixels of boundaries
ACM 7.7 92.3 3.7
GARM 19.8 80.2 19.1
WB-GARM 83.4 16.6 37.7
The GARM performed better with this specimen than it did with some of the prior tests.
Unfortunately due to the complexity of the lumen borders and the increased resolution of each
area to be captured, it was unable to meet the criteria for falling on the majority of the 398
boundary points of indentation in the ground truth. The WB-GARM, however, managed to fall
through 83.4% of these points with minimal error-artefacts being captured in the foreground.
Comparison of results
0
50
100
150
200
250
300
350
31
79
332
398
ACM
GARM
WBGARM
Gold
Standard
91
4.5.5.2 Improvements obtained through contrast adjustment
(a) GARM Result after contrast adjustment (b) WB-GARM Segmentation after
contrast adjustment
(c) 395 boundary points in contrast adjusted (d) Boundary comparison
ground truth
Figure 4.24 - Comparison of results after contrast adjustment
Comparison of results
0
50
100
150
200
250
300
350
54
263
395
GARM
WBGARM
(without
thresholding)
Gold
Standard
92
Table 4.11 Comparison table for segmentation results after contrast adjustment
Algorithm % of points passing
through correct
boundaries
% of points outside
correct boundaries
% of these points that are
within 3 pixels of the
boundaries
GARM 13.67 86.33 8.2
WB-GARM 66.5 33.5 12.3
Once again, we are presented with two segmentations of varying quality. The strict nature of the
evaluation technique being used leaves many of the GARM contours (which fall on the incorrect
boundary) not being counted, resulting in a poor pass-through rating. The WB-GARM here
performs to a higher level of accuracy but is not as high as the previous non-contrast experiment.
This is still a usable result which highlights the WB-GARMs ability to perform well with and
without external morphological operations outside of those within the model itself. Overall
across both tests, the WB-GARMs demonstrates that it is capable of providing improved
segmentation results over those offered by both the ACM and the GARM.
4.6 Overview and discussion of results
Figure 4.25 - Percentage of correctly segmented boundary points a distribution comparison
0
10
20
30
40
50
60
70
80
90
100
Sample 1 Sample 2 Sample 3 Sample 4 Sample 5
ACM
GARM
WB-GARM
93
4.6.1 Summary of the algorithms performance
As can be observed in Figure 4.13, the above results which have been evaluated using boundary-
point vertex models based on the average intra-observer contours, show a clear indication that
the new Geodesic WB-GARM offers a significant improvement in lumen segmentation of the
colon glands than the other two models analysed. The advantages attained by the description
enhancements provided by the Wavelet Packet basis are further reaffirmed by the WB-GARMs
ability to perform well in both original and contrast-adjusted colour spaces. From both visual and
quantitive analysis, the results appear to be promising.
4.6.2 Areas for improvement
Certain results still appear to be affected by minor misclassifications of the foreground, resulting
in minor error-contours. While the majority of these artefacts have been effectively handled
using initial speckle thresholding, there is still a lot of room for improvement. One area where
improvements could be made is speckle thresholding, which could be advanced to include
adaptive matrices with more complex intensity maps to increase the probability of successfully
cleaning of the human colon tissue samples prior to segmentation being initialised.
4.6.3 Summary
The approach for image segmentation previously proposed has been adapted to solve the
problem of glandular lumen segmentation of human colon tissue. Our approach uses a
combination of boundary and region forces coupled with enhanced Wavelet Packet texture
descriptors which allow us to more clearly define detailed boundary information than the original
source algorithm, the Geodesic Active Region Model. The resulting framework, the WB-GARM
model has been optimized for use on the particular application of lumen segmentation with the
inclusion of exterior speckle thresholding for further improved results. Based on a median
performance rating of 83.4% (the closest to a perfect result achieved was 92.5%), The WB-
GARM seems to be a good candidate for usage on real-world histology images and would offer a
resourceful computational alternative for segmenting lumen in histopathlogical applications.
94
Chapter 5
Thesis Summary and Conclusions
5.1 Summary
The subjects of this thesis are: (i) the proposal of a Wavelet-based texture descriptor with
boundary enhancement for use in texture segmentation applications and (ii) the effects of this
texture descriptor when compared to the conventional unenhanced Gabor filters found in an
existing region-based segmentation approach - the Geodesic Active Region model. This
comparison is made in particular between the segmentation results of the newly presented
method and the GARM's untouched Gabor filters on a set of grayscale histopathlogical images,
where the improvements offered by the new method are promising.
Chapter 2 investigated existing supervised methods used to segment textured images. A
summary of these included discussions of edge-based, region-based and finally contour-based
segmentation models which are prevalent in medical imaging for the past few years. In reference
to snake-based models - Active Contour Model and Geodesic Active region model were
reviewed in great detail as they which directly relate to new texture descriptor proposed in this
thesis. The latter, GARM is used as part of a demonstration on how the new texture descriptors
can be used in conjunction with existing Gabor filter texture descriptors to provide an improved
segmentation solution. Morphological image enhancement methods such as unsharp masks and
sharpening were also illustrated in this chapter as part of an investigation into techniques for
improving the visibility of object boundaries inside a source image.
Chapter 3 introduced a new Wavelet-based texture descriptor with boundary enhancement which
is the methodology proposed in this thesis. The chapter began by detailing Wavelet-theory
including forward and inverse Wavelet and Wavelet Packet transforms. Due to their multi-scale
nature these were found to provide a wider set of edge and boundary information than other
edge-detection methods. It was also shown that wavelet packets are capable of representing some
95
of the primary edges of image objects in such a way their features may be morphologically
altered to generate a set of images containing only region outlines. Sample "patches" from
images in this set were then taken and combined via a pixel additional operation with equivalent
patches from the foreground samples supplied to the Gabor kernels in the GARM. This
effectively results in a segmentation approach which is then, rather than simply segmenting a
source image, is segmenting an image whose primary region and boundary information will be
further taken into account yielding improved segmentation.
In Chapter 4 a series of experiments was carried out to investigate and validate the wavelet
packet texture descriptors outlined in Chapter 3. Segmentation tests were performed on sets of
both real-world and medical images with a heavier focus being placed on the latter due to the
emphasis placed in this thesis on improving the quality of histopathological image
segmentations. The results of these experiments confirmed that boundary enhancement of images
by means of wavelet packets can have a significant impact on the quality and accuracy of a 2-
class texture segmentation problem with interesting improvements made in comparison to both
the ACM and GARM. Having established that the proposed method had a positive effect on
snake, boundary and region-based segmentation quality, the next step was to assess the estimated
amount of improvement offered over existing methods. For this purpose ground truth images
based on the average of three externally hand-segmented sources were treated as a series of
deformed points.
Results from the ACM, GARM and WB-GARM were then evaluated based on the quantity of
these points through which their segmented foreground boundaries passed through successfully.
This test concluded that the proposed wavelet based texture descriptors resulted in an improved
segmentation in each of the tests presented when compared to the other two methods being
evaluated. A relationship between the contrast of histopathlogical images and segmentation
quality was also found to affect segmentation accuracy and once established, this was shown in
some instances to provide further improvements in the segmentation quality.
96
5.2 Conclusions
This thesis has investigated the effects of multi-scale wavelet packet sub-bands with boundary
enhancement on the quality of a texture segmentation using an existing model - the Geodesic
Active Region Model. Both of these factors combined together have been shown to positively
affect the output of a texture segmentation algorithm such that a significant increase in
segmentation accuracy may be observed in many cases. To the authors knowledge, the above
points have not been explicitly addressed previously as part of a combined boundary
enhancement routine in texture image segmentation previously.
As part of a supervised segmentation problem, the WB-GARM was demonstrated in both normal
and contrast-based cases as having improved the accuracy of texture segmentation when
compared to the output generated by existing models and texture descriptors when applied to the
same image. This was shown to be true for a variety of images and it was concluded that wavelet
packet texture descriptors could offer a computationally inexpensive means of improving
segmentation results in contour based segmentation models. As with the GARM, the WB-
GARM does not perform well with source images of a very poor quality, however as mentioned,
they are capable of producing segmentations of a higher degree of accuracy with images of a
respectable quality.
A texture descriptor has been modified to take into account additional hidden boundary and edge
information from a source image through wavelet packet sub-bands. Through empirical
observations, this has been used to create a segmentation enhancement routine which may be
used as a pre-processing step. The application of this texture descriptor to textured images of
varying size and type reduced the segmentation error associated with using the conventional
segmentation model. In addition, the relative increase in segmentation quality suggests that this
method has the potential to improve the image segmentation of pictures across a variety of
different applications including the glandular segmentation of colon biopsy images and object
selection in laser-guided surgery.
Future work in this area could see the introduction of an algorithm for intelligently selecting the
most descriptive wavelet packet sub-bands for use as part of the proposed texture descriptor -
this could include the best basis if a cost function was supplied for a particular application or
97
image type. The current selection method uses a fixed set of sub-bands from different scales for
each segmentation, however, narrowing this down to only those sub-bands which provide the
most useful edge and boundary information could offer further improvements in segmentation
quality with textured images. This would allow the WB-GARM to become an even more
powerful tool for accurate texture segmentation.
98
Bibliography
1.K. Tingelhoff, K.E.G. Eichjorn -"Analysis of manual segmentation in paranasal CT
images", In European Archives of Oto-Rhino-Laryngology. Springer, Berlin. Volume
265, Pages 1061-1070. September. 2008.
2.Liapis, S., Sifakis, E. and Tziritas, G - "Colour and texture segmentation using wavelet
frame analysis, deterministic relaxation and fast marching algorithms" In Journal of
Visual Communication and Image Representation, Volume 15, Pages 1-26, 2004.
3.Y. Sinal Akgul -"Image Guided Surgery", Video/Image Modelling and Synthesis Lab,
Dept. Computer Science and Information Sciences, Delarware, Newark, Delware 19716.
4.R.S. Brindle, "Serial Composition", Oxford University Press, 1966.
5.R. Azencott, J. Wang, L. Younes - "Texture Classification using Windowed Fourier
Filters", In IEEE Transactions on Pattern Analysis and Machine Intelligence archive,
Volume 19, Issue 2, Pages 148-153, 1997.
6.J. O. Smith III - "Mathematics of the Discrete Fourier Transform (DFT)", W3K Publishing,
2007.
7.A.Jenoubi, A. Jianchao Zeng, Chouikha, M.F - Top-down approach to segmentation of
prostate boundaries in ultrasound images . In Proceedings of the 33rd Applied Imagery
Pattern Recognition Workshop. Pages 13-15. Oct. 2004
8.L. Li, D. Chen, S. Lakare, K. Kreeger, I. Bitter, A. Kaufman, M. R. Wax, P. M. Djuric, Z.
Liang - " An Image Segmentation Approach to Extract Colon Lumen through Colonic
Material Tagging and Hidden Markov Random Field Model for Virtual Colonoscopy ,"
In SPIE 2002 Symposium on Medical Imaging, San Diego, CA, USA, February 2002
9.A.Todman, R. Naguib, M. Bennen - Visual characteristics of colon images. IEEE
CCECE, 2001.
10. K.Brady, I.Jermyn, J.Zerubia - "Adaptive probabilistic models of wavelet packets for the
analysis and segmentation of textured remote sensing images", British Machine Vision
Conference, 2003
11. Y.Meyer, R.Coifman - "Wavelets", In Cambridge Studies in Advanced Mathematics,
Volume 48, Cambridge University Press, Cambridge, 1997.
12. V. Caselles, F. Catte, T. Coll, et al - "A Geometric Model for Active Contours in Image
Processing", In umerische Mathematik, Pages: 1-31 October 1993.
13. Rafael C. Gonzalez, "Digital Image Processing Using Matlab", Prentice Hall, 12 Feb
2004.
14. G.Mu, H.Zhai, S. Zhang - "Non-linearly weighted fuzzy correlation for colour-image
retrieval", In Chinese Optics Letters, Volume 1, Issue 10, Pages: 583-584. 2003.
15. Pichumani, R - Model-based vision, URL:
http://www.visionbib.com/bibliography/match597.html#TT45493, CV-Online, 1997.
16. N.R, S. Marshall. - "The use of genetic algorithms in morphological filter design". In
Signal Processing: Image Communication, Volume 8, Pages: 55-71, Jan 1996.
17. S.C.Zhu - "Region Competition: Unifying Snakes, Region Growing, and Bayes/MDL for
Multiband Image Segmentation", In IEEE Transactions on Pattern Analysis and Machine
Intelligence, Volume 18, Pages: 884-900, 1996
18. E. Wesley, W. E. Snyder, H. Qi - "Machine Vision", Cambridge University Press,
Cambridge, UK, 2004.
99
19. H. Choi, R. Baraniuk - "Analysis of wavelet-domain Wiener filters", In Proceedings of
IEEE--SP International Symposium on Time-frequency and Time-scale Analysis, Pages:
613-616, October 1998.
20. J. Chen, T. N. Pappas, A. Mojsilovic, B. E. Rogowitz - "Adaptive perceptual colour-
texture image segmentation," In IEEE Trans. Image Processing, Volume 14, Pages:
1524-1536, Oct. 2005.
21. F. W. Campbell, J. G. Robson - "Application of Fourier analysis to the visibility of
gratings,", Journel of Physiolology (London), Volume197, Pages 551-566, 1968.
22. S.J. Osher , J. A. Sethian - "Fronts propagating with curvature dependent speed:
algorithms based on Hamilton-Jacobi formulations", In Journal of Computational
Physics, Pages: 12-49, 1988
23. Gonzalez, R. C.Woods - "Digital Image Processing, First Edition" Addison-Wesley,
1992.
24. Y.Mallet, D. Coomans, J. Kautsky, O. De vel - "Classification using Adaptive Wavelets
for Feature Extraction", In IEEE Transactions on Pattern Analysis and Machine
Intelligence, Volume 19, No. 10, Pages: 1058-1066, October 1997.
25. L.Zhang, D. Zhang - Characterization of palmprints by wavelet signatures via
directional context modeling", In IEEE Transactions on System, Man and Cybernetic,
Part B. Volume 34, Pages: 1335-1347, June, 2004.
26. A.H Bhalerao, R. Wilson Unsupervised image segmentation combing region and
boundary estimation, in IVC Volume 19 umber 6, Pages: 353-368, April 2001.
27. Qian, Y.T, Zhao, R.C - "Image Segmentation Based on Combination of the Global and
Local Information", In ICIP97, Volume 1, Pages: 204-207, 1997.
28. W.A Perkins - "Region segmentation of Images by Expansion and Contraction of Edge
points", In IJCAI79, Pages: 699-701, 1979.
29. A.Gouze, C. De Roover, A. Herbulot, E. Debreuve, B. Macq and M. Barlaud -
"Watershed-driven active contours for moving object segmentation". In IEEE
International Conference on Image Processing, September 2005.
30. T.Abe, Y.Matsuzawa - "Region Extraction with Multiple Active Contour Models". In
Workshop on Digital and Computational Video. Pages 56-63. 2001
31. R. J. Lapeer, A. C. Tan, R. Aldridge - "Active Watersheds: Combining 3D Watershed
Segmentation and Active Contours to Extract Abdominal Organs from MR Images". In
MICCAI. Pages: 596-603. 2002.
32. M. Kass, A. Witkin, D. Terzopoulos - "Snakes: active contour models". In First
International Conference on Computer Vision, Pages 259-268, 1987.
33. S. J. Osher , J. A. Sethian - "Fronts propagating with curvature dependent speed:
algorithms based on Hamilton-Jacobi formulations", In Journal of Computational
Physics, Pages: 12-49, 1988.
34. L.D Cohen, R.Kimmel - Global Minimum for Active Contour Models: A Minimal Path
Approach, International Journal of Computer Vision.", 1997.
35. V. Caselles, F. Catte, T. Coll, et al - "A Geometric Model for Active Contours in Image
Processing", In umerische Mathematik, Pages: 1-31 October 1993.
36. R. Malladi, J. Sethian, B. Vemuri - "Shape modeling with front propagation: a level set
approach", In IEEE Trans. Pattern Anal. Machine Intelligence, Volume 17, Pages: 158-
175. 1995.
37. G.A. Giraldi, L.M Gonalves, A.F Oliveira - "Dual topologically adaptable snakes", In
Proceedings of the Fifth Joint Conference on In-formation Sciences (JCIS'2000, Vol. 2),
Third In-ternational Conference on Computer Vision, Pattern Recognition, and Image
Processing, Pages: 103-106, February 2000.
100
38. H. Delingette, J. Montagnat - "Shape and topology constraints on parametric active
contours", Computer Vision and Image Understanding, Volume. 83, Pages 140-171,
2001.
39. J.S Suri, A.Farag Deformable Models: Theory and Biomedical Applications,
Pages:35-38, Springer, 2007.
40. M. Kim , J. Choi , D. Kim - "A VOP generation tool: automatic segmentation of moving
objects in image sequences based on spatio-temporal information. Circuits and Systems
for Video Technology", In IEEET. Volume 8, December 1999.
41. J.A Sethian, Hogea.- "Computational Modelling of Solid Tumor Evolution via a General
Cartesian Mesh/level set method", In Fluid Dynamics & Materials Processing, Volume.
1, February 2005.
42. G. Aubert , L. Blanc Fraud -"Some remarks on the equivalence between classical snakes
and geodesic active contours", In International Journal of Computer Vision, Volume 34,
1999.
43. P. Kornprobst, R.Deriche, G.Aubert - "Image Sequence Restoration: A PDE Based
Coupled Method for Image Restoration and Motion Segmentation". In Proceedings of the
5th European Conference on Computer Vision, Volume 2, Pages: 548-562, 1998.
44. S.Kichenassamy, A.Kumar, A J. Yezzi - "Gradient Flows and Geometric Active Contour
Models", In Proceedings of the Fifth International Conference on Computer Vision,
Pages: 810-815, 1995.
45. N. Paragios, O. Mellina-Gottardo, and V. Ramesh -"Gradient vector flow fast geometric
active contours". In IEEE Trans. Pattern Anal. Machine Intelligence, Volume 1, Pages:
67-73, 2004.
46. T. Chan and L. Vese - An active contour model without edges, In International
Conference on Scale-Space Theories in Computer Vision, Pages 141-151, 1999.
47. D. Mumford, J. Shah- "Boundary detection by minimizing functionals". In Proceedings
of IEEE ICASSP, Pages: 22-26, 1985.
48. A. Chakraborty, L. H. Staib, J. S. Duncan - "An Integrated Approach to Boundary
Finding in Medical Images", In IEEE Workshop on Biomedical Image Analysis, Pages:
13-22, 1994.
49. N. Paragios, R. Deriche - "Geodesic Active regions for Supervised Texture
Segmentation". In IEEE International Conference on Computer Vision (ICCV), Pages:
926-932, Corfu, Greece, 1999.
50. N. Paragios, R. Deriche - "Geodesic Active Regions: A New Framework to Deal with
Frame Partition Problems in Computer Vision", In Journal of Visual Communication and
Image Representation 13, Pages: 249- 268, 2002
51. T.Brox, M.Rousson, R. Deriche, J.Weickert - "Unsupervised segmentation incorporating
colour, texture, and motion" - In Computer Analysis of Images and Patterns, volume
2756 of Lecture Notes in Computer Science, 2003.
52. D. Cremers, T. Kohlberger, C. Schnorr - "Nonlinear Shape Statistics in Mumford-Shah
Based Segmentation". In European Conference on Computer Vision, Volume 2, Pages:
93-108, Copenhagen, Denmark, June 2002.
53. T. Brox, J. Weickert - "Level Set Segmentation with multiple regions". In IEEE
Transactions on Image Processing, Volume 15, Pages 3213-3218, 2006.
54. A. Cohen, I. Daubechies - "Non-separable bidimensional wavelet bases," In Revista
Matematica Iberoamericana, Volume 9, Pages: 51-137, 1993.
55. J. S. Duncan, N. Ayache - "Medical Image Analysis: Progress over Two Decades and the
Challenges Ahead," In IEEE Transactions on Pattern Analysis and Machine Intelligence,
Volume 22, Pages: 85-106, January 2000
101
56. C.P Lee, W.E. Snyder, C.Wang -"Supervised Multispectral Image Segmentation using
Active Contours", In International Conference on Automation and Robotics, Barcelona,
Pages: 4242- 4247, April, 2005.
57. W.E.L. Grimson, G.J. Ettinger, T. Kapur, M.E. Leventon, W.M. Wells III, R. Kikinis -
"Utilizing Segmented MRI Data in Image-Guided Surgery." In International Journal of
Pattern Recognition and Artificial Intelligence, Pages: 1367-1397, July 9
th
, 1996.
58. Gonzales, Woods. Digital Image Processing, Second Edition, Prentice Hall, January,
2002.
59. Imatest measurements: Image quality factors, Imatest, URL:
(http://www.imatest.com/docs/iqf.html)
60. J.Sachs, Sharpening filters. Digital Light and Colour, 1999.
61. E. Mach -Mach Bands On the effect of the spatial distribution of the light stimulus on
the retina Pages 253-71. 1865.
62. W.K. Pratt, J.Wiley & Sons, Digital Image Processing (second edition), Addison-
Wesley, New York, USA, 1991.
63. N. Paragios, R. Deriche - "Geodesic Active Regions: A New Framework to Deal with
Frame Partition Problems in Computer Vision", In Journal of Visual Communication and
Image Representation 13, Pages: 249- 268, 2002
64. W. E. Higgs, D.F. Dunn - Gabor filter design for multiple texture segmentation, In
Journal of Optical Engineering, Volume 35, Pages: 2852-2863,1996.
65. R.C. Staunton, M. Li - Unsupervised Texture Segmentation Based on Immune Genetic
Algorithms and Fuzzy Clustering, 8
th
International Conference on Signal Processing, In
IEEE ICSP'06, Volume 2, Pages: 957-961, November 2006.
66. R.R Coifman, Y. Meyer, M.V. Wickerhauser -"Wavelet analysis and signal processing,",
In In Wavelets and their Applications, Pages: 153-178, 1992.
67. N. Paragios, R. Deriche - Geodesic Active Contours for Supervised Texture
Segmentation. In IEEE Computer Society Conference Computer Vision and Pattern
Recognition, Volume 2, 1999.
68. Ian Kaplan -"Applying the Haar Wavelet Transform to Time Series Information" - URL:
http://www.bearcave.com/misl/misl_tech/wavelets/haar.html, Bearcave, February 2004.
69. F.H. Elfouly, M.I. Mahmoud, M.I. M. Dessouky, and Salah Deya - Comparison between
Haar and Daubechies Wavelet Transformations on FPGA Technology In International
Journal of Computer, Information, and Systems Science, and Engineering, Winter 2008.
70. D.F.Walnut - "An Introduction to Wavelet Analysis: With 88 Figures", Birkhuser
Boston, January 2004.
71. A. Jense, A. La Cour-Harbo - Ripples in Mathematics: The Discrete Wavelet
Transform, Springer, 2001.
72. A.Linderhead, S. Sjokvist, S.Nyberg, M.Uppsall, C. Gronwall, P.Andersson, D. Letalick
- Temporal analysis for land mine detection . In Proceedings of the 4th International
Symposium on Image and Signal Processing and Analysis (ISPA 2005), Pages: 389- 394.
September 2005.
73. L. Debnath - "Wavelet Transforms and their applications", Birkhauser Boston. November
2001.
74. C. T. Leondes -Medical Imaging Systems Technology / Analysis And Computational
Methods (V. 1). World Scientific Publishing Co Pte Ltd, 2005
75. J. Ivins, J. Porrill - Active Region Models For Segmenting Medical Images, First IEEE
International Conference on Image Processing (ICIP'94; Austin, Texas): Volume 2,
Pages: 227-231. November 1994.
102
76. A. Chakraborty, L. Staib, and J. Duncan - Deformable Boundary Finding in Medical
Images by Integrating Gradient and Region In-formation, In IEEE Trans. in Medical
Imaging, Volume 15, no. 6, Pages 859870, Dec. 1996.
77. R. Ronfard - Region-Based Strategies for Active Contour Models,. In International
Journal of Computer Vision, Volume. 2, Pages 229-251. January 1994.
78. M. Hernandez, A. Frang - Non-parametric geodesic active regions: method and
evaluation for cerebral aneurysms segmentation in 3DRA and CTA",
Spain Computational Imaging Lab, Department of Technology, Pompeu Fabra
University, Barcelona, 2007.
79. O.Ecabert, J.Thiran - "Variational Image Segmentation by Unifying Region and
Boundary Information," In 16th International Conference on Pattern Recognitio(n
ICPR'02). Volume 2, Page(s): 885 - 888, 2002
80. J. Bigun, G. H. Granlund, J. Wiklund. "Multidimensional orientation estimation with
applications to texture analysis and optical flow", In IEEE Transactions on Pattern
Analysis and Machine Intelligence, Pages: 775790, August 1991.
81. T. Brox, M. Rousson, R. Deriche, J. Weickert - Unsupervised segmentation
incorporating colour, texture, and motion. In IRIA, Technical Report 4760, March
2003.
82. D. Xiano, O. Jun -Study of Colour Image Enhancement Based on Wavelet Analysis, In
IPSJ Technical Reports, Volume 93. Pages: 35-40. 2006.
83. P. Sakellaropoulos, L.Costaridou, G. Panayiotakis - A Wavelet-based Spatially
Adaptive Method for Mammographic Contrast Enhancement. In Physics in Medicine
and Biology. Volume 48, Pages 787-803, 2003.
84. A. A. Michelson - Studies in Optics, University of Chicago Press, Chicago,
Illinois, USA, 1927
85. A. Marion, An Introduction to Image Processing, Chapman and Hall, Pages 242 244,
1991.
86. R.Fisher, S. Perkins, A. Walker and E. Wolfart, "Pixel Addition" URL:
http://homepages.inf.ed.ac.uk/rbf/HIPR2/pixadd.htm, Department of Informatics, The
University of Edinburgh, 2003.
87. C.Braccini, L.De Floriani, G.Vernazza - "Image Analysis and Processing", In 8th
International Conference (ICIAP '95), Springer, San Remo, Italy, September 1995.
88. D.A. Burkhardt and P. K. Fahey -Contrast Enhancement and Distributed Encoding by
Bipolar Cells in the Retina, In The Journal of europhysiology, Volume. 80, Pages
1070-1081, September 1998.
89. J.Becker - "Scanning Tunneling Microscope Computer Automation", In Surface Science,
Pages 200-209, 1987.
90. R.Owens - Spatial Domain methods.
URL:http://homepages.inf.ed.ac.uk/rbf/CVonline/LOCAL_COPIES/OWENS/LECT5/no
de3.html , University of Edinburgh, School of Informatics. 1997.
91. S.Pizer, J. Austin, R. Cromartie - Adaptive Histogram Equalization and its Variations.
In Computer Vision, Graphics and Image Processing. Volume 39. Number 3 Page:
355-368. 1987.
92. S.Wook, K. Lee, Y. Bae, K. Min, M. Kwon.- "Genetic classification of colorectal cancer
based on chromosomal loss and microsatellite instability predicts survival.", Clinical
Cancer Research, Seoul 137-701, Korea. (7):2311-22, 2002
93. K.Masood, N.M Rajpoot - Classification of Colon Biopsy Samples by Spatial Analysis
of a Single Spectral Band from its Hyperspectral Cube. In Proceedings Medical Image
Understanding and Analysis 2007.
103
94. K.Masood, N.Rajpoot, H.Qureshi, N.Rajpoot -"Hyperspectral Texture Analysis for Colon
Tissue Biopsy Classification", In International Symposium on Health Informatics and
Bioinformatics, Turkey 2007.
95. M.Sato, S. Lakare, M. Wan, A. Kaufman, Z. Liang, M. Wax - "An automatic colon
segmentation for 3D virtual colonoscopy". In IEICE Trans. Information and Systems,
Volume. E84-D, No. 1, Pages 201-208, 2001
96. A.Toddman, Naguib, M.K. Bennett, M.K - Visual characterisation of colon images, In
Proceedings of Medical Image Understanding and Analysis (MIUA 2001), Pages 161-
164. 2001.
97. R.L. Koretz - Malignant polyps: are they sheep in wolves' clothing?. In Ann Intern
Med. 118:63-8, 1993.
98. J.S Mandel, J.H Bond, T.R Church, D.C Snover, G.M Bradley, L.M Schuman, F Ederer -
"Reducing mortality from colorectal cancer by screening for fecal occult blood.
Minnesota Colon Cancer Control Study." - In Engl J Med, Volume 328, Issue 19,
Pages 1365-71. May 1993.
99. L.Li, D. Chen, S. Lakare, K. Kreeger, I. Bitter, A. Kaufman, M. R. Wax, P. M. Djuric,
and Z. Liang - "An Image Segmentation Approach to Extract Colon Lumen through
Colonic Material Tagging and Hidden Markov Random Field Model for Virtual
Colonoscopy ," In SPIE 2002 Symposium on Medical Imaging, San Diego, CA, February
2002.
100. L. Hong, A. Kaufman, T. Wei,M. Wax - "3D Virtual Colonoscopy", In Proc. Symposium
on Biomedical Visualization. Pages 26-32. 1995.
101. L. Chen, N. Tokuda and A. Nagai - Robustness of Regional Matching Over Global
Matching -Experiments and Applications to Eigenface-Based Face Recognition, :
Proceedings of 2001 International Conference on Intelligent Multimedia and Distance
Education, Pages 38-47, John Wiley & Sons, Inc, 2001.
102. A. Todman, R. Naguib, M. Bennen - Visual characteristics of colon images. IEEE
CCECE, 2001.
103. K. Chen, D. Wang, X. Liu - Weight adaptation and oscillatory correlation for image
segmentation, In IEEE Transactions on eural networks, Volume 11, Issue 5, Pages: 1106
-1123, September 2000.
104. L.P. Clarke, R.P. Velthuizen,M.A. Camacho, J.J. Heine- "MRI segmentation: methods
and applications.", In Magnetic. Resonance Imaging,Volume: 13, Issue: 3, Pages 343-36,
1995
105. R.M Summers, J.Yao, P.J Pickhardt, M.Franaszek, I.Bitter, D.Brickman, V.Krishna, J.R
Choi - "Computed tomographic virtual colonoscopy computer-aided polyp detection in a
screening population". In Gastroenterology. Pages 1832-1844. December 2005.
106. I.Bitter, R. Van Uitert, R.Summers - Detection of Colon Wall Outer Boundary and
Segmentation of the Colon Wall Based on Level Set Methods, International Conference of
the IEEE Engineering in Medicine and Biology Society. 2006.
107. Cao, Tavanapong, Li - Parsing and browsing tools for colonoscopy videos. In
Proceedings of the 12th annual ACM international conference on Multimedia New York,
NY, USA. Pages: 844 851. 2004
108. V. Raad, A. Bradley - "Active Contour Model Based Segmentation of Colposcopy
Images of Cervix Uteri Using Gaussian Pyramids". In 6th International Symposium on
Digital Signal Processing for Communication Systems (DSPCS'02), Sydney, Australia.
January, 2002