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A Wavelet-packet based Geodesic Active RegionModel (WB-GARM) for Glandular segmentationof histopathology images
Adnan Osmani B.S.c
Supervisor: Dr. asir M. Rajpoot
Department of Computer Science,University of Warwick,Coventry CV4 7AL,UK A thesis submitted for the award of aMaster's degree by Research in Computer ScienceJuly 2009
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Abstract
This thesis discusses wavelet-based boundary enhancement techniques for improving thesegmentation quality of contour based texture segmentation algorithms. With a focus onimproving the glandular segmentations of clinical histopathology images, a number of issueswith existing approaches are investigated before arriving at the conclusion that image and boundary enhancement techniques play a significant role in improving image segmentationquality.We present a method for enhancing the visibility of region-of-interest (ROI) boundaries inChapter 3. This method takes advantage of the information in wavelet-packet sub-bandsoverlaying wavelet feature information over a group of selected texture samples as part of asupervised segmentation approach. This builds on the existing Geodesic Active Region modeland aims to improve the probability that a more accurate segmentation may be achieved post-enhancement. Further insight into our algorithmic design process is also provided.In Chapter 4, the proposed technique is validated against sets of both real world and medicalimages. Experiments are demonstrated to present the improvement in segmentation qualityachieved with encouraging results being observed on both sets. Simple further adjustments arealso made to the algorithm providing additional benefits in the quality of results for theapplication of glandular segmentation. The method proposed in this thesis is flexible enough to be used in other segmentation problems, offering a computationally cheap qualitativeenhancement to their existing capabilities. It may also be powerful enough to offer real-worldsolutions in the area of glandular segmentation.
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Contents
Abstract
....................................................................................................................................... i
List of Figures
........................................................................................................................ iv
List of Tables
.......................................................................................................................... vi
Acknowledgements
............................................................................................................ vii
Chapter 1 – Introduction and Objectives
................................................................... 1
1.1 Problem Description
................................................................................................................. 3
1.2 Main Contributions
................................................................................................................... 4
1.3 Thesis Organization
.................................................................................................................. 4
Chapter 2 – Literature Review
........................................................................................ 6
2.1.1 Edge-based segmentation
....................................................................................................... 6
2.2 Region-based segmentation
...................................................................................................... 8
2.3 Texture-based segmentation
................................................................................................... 10
2.4 Hybrid segmentation methods
................................................................................................ 12
2.5 Contour-based segmentation
................................................................................................... 12
2.6 Snakes: Active Contour Models
............................................................................................. 13
2.7 Level-set methods
................................................................................................................... 17
2.8 Chan-Vese Active Contour Model
.......................................................................................... 20
2.9 Geodesic Active Region Model (GARM)
.............................................................................. 21
2.10 Summary
............................................................................................................................... 25
Chapter 3 - Wavelet-based Geodesic Active Region Model
......................... 27
3.1 Texture descriptors
.................................................................................................................. 28
3.2 The Wavelet transform
........................................................................................................... 30
3.3 The Inverse Wavelet transform
............................................................................................... 31
3.4 Wavelet Packets
...................................................................................................................... 32
3.5 The Forward Wavelet-packet transform
................................................................................. 33
3.6 Cost functions
......................................................................................................................... 34
3.7 Weaknesses of the GARM
...................................................................................................... 35
3.8 Improving the GARM
............................................................................................................. 37
3.9 A Wavelet-packet texture descriptor
...................................................................................... 38
3.10 A Pseudo-code description of the WB-GARM texture descriptor enhancement technique
. 40
3.11 Generating Multi-Scale Wavelet Packet Texture Features
................................................... 40
3.12 Preparing WPF feature images for usage
.............................................................................. 45
3.14 Rescaling pixel values
........................................................................................................... 46
3.15 Pixel Addition
....................................................................................................................... 50
3.16 Adjustments for improved results in Medical Applications
................................................. 53
3.17 Summary
............................................................................................................................... 54
Chapter 4
.................................................................................................................................. 55
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