- •Biological and Medical Physics, Biomedical Engineering
- •Medical Image Processing
- •Preface
- •Contents
- •Contributors
- •1.1 Medical Image Processing
- •1.2 Techniques
- •1.3 Applications
- •1.4 The Contribution of This Book
- •References
- •2.1 Introduction
- •2.2 MATLAB and DIPimage
- •2.2.1 The Basics
- •2.2.2 Interactive Examination of an Image
- •2.2.3 Filtering and Measuring
- •2.2.4 Scripting
- •2.3 Cervical Cancer and the Pap Smear
- •2.4 An Interactive, Partial History of Automated Cervical Cytology
- •2.5 The Future of Automated Cytology
- •2.6 Conclusions
- •References
- •3.1 The Need for Seed-Driven Segmentation
- •3.1.1 Image Analysis and Computer Vision
- •3.1.2 Objects Are Semantically Consistent
- •3.1.3 A Separation of Powers
- •3.1.4 Desirable Properties of Seeded Segmentation Methods
- •3.2 A Review of Segmentation Techniques
- •3.2.1 Pixel Selection
- •3.2.2 Contour Tracking
- •3.2.3 Statistical Methods
- •3.2.4 Continuous Optimization Methods
- •3.2.4.1 Active Contours
- •3.2.4.2 Level Sets
- •3.2.4.3 Geodesic Active Contours
- •3.2.5 Graph-Based Methods
- •3.2.5.1 Graph Cuts
- •3.2.5.2 Random Walkers
- •3.2.5.3 Watershed
- •3.2.6 Generic Models for Segmentation
- •3.2.6.1 Continuous Models
- •3.2.6.2 Hierarchical Models
- •3.2.6.3 Combinations
- •3.3 A Unifying Framework for Discrete Seeded Segmentation
- •3.3.1 Discrete Optimization
- •3.3.2 A Unifying Framework
- •3.3.3 Power Watershed
- •3.4 Globally Optimum Continuous Segmentation Methods
- •3.4.1 Dealing with Noise and Artifacts
- •3.4.2 Globally Optimal Geodesic Active Contour
- •3.4.3 Maximal Continuous Flows and Total Variation
- •3.5 Comparison and Discussion
- •3.6 Conclusion and Future Work
- •References
- •4.1 Introduction
- •4.2 Deformable Models
- •4.2.1 Point-Based Snake
- •4.2.1.1 User Constraint Energy
- •4.2.1.2 Snake Optimization Method
- •4.2.2 Parametric Deformable Models
- •4.2.3 Geometric Deformable Models (Active Contours)
- •4.2.3.1 Curve Evolution
- •4.2.3.2 Level Set Concept
- •4.2.3.3 Geodesic Active Contour
- •4.2.3.4 Chan–Vese Deformable Model
- •4.3 Comparison of Deformable Models
- •4.4 Applications
- •4.4.1 Bone Surface Extraction from Ultrasound
- •4.4.2 Spinal Cord Segmentation
- •4.4.2.1 Spinal Cord Measurements
- •4.4.2.2 Segmentation Using Geodesic Active Contour
- •4.5 Conclusion
- •References
- •5.1 Introduction
- •5.2 Imaging Body Fat
- •5.3 Image Artifacts and Their Impact on Segmentation
- •5.3.1 Partial Volume Effect
- •5.3.2 Intensity Inhomogeneities
- •5.4 Overview of Segmentation Techniques Used to Isolate Fat
- •5.4.1 Thresholding
- •5.4.2 Selecting the Optimum Threshold
- •5.4.3 Gaussian Mixture Model
- •5.4.4 Region Growing
- •5.4.5 Adaptive Thresholding
- •5.4.6 Segmentation Using Overlapping Mosaics
- •5.6 Conclusions
- •References
- •6.1 Introduction
- •6.2 Clinical Context
- •6.3 Vessel Segmentation
- •6.3.1 Survey of Vessel Segmentation Methods
- •6.3.1.1 General Overview
- •6.3.1.2 Region-Growing Methods
- •6.3.1.3 Differential Analysis
- •6.3.1.4 Model-Based Filtering
- •6.3.1.5 Deformable Models
- •6.3.1.6 Statistical Approaches
- •6.3.1.7 Path Finding
- •6.3.1.8 Tracking Methods
- •6.3.1.9 Mathematical Morphology Methods
- •6.3.1.10 Hybrid Methods
- •6.4 Vessel Modeling
- •6.4.1 Motivation
- •6.4.1.1 Context
- •6.4.1.2 Usefulness
- •6.4.2 Deterministic Atlases
- •6.4.2.1 Pioneering Works
- •6.4.2.2 Graph-Based and Geometric Atlases
- •6.4.3 Statistical Atlases
- •6.4.3.1 Anatomical Variability Handling
- •6.4.3.2 Recent Works
- •References
- •7.1 Introduction
- •7.2 Linear Structure Detection Methods
- •7.3.1 CCM for Imaging Diabetic Peripheral Neuropathy
- •7.3.2 CCM Image Characteristics and Noise Artifacts
- •7.4.1 Foreground and Background Adaptive Models
- •7.4.2 Local Orientation and Parameter Estimation
- •7.4.3 Separation of Nerve Fiber and Background Responses
- •7.4.4 Postprocessing the Enhanced-Contrast Image
- •7.5 Quantitative Analysis and Evaluation of Linear Structure Detection Methods
- •7.5.1 Methodology of Evaluation
- •7.5.2 Database and Experiment Setup
- •7.5.3 Nerve Fiber Detection Comparison Results
- •7.5.4 Evaluation of Clinical Utility
- •7.6 Conclusion
- •References
- •8.1 Introduction
- •8.2 Methods
- •8.2.1 Linear Feature Detection by MDNMS
- •8.2.2 Check Intensities Within 1D Window
- •8.2.3 Finding Features Next to Each Other
- •8.2.4 Gap Linking for Linear Features
- •8.2.5 Quantifying Branching Structures
- •8.3 Linear Feature Detection on GPUs
- •8.3.1 Overview of GPUs and Execution Models
- •8.3.2 Linear Feature Detection Performance Analysis
- •8.3.3 Parallel MDNMS on GPUs
- •8.3.5 Results for GPU Linear Feature Detection
- •8.4.1 Architecture and Implementation
- •8.4.2 HCA-Vision Features
- •8.4.3 Linear Feature Detection and Analysis Results
- •8.5 Selected Applications
- •8.5.1 Neurite Tracing for Drug Discovery and Functional Genomics
- •8.5.2 Using Linear Features to Quantify Astrocyte Morphology
- •8.5.3 Separating Adjacent Bacteria Under Phase Contrast Microscopy
- •8.6 Perspectives and Conclusions
- •References
- •9.1 Introduction
- •9.2 Bone Imaging Modalities
- •9.2.1 X-Ray Projection Imaging
- •9.2.2 Computed Tomography
- •9.2.3 Magnetic Resonance Imaging
- •9.2.4 Ultrasound Imaging
- •9.3 Quantifying the Microarchitecture of Trabecular Bone
- •9.3.1 Bone Morphometric Quantities
- •9.3.2 Texture Analysis
- •9.3.3 Frequency-Domain Methods
- •9.3.4 Use of Fractal Dimension Estimators for Texture Analysis
- •9.3.4.1 Frequency-Domain Estimation of the Fractal Dimension
- •9.3.4.2 Lacunarity
- •9.3.4.3 Lacunarity Parameters
- •9.3.5 Computer Modeling of Biomechanical Properties
- •9.4 Trends in Imaging of Bone
- •References
- •10.1 Introduction
- •10.1.1 Adolescent Idiopathic Scoliosis
- •10.2 Imaging Modalities Used for Spinal Deformity Assessment
- •10.2.1 Current Clinical Practice: The Cobb Angle
- •10.2.2 An Alternative: The Ferguson Angle
- •10.3 Image Processing Methods
- •10.3.1 Previous Studies
- •10.3.2 Discrete and Continuum Functions for Spinal Curvature
- •10.3.3 Tortuosity
- •10.4 Assessment of Image Processing Methods
- •10.4.1 Patient Dataset and Image Processing
- •10.4.2 Results and Discussion
- •10.5 Summary
- •References
- •11.1 Introduction
- •11.2 Retinal Imaging
- •11.2.1 Features of a Retinal Image
- •11.2.2 The Reason for Automated Retinal Analysis
- •11.2.3 Acquisition of Retinal Images
- •11.3 Preprocessing of Retinal Images
- •11.4 Lesion Based Detection
- •11.4.1 Matched Filtering for Blood Vessel Segmentation
- •11.4.2 Morphological Operators in Retinal Imaging
- •11.5 Global Analysis of Retinal Vessel Patterns
- •11.6 Conclusion
- •References
- •12.1 Introduction
- •12.1.1 The Progression of Diabetic Retinopathy
- •12.2 Automated Detection of Diabetic Retinopathy
- •12.2.1 Automated Detection of Microaneurysms
- •12.3 Image Databases
- •12.4 Tortuosity
- •12.4.1 Tortuosity Metrics
- •12.5 Tracing Retinal Vessels
- •12.5.1 NeuronJ
- •12.5.2 Other Software Packages
- •12.6 Experimental Results and Discussion
- •12.7 Summary and Future Work
- •References
- •13.1 Introduction
- •13.2 Volumetric Image Visualization Methods
- •13.2.1 Multiplanar Reformation (2D slicing)
- •13.2.2 Surface-Based Rendering
- •13.2.3 Volumetric Rendering
- •13.3 Volume Rendering Principles
- •13.3.1 Optical Models
- •13.3.2 Color and Opacity Mapping
- •13.3.2.2 Transfer Function
- •13.3.3 Composition
- •13.3.4 Volume Illumination and Illustration
- •13.4 Software-Based Raycasting
- •13.4.1 Applications and Improvements
- •13.5 Splatting Algorithms
- •13.5.1 Performance Analysis
- •13.5.2 Applications and Improvements
- •13.6 Shell Rendering
- •13.6.1 Application and Improvements
- •13.7 Texture Mapping
- •13.7.1 Performance Analysis
- •13.7.2 Applications
- •13.7.3 Improvements
- •13.7.3.1 Shading Inclusion
- •13.7.3.2 Empty Space Skipping
- •13.8 Discussion and Outlook
- •References
- •14.1 Introduction
- •14.1.1 Magnetic Resonance Imaging
- •14.1.2 Compressed Sensing
- •14.1.3 The Role of Prior Knowledge
- •14.2 Sparsity in MRI Images
- •14.2.1 Characteristics of MR Images (Prior Knowledge)
- •14.2.2 Choice of Transform
- •14.2.3 Use of Data Ordering
- •14.3 Theory of Compressed Sensing
- •14.3.1 Data Acquisition
- •14.3.2 Signal Recovery
- •14.4 Progress in Sparse Sampling for MRI
- •14.4.1 Review of Results from the Literature
- •14.4.2 Results from Our Work
- •14.4.2.1 PECS
- •14.4.2.2 SENSECS
- •14.4.2.3 PECS Applied to CE-MRA
- •14.5 Prospects for Future Developments
- •References
- •15.1 Introduction
- •15.2 Acquisition of DT Images
- •15.2.1 Fundamentals of DTI
- •15.2.2 The Pulsed Field Gradient Spin Echo (PFGSE) Method
- •15.2.3 Diffusion Imaging Sequences
- •15.2.4 Example: Anisotropic Diffusion of Water in the Eye Lens
- •15.2.5 Data Acquisition
- •15.3 Digital Processing of DT Images
- •15.3.2 Diagonalization of the DT
- •15.3.3 Gradient Calibration Factors
- •15.3.4 Sorting Bias
- •15.3.5 Fractional Anisotropy
- •15.3.6 Other Anisotropy Metrics
- •15.4 Applications of DTI to Articular Cartilage
- •15.4.1 Bovine AC
- •15.4.2 Human AC
- •References
- •Index
76 |
A. Alfiansyah |
Fig. 4.9 Role of the elastic term in geodesic active contour: In the upper row, the model is evolved without the elastic term; in the lower row, an elastic term is used
boundaries C. A reduced form of this problem consists simply in the restriction of EMS to piecewise constant functions and finding a partition of Ω such that f in Ω equals a constant.
To minimize the functional energy, Chan and Vese proposed a two-phase segmentation as follows:
C,Co,Cb |
μ δ (φ )| φ | |
+ ν |
|
(φ ) |
+ λo |
| |
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− |
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o| |
2H |
(φ ) |
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+ |
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min |
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dxdy |
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H |
dxdy |
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f |
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c |
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dxdy |
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Ω |
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Ω |
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inside(C) |
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+ λo |
| f − co|2(1 − H(φ ))dxdy, |
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||||
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outside(C) |
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where φ is the level set function and H(φ ) is the Heaviside function.
Generally, the above deformable models implemented by means of the level set method suffer from a slower speed of convergence than parametric deformable models due to their computational complexity. Application of the Chan-Vese deformable model to segmentation on a low signal, noisy image is shown in Fig. 4.10.
4.3 Comparison of Deformable Models
Whereas geometric deformable models often have been presented as an improvement (and even superior) to classical snakes [23, 25, 30], one might argue that they actually are complementary to each other. In a wide range of image segmentation
4 Deformable Models and Level Sets in Image Segmentation |
77 |
Fig. 4.10 Image segmentation using a Chan–Vese deformable model: (a) The original image; note that it has a very weak border; (b) The degraded image with added salt-and-paper noises; (c) A segmentation result represented as a binary mask (the white area is the detected object)
applications there is a trade-off between desirable properties. Instances of such important trade-offs are the level of automation versus control, and topological flexibility versus a priori constraints. Other important properties are the role of the initialization, existence of a unique solution, dependence of the result on parameter choice and the robustness of the method with respect to noise, and imperfect image data.
Table 4.1 summarizes the main properties of a number of deformable model types which have been described in the previous section. We categorize the deformable models into three approaches following the previous presentation.
Classical and explicit parametric snakes are well-known in performing well if the initialization is close to the desired objects. Moreover, since a parameterization is