- •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
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Unlike run-length classifiers and co-occurrence classifiers, Laws’ energy metrics [45] are local neighborhood values obtained by convolving the image with two out of five one-dimensional convolution kernels to yield a feature vector with up to 25 elements. Laws proposes a three-step process where the image is first subjected to background removal (for example, a highpass filter step), subsequently convolved with the kernel pair, and finally lowpass filtered. The resulting image is referred to as the energy map. Typically, Laws’ energy maps result in a high-dimensional feature vector per pixel and advertises itself for classification or segmentation with highdimensional clustering techniques or artificial intelligence methods. In one example [48], classical statistical parameters were obtained from the texture energy maps, and the discrete first-order finite difference convolution kernel that approximates ∂ 2/∂ x∂ y showed some ability to discriminate between cases with and without fractures. However, Laws’ texture maps are not in common use for this special application of texture analysis. One possible reason is the fixed scale on which the texture maps operate. Laws’ convolution kernels are fixed to 5 by 5 pixels, and pixel noise dominates this scale. Thus, the method suffers from the same problems as the co-occurrence matrix with short displacements. However, it is conceivable that a combination of multiscale decomposition (such as a wavelet decomposition) with Laws’ texture energy maps provides a more meaningful basis to obtain a quantitative description of the texture.
In summary, texture analysis methods in the spatial domain provide, to some extent, information that is related to actual trabecular structure. Therefore, texture analysis methods have the potential to provide information on bone architecture that is independent from bone density. However, texture analysis methods are sensitive towards the image formation function (e.g., projection image versus tomography), towards the point-spread function, the pixel size relative to trabecular size, and towards image artifacts, most notably noise.
9.3.3 Frequency-Domain Methods
The Fourier transform decomposes an image into its periodic components. A regular, repeating pattern of texture elements (sometimes referred to as texels), causes distinct and narrow peaks in the Fourier transform. A comprehensive discussion of the Fourier transform and its application in image analysis can be found in the pertinent literature [39, 40]. Since the Fourier transform reveals periodic components, i.e., the distances at which a pattern repeats itself, operations acting on the Fourier-transform of an image are referred to as frequency-domain operations in contrast to the spatial-domain operations that were covered in the previous section. The magnitude of the Fourier transform is often referred to as the frequency spectrum. In two-dimensional images, the frequency spectrum is two-dimensional with two orthogonal frequency components u and v. It is possible to analyze those frequency components separately and include properties such as texture anisotropy.
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M.A. Haidekker and G. Dougherty |
Alternatively, the spectrum can be reduced to one dimension by averaging all frequency coefficients at the same spatial frequency ω = √u2 + v2. Intuitively, the frequency spectrum can be interpreted as a different representation of the spatialdomain image data that emphasizes a specific property, namely, the periodicity.
Trabecular bone does not exhibit any strict periodicity, because trabeculae are to some extent randomly oriented and have random size. The Fourier transform of random structures does not show distinct peaks. Rather, the frequency components decay more or less monotonically with increasing spatial frequency. This property is demonstrated in Fig. 9.7. The Fourier transform images (more precisely, the logtransformed magnitude of the Fourier transform) of a relatively regular texture and an irregular, bone-like structure are shown. Peaks that indicate the periodicity of the knit pattern do not exist in the Fourier transform of the bone-like structure. However, the decay behavior of the central maximum contains information about the texture. A fine, highly irregular texture, typically associated with healthy bone architecture, would show a broad peak with slow drop-off towards higher frequencies. Conversely, osteoporotic bone with large intratrabecular spacing would show a narrow peak with a faster drop-off towards higher frequencies.
In the analysis of trabecular bone texture, frequency-domain methods are often used to detect self-similar properties. These methods are described in the next section. Moreover, a number of single-value metrics can be derived from the Fourier transform. These include the root mean square variation and the first moment of the power spectrum (FMP, (9.8)):
|
∑u ∑v √ |
|
|
|F(u, v)|2 |
|
|
FMP = |
u2 |
+ v2 |
(9.8) |
|||
∑u ∑v |F(u, v)|2 |
||||||
|
|
|||||
Here, F(u, v) indicates the Fourier coefficients at the spatial frequencies u and v, and the summation takes place over all u, v. The computation of the FMP-value can be restricted to angular “wedges” of width θ , where the angle-dependent FMP (θi) is computed over all u, v with tan(θi) < v/u ≤ tan(θi + θ ). In this case, the minimum and maximum value of FMP (θi) provide additional information on the anisotropy of the texture. For example, if the texture has a preferredly horizontal and vertical orientation, FMP(θ ) shows very distinct maxima for θ around 0◦, ±90◦, and 180 ◦. Conversely, the FMP-index for a randomly oriented texture has less distinct maxima, and the coefficient of variation of FMP(θ ) is lower. Two recent representative studies describe the use of frequency-domain metrics in radiographic images of the femur in patients with osteoprosis [49] and osteolysis [50]. Special use of the anisotropy was made in a study by Chappard et al. [51] and Brunet-Imbault et al. [52].
Frequency-domain methods have two major advantages over spatial-domain methods for the analysis of bone structure and its texture representation in images. First, frequency-domain methods are less sensitive against background irregularities and inhomogeneous intensity distributions. Trend-like background inhomogeneities map to very low spatial frequencies, and the corresponding Fourier coefficients
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Fig. 9.7 Frequency-domain representation of texture. (a): Photography of a knit texture that contains a somewhat regular repeating pattern. The regularity of the pattern is represented by distinct peaks in the Fourier transform (b). The slight off-vertical orientation of the knit texture finds a correspondence of the off-horizontal orientation of the Fourier-transform pattern. (c): Synthetic trabecular pattern from Fig. 9.5. Such a pattern does not have repeated texture elements, and the frequency coefficients decay mostly monotonically with increasing frequencies (d). The decay behavior can be used to characterize any irregular texture
are close to the center of the Fourier spectrum image. By omitting the F(u, v) from any single-value metric computation for small u,v, trends are automatically excluded from the metric. Second, frequency-domain methods are usually less noise-sensitive than spatial-domain methods. Many spatial-domain methods act on the pixel level (examples are Laws’ texture energies or the co-occurrence matrix with low displacements), and pixel noise directly influences the measured values. In the frequency domain, the energy of the noise is broadly distributed over the entire frequency spectrum. High spatial frequencies, i.e., those frequencies that are
