- •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
13 Medical Image Volumetric Visualization: Algorithms, Pipelines... |
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Fig. 13.14 Shell rendering examples. Top row, shell SR [174]: skull CT data (left) and CT data of a “dry” child’s skull (right). Bottom row, shell DVR [175]: CT skull (left), and MR head (right)
13.7 Texture Mapping
The pioneering work of exploiting texture hardware for DVR was performed by Cullip and Neumann [90] and Cabral et al. [91]. When graphics hardware does not support trilinear interpolation, 2D texture mapping (2DTM) must be adopted. In this case, the volume is decomposed into three stacks of perpendicularly object-aligned polygons. For the current viewing direction, the stack whose slicing direction (normal) must be within 45 degrees of the current viewing direction is chosen for rendering. During rasterization, each of the polygon slices is textured with the image information obtained from the volume via bilinear interpolation. Finally, the textured slices are alpha-blended in a back-to-front order to produce the final image.
308 |
Q. Zhang et al. |
Fig. 13.15 The working pipeline of 3DTM for 3D head rendering
Fig. 13.16 Medical image rendered with 3DTM: (a) CT skull; (b) MR brain; (c) CT jaw, and (d) MR cerebral blood vessel
Figure 13.15 describes the working pipeline, and Fig. 13.16 illustrates the rendering results with this algorithm. 3DTM uploads the volume to the graphics memory as a single 3D texture, and a set of polygons perpendicular to the viewing direction is placed within the volume and textured with the image information by trilinear interpolation. Compared with 2DTM, there are no orientation limitations
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for the decomposed polygon slices, making the texture access more flexible. The compositing process is similar to 2DTM, in that the set of textured polygon planes are alpha-blended in a back-to-front order.
13.7.1 Performance Analysis
Compared with 3DTM, the main advantage of 2DTM is higher rendering speed and lower hardware requirements, since it uses efficient in-slice bilinear interpolations, instead of expensive trilinear interpolations. However, this algorithm is prone to aliasing artifacts at the edges of the slice polygons, and has to maintain three copies of the volume in graphics memory. The shift of viewing directions causes the algorithm to switch from one texture stack to another, resulting in the “popping” artifacts mentioned earlier. In 3DTM, the extracted slices can have arbitrary orientations and only a single copy of the data is required; therefore, there are no artifacts caused by the texture stack switching during the viewing direction changing process. In addition, the extracted slices are textured with trilinear instead of bilinear interpolation, so the mapped texture information has a higher accuracy. For orthographic projections, the viewport-aligned slices can be employed to achieve a consistent sampling step, but because the sampling distance cannot be uniform for projective views, “striping” artifacts are introduced. This limitation may be overcome using spherical rendering primitives [92], albeit with an increased computational cost.
13.7.2 Applications
In the published literature, there are three main types of medical applications for TM-based DVR. The first is multimodal medical image rendering and tissue separation. Sato et al. [93] designed a multidimensional TF to identify tissue structures in multimodal medical images generated with 3DTM. A two-level rendering technique was integrated with 3DTM by Hauser et al. [94], allowing different rendering techniques to be selected for different tissues based on segmentation information. Later, Hadwiger et al. [95] improved this 3DTM-based two-level DVR algorithm in the aspects of image quality and performance, minimizing the number of rendering passes and the computational cost of each pass, adding dynamic filtering, and using depth and stencil buffering to achieve correct compositing of objects created with different rendering techniques.
The second application area is in the display of specific tissues and organs for diagnosis and therapy. Holmes et al. [96] used 3DTM to achieve a real-time display of transurethral ultrasound (TUUS) for prostate treatment. This technique was also used by Etlik et al. [97] to find bone fractures, and also by Wenger et al. [98] to visualize diffusion tensor MRI (DTI) data in the brain. Wang et al. [99] exploited