E-grāmata: Visualization in Medicine: Theory, Algorithms, and Applications

Foreword		xix
Preface		xxi
Introduction		1	(10)
Visualization in Medicine		1	(2)
Computerized Medical Imaging		3	(3)
2D and 3D Visualizations		6	(1)
Organization		7	(4)
PART I ACQUSITION, ANALYSIS, AND INTERPRETATION		11	(124)
Medical Image Data and Visual Perception		13	(22)
Medical Image Data		13	(4)
Data Artifacts		17	(9)
Sampling Theorem		18	(1)
Under Sampling and Aliasing		19	(2)
Partial Volume Effect		21	(1)
Interpolation Artifacts		22	(3)
Signal Artifacts		25	(1)
Sensitivity and Specificity		26	(1)
Visual Perception		27	(7)
Gray Value Perception		27	(3)
Color Spaces, Color Scales, and Color Perception		30	(4)
Summary		34	(1)
Acquisition of Medical Image Data		35	(30)
X-ray Imaging		36	(5)
Angiography		39	(1)
Rotational X-ray		39	(2)
Discussion		41	(1)
Computed Tomography		41	(7)
Computed Tomography Compared with X-ray Imaging		41	(1)
Principle of CT Data Generation		42	(3)
Parameters of CT Scanning		45	(2)
Standardization with Hounsfield units		47	(1)
Magnetic Resonance Imaging		48	(9)
Parameters of MRI Scanning		50	(4)
Intraoperative MRI Data		54	(1)
Functional MRI		54	(1)
Diffusion Tensor Imaging		55	(1)
Historic Remarks		56	(1)
CT versus MRI Data		56	(1)
Ultrasound		57	(3)
Position Emission Tomography (PET)		60	(1)
Single-Photon Emission Computed Tomography (SPECT)		61	(2)
Summary		63	(2)
Medical Volume Data in Clinical Practice		65	(18)
Storage of Medical Image Data		65	(2)
Scope of DICOM		65	(1)
Structure of DICOM Data		66	(1)
Conventional Film-based Diagnosis		67	(2)
Cooperation of Radiologists and Radiology Technician		67	(1)
Tasks in Conventional Film-based Diagnosis		68	(1)
Soft-copy Reading		69	(11)
Integration of Soft-copy Reading in Digital Radiology Departments		69	(2)
Tasks in Soft-copy Reading		71	(2)
Quantitative Image Analysis		73	(3)
Digital Hanging Protocol		76	(1)
Guidelines for Software Assistants to Support Soft-copy Reading		76	(1)
Diagnosis with 3D Visualizations		77	(3)
Summary		80	(3)
Image Analysis for Medical Visualization		83	(52)
Requirements		84	(1)
Preprocessing and Filtering		85	(10)
ROI Selection		85	(1)
Resampling		86	(1)
Histogram and Histogram Equalization		87	(1)
General Noise Reduction Techniques		88	(5)
Inhomogeneity Correction		93	(1)
Gradient Filtering		93	(1)
Enhancement of Relevant Structures		94	(1)
General Segmentation Approaches		95	(14)
Manual Segmentation		96	(1)
Threshold-based Segmentation		96	(2)
Region Growing		98	(2)
Watershed Segmentation		100	(4)
Live Wire Segmentation		104	(5)
Model-based Segmentation Methods		109	(7)
Active Contour Models		109	(2)
Level Sets and Fast Marching Methods		111	(1)
Active Shape Models		111	(3)
Active Appearance Models		114	(1)
Incorporating Model Assumptions in Region-Growing Segmentation		115	(1)
Interaction Techniques		116	(3)
Interaction Techniques for Region Growing		117	(1)
Interaction Techniques for Watershed Segmentation		118	(1)
Interaction Techniques for LiveWire		118	(1)
Postprocessing of Segmentation Results		119	(3)
Morphological Image Analysis		119	(1)
Smoothing Segmentation Results for Visualization		120	(2)
Skeletonization		122	(2)
Validation of Segmentation Methods		124	(2)
Phantom studies versus Clinical Data		125	(1)
Validation Metrics		125	(1)
Discussion		126	(1)
Registration and Fusion of Medical Image Data		126	(5)
Summary		131	(4)
PART II VOLUME VISUALIZATION		135	(124)
Fundamentals of Volume Visualization		137	(18)
The Volume Visualization Pipeline		137	(1)
Histograms and Volume Classification		137	(8)
Histograms		139	(3)
Transfer Function Specification		142	(3)
Selection of Isovalues		145	(1)
Illumination in Scalar Volume Datasets		145	(7)
Phong's Illumination Model		146	(2)
Approximation of Normal Vectors		148	(4)
Summary		152	(3)
Indirect Volume Visualization		155	(28)
Plane-based Volume Rendering		155	(1)
Surface-based Volume Rendering		156	(17)
Contour Tracing		158	(1)
Cuberille Voxel Representation		158	(1)
Polygonal Isosurface Extraction		159	(9)
Other Isosurface Extraction Algorithms		168	(1)
Data Structures for Accelerating Isosurface Extraction		169	(4)
Surface Postprocessing		173	(7)
Geometry Culling		173	(2)
Mesh Reduction		175	(1)
Mesh Smoothing		176	(3)
Voxelization		179	(1)
Summary		180	(3)
Direct Volume Visualization		183	(14)
Theoretical Models for Direct Volume Rendering		183	(4)
Emission		184	(1)
Absorption		184	(1)
Volume Rendering Equation		185	(2)
The Volume Rendering Pipeline		187	(2)
Compositing		189	(6)
Compositing Variations: Pseudo X-ray, MIP, and CVP		190	(3)
Thin Slab Volume Rendering		193	(1)
Pre-Integrated Volume Rendering		194	(1)
Summary		195	(2)
Algorithms for Direct Volume Visualization		197	(40)
Ray Casting		197	(6)
Quality		199	(1)
Acceleration Methods		200	(3)
Shear Warp		203	(3)
Quality		205	(1)
Splatting		206	(6)
Quality		208	(2)
Acceleration Methods		210	(2)
Texture-Mapping		212	(7)
Quality		215	(3)
Dataset Management		218	(1)
Other Direct Volume Rendering Approaches		219	(2)
Shell Rendering		220	(1)
Direct Volume Rendering of Segmented Volume Data		221	(2)
Hybrid Volume Rendering		223	(5)
Validation of Volume Visualization Algorithms		228	(7)
Validation Criteria		229	(1)
Geometric Models for Validation		230	(2)
Image and Datalevel Comparisons		232	(1)
Presentation of Results		232	(3)
Summary		235	(2)
Exploration of Dynamic Medical Volume Data		237	(22)
Introduction		237	(1)
Medical Background		238	(3)
Basic Visualization Techniques		241	(1)
Data Processing		242	(2)
Advanced Visualization Techniques		244	(4)
Multiparameter Visualization		245	(3)
Integrating Dynamic Information and Morphology		248	(1)
Case Study: Tumor Perfusion		248	(5)
Imaging		250	(1)
Computer Support		250	(1)
Visualization Techniques		251	(2)
Case Study: Brain Perfusion		253	(3)
Imaging		254	(1)
Computer Support		255	(1)
Visualization Techniques		255	(1)
Summary		256	(3)
PART III EXPLORATION OF MEDICAL VOLUME DATA		259	(82)
Transfer Function Specification		261	(30)
Strategies for One-dimensional Transfer Functions		262	(8)
Data-Driven TF Specification		263	(3)
Employing Reference Transfer Functions		266	(1)
Image-Driven TF Specification		267	(3)
Multidimensional Transfer Functions		270	(5)
Histograms for 2D TF Specification		271	(1)
2D Component Functions		272	(2)
Representation of 2D Transfer Functions		274	(1)
Gradient-based Transfer Functions		275	(5)
Gradient Estimation and Storage		275	(1)
User Interfaces for Gradient-based Transfer Functions		276	(4)
Distance-based transfer functions		280	(6)
Distance Calculation and Storage		281	(1)
Applications		282	(3)
Discussion		285	(1)
Local and Spatialized Transfer Functions		286	(2)
Summary		288	(3)
Clipping, Cutting, and Virtual Resection		291	(22)
Clipping		291	(3)
Selective Clipping		293	(1)
Box Clipping		294	(1)
Virtual Resection		294	(3)
Specification of Virtual Resections by Erasing		296	(1)
Specification of Virtual Resections by Drawing on Slices		296	(1)
Virtual Resection with a Deformable Cutting Plane		297	(10)
Defining Cutting Plane Boundaries		298	(1)
Generation of the Initial Cutting Plane		298	(4)
Modification of Virtual Resections		302	(1)
Discussion		303	(2)
Efficient Visualization of Virtual Resections		305	(1)
Visualization Parameters		306	(1)
Evaluation		306	(1)
Combination of Resection Proposals and Virtual Resection		307	(1)
Cutting Medical Volume Data		307	(3)
High-quality Representation of Cut Surfaces		308	(2)
Virtual Resection and Surgery Simulation		310	(1)
Summary		310	(3)
Measurements in Medical Visualization		313	(28)
General Design Issues		315	(2)
Usability		315	(2)
Accuracy and Uncertainty		317	(1)
3D Distance Measurements		317	(4)
Distance Lines		317	(2)
Interactive Rulers		319	(1)
Path Measurement		320	(1)
Angular Measurements		321	(2)
Interactive Volume Measurements		323	(1)
Interactive Volume Measurements		324	(5)
Volume Selection		324	(3)
Volume Approximation		327	(1)
Validation		328	(1)
Minimal Distance Computation		329	(7)
Distance Calculation in Robotics and Medical Visualization		330	(1)
Minimal Distance Computation based on Bounding Spheres		331	(5)
Further Automatic Measurements		336	(1)
Measuring the Extents of Objects		336	(1)
Measurement of Angles between Elongated Objects		337	(1)
Summary		337	(4)
PART IV ADVANCED VISUALIZATION TECHNIQUES		341	(156)
Visualization of Anatomic Tree Structures		343	(38)
Vessel Analysis		345	(5)
Preprocessing to Enhance Vessel-like Structures		345	(1)
Vessel Segmentation		346	(1)
Skeletonization		346	(4)
Overview of Vessel Visualization		350	(2)
Reconstruction of Vessels for Visualization		351	(1)
Reconstruction of Vessels for Interaction		352	(1)
Explicit and Implicit Surface Reconstruction		352	(1)
Explicit Surface Reconstruction		352	(5)
Visualization with Parametric Surfaces		353	(1)
Visualization with Truncated Cones		353	(2)
Visualization with Subdivision Surfaces		355	(2)
Modeling Tree Structures with Implicit Surfaces		357	(4)
Introduction		358	(1)
Implicit Surfaces: a Brief Introduction		358	(1)
Convolution Surfaces		358	(2)
Blending		360	(1)
Visualization with Convolution Surfaces		361	(4)
Filter Modification		361	(1)
Computational Complexity		362	(2)
Construction of a Geometric Model		364	(1)
Validation and Evaluation		365	(6)
Qualitative Validation		365	(1)
Quantitative Validation		366	(3)
Determination of the Width Coefficient		369	(1)
Evaluation		370	(1)
Visualization of the Error		370	(1)
Examples		371	(1)
Exploration of Vasculature		372	(2)
Vessel Visualization for Diagnosis		374	(3)
Summary		377	(4)
Virtual Endoscopy		381	(22)
Application Scenarios for Virtual Endoscopy		382	(2)
Technical Issues		384	(3)
Rendering for Virtual Endoscopy		384	(1)
Navigating through Body Cavities		385	(2)
User Interface		387	(1)
Virtual Colonoscopy		387	(2)
Virtual Bronchoscopy		389	(2)
Virtual Neuroendoscopy		391	(6)
Cerebral Ventricular System		391	(3)
Multimodal Visualization for Neuroendoscopic Interventions		394	(1)
Minimally Invasive Surgery of the Pituitary Gland		395	(2)
Virtual Angioscopy		397	(3)
Angioscopy of Cerebral Blood Vessels		397	(2)
Angioscopy of Coronary Blood Vessels		399	(1)
Summary		400	(3)
Image-Guided Surgery and Virtual Reality		403	(16)
Prerequisites for Intraoperative Visualization		403	(4)
Tissue Deformation and Brain Shift		404	(1)
Registration		405	(2)
Image-Guided Surgery		407	(4)
Tracking Systems		407	(2)
Navigating Instruments in the OR		409	(2)
Virtual and Mixed Reality in the OR		411	(5)
The Occlusion Problem of Mixed Reality		412	(1)
Alignment of the Mixed Reality Camera		413	(1)
Interaction in the OR		414	(2)
Summary		416	(3)
Emphasis Techniques and Illustrative Rendering		419	(36)
Illustrative Surface and Volume Rendering		420	(14)
Emphasis and Illustrative Rendering		422	(1)
Silhouette and Feature Lines from Polygonal Models		423	(3)
Hatching Surface Models		426	(1)
Illustrative Rendering of Medical Volume Data		427	(2)
Hatching Volume Models		429	(1)
Illustrative Shading Styles		430	(3)
Style Specification for Illustrative Volume Rendering		433	(1)
Combining Line, Surface, and Volume Visualization		434	(5)
Hybrid Rendering with Object-based Methods		434	(1)
Emphasis with Hybrid Visualizations		435	(4)
Visibility Analysis		439	(1)
Local Emphasis Techniques		440	(3)
Emphasis Using Color		440	(1)
Focus-and-Context-Views		440	(1)
Emphasis with Arrows		441	(1)
Emphasis with Shadow Volumes		442	(1)
Regional and Global Emphasis Techniques		443	(3)
Cutaway and Ghost Views		443	(2)
Defining Contrasts for Emphasis		445	(1)
Dynamic Emphasis Techniques		446	(1)
Synchronized Emphasis		447	(2)
Slice Selection		447	(1)
Emphasis in 2D Slices		448	(1)
Range Visualization		448	(1)
Classification of Emphasis Techniques		449	(2)
Summary		451	(4)
Exploration of MRI Diffusion Tensor Images		455	(42)
Medical Background And Image Acquisition		457	(7)
Neuroanatomy		457	(1)
Image Acquisition		458	(5)
Clinical Applications		463	(1)
Image Analysis of DTI Data		464	(3)
Interpolation of DTI Data		465	(1)
Filtering DTI Data		466	(1)
Discussion		467	(1)
Quantitative Characterization of Diffusion Tensors		467	(3)
Diffusivity Metrics		467	(1)
Anisotropy Metrics		467	(2)
Coherence Metrics		469	(1)
Discussion		470	(1)
Slice-based Visualizations of Tensor Data		470	(3)
Visualization with Tensor Glyphs		473	(4)
Ellipsoids as Tensor Glyphs		474	(1)
Superquadric Tensor Glyphs		474	(1)
Visualization of Tensor Glyphs		475	(1)
Color Schemes for Tensor Glyphs		476	(1)
Direct Volume Rendering of Diffusion Tensor Fields		477	(1)
Fiber Tract Modeling		477	(9)
Streamline Computation and Visualization		478	(5)
Hyperstreamlines and Streamsurfaces		483	(3)
Exploration of Fiber Tracts through Clustering		486	(7)
Proximity Metrics for Clustering		487	(1)
Clustering Algorithms		488	(1)
Visualization and Quantification of Fiber Bundles		489	(3)
Validation of Fiber Clustering		492	(1)
Software Tools for the Exploration of DTI Data		493	(1)
Summary		493	(4)
PART V APPLICATION AREAS AND CASE STUDIES		497	(78)
Image Analysis and Visualization for Liver Surgery Planning		499	(26)
Medical Background		500	(5)
Liver Anatomy		500	(2)
Preoperative Imaging		502	(1)
Liver Surgery		503	(2)
Image Analysis for Liver Surgery Planning		505	(3)
Risk Analysis for Oncologic Liver Surgery Planning		508	(3)
Risk Analysis for Live Donor Liver Transplantation		511	(3)
Grafts with or without Middle Hepatic Vein		511	(1)
Case Study		512	(2)
Simulation and Visualization for Planning		514	(2)
Applicator Positioning		514	(1)
Physical Effects of Thermoablation		515	(1)
Software Assistants for Liver Sufgery Planning		516	(3)
Image Analysis with Hepa Vision		517	(1)
Surgery Planning with the Intervention Planner		517	(2)
Clinical Application		519	(1)
Planning Pancreatic and Renal Surgery		520	(1)
Summary		521	(4)
Visualization for Medical Education		525	(44)
Datasets and Knowledge Representation		526	(4)
Datasets for Medical Education		526	(2)
Knowledge Representation		528	(2)
Labeling Medical Visualizations		530	(11)
Placement of External Labels		531	(4)
Placement of Internal Labels		535	(2)
Labeling Branching and Partially Visible Objects		537	(2)
Labeling Cross-sectional Images		539	(1)
Presentation Variables for Labeling		539	(2)
Animating Medical Visualizations		541	(4)
Script-based Specification of Animations		542	(3)
Changing the Object Focus with Animations		545	(1)
Basics of Computer-based Training		545	(1)
Anatomy Education		546	(6)
Voxel Man		547	(1)
Digital Anatomist		547	(2)
Anatomy Browser		549	(1)
ZoomIllustrator and 3D Puzzle		549	(3)
Surgery Education and Simulation		552	(14)
CBT Systems for Studying Clinical Surgery		553	(1)
Tasks and Concepts for Surgery Simulation		553	(9)
CBT Systems for Studying Operative Techniques		562	(4)
Summary		566	(3)
Outlook		569	(6)
Integrating Simulation and Visualization		570	(1)
Integrated Visualization of Preoperative and Intraoperative Visualization		571	(1)
Integrated Visualization of Morphologic and Functional Image Data		572	(1)
Model-based Visualization		572	(3)
Appendix		575	(14)
Bibliography		589	(52)
Index		641

Bernhard Preim was born in 1969 in Magdeburg, Germany. He received the diploma in computer science in 1994 (minor in mathematics) and a Ph.D. in 1998 for a thesis on interactive visualization for anatomy education from the Otto-von-Guericke University of Magdeburg. In 1999 he moved to Bremen where he joined the staff of MEVIS and directed the computer-aided planning in liver surgery” group. Since Mars 2003 he is full professor for Visualization at the computer science department at the Otto-von-Guericke-University of Magdeburg, heading a research group focussed on medical visualization. His research interests include vessel visualization, exploration of blood flow, visual analytics in public health, virtual reality in medical education and since recently narrative visualization. He authored Visualization in Medicine” (Co-author Dirk Bartz, 2007) and Visual Computing in Medicine” (Co-author: C. Botha, 2013). Bernhard Preim founded the working group Medical Visualization in the German Society for Computer Science and served as speaker from 2003-2012. He was president of the German Society for Computer- and Robot-Assisted Surgery (www.curac.org). He was Co-Chair and Co-Organizer of the first and second Eurographics Workshop on Visual Computing in Biology and Medicine (VCBM) in 2008 and 2010 and lead the steering committee of that workshop until 2019. He is the chair of the scientific advisory board of ICCAS (International Competence Center on Computer-Assisted Surgery Leipzig, since 2010). From 2011-2018 he was an associate editor of IEEE Transactions on Medical Imaging and and IEEE Transactions on Visualization and Graphics (2017-2022). Currently he serves in the editorial board of Computers & Graphics (since 2019). He was also regularly a Visiting Professor at the University of Bremen where he closely collaborates with Fraunhofer MEVIS (2003-2012) and was Visiting Professor at TU Vienna (2016). Dirk Barz was Professor for Computer-Aided Surgery at the U of Leipzig. He was also member of the executive committee of the IEEE Visualization and Graphics Technical Committee. He received the NDI Young Investigator Award for his work on virtual endoscopy and intra-operative navigation.