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A widely used, classroom-tested text, Applied Medical Image Processing: A Basic Course delivers an ideal introduction to image processing in medicine, emphasizing the clinical relevance and special requirements of the field. Avoiding excessive mathematical formalisms, the book presents key principles by implementing algorithms from scratch and using simple MATLAB(R)/Octave scripts with image data and illustrations on an accompanying CD-ROM or companion website. Organized as a complete textbook, it provides an overview of the physics of medical image processing and discusses image formats and data storage, intensity transforms, filtering of images and applications of the Fourier transform, three-dimensional spatial transforms, volume rendering, image registration, and tomographic reconstruction. This Second Edition of the bestseller: * Contains two brand-new chapters on clinical applications and image-guided therapy * Devotes more attention to the subject of color space * Includes additional examples from radiology, internal medicine, surgery, and radiation therapy * Incorporates freely available programs in the public domain (e.g., GIMP, 3DSlicer, and ImageJ) when applicable Beneficial to students of medical physics, biomedical engineering, computer science, applied mathematics, and related fields, as well as medical physicists, radiographers, radiologists, and other professionals, Applied Medical Image Processing: A Basic Course, Second Edition is fully updated and expanded to ensure a perfect blend of theory and practice.
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Table of Contents

List of Figures List of Tables Foreword Preface to the First Edition Preface to the Second Edition User Guide Acknowledgments Chapter 1: A Few Basics of Medical Image Sources Radiology The Electromagnetic Spectrum Basic X-Ray Physics Attenuation and Imaging Computed Tomography Magnetic Resonance Tomography Ultrasound Nuclear Medicine and Molecular Imaging Other Imaging Techniques Radiation Protection and Dosimetry Summary and Further References Chapter 2: Image Processing in Clinical Practice Application Examples Image Databases Intensity Operations Filter Operations Segmentation Spatial Transforms Rendering and Surface Models Registration CT Reconstruction Summary Chapter 3: Image Representation Pixels and Voxels Gray Scale and Color Representation Image File Formats DICOM Other Formats - Analyze 7.5, NIfTI, and Interfile Image Quality and the Signal-to-Noise Ratio Practical Lessons Summary and Further References Chapter 4: Operations in Intensity Space The Intensity Transform Function and the Dynamic Range Windowing Histograms and Histogram Operations Dithering and Depth Practical Lessons Summary and Further References Chapter 5: Filtering and Transformations The Filtering Operation The Fourier Transform Other Transforms Practical Lessons Summary and Further References Chapter 6: Segmentation The Segmentation Problem ROI Definition and Centroids Thresholding Region Growing More Sophisticated Segmentation Methods Morphological Operations Evaluation of Segmentation Results Practical Lessons Summary and Further References Chapter 7: Spatial Transforms Discretization - Resolution and Artifacts Interpolation and Volume Regularization Translation and Rotation Reformatting Tracking and Image-Guided Therapy Practical Lessons Summary and Further References Chapter 8: Rendering and Surface Models Visualization Orthogonal and Perspective Projection, and the Viewpoint Raycasting Surface-Based Rendering Practical Lessons Summary and Further References Chapter 9: Registration Fusing Information Registration Paradigms Merit Functions Optimization Strategies Some General Comments Camera Calibration Registration to Physical Space Evaluation of Registration Results Practical Lessons Summary and Further References Chapter 10: CT Reconstruction Introduction Radon Transform Algebraic Reconstruction Some Remarks on Fourier Transform and Filtering Filtered Backprojection Practical Lessons Summary and Further References Chapter 11: A Tutorial on Image Guided Therapy A Hands-On Approach to Camera Calibration and Image-Guided Therapy Transformations Camera Calibration Image-Guided Therapy, Introduction Image-Guided Therapy, Navigation System Image-Guided Therapy, Theory in Practice Summary Chapter 12: A Selection of MATLAB(R) Commands Control Structures and Operators I/O and Data Structures Mathematical Functions Further References Index

About the Author

Wolfgang Birkfellner studied theoretical physics at, and holds a Ph.D in medical physics from, the University of Vienna, Austria. Currently, he is heading the Digital Image Processing Laboratory at the Center for Biomedical Engineering and Physics at the Medical University of Vienna. He is also a reviewer and editorial board member for major journals in the field, program committee member for international conferences, and principal investigator for several third-party funded research projects. Previously, he served as senior researcher at the University Hospital Basel/Switzerland and associate professor of medical physics at the Center for Biomedical Engineering and Physics of Vienna Medical School.


"... very well constructed and extremely useful within its stated scope. The completeness of the treatment of topics, combined with the MATLAB examples of individual functions, is impressive. Examples are explained in great detail, with the command-line code presented, and explained, piece by piece. A student, or anyone else needing to develop image processing functions, will find this book very functional and valuable, both as a textbook and a self-contained reference." -Computing in Science & Engineering, July/August 2015 "The book is practical and accessible and has limited formalism. I do not know of any other books with this approach for medical image processing." -Professor Amir A. Amini, University of Louisville, Kentucky, USA "... a very useful book in an area that needs ongoing information transfer." -Professor Robert L. Galloway, Vanderbilt University, Nashville, Tennessee, USA "I mention the book every time I meet someone who asks what the best way is to get into this field." -Professor Leo Joskowicz, Head of Computer-Assisted Surgery and Medical Image Processing Laboratory, The Hebrew University of Jerusalem, Israel "The strengths of the book are undulated - it is an exceptionally useful, practical, and approachable tool for teaching medical image computing to undergraduate students." -Professor Gabor Fichtinger, Queen's University, Kingston, Ontario, Canada Praise for the First Edition: "The topics covered are clearly explained, including explanations of the mathematical operations that are required, therefore making it an ideal text for anyone who is new to medical image processing. ... an interesting and helpful introduction to medical image processing. ... This text is likely to be of interest to students starting work in medical image processing and would be a useful library text for hospital departments offering training in medical imaging." -Sarah Cade, Scope, December 2011 "The book ... achieves its purpose very well. ... The CD adds substantial value to the text and serves as an excellent guide to practice the information covered in the text. ... Several books on image processing have been published recently, and this book takes a backseat to none of them. ... Students who take a course where this book is used as the course text will be fortunate indeed." -William Hendee, Medical Physics, Vol. 37, December 2010 "... an outstanding work that will be of interest to virtually all biomedical engineers. The text is easy to follow, supposing only that the reader has a modest knowledge of linear algebra, basic engineering principles, and computer programming. I was impressed by the content as well as by the amount of information that is packed on each page. In each well-organized chapter, important concepts and definitions are described concisely and well. Relevant medical images used for processing complement many of the concepts discussed. Where important, the mathematical formulation is provided. The text and images refer to several MATLAB-based programming examples that are provided at the end of each chapter. These are useful to apply the concepts to actual medical image processing. The book can be used in part as an excellent reference work for biomedical engineers, scientists, and clinicians. This is a well-written, coherent, and comprehensive work covering the major topics in the field, suitable as a standalone text ... . The book is enjoyable to read, and students and professionals will not be bored when doing so. Engineers and scientists will find useful coverage of the field, and students will find the entire volume to be filled with important information." -Edward J. Ciaccio, Columbia University, New York, USA, BioMedical Engineering OnLine, 2011 "I have found this book very useful ... . It is comprehensive and well written." -Professor Terry Peters, Robarts Research Institute, University of Western Ontario, London, Ontario, Canada "This is a lucid, well-written, and hands-on textbook that explains in simple terms and with examples the basic issues of medical image processing. It contains many examples and useful programs." -Professor Leo Joskowicz, Head of Computer-Assisted Surgery and Medical Image Processing Laboratory, The Hebrew University of Jerusalem, Israel "The plethora of examples in each chapter ... allows the reader to apply the theory and visually assess the outcomes. This book is a perfect blend of theory and practice. I highly recommend it." -Dr. Pascal Fallavollita, Technical University of Munich, Germany "... significant and timely. It provides a cogent, not overly simplified, not excessively mathematical treatise of basic principles that the student, trainee, young scientist, and junior practitioner can readily grasp and apply. ... will help facilitate the ongoing, almost magical evolution of modem medical imaging ... they who read this book will be able to make 'a truly useful picture'." -From the Foreword by Richard A. Robb, Ph.D, Mayo Medical School, Rochester, Minnesota, USA

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