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This section incorporates all aspects of imaging and bioimage informatics, including but not limited to: microscopic and biomedical image acquisition methods and applications, methods and applications of image analysis and related machine learning, pattern recognition and data mining techniques, image oriented multidimensional data and metadata visualization techniques, methods and applications of bioimage annotation and ontology generation. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta Citation: BMC Bioinformatics 21 Content type: Methodology article.
Imaging, image analysis and data visualization
Editorial Reviews. From the Back Cover. This content was uploaded by our users and we assume good faith they have the permission to share this book. If you own the copyright to this book and it is wrongfully on our website, we offer a simple DMCA procedure to remove your content from our site. Start by pressing the button below! All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed.
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The publisher makes no warranty, express or implied, with respect to the material contained herein. Philip Batchelor, who tragically died in a climbing accident while close to completing work on Chapter Born in Cornwall in England but brought up in Vouvry in Switzerland he was always proud of both sides to his heritage. A truly gifted mathematician, he devoted his talents to medical imaging, where he made many valuable contributions.
In diffusion imaging, he provided a mathematical framework for the treatment of tensors, leading to the geodesic anisotropy measure. More recently, he and co-workers made significant progress in tackling the hugely difficult task of diffusion tensor imaging of the beating heart. He always had time for students, colleagues and anyone who sought his advice. His insight into problems in three dimensions and higher benefited many who were lucky enough to work with him.
He would have been delighted to pass on some of his knowledge in this book. Beyond his scientific abilities, it is his warmth, generosity of spirit and consistent smile that will be remembered with affection by colleagues, friends and family alike.
Preface This book is primarily a graduate text on 3D imaging, shape analysis and associated applications. In addition to serving masters-level and doctoral-level research students, much of the text is accessible enough to be useful to final-year undergraduate project students.
Also, we hope that it will serve wider audiences; for example, as a reference text for professional academics, people working in commercial research and development labs and industrial practitioners. We believe that this text is unique in the literature on 3D imaging in several respects: 1 it provides a wide coverage of topics in 3D imaging; 2 it pays special attention to the clear presentation of well-established core techniques; 3 it covers a wide range of the most promising recent techniques that are considered to be stateof-the-art; 4 it is the first time that so many world-leading academics have come together on this range of 3D imaging topics.
Firstly, we ask: why is 3D imaging so interesting to study, research and develop? Why is it so important to our society, economy and culture? This leads us to the field of computer vision and ultimately to the subject of this book: 3D imaging.
Biological Vision Systems It is worth reflecting on the obvious fact that the importance of images, in their very general sense paintings, digital photographs, etc. For many animals, including humans, the eye-brain vision system constitutes an indispensable, highly information-rich mode of sensory perception. The evolution of this system has been driven by aspects of our particular optical world: with the Sun we have a natural source of light; air is transparent, which allows our environment to be illuminated; the wavelength of light is small enough to be scattered by vii viii Preface most surfaces, which means that we can gather light reflected off them from many different viewpoints, and it is possible to form an image with a relatively simple structure such as a convex lens.
It is easy to appreciate the utility and advantages of visual perception, which provides a means to sense the environment in a comprehensive, non-contact way. Indeed, evolutionary biologists have proposed that the development of vision intensified predation and sparked an evolutionary arms race between predators and prey.
Thus biological vision systems exist as a result of evolutionary survival and have been present on Earth for a very long time. Today, there is comprehensive research literature in visual psychophysics, the study of eyesight.
Visual illusions suggest that, for some 3D cues, humans use a lot of assumptions about their environment, when inferring 3D shape. The study of how depth perception depends on several visual and oculomotor cues has influenced the development of modern techniques in 3D imaging. Ideas have also flowed in the opposite direction: results from computer vision indicate what information can be extracted from raw visual data, thereby inspiring theories of human visual perception.
Visual Representations from Paintings to Photographs A drawing, painting or photograph can be viewed as a form of visual expression and communication.
Drawing and painting has a very long history and several discoveries of very old cave paintings have been made, for example, those in the Chauvet cave France are more than 32, years old. Throughout the history of mankind, the use of paintings, drawings and automatically captured images has been culturally important in many different ways. In terms of the subject matter of this book, the advent of photography in the early 19th century was an important milestone, enabling light reflected from an object or scene to be recorded and retained in a durable way.
Photographs have many advantages, such as an accurate, objective visual representation of the scene and a high level of autonomy in image capture. Once photography was born, it was soon realized that measurements of the imaged scene could be made; for example, a map could be built from photographs taken from a balloon.
Thus the field of photogrammetry was born, which focuses on extracting accurate measurements from images this is now often included under the banner of remote sensing. The work done in this field, from the midth to the midth century, is an essential historical precursor to the material presented in this book. The creation, distribution, analysis and intelligent use of digital information now has a wide range of impacts on everyone in the developed world, throughout all stages of their lives.
This can be Preface ix anything from the way in which we do our jobs, to the way our health is managed by our doctors; to how our safety is secured on public transport, during air travel and in public spaces; to how our financial systems work; to how we manage our shopping and leisure time.
Of course, many of these impacts have been brought about by the advances in computing and communications technology over the past few decades, with the most obvious examples being the Internet, the world wide web and, more recently, mobile access to these resources over wide-bandwidth, wireless technologies. The information that we use is often described as being multi-media, in the sense that it includes text, audio, graphical figures, images, video and interactive content. Of these different forms, images have always played a hugely important role for obvious reasons: they can convey a huge amount of information in a compact form, they clarify concepts and ideas that are difficult to describe in words, they draw in their audience by making documents more visually appealing and they relate directly to our primary non-contact mechanism for sensing our environment we humans live and interact in a visual world.
For these reasons, images will always be important, but recent advances in both hardware and software technologies are likely to amplify this. For example, digital cameras are now embedded in many devices such as smartphones and the relatively recent explosion in social networking allows groups of people to share images.
Computer Vision The information society brings with it such a large number of images that we can not hope to analyze them all manually-consider for example the number of images from the security surveillance of a large city over a 24 hour period.
The goal of computer vision is to automate the analysis of images through the use of computers and the material presented in this book fits that high level aim. Since there are a large number of ways in which we use images, there is a correspondingly large number of applications of computer vision. In general, automation can improve image analysis performance people get boredit increases coverage, it reduces operating costs and, in some applications, it leads to improved safety e.
The last four decades has seen the rapid evolution of imaging technology and computing power, which has fed the growth of the field of computer vision and the related fields of image analysis and pattern recognition. The Limitations of Standard 2D Images Most of the images in our information society are standard 2D color-texture images i.
Many of these difficulties stem from the fact that the 3D world is projected down onto a 2D image, thus losing depth information and creating ambiguity. For example, in a 2D image: how do we segment foreground objects from the background? How can we recognize the same object from different viewpoints?
How do we deal with ambiguity between object size and distance from the camera? To compound these problems, there is also the issue of how to deal with varying illumination, which can make the same object appear quite different when imaged. This is referred to as a 3D scan or 3D image and it often comes with a registered color-texture image that can be pasted over the captured shape and rendered from many viewpoints if desired on a computer display. The techniques developed include both active systems, where some form of illumination is projected onto the scene and passive systems, where the natural illumination of the scene is used.
Perhaps the most intensively researched area of 3D shape acquisition has been focused on stereo vision systems, which, like the human visual system, uses a pair of views images in order to compute 3D structure.
Here, researchers have met challenging problems such as the establishment of correspondences between overlapping images for the dense reconstruction of the imaged scene.
Many applications require further processing and data analysis, once 3D shape data has been acquired. For example, identification of salient points within the 3D data, registration of multiple partial 3D data scans, computation of 3D symmetry planes and matching of whole 3D objects. The different steps of this pipeline have raised important topics in the research community for decades, owing to the numerous theoretical and technical problems that they induce.
Capturing the 3D shape, instead of just a 2D projection as a standard camera does, makes an extremely wide array of new kinds of application possible. For instance, 3D and free-viewpoint TV, virtual and augmented reality, natural user interaction based on monitoring gestures, 3D object recognition and 3D recognition for biometry, 3D medical imaging, 3D remote sensing, industrial inspection, robot navigation, to name just a few. These applications, of course, involve much more technological advances than just 3D shape capture: storage, analysis, transmission and visualization of the 3D shape are also part of the whole pipeline.
Preface xi 3D imaging and analysis is closely associated with computer vision, but it also intersects with a number of other fields, for example: image processing, pattern recognition, computer graphics, computational geometry and physics. It involves building sensors, modeling them and then processing the output images.
In particular, 3D image analysis bridges the gap between low-level and high-level vision in order to deduce high-level semantic information from basic 3D data. Book Objective and Content The objective of this book is to bring together a set of core topics in 3D imaging, analysis and applications, both in terms of well-established fundamental techniques and the most promising recent techniques.
Indeed, we see that many similar techniques are being used in a variety of subject areas and applications and we feel that we can unify a range of related ideas, providing clarity to both academic and industrial practitioners, who are acquiring and processing 3D datasets. To ensure the quality of the book, all contributors have attained a world-class standing by publishing in the top conferences and journals in this area.
Thus, the material presented in this book is informative and authoritative and represents mainstream work and opinions within the community. After an introductory chapter, the book covers 3D image capture methods, particularly those that use two cameras, as in passive stereo vision, or a camera and light projector, as in active stereo vision.
It also covers how 3D data is represented, stored and visualized. Later parts of the book cover the analysis and processing of 3D images, firstly in a general sense, which includes feature extraction, shape registration and shape matching, and then with a view to a range of applications including 3D object recognition, 3D object retrieval shape search3D face recognition, 3D mapping and 3D medical imaging.
The idea to produce a new book on 3D imaging was originated by Yonghuai Liu, while Nick Pears was responsible for coordinating the authoring. Acknowledgements We would like to express our sincere gratitude to all chapter authors for their contributions, their discussions and their support during the book preparation.
It has been our honor to work with so many truly world leading academics and, without them, the production of this book would have not been possible.
We would also like to thank all of the chapter reviewers for their insightful comments, which have enabled us to produce a high quality book. Special thanks to Adrien Bartoli and Umberto Castellani for contributing ideas to the preface of this book. We are grateful for the support of our publisher, Springer; in particular, we would like to thank Helen Desmond, Ben Bishop, Beverley Ford and Catherine Moore from Springer UK, who worked with us in a friendly and effective way throughout all stages of the book production process.
Bronstein, Michael M. Batchelor, P. King Index. The former uses ambient illumination i. Chapter 4 discusses how to represent the captured data, both for efficient algorithmic 3D data processing and efficient data storage. This provides a bridge to the following part of the book, which deals with 3D shape analysis and processing.
Chapter 2 Passive 3D Imaging Stephen Se and Nick Pears Abstract We describe passive, multiple-view 3D imaging systems that recover 3D information from scenes that are illuminated only with ambient lighting.
Much of the material is concerned with using the geometry of stereo 3D imaging to formulate estimation problems. Firstly, we present an overview of the common techniques used to recover 3D information from camera images. Secondly, we discuss camera modeling and camera calibration as an essential introduction to the geometry of the imaging process and the estimation of geometric parameters.
Thirdly, we focus on 3D recovery from multiple views, which can be obtained using multiple cameras at the same time stereoor a single moving camera at different times structure from motion. Epipolar geometry and finding image correspondences associated with the same 3D scene point are two key aspects for such systems, since epipolar geometry establishes the relationship between two camera views, while depth information can be inferred from the correspondences.
3d imaging analysis and applications pdf reader
This textbook is designed for postgraduate studies in the field of 3D Computer Vision. It also provides a useful reference for industrial practitioners; for example, in the areas of 3D data capture, computer-aided geometric modelling and industrial quality assurance. This second edition is a significant upgrade of existing topics with novel findings. Additionally, it has new material covering consumer-grade RGB-D cameras, 3D morphable models, deep learning on 3D datasets, as well as new applications in the 3D digitization of cultural heritage and the 3D phenotyping of crops. Overall, the book covers three main areas:nbsp; 3D imaging, including passive 3D imaging, active triangulation 3D imaging, active time-of-flight 3D imaging, consumer RGB-D cameras, and 3D data representation and visualisation; nbsp; 3D shape analysis, including local descriptors, registration, matching, 3D morphable models, and deep learning on 3D datasets; and nbsp; 3D applications, including 3D face recognition, cultural heritage and 3D phenotyping of plants. There are many real-world applications that demand high-performance 3D imaging and analysis and, as a result, many new techniques and commercial products have been developed. However, many challenges remain on how to analyse the captured data in a way that is sufficiently fast, robust and accurate for the application.
Image analysis is the extraction of meaningful information from images ; mainly from digital images by means of digital image processing techniques. Computers are indispensable for the analysis of large amounts of data, for tasks that require complex computation, or for the extraction of quantitative information. On the other hand, the human visual cortex is an excellent image analysis apparatus, especially for extracting higher-level information, and for many applications — including medicine, security, and remote sensing — human analysts still cannot be replaced by computers. For this reason, many important image analysis tools such as edge detectors and neural networks are inspired by human visual perception models. Digital Image Analysis or Computer Image Analysis is when a computer or electrical device automatically studies an image to obtain useful information from it.
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3D Imaging, Analysis and Applications by Nick Pears
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It seems that you're in Germany. We have a dedicated site for Germany. Many similar techniques are being used in a variety of subject areas and applications and the authors attempt to unify a range of related ideas. With contributions from high profile researchers and practitioners, the material presented is informative and authoritative and represents mainstream work and opinions within the community. Composed of three sections, the first examines 3D imaging and shape representation, the second, 3D shape analysis and processing, and the last section covers 3D imaging applications. Although 3D Imaging, Analysis and Applications is primarily a graduate text, aimed at masters-level and doctoral-level research students, much material is accessible to final-year undergraduate students. It will also serve as a reference text for professional academics, people working in commercial research and development labs and industrial practitioners.
Once production of your article has started, you can track the status of your article via Track Your Accepted Article. Help expand a public dataset of research that support the SDGs. Medical Image Analysis provides a forum for the dissemination of new research results in the field of medical and biological image analysis , with special emphasis on efforts related to the applications of computer vision , virtual reality and robotics to biomedical imaging problems. The journal publishes The journal publishes the highest quality, original papers that contribute to the basic science of processing, analysing and utilizing medical and biological images for these purposes.
Editorial Reviews. From the Back Cover. This content was uploaded by our users and we assume good faith they have the permission to share this book. If you own the copyright to this book and it is wrongfully on our website, we offer a simple DMCA procedure to remove your content from our site.
Many similar techniques are beingMore3D Imaging, Analysis and Applications brings together core topics, both in terms of well-established fundamental techniques and the most promising recent techniques in the exciting field of 3D imaging and analysis. Many similar techniques are being used in a variety of subject areas and applications and the authors attempt to unify a range of related ideas. With contributions from high profile researchers and practitioners, the material presented is informative and authoritative and represents mainstream work and opinions within the community. Composed of three sections, the first examines 3D imaging and shape representation, the second, 3D shape analysis and processing, and the last section covers 3D imaging applications.
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