3d Virtual Histology Of Neuronal Tissue By Propagation Based X Ray Phase Contrast Tomography

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3d virtual histology of neuronal tissue by propagation-based x-ray phase-contrast tomography

Author : Mareike Töpperwien
Publisher : Göttingen University Press
ISBN 13 : 3863953649
Total Pages : 286 pages
Book Rating : 4.8/5 (639 download)

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Book Synopsis 3d virtual histology of neuronal tissue by propagation-based x-ray phase-contrast tomography by : Mareike Töpperwien

Download or read book 3d virtual histology of neuronal tissue by propagation-based x-ray phase-contrast tomography written by Mareike Töpperwien and published by Göttingen University Press. This book was released on 2018 with total page 286 pages. Available in PDF, EPUB and Kindle. Book excerpt: Deciphering the three-dimensional (3d) cytoarchitecture of neuronal tissue is an important step towards understanding the connection between tissue function and structure and determining relevant changes in neurodegenerative diseases. The gold standard in pathology is histology, in which the tissue is examined under a light microscope after serial sectioning and subsequent staining. It is an invasive and labor-intensive technique which is prone to artifacts due to the slicing procedure. While it provides excellent results on the 2d slices, the 3d anatomy can only be determined after aligning the individual sections, leading to a non-isotropic resolution within the tissue. X-ray computed tomography (CT) offers a promising alternative due to its potential resolution and large penetration depth which allows for non-invasive imaging of the sample's 3d density distribution. In classical CT, contrast formation is based on absorption of the x-rays as they pass through the sample. However, weakly absorbing samples like soft tissue from the central nervous system give nearly no contrast. By exploiting the much stronger phase shifts for contrast formation, which the sample induces in a (partially) coherent wavefront, it can be substantially increased. During free-space propagation behind the sample, these phase shifts are converted to a measurable intensity image by interference of the disturbed wave fronts. In this thesis, 3d virtual histology is performed by means of propagation-based x-ray phase-contrast tomography on tissue from the central nervous system of humans and mice. A combination of synchrotron-based and laboratory setups is used to visualize the 3d density distribution on varying lengths scales from the whole organ down to single cells. By comparing and optimizing different preparation techniques and phase-retrieval approaches, even sub-cellular resolution can be reached in mm-sized tissue blocks. The development of an automatic cell segmentation workflow provides access to the 3d cellular distribution within the tissue, enabling the quantification of the cellular arrangement and allowing for extensive statistical analysis based on several thousands to millions of cells. This paves the way for biomedical studies aimed at changes in cellular distribution, e.g., in the course of neurodegenerative diseases such as multiple sclerosis, Alzheimer's disease or ischemic stroke.

3d Virtual Histology of Neuronal Tissue by Propagation-based X-ray Phase-contrast Tomography

Author : Mareike Töpperwien
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (14 download)

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Book Synopsis 3d Virtual Histology of Neuronal Tissue by Propagation-based X-ray Phase-contrast Tomography by : Mareike Töpperwien

Download or read book 3d Virtual Histology of Neuronal Tissue by Propagation-based X-ray Phase-contrast Tomography written by Mareike Töpperwien and published by . This book was released on 2018 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Deciphering the three-dimensional (3d) cytoarchitecture of neuronal tissue is an important step towards understanding the connection between tissue function and structure and determining relevant changes in neurodegenerative diseases. The gold standard in pathology is histology, in which the tissue is examined under a light microscope after serial sectioning and subsequent staining. It is an invasive and labor-intensive technique which is prone to artifacts due to the slicing procedure. While it provides excellent results on the 2d slices, the 3d anatomy can only be determined after alignin...

Multi-scale 3D Virtual Histology Via Phase-contrast X-ray Tomography with Synchrotron Radiation

Author : Jasper Frohn
Publisher : Universitätsverlag Göttingen
ISBN 13 : 386395601X
Total Pages : 148 pages
Book Rating : 4.8/5 (639 download)

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Book Synopsis Multi-scale 3D Virtual Histology Via Phase-contrast X-ray Tomography with Synchrotron Radiation by : Jasper Frohn

Download or read book Multi-scale 3D Virtual Histology Via Phase-contrast X-ray Tomography with Synchrotron Radiation written by Jasper Frohn and published by Universitätsverlag Göttingen. This book was released on 2023 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: To this day, the standard method for investigating biological tissue with cellular resolution is the examination under a light microscope, first denoted as histology by Karl Meyer in 1819. Despite the enormous success and importance of histology, it has two major disadvantages. Firstly, the specimen must be physically cut into thin sections due to the limited penetrating power of optical light, and secondly, additional staining of the specimen is required to achieve sufficient image contrast. Both disadvantages can be overcome by the non-destructive method of propagation-based X-ray phase-contrast tomography. While the mechanism of phase-contrast provides sufficient image contrast to image single cells, a tomographic imaging scheme with penetrating X-rays allows for an undamaged sample by virtually slicing the reconstructed 3D sample volume. In this work, the holotomography setup of the synchrotron endstation „GINIX“ (The Göttingen Instrument for Nanoscale-Imaging with X-Rays) was extended to a multi-scale X-ray phase-contrast tomography setup suitable for 3D virtual histology by adding two acquisition schemes. Compared to the existing setup, the first additional scheme is a propagation-based microtomography setup, which enlarges the reconstructed 3D volumes by a factor of approx. 64 at a fraction of the acquisition time (ca. 2 min). The second additional scheme aims for higher resolutions. To this end, the X-ray waveguide illumination was combined with photon counting detector with a large field of view and a novel phase reconstruction scheme, which is based on iterative farfield phase retrieval without an „empty-beam correction“ in the detector plane.

Advancing the Characterization of Neuronal Cyto-Architecture by X-ray Phase-Contrast Tomography

Author : Marina Eckermann
Publisher : Universitätsverlag Göttingen
ISBN 13 : 3863955285
Total Pages : 276 pages
Book Rating : 4.8/5 (639 download)

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Book Synopsis Advancing the Characterization of Neuronal Cyto-Architecture by X-ray Phase-Contrast Tomography by : Marina Eckermann

Download or read book Advancing the Characterization of Neuronal Cyto-Architecture by X-ray Phase-Contrast Tomography written by Marina Eckermann and published by Universitätsverlag Göttingen. This book was released on 2021 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: To bring physiology and pathology of the human brain into better micro-anatomical and histological context, studies with different methodologies are required. Established techniques such as electron microscopy or histology show limitations in view of invasiveness, labor-intense and artifact-prone sample preparation, as well as an adequate ratio between resolution and volume throughput. For this reason, X-ray phase-contrast tomography (PC-CT) has been proposed as a three-dimensional non-destructive imaging technique, which requires less effort in sample preparation and can assess larger volumes. Furthermore, it offers quantitative electron density based contrast even for unstained tissue. Up to now, however, PC-CT studies fell short in number of samples, so that structural alterations caused by neurodegenerative diseases cannot be distinguished from physiological inter-subject variations. In this thesis, the scalability of PC-CT with respect to the required number of samples and resolution-to-volume-throughput is demonstrated, and the methodology is advanced with respect to data acquisition, processing and segmentation. In addition to the human cerebellum, cortex and hippocampus are studied. Concerning quantification and analysis of PC-CT data, this work introduces optimal transport analysis to obtain quantitative metrics of the cyto-architecture and to identify changes due to neurodegenerative diseases. For the case of Alzheimer’s disease, this workflow reveals a yet undescribed compactification of granular cells in the human hippocampus. This thesis also provides optimized configurations to study neural tissues with laboratory instrumentation, and – finally – provides new correlative imaging approaches, in particular with scanning electron microscopy.

Nanoscale Photonic Imaging

Author : Tim Salditt
Publisher : Springer Nature
ISBN 13 : 3030344134
Total Pages : 634 pages
Book Rating : 4.0/5 (33 download)

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Book Synopsis Nanoscale Photonic Imaging by : Tim Salditt

Download or read book Nanoscale Photonic Imaging written by Tim Salditt and published by Springer Nature. This book was released on 2020-06-09 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book, edited and authored by a team of world-leading researchers, provides a broad overview of advanced photonic methods for nanoscale visualization, as well as describing a range of fascinating in-depth studies. Introductory chapters cover the most relevant physics and basic methods that young researchers need to master in order to work effectively in the field of nanoscale photonic imaging, from physical first principles, to instrumentation, to mathematical foundations of imaging and data analysis. Subsequent chapters demonstrate how these cutting edge methods are applied to a variety of systems, including complex fluids and biomolecular systems, for visualizing their structure and dynamics, in space and on timescales extending over many orders of magnitude down to the femtosecond range. Progress in nanoscale photonic imaging in Göttingen has been the sum total of more than a decade of work by a wide range of scientists and mathematicians across disciplines, working together in a vibrant collaboration of a kind rarely matched. This volume presents the highlights of their research achievements and serves as a record of the unique and remarkable constellation of contributors, as well as looking ahead at the future prospects in this field. It will serve not only as a useful reference for experienced researchers but also as a valuable point of entry for newcomers.

X-ray Phase-Contrast Imaging Using Near-Field Speckles

Author : Marie-Christine Zdora
Publisher : Springer Nature
ISBN 13 : 3030663299
Total Pages : 337 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis X-ray Phase-Contrast Imaging Using Near-Field Speckles by : Marie-Christine Zdora

Download or read book X-ray Phase-Contrast Imaging Using Near-Field Speckles written by Marie-Christine Zdora and published by Springer Nature. This book was released on 2021-02-16 with total page 337 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis presents research on novel X-ray imaging methods that improve the study of specimens with small density differences, revealing their inner structure and density distribution. Exploiting the phase shift of X-rays in a material can significantly increase the image contrast compared to conventional absorption imaging. This thesis provides a practical guide to X-ray phase-contrast imaging with a strong focus on X-ray speckle-based imaging, the most recently developed phase-sensitive method. X-ray speckle-based imaging only requires a piece of abrasive paper in addition to the standard X-ray imaging setup. Its simplicity and robustness combined with the compatibility with laboratory X-ray sources, make it an ideal candidate for wide user uptake in a range of fields. An in-depth overview of the state of the art of X-ray speckle-based imaging and its latest developments is given in this thesis. It, furthermore, explores a broad range of applications, from X-ray optics characterisation, to biomedical imaging for 3D virtual histology and geological studies of volcanic rocks, demonstrating is promising potential. Moreover, the speckle-based technique is placed in the context of other phase-sensitive X-ray imaging methods to assist in the choice of a suitable method, hence serving as a guide and reference work for future users.

Advanced High-Resolution Tomography in Regenerative Medicine

Author : Alessandra Giuliani
Publisher : Springer
ISBN 13 : 303000368X
Total Pages : 232 pages
Book Rating : 4.0/5 (3 download)

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Book Synopsis Advanced High-Resolution Tomography in Regenerative Medicine by : Alessandra Giuliani

Download or read book Advanced High-Resolution Tomography in Regenerative Medicine written by Alessandra Giuliani and published by Springer. This book was released on 2018-11-19 with total page 232 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the state-of-the-art research on advanced high-resolution tomography, exploring its role in regenerative medicine. and also explores the 3D interactions between tissues, cells, and biomaterials. Various multidisciplinary paths in regenerative medicine are covered, including X-ray microtomography and its role in regenerative medicine, synchrotron radiation-based microtomography and phase contrast tomography, the challenge of the vascularization of regenerated tissues, lung and cartilage imaging, and more. This is an ideal book for biomedical engineers, biologists, physicists, clinicians, and students who want to pursue their studies in the field of regenerative medicine. This book also: Reviews in detail the algorithms and software used for the 3D exploration of regenerated tissue Covers the latest research on the use of X-ray microtomography for muscle diseases Details applications of synchrotron radiation tomography in orthopedics and dentistry

Medical Imaging Informatics

Author : Alex A.T. Bui
Publisher : Springer Science & Business Media
ISBN 13 : 1441903852
Total Pages : 454 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Medical Imaging Informatics by : Alex A.T. Bui

Download or read book Medical Imaging Informatics written by Alex A.T. Bui and published by Springer Science & Business Media. This book was released on 2009-12-01 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Medical Imaging Informatics provides an overview of this growing discipline, which stems from an intersection of biomedical informatics, medical imaging, computer science and medicine. Supporting two complementary views, this volume explores the fundamental technologies and algorithms that comprise this field, as well as the application of medical imaging informatics to subsequently improve healthcare research. Clearly written in a four part structure, this introduction follows natural healthcare processes, illustrating the roles of data collection and standardization, context extraction and modeling, and medical decision making tools and applications. Medical Imaging Informatics identifies core concepts within the field, explores research challenges that drive development, and includes current state-of-the-art methods and strategies.

MicroComputed Tomography

Author : Stuart R. Stock
Publisher : CRC Press
ISBN 13 : 1351835076
Total Pages : 299 pages
Book Rating : 4.3/5 (518 download)

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Book Synopsis MicroComputed Tomography by : Stuart R. Stock

Download or read book MicroComputed Tomography written by Stuart R. Stock and published by CRC Press. This book was released on 2018-10-03 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to the availability of commercial laboratory systems and the emergence of user facilities at synchrotron radiation sources, studies of microcomputed tomography or microCT have increased exponentially. MicroComputed Technology provides a complete introduction to the technology, describing how to use it effectively and understand its results. The first part of the book focuses on methodology, covering experimental methods, data analysis, and visualization approaches. The second part addresses various microCT applications, including porous solids, microstructural evolution, soft tissue studies, multimode studies, and indirect analyses. The author presents a sufficient amount of fundamental material so that those new to the field can develop a relative understanding of how to design their own microCT studies. One of the first full-length references dedicated to microCT, this book provides an accessible introduction to field, supplemented with application examples and color images.

Neurohistology and Imaging Techniques

Author : Radek Pelc
Publisher : Humana
ISBN 13 : 9781071604267
Total Pages : 471 pages
Book Rating : 4.6/5 (42 download)

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Book Synopsis Neurohistology and Imaging Techniques by : Radek Pelc

Download or read book Neurohistology and Imaging Techniques written by Radek Pelc and published by Humana. This book was released on 2020-06-25 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores major light microscopic imaging modalities that can be used to view nervous tissue, and discusses the steps needed to use each of them, and ways to interpret the data. The chapters in this book cover topics such as atlasing of insect brain; neuroanatomical tracing through fluorochrome expression; fluorescent probes for amyloids; or optical clearing for ultramicroscopy of GFP-expressing tissues. In the Neuromethods series style, chapters include the kind of detail and key advice from the specialists needed to get successful results in your laboratory. Authoritative and cutting-edge, Neurohistology and Imaging Techniques is a valuable resource for both expert and novice users of major light microscopic imaging techniques, and those interested in exploring alternate imaging tools.

Phase-Contrast and Dark-Field Imaging

Author : Simon Zabler
Publisher : MDPI
ISBN 13 : 3038972843
Total Pages : 147 pages
Book Rating : 4.0/5 (389 download)

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Book Synopsis Phase-Contrast and Dark-Field Imaging by : Simon Zabler

Download or read book Phase-Contrast and Dark-Field Imaging written by Simon Zabler and published by MDPI. This book was released on 2019-01-08 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "Phase-Contrast and Dark-Field Imaging" that was published in J. Imaging

Molecular Imaging

Author : Brian D. Ross
Publisher : Elsevier
ISBN 13 : 0128206365
Total Pages : 1074 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Molecular Imaging by : Brian D. Ross

Download or read book Molecular Imaging written by Brian D. Ross and published by Elsevier. This book was released on 2021 with total page 1074 pages. Available in PDF, EPUB and Kindle. Book excerpt:

X-ray waveguide optics

Author : Sarah Hoffmann-Urlaub
Publisher : Göttingen University Press
ISBN 13 : 3863953088
Total Pages : 134 pages
Book Rating : 4.8/5 (639 download)

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Book Synopsis X-ray waveguide optics by : Sarah Hoffmann-Urlaub

Download or read book X-ray waveguide optics written by Sarah Hoffmann-Urlaub and published by Göttingen University Press. This book was released on 2017 with total page 134 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modern x-ray sources and analysis techniques such as lens less imaging combined with phase retrieval algorithms allow for resolving structure sizes in the nanometer range. For this purpose optics have to be employed, ensuring small focal spot dimensions simultaneously with high photon densities. Furthermore, the wave front behind the optics is required to be smooth enabling for high resolution imaging. Combining all these properties, x-ray waveguides are well suited to perform this task, since the intensity distribution behind the guide is restricted in two dimensions serving as a secondary quasi point-source without wave-front aberrations, showing also a high divergence, suitable for resolving fine features. Importantly, the radiation provided by the waveguide reveals a high degree of coherence, required by many imaging techniques. The waveguide itself consists of an air-filled channel embedded in a solid matrix; typical materials are silicon, germanium or quartz. While the entrance area is nano-sized, the channel length is in the millimeter-range, this way posing challenges to fabricate high aspect ratio geometries. Since the functioning of x-ray waveguides is based on the total reflection at small incident angles, the surface roughness of the channel walls must be as low as possible to avoid scattering and hence loss of intensity. To fulfill these demanding conditions, a process scheme involving spin-coating, electron beam lithography, wet development, reactive ion etching and wafer bonding is optimized within this work. To gain deeper insights into the principle of wave guiding finite difference simulations are performed, also opening access for advanced design considerations such as gratings, tapered and curved channels, or beamsplitters, enabling for constructing novel x-ray tools as for example time delay devices or interferometers. Waveguides in all geometries are tested at synchrotron sources, accomplishing new benchmarks in x-ray optical performance. Here, the x-ray beam leaving the channel, propagates out to a pixel array detector in the far-field region. From the recorded data the intensity distribution in the near-field directly behind the waveguide is reconstructed, revealing an outstanding agreement with the simulations and electron micrographs. Since the radiation field of the waveguide is well-characterized and also tunable to meet the requirements of both the measurement setup and the sample, they are suited of a broad field of applications in coherent x-ray imaging.

Medical Imaging Systems

Author : Andreas Maier
Publisher : Springer
ISBN 13 : 3319965204
Total Pages : 263 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis Medical Imaging Systems by : Andreas Maier

Download or read book Medical Imaging Systems written by Andreas Maier and published by Springer. This book was released on 2018-08-02 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book gives a complete and comprehensive introduction to the fields of medical imaging systems, as designed for a broad range of applications. The authors of the book first explain the foundations of system theory and image processing, before highlighting several modalities in a dedicated chapter. The initial focus is on modalities that are closely related to traditional camera systems such as endoscopy and microscopy. This is followed by more complex image formation processes: magnetic resonance imaging, X-ray projection imaging, computed tomography, X-ray phase-contrast imaging, nuclear imaging, ultrasound, and optical coherence tomography.

Fish as Model Organism for Skeletal Diseases

Author : Erika Kague
Publisher : Frontiers Media SA
ISBN 13 : 2832540562
Total Pages : 224 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Fish as Model Organism for Skeletal Diseases by : Erika Kague

Download or read book Fish as Model Organism for Skeletal Diseases written by Erika Kague and published by Frontiers Media SA. This book was released on 2023-11-30 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Coherent X-Ray Optics

Author : David Paganin
Publisher : OUP Oxford
ISBN 13 : 019152431X
Total Pages : 424 pages
Book Rating : 4.1/5 (915 download)

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Book Synopsis Coherent X-Ray Optics by : David Paganin

Download or read book Coherent X-Ray Optics written by David Paganin and published by OUP Oxford. This book was released on 2006-01-12 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book gives a thorough treatment of the rapidly-expanding field of coherent x-ray optics, which has recently experienced something of a renaissance with the availability of third-generation synchrotron sources. It is the first book of its kind. The author begins with a treatment of the fundamentals of x-ray diffraction for both coherent and partially coherent radiation, together with the interactions of x-rays with matter. X-ray sources, optics elements and detectors are then discussed, with an emphasis on their role in coherent x-ray optics. Various facets of coherent x-ray imaging are then discussed, including holography, interferometry, self imaging, phase contrast and phase retrieval. Lastly, the foundations of the new field of singular x-ray optics are examined. Most topics are developed from first principles, with numerous references given to the contemporary research literature. This book will be useful to x-ray physicists and students, together with optical physicists and engineers who wish to learn more about the fascinating subject of coherent x-ray optics.

Biomedical Data Mining for Information Retrieval

Author : Sujata Dash
Publisher : John Wiley & Sons
ISBN 13 : 111971124X
Total Pages : 450 pages
Book Rating : 4.1/5 (197 download)

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Book Synopsis Biomedical Data Mining for Information Retrieval by : Sujata Dash

Download or read book Biomedical Data Mining for Information Retrieval written by Sujata Dash and published by John Wiley & Sons. This book was released on 2021-08-24 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: BIOMEDICAL DATA MINING FOR INFORMATION RETRIEVAL This book not only emphasizes traditional computational techniques, but discusses data mining, biomedical image processing, information retrieval with broad coverage of basic scientific applications. Biomedical Data Mining for Information Retrieval comprehensively covers the topic of mining biomedical text, images and visual features towards information retrieval. Biomedical and health informatics is an emerging field of research at the intersection of information science, computer science, and healthcare and brings tremendous opportunities and challenges due to easily available and abundant biomedical data for further analysis. The aim of healthcare informatics is to ensure the high-quality, efficient healthcare, better treatment and quality of life by analyzing biomedical and healthcare data including patient’s data, electronic health records (EHRs) and lifestyle. Previously, it was a common requirement to have a domain expert to develop a model for biomedical or healthcare; however, recent advancements in representation learning algorithms allows us to automatically to develop the model. Biomedical image mining, a novel research area, due to the vast amount of available biomedical images, increasingly generates and stores digitally. These images are mainly in the form of computed tomography (CT), X-ray, nuclear medicine imaging (PET, SPECT), magnetic resonance imaging (MRI) and ultrasound. Patients’ biomedical images can be digitized using data mining techniques and may help in answering several important and critical questions relating to healthcare. Image mining in medicine can help to uncover new relationships between data and reveal new useful information that can be helpful for doctors in treating their patients. Audience Researchers in various fields including computer science, medical informatics, healthcare IOT, artificial intelligence, machine learning, image processing, clinical big data analytics.