In Vivo Assessment of the Neural Substrate Linked with Vocal Imitation
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Management of Large Sets of Image Data Capture, Databases, Image Processing, Storage, Visualization Karol Kozak
Management of large sets of image data Capture, Databases, Image Processing, Storage, Visualization Karol Kozak Download free books at Karol Kozak Management of large sets of image data Capture, Databases, Image Processing, Storage, Visualization Download free eBooks at bookboon.com 2 Management of large sets of image data: Capture, Databases, Image Processing, Storage, Visualization 1st edition © 2014 Karol Kozak & bookboon.com ISBN 978-87-403-0726-9 Download free eBooks at bookboon.com 3 Management of large sets of image data Contents Contents 1 Digital image 6 2 History of digital imaging 10 3 Amount of produced images – is it danger? 18 4 Digital image and privacy 20 5 Digital cameras 27 5.1 Methods of image capture 31 6 Image formats 33 7 Image Metadata – data about data 39 8 Interactive visualization (IV) 44 9 Basic of image processing 49 Download free eBooks at bookboon.com 4 Click on the ad to read more Management of large sets of image data Contents 10 Image Processing software 62 11 Image management and image databases 79 12 Operating system (os) and images 97 13 Graphics processing unit (GPU) 100 14 Storage and archive 101 15 Images in different disciplines 109 15.1 Microscopy 109 360° 15.2 Medical imaging 114 15.3 Astronomical images 117 15.4 Industrial imaging 360° 118 thinking. 16 Selection of best digital images 120 References: thinking. 124 360° thinking . 360° thinking. Discover the truth at www.deloitte.ca/careers Discover the truth at www.deloitte.ca/careers © Deloitte & Touche LLP and affiliated entities. Discover the truth at www.deloitte.ca/careers © Deloitte & Touche LLP and affiliated entities. -
Accurate Segmentation of Brain MR Images
Accurate segmentation of brain MR images Master of Science Thesis in Biomedical Engineering ANTONIO REYES PORRAS PÉREZ Department of Signals and Systems Division of Biomedical Engineering CHALMERS UNIVERSITY OF TECHNOLOGY Göteborg, Sweden, 2010 Report No. EX028/2010 Abstract Full brain segmentation has been of significant interest throughout the years. Recently, many research groups worldwide have been looking into development of patient-specific electromagnetic models for dipole source location in EEG. To obtain this model, accurate segmentation of various tissues and sub-cortical structures is thus required. In this project, the performance of three of the most widely used software packages for brain segmentation has been analyzed: FSL, SPM and FreeSurfer. For the analysis, real images from a patient and a set of phantom images have been used in order to evaluate the performance r of each one of these tools. Keywords: dipole source location, brain, patient-specific model, image segmentation, FSL, SPM, FreeSurfer. Acknowledgements To my advisor, Antony, for his guidance through the project. To my partner, Koushyar, for all the days we have spent in the hospital helping each other. To the staff in Sahlgrenska hospital for their collaboration. To MedTech West for this opportunity to learn. Table of contents 1. Introduction ......................................................................................................................................... 1 2. Magnetic resonance imaging .............................................................................................................. -
1 Structural and Functional Alterations in the Brain Gray Matter
Structural and functional alterations in the brain gray matter among first-degree relatives of schizophrenia patients: a multimodal meta-analysis of fMRI and VBM studies Running title: Familial risk for schizophrenia and alterations in the brain Aino I. L. Saarinen, PhD1,2,3,*, Sanna Huhtaniska, MD, PhD4, Juho Pudas, MB3, Lassi Björnholm, MD3, Tuomas Jukuri, MD, PhD3, Jussi Tohka, MD, PhD5, Niklas Granö, PhD6, Jennifer H. Barnett, PhD7,8, Vesa Kiviniemi, MD, PhD9,10, Juha Veijola, MD, PhD3,10,11, Mirka Hintsanen, PhD1, Johannes Lieslehto, MD, PhD 12 1 Research Unit of Psychology, University of Oulu, Finland 2 Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland 3 Research Unit of Clinical Neuroscience, Department of Psychiatry, University of Oulu, Finland 4 Center for Life Course Health Research, University of Oulu, Finland 5 A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland 6 Helsinki University Hospital, Department of Adolescent Psychiatry, Finland 7 Cambridge Cognition, Cambridge, UK 8 Department of Psychiatry, University of Cambridge, Cambridge, UK 9 Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland 10 Department of Psychiatry, Oulu University Hospital, Oulu, Finland 11 Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland 12 Section for Neurodiagnostic Applications, Department of Psychiatry, Ludwig Maximilian University, Nussbaumstrasse 7, 80336 Munich, Bavaria, * Corresponding author: Aino Saarinen. Department of Psychology and Logopedics, Faculty of Medicine, Haartmaninkatu 3, P.O. Box 21, 00014 University of Helsinki, Finland. E-mail: [email protected], Tel.: +35844 307 1204. 1 Abstract Objective: Schizophrenia has one of the highest heritability estimates in psychiatry, but the genetically- based underlying neuropathology has mainly remained unclear. -
Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting
UNIVERSITY OF PADOVA Department of Information Engineering Ph.D. School on Information Engineering Curriculum: Bioengineering - Cycle: XXX Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting Headmaster of the School: Prof. Andrea NEVIANI Supervisor: Prof. Alessandra BERTOLDO PhD. Candidate: Eng. Erica SILVESTRI 2018 iii University of Padova Abstract Ph.D. School on Information Engineering Simultaneous PET/MRI for Connectivity Mapping: Quantitative Methods in Clinical Setting by Eng. Erica SILVESTRI In recent years, the study of brain connectivity has received growing inter- est from neuroscience field, from a point of view both of analysis of patho- logical condition and of a healthy brain. Hybrid PET/MRI scanners are promising tools to study this complex phenomenon. This thesis presents a general framework for the acquisition and analysis of simultaneous multi- modal PET/MRI imaging data to study brain connectivity in a clinical set- ting. Several aspects are faced ranging from the planning of an acquisition protocol consistent with clinical constraint to the off-line PET image recon- struction, from the selection and implementation of methods for quantifying the acquired data to the development of methodologies to combine the com- plementary informations obtained with the two modalities. The developed analysis framework was applied to two different studies, a first conducted on patients affected by Parkinson’s Disease and dementia, and a second one on high grade gliomas, as proof of concept evaluation that the pipeline can be extended in clinical settings. v Università degli Studi di Padova Sommario Scuola di Dottorato in Ingegneria dell’Informazione Acquisizioni simultanee PET/MR per lo studio della connettività: metodi quantitativi in ambito clinico di Ing. -
Medical Image Processing Software
Wohlers Report 2018 Medical Image Processing Software Medical image Patient-specific medical devices and anatomical models are almost always produced using radiological imaging data. Medical image processing processing software is used to translate between radiology file formats and various software AM file formats. Theoretically, any volumetric radiological imaging dataset by Andy Christensen could be used to create these devices and models. However, without high- and Nicole Wake quality medical image data, the output from AM can be less than ideal. In this field, the old adage of “garbage in, garbage out” definitely applies. Due to the relative ease of image post-processing, computed tomography (CT) is the usual method for imaging bone structures and contrast- enhanced vasculature. In the dental field and for oral- and maxillofacial surgery, in-office cone-beam computed tomography (CBCT) has become popular. Another popular imaging technique that can be used to create anatomical models is magnetic resonance imaging (MRI). MRI is less useful for bone imaging, but its excellent soft tissue contrast makes it useful for soft tissue structures, solid organs, and cancerous lesions. Computed tomography: CT uses many X-ray projections through a subject to computationally reconstruct a cross-sectional image. As with traditional 2D X-ray imaging, a narrow X-ray beam is directed to pass through the subject and project onto an opposing detector. To create a cross-sectional image, the X-ray source and detector rotate around a stationary subject and acquire images at a number of angles. An image of the cross-section is then computed from these projections in a post-processing step. -
Avizo Software for Industrial Inspection
Avizo Software for Industrial Inspection Digital inspection and materials analysis Digital workflow Thermo Scientific™ Avizo™ Software provides a comprehensive set of tools addressing the whole research-to-production cycle: from materials research in off-line labs to automated quality control in production environments. 3D image data acquisition Whatever the part or material you need to inspect, using © RX Solutions X-ray CT, radiography, or microscopy, Avizo Software is the solution of choice for materials characterization and defect Image processing detection in a wide range of areas (additive manufacturing, aerospace, automotive, casting, electronics, food, manufacturing) and for many types of materials (fibrous, porous, metals and alloys, ceramics, composites and polymers). Avizo Software also provides dimensional metrology with Visual inspection Dimensional metrology Material characterization advanced measurements; an extensive set of programmable & defect analysis automated analysis workflows (recipes); reporting and traceability; actual/nominal comparison by integrating CAD models; and a fully automated in-line inspection framework. With Avizo Software, reduce your design cycle, inspection times, and meet higher-level quality standards at a lower cost. + Creation and automation of inspection and analysis workflows + Full in-line integration Reporting & traceability On the cover: Porosity analysis and dimensional metrology on compressor housing. Data courtesy of CyXplus 2 3 Avizo Software for Industrial Inspection Learn more at thermofisher.com/amira-avizo Integrating expertise acquired over more than 10 years and developed in collaboration with major industrial partners in the aerospace, Porosity analysis automotive, and consumer goods industries, Avizo Software allows Imaging techniques such as CT, FIB-SEM, SEM, and TEM, allow detection of structural defects in the to visualize, analyze, measure and inspect parts and materials. -
Respiratory Adaptation to Climate in Modern Humans and Upper Palaeolithic Individuals from Sungir and Mladeč Ekaterina Stansfeld1*, Philipp Mitteroecker1, Sergey Y
www.nature.com/scientificreports OPEN Respiratory adaptation to climate in modern humans and Upper Palaeolithic individuals from Sungir and Mladeč Ekaterina Stansfeld1*, Philipp Mitteroecker1, Sergey Y. Vasilyev2, Sergey Vasilyev3 & Lauren N. Butaric4 As our human ancestors migrated into Eurasia, they faced a considerably harsher climate, but the extent to which human cranial morphology has adapted to this climate is still debated. In particular, it remains unclear when such facial adaptations arose in human populations. Here, we explore climate-associated features of face shape in a worldwide modern human sample using 3D geometric morphometrics and a novel application of reduced rank regression. Based on these data, we assess climate adaptations in two crucial Upper Palaeolithic human fossils, Sungir and Mladeč, associated with a boreal-to-temperate climate. We found several aspects of facial shape, especially the relative dimensions of the external nose, internal nose and maxillary sinuses, that are strongly associated with temperature and humidity, even after accounting for autocorrelation due to geographical proximity of populations. For these features, both fossils revealed adaptations to a dry environment, with Sungir being strongly associated with cold temperatures and Mladeč with warm-to-hot temperatures. These results suggest relatively quick adaptative rates of facial morphology in Upper Palaeolithic Europe. Te presence and the nature of climate adaptation in modern humans is a highly debated question, and not much is known about the speed with which these adaptations emerge. Previous studies demonstrated that the facial morphology of recent modern human groups has likely been infuenced by adaptation to cold and dry climates1–9. Although the age and rate of such adaptations have not been assessed, several lines of evidence indicate that early modern humans faced variable and sometimes harsh environments of the Marine Isotope Stage 3 (MIS3) as they settled in Europe 40,000 years BC 10. -
3D Medical Image Segmentation in Virtual Reality
3D Medical Image Segmentation in Virtual Reality Shea B. Yonker, Oleksandr O. Korshak, Timothy Hedstrom, Alexander Wu, Siddharth Atre, Jürgen P. Schulze University of California San Diego, La Jolla, CA Abstract inside, all by using their hands like they would in the real world. The possible achievements of accurate and intuitive 3D In fact, our application goes beyond simulating what one could image segmentation are endless. For our specific research, we do in the real world by allowing the user to reach into the data aim to give doctors around the world, regardless of their set as if it is a hologram. computer knowledge, a virtual reality (VR) 3D image Finally, to more particularly examine one aspect of the segmentation tool which allows medical professionals to better data, our program allows for segmentation of this 3D image. For visualize their patients' data sets, thus attaining the best humans, looking at an image and deciphering foreground vs. understanding of their respective conditions. background is in most cases trivial. Whereas for computers, it We implemented an intuitive virtual reality interface that can be one of the most difficult and computationally taxing can accurately display MRI and CT scans and quickly and problems. For this reason, we will introduce several precisely segment 3D images, offering two different segmentation solutions, each of which is tailored to a specific segmentation algorithms. Simply put, our application must be application of medical imaging. able to fit into even the most busy and practiced physicians' workdays while providing them with a new tool, the likes of Related Work which they have never seen before. -
Official Program
OFFICIAL PROGRAM ___________________________________________________________________ Generously Sponsored by: TABLE OF CONTENTS SCHEDULE 3 KEYNOTE SPEAKERS 5 BREAKOUT SESSIONS 7 ORAL PRESENTATIONS 11 POSTER SESSION 1 (ORGANIZED BY POSTER NUMBER) 13 POSTER SESSION 2 (ORGANIZED BY POSTER NUMBER) 16 ABSTRACTS – ORAL PRESENTATIONS 19 ABSTRACTS – POSTER SESSION 1 44 ABSTRACTS – POSTER SESSION 2 91 SEMSS ORGANIZING COMMITTEE 135 LIGHT HALL & CAMPUS MAPS 136 SEMSS encourages open and honest intellectual debate as part of a welcoming and inclusive atmosphere at every conference. SEMSS asks each participant to foster rigorous analysis of all science presented or discussed in a manner respectful to all conferees. To help maintain an open and respectful community of scientists, SEMSS does not tolerate illegal or inappropriate behavior at any conference site, including violations of applicable laws pertaining to sale or consumption of alcohol, destruction of property, or harassment of any kind, including sexual harassment. SEMSS condemns inappropriate or suggestive acts or comments that demean another person by reason of his or her gender, gender identity or expression, race, religion, ethnicity, age or disability or that are unwelcome or offensive to other members of the community or their guests. * *Adapted from the language of Gordon Research Conferences 2 SEMSS 2018 SCHEDULE SATURDAY, NOVEMEBER 10, 2018 _____________________________________________________________________________________ REGISTRATION 12:30 – 1:00 PM Location: Light Hall, North -
A Simple Rapid Process for Semi-Automated Brain Extraction from Magnetic Resonance Images of the Whole Mouse Head
Accepted Manuscript Title: A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head Author: Adam Delora Aaron Gonzales Christopher S. Medina Adam Mitchell Abdul Faheem Mohed Russell E. Jacobs Elaine L. Bearer PII: S0165-0270(15)00370-2 DOI: http://dx.doi.org/doi:10.1016/j.jneumeth.2015.09.031 Reference: NSM 7360 To appear in: Journal of Neuroscience Methods Received date: 10-8-2015 Revised date: 28-9-2015 Accepted date: 30-9-2015 Please cite this article as: Delora A, Gonzales A, Medina CS, Mitchell A, Mohed AF, Jacobs RE, Bearer EL, A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head, Journal of Neuroscience Methods (2015), http://dx.doi.org/10.1016/j.jneumeth.2015.09.031 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Graphical Abstract (for review) Accepted Manuscript Page 1 of 27 A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head Delora, Gonzales, Medina, Mitchell, Mohed, Jacobs and Bearer Highlights • We present a new software tool for automated mouse brain extraction • The new software tool is rapid and applies to any MR dataset • We validate the output by comparing with manual extraction (the gold standard) • Brain extraction with this tool preserves individual volume, and improves alignments Accepted Manuscript Page 2 of 27 Fast automated skull-stripping Delora et al. -
An Open Source Freeware Software for Ultrasound Imaging and Elastography
Proceedings of the eNTERFACE’07 Workshop on Multimodal Interfaces, Istanbul,˙ Turkey, July 16 - August 10, 2007 USIMAGTOOL: AN OPEN SOURCE FREEWARE SOFTWARE FOR ULTRASOUND IMAGING AND ELASTOGRAPHY Ruben´ Cardenes-Almeida´ 1, Antonio Tristan-Vega´ 1, Gonzalo Vegas-Sanchez-Ferrero´ 1, Santiago Aja-Fernandez´ 1, Veronica´ Garc´ıa-Perez´ 1, Emma Munoz-Moreno˜ 1, Rodrigo de Luis-Garc´ıa 1, Javier Gonzalez-Fern´ andez´ 2, Dar´ıo Sosa-Cabrera 2, Karl Krissian 2, Suzanne Kieffer 3 1 LPI, University of Valladolid, Spain 2 CTM, University of Las Palmas de Gran Canaria 3 TELE Laboratory, Universite´ catholique de Louvain, Louvain-la-Neuve, Belgium ABSTRACT • Open source code: to be able for everyone to modify and reuse the source code. UsimagTool will prepare specific software for the physician to change parameters for filtering and visualization in Ultrasound • Efficiency, robust and fast: using a standard object ori- Medical Imaging in general and in Elastography in particular, ented language such as C++. being the first software tool for researchers and physicians to • Modularity and flexibility for developers: in order to chan- compute elastography with integrated algorithms and modular ge or add functionalities as fast as possible. coding capabilities. It will be ready to implement in different • Multi-platform: able to run in many Operating systems ecographic systems. UsimagTool is based on C++, and VTK/ITK to be useful for more people. functions through a hidden layer, which means that participants may import their own functions and/or use the VTK/ITK func- • Usability: provided with an easy to use GUI to interact tions. as easy as possible with the end user. -
Modelling of the Effects of Entrainment Defects on Mechanical Properties in Al-Si-Mg Alloy Castings
MODELLING OF THE EFFECTS OF ENTRAINMENT DEFECTS ON MECHANICAL PROPERTIES IN AL-SI-MG ALLOY CASTINGS By YANG YUE A dissertation submitted to University of Birmingham for the degree of DOCTOR OF PHILOSOPHY School of Metallurgy and Materials University of Birmingham June 2014 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Liquid aluminium alloy is highly reactive with the surrounding atmosphere and therefore, surface films, predominantly surface oxide films, easily form on the free surface of the melt. Previous researches have highlighted that surface turbulence in liquid aluminium during the mould-filling process could result in the fold-in of the surface oxide films into the bulk liquid, and this would consequently generate entrainment defects, such as double oxide films and entrapped bubbles in the solidified casting. The formation mechanisms of these defects and their detrimental e↵ects on both mechani- cal properties and reproducibility of properties of casting have been studied over the past two decades. However, the behaviour of entrainment defects in the liquid metal and their evolution during the casting process are still unclear, and the distribution of these defects in casting remains difficult to predict.