Review of Graph, Medical and Color Image Base Segmentation Techniques
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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. -
Survey of Databases Used in Image Processing and Their Applications
International Journal of Scientific & Engineering Research Volume 2, Issue 10, Oct-2011 1 ISSN 2229-5518 Survey of Databases Used in Image Processing and Their Applications Shubhpreet Kaur, Gagandeep Jindal Abstract- This paper gives review of Medical image database (MIDB) systems which have been developed in the past few years for research for medical fraternity and students. In this paper, I have surveyed all available medical image databases relevant for research and their use. Keywords: Image database, Medical Image Database System. —————————— —————————— 1. INTRODUCTION Measurement and recording techniques, such as electroencephalography, magnetoencephalography Medical imaging is the technique and process used to (MEG), Electrocardiography (EKG) and others, can create images of the human for clinical purposes be seen as forms of medical imaging. Image Analysis (medical procedures seeking to reveal, diagnose or is done to ensure database consistency and reliable examine disease) or medical science. As a discipline, image processing. it is part of biological imaging and incorporates radiology, nuclear medicine, investigative Open source software for medical image analysis radiological sciences, endoscopy, (medical) Several open source software packages are available thermography, medical photography and for performing analysis of medical images: microscopy. ImageJ 3D Slicer ITK Shubhpreet Kaur is currently pursuing masters degree OsiriX program in Computer Science and engineering in GemIdent Chandigarh Engineering College, Mohali, India. E-mail: MicroDicom [email protected] FreeSurfer Gagandeep Jindal is currently assistant processor in 1.1 Images used in Medical Research department Computer Science and Engineering in Here is the description of various modalities that are Chandigarh Engineering College, Mohali, India. E-mail: used for the purpose of research by medical and [email protected] engineering students as well as doctors. -
Sistema De Detección Y Ubicación De Marcadores Visuales Para El Rastreo De Robots Móviles
1 UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO FACULTAD DE INGENIERÍA SISTEMA DE DETECCIÓN Y UBICACIÓN DE MARCADORES VISUALES PARA EL RASTREO DE ROBOTS MÓVILES T E S I S Que para obtener el título de INGENIERO MECATRÓNICO P R E S E N T A EMMANUEL TAPIA BRITO DIRECTOR DE TESIS: DR. VÍCTOR JAVIER GONZÁLEZ VILLELA MÉXICO D.F. JULIO 2013 Dedicatoria A mis padres, por su incondicional apoyo, por ser fuente de inspiración, por su esfuerzo derramado día a día y por aguantarme durante todos estos años. * A Getsemaní por llenar de inmenso amor y alegría mi corazón y por haber compartido conmigo una gran etapa de mi vida. * A Sofía por brindarme tu apoyo y el amor que me dio ánimos para alcanzar esta meta. * A todos mis amigos por haber formado parte de mi vida universitaria. 3 4 Agradecimientos A la Universidad Nacional Autónoma de México por la excelente educación recibida. * A los profesores de la Facultad de Ingeniería, en especial a los del Departamento de Ingeniería Mecatrónica, a quienes debo mi formación profesional. * Al grupo de trabajo MRG, por su soporte técnico y ayuda en la realización de esta Tesis. * Al Dr. Víctor Javier González Villela por la oportunidad, motivación y confianza brindada durante la realización de este proyecto. * A Oscar X. Hurtado Reynoso, por su gran ayuda en la etapa de pruebas con el robot. * A la DGAPA por el apoyo brindado a través del proyecto PAPIIT 1N115811 con título “Investigación y desarrollo en sistemas mecatrónicos: robótica móvil, robótica paralela, robótica híbrida y teleoperación”. 5 6 Resumen Esta tesis presenta los puntos principales del desarrollo de un sistema de visión por computadora con el objetivo de emplearlo como medio de asistencia para el con- trol de robots móviles. -
CT Image Based 3D Reconstruction for Computer Aided Orthopaedic Surgery
CT Image Based 3D Reconstruction for Computer Aided Orthopaedic Surgery F. Blanco IDMEC-IST, Technical University of Lisbon, Av Rovisco Pais, 1049-001 Lisboa, Portugal P.J.S. Gonçalves Polytechnic Institute of Castelo Branco, Av Empresario, 6000-767 Castelo Branco, Portugal IDMEC-IST, Technical University of Lisbon, Av Rovisco Pais, 1049-001 Lisboa, Portugal J.M.M. Martins & J.R. Caldas Pinto IDMEC-IST, Technical University of Lisbon, Av Rovisco Pais, 1049-001 Lisboa, Portugal Abstract This paper presents an integrated system of 3D medical image visualization and robotics to assist orthopaedic surgery, namely by positioning a manipulator robot end-effector using a CT image based femur model. The 3D model is generated from CT images, acquired in a preoperative exam, using VTK applied to the free medical visualization software InVesalius. Add-ons were developed for communication with the robot which will be forwarded to the designated position to perform surgical tasks. A stereo vision 3D reconstruction algorithm is used to determine the coordinate transform between the virtual and the real femur by means of a fiducial marker attached to the bone. Communication between the robot and 3D model is bi-directional since visualization is updated in real time from the end-effector movement. 1. Introduction In recent years, robotic applications regarding surgical assistance have been appearing more often. Their advantages in precision, accuracy, repeatability and the ability to use specialized manipulators are granting them a place in the operating theatre. By introducing robotic technology in surgery, the goal is not to replace the surgeon but, instead, to develop new tools to assist in accurate surgical tasks. -
Development and Characterization of the Invesalius Navigator Software for Navigated Transcranial Magnetic Stimulation T ⁎ Victor Hugo Souzaa, ,1, Renan H
Journal of Neuroscience Methods 309 (2018) 109–120 Contents lists available at ScienceDirect Journal of Neuroscience Methods journal homepage: www.elsevier.com/locate/jneumeth Development and characterization of the InVesalius Navigator software for navigated transcranial magnetic stimulation T ⁎ Victor Hugo Souzaa, ,1, Renan H. Matsudaa, André S.C. Peresa,b, Paulo Henrique J. Amorimc, Thiago F. Moraesc, Jorge Vicente L. Silvac, Oswaldo Baffaa a Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, 14040-901, Ribeirão Preto, SP, Brazil b Instituto Internacional de Neurociência de Natal Edmond e Lily Safra, Instituto Santos Dumont, Rodovia RN 160 Km 03, 3003, 59280-000, Macaíba, RN, Brazil c Núcleo de Tecnologias Tridimensionais, Centro de Tecnologia da Informação Renato Archer, Rodovia Dom Pedro I Km 143, 13069-901, Campinas, SP, Brazil GRAPHICAL ABSTRACT ARTICLE INFO ABSTRACT Keywords: Background: Neuronavigation provides visual guidance of an instrument during procedures of neurological in- Neuronavigation terventions, and has been shown to be a valuable tool for accurately positioning transcranial magnetic stimu- Transcranial magnetic stimulation lation (TMS) coils relative to an individual’s anatomy. Despite the importance of neuronavigation, its high cost, Localization error low portability, and low availability of magnetic resonance imaging facilities limit its insertion in research and Co-registration clinical environments. Coil positioning New method: We have developed and validated the InVesalius Navigator as the first free, open-source software Surgical planning for image-guided navigated TMS, compatible with multiple tracking devices. A point-based, co-registration al- gorithm and a guiding interface were designed for tracking any instrument (e.g. -
Journal of Epilepsy and Clinical Neurophysiology
ISSN 1676-2649 Journal of Epilepsy and Clinical Neurophysiology Volume 25 l Number 1 l Year 2019 ABSTRACTS PRESENTED AT THE 6TH BRAINN CONGRESS BRAZILIAN INSTITUTE OF NEUROSCIENCE AND NEUROTECHNOLOGY (BRAINN-UNICAMP) APRIL 1th TO 3th 2019 - CAMPINAS, SP, BRAZIL J Epilepsy Clin Neurophysiol 2019; 25(1): 1-51 www.jecn.org Órgão Oficial da Liga Brasileira de Epilepsia Indexada no LILACS – Literatura Latino-americana e do Caribe em Ciências da Saúde CORPO EDITORIAL Editores Científicos Fernando Cendes – Departamento de Neurologia, Faculdade de Ciências João Pereira Leite – Departamento de Neurociências e Ciências do Médicas, Unicamp, Campinas/SP/Brasil. Comportamento, Faculdade de Medicina, USP, Ribeirão Preto/SP/Brasil. Editores Associados Li Li Min – Departamento de Neurologia, Faculdade de Ciências Carlos Eduardo Silvado – Setor de Epilepsia e EEG, Hospital de Clínicas, Médicas, Unicamp, Campinas/SP/Brasil. UFPR, Curitiba, PR/Brasil. Conselho Editorial • André Palmini – Divisão de Neurologia, PUC • Gilson Edmar Gonçalves e Silva – Departamento Pediatria, Faculdade de Medicina, PUC, Porto Porto Alegre, RS/Brasil. de Neurologia, Faculdade de Medicina, UFPE, Alegre, RS/Brasil. • Áurea Nogueira de Melo – Departamento de Recife, PE/Brasil. • Natalio Fejerman – Hospital de Pediatria “Juan Medicina Clínica, Centro de Ciências da Saúde, • Íscia Lopes-Cendes – Departamento de Genética P. Garrahan”, Buenos Aires/Argentina. UFRN, Natal, RN/Brasil. Médica, Faculdade de Ciências Médicas, Uni- • Norberto Garcia Cairasco – Departamento de • Bernardo Dalla Bernardina – Universitá de camp, Campinas, SP/Brasil. Fisiologia, Faculdade de Medicina, USP, Ribeirão Verona,Verona/Itália. • J. W. A. S. Sander – National Hospital for Neu- Preto, SP/Brasil. • Elza Marcia Yacubian – Unidade de Pesquisa e rology and Neurosurgery, London/UK • Paula T. -
Current Applications and Future Perspectives of the Use of 3D Printing in Anatomical Training and Neurosurgery
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector TECHNOLOGY REPORT published: 24 June 2016 doi: 10.3389/fnana.2016.00069 Current Applications and Future Perspectives of the Use of 3D Printing in Anatomical Training and Neurosurgery Vivek Baskaran 1, Goran Štrkalj 2, Mirjana Štrkalj 3 and Antonio Di Ieva 4, 5* 1 ACT Health, Canberra, ACT, Australia, 2 Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia, 3 Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia, 4 Neurosurgery Unit, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia, 5 Cancer Division, Garvan Institute of Medical Research, Sydney, NSW, Australia 3D printing is a form of rapid prototyping technology, which has led to innovative new applications in biomedicine. It facilitates the production of highly accurate three dimensional objects from substrate materials. The inherent accuracy and other properties of 3D printing have allowed it to have exciting applications in anatomy education and surgery, with the specialty of neurosurgery having benefited particularly well. This article presents the findings of a literature review of the Pubmed and Web of Science databases investigating the applications of 3D printing in anatomy and surgical education, and Edited by: neurosurgery. A number of applications within these fields were found, with many Zoltan F. Kisvarday, University of Debrecen, Hungary significantly improving the quality of anatomy and surgical education, and the practice of Reviewed by: neurosurgery. They also offered advantages over existing approaches and practices. It is Ricardo Insausti, envisaged that the number of useful applications will rise in the coming years, particularly University of Castilla -la Mancha, as the costs of this technology decrease and its uptake rises. -
Three-Dimensional Printing of Customized Bioresorbable Airway
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.12.294751; this version posted September 13, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Three-dimensional Printing of Customized Bioresorbable Airway Stents Nevena Paunović1,ǂ; Yinyin Bao1,ǂ; Fergal Brian Coulter2; Kunal Masania2,3; Anna Karoline Geks4; Karina Klein4; Ahmad Rafsanjani2,5; Jasmin Cadalbert1; Peter W. Kronen4,6,7; Nicole Kleger2; Agnieszka Karol4; Zhi Luo1; Fabienne Rüber8; Davide Brambilla1,9; Brigitte von Rechenberg4; Daniel Franzen8,*; André R. Studart2,*; Jean-Christophe Leroux1,* 1Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland. 2Complex materials, Department of Materials, ETH Zurich, Zurich, Switzerland. 3Shaping Matter Lab, Faculty of Aerospace Engineering, TU Delft, Delft, Netherlands. 4Musculoskeletal Research Unit, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland. 5The Maersk Mc-Kinney Moller Institute, University of Southern Denmark, Odense, Denmark. 6Veterinary Anaesthesia Services-International, Winterthur, Switzerland. 7Center for Applied Biotechnology and Molecular Medicine, University of Zurich, Zurich, Switzerland. 8Department of Pulmonology, University Hospital Zurich, Zurich, Switzerland. 9Faculty of Pharmacy, Université de Montréal, Montréal, QC, Canada. ǂThese authors contributed equally. *Corresponding authors. E-mail: [email protected], [email protected], [email protected]. Abstract Central airway obstruction is a life-threatening disorder causing a high physical and psychological burden to patients due to severe breathlessness and impaired quality of life. Standard-of-care airway stents are silicone tubes, which cause immediate relief, but are prone to migration, especially in growing patients, and require additional surgeries to be removed, which may cause further tissue damage. -
Process to Convert DICOM Data to 3D Printable STL Files Mac Cameron, Application Engineer
HOW-TO GUIDE Process to Convert DICOM Data to 3D Printable STL Files Mac Cameron, Application Engineer Anatomical models have several applications in the medical space — from patient-specific models used to plan and optimize surgical approaches, to sophisticated training simulators to educate physicians, to clinically relevant models for preclinical device testing. Developing these models can be a challenge due to the complexity and irregularity of human anatomy. One starting point is to use data readily available in the form of patient imaging studies generated by non-invasive MRI, CT, or 3D Ultrasound testing. Using data from patients, model designers can recreate the complexity of any disease, abnormal anatomy or variation that exists in the natural world. Using this approach, the first challenge is to take the data from imaging studies, isolate the anatomy of interest (referred to as segmentation) and convert it into a file format readable by CAD and 3D printing software. The final product depends on the quality of the original data. Image resolution, the use of contrast to enhance the anatomy, and sophistication of the software used to perform segmentation can all significantly affect the final product. There are a variety of professional, freeware, and open-source solutions available to perform these steps. This document describes the approach using InVesalius and Materialise Magics as an example, but the process can be replicated by many available solutions. Software used in this tutorial: • InVesalius free software to convert DICOM images to STL files. svn.softwarepublico.gov.br/trac/invesalius • Magics for editing STL files. software.materialise.com/magics THE 3D PRINTING SOLUTIONS COMPANY™ PROCESS TO CONVERT DICOM DATA TO 3D PRINTABLE STL FILES STEP ONE: GET DICOM DATA Digital Imaging and Communications in Medicine (DICOM) is a standard for handling, storing, printing and transmitting information in medical imaging. -
Software for Bioprinting Catherine Pakhomova1,2*, Dmitry Popov1, Eugenii Maltsev1, Iskander Akhatov1, Alexander Pasko1,3
REVIEW ARTICLE Software for Bioprinting Catherine Pakhomova1,2*, Dmitry Popov1, Eugenii Maltsev1, Iskander Akhatov1, Alexander Pasko1,3 1Center for Design, Manufacturing and Materials, Skolkovo Institute of Science and Technology, Moscow 2Institute of Engineering Physics for Biomedicine, NRNU Mephi, Moscow 3The National Centre for Computer Animation, Bournemouth University, UK Abstract: The bioprinting of heterogeneous organs is a crucial issue. To reach the complexity of such organs, there is a need for highly specialized software that will meet all requirements such as accuracy, complexity, and others. The primary objective of this review is to consider various software tools that are used in bioprinting and to reveal their capabilities. The sub-objective was to consider different approaches for the model creation using these software tools. Related articles on this topic were analyzed. Software tools are classified based on control tools, general computer-aided design (CAD) tools, tools to convert medical data to CAD formats, and a few highly specialized research-project tools. Different geometry representations are considered, and their advantages and disadvantages are considered applicable to heterogeneous volume modeling and bioprinting. The primary factor for the analysis is suitability of the software for heterogeneous volume modeling and bioprinting or multimaterial three- dimensional printing due to the commonality of these technologies. A shortage of specialized suitable software tools is revealed. There is a need to develop -
Evaluation of Imaging Software Accuracy for 3-Dimensional Analysis of the Mandibular Condyle
International Journal of Environmental Research and Public Health Article Evaluation of Imaging Software Accuracy for 3-Dimensional Analysis of the Mandibular Condyle. A Comparative Study Using a Surface-to-Surface Matching Technique Antonino Lo Giudice 1 , Vincenzo Quinzi 2 , Vincenzo Ronsivalle 1 , Marco Farronato 3 , Carmelo Nicotra 1, Francesco Indelicato 4 and Gaetano Isola 4,* 1 Department of General Surgery and Surgical-Medical Specialties, Section of Orthodontics, School of Dentistry, University of Catania, 95123 Catania, Italy; [email protected] (A.L.G.); [email protected] (V.R.); [email protected] (C.N.) 2 Post Graduate School of Orthodontics, Department of Life, Health and Environmental Sciences, University of L’Aquila, V.le San Salvatore, 67100 L’Aquila, Italy; [email protected] 3 Department of Medicine, Surgery and Dentistry, Section of Orthodontics, University of Milan, 20122 Milan, Italy; [email protected] 4 Department of General Surgery and Surgical-Medical Specialties, Section of Oral Surgery and Periodontology, School of Dentistry, University of Catania, 95123 Catania, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-095-3782453 Received: 29 May 2020; Accepted: 1 July 2020; Published: 3 July 2020 Abstract: The aim of this study was to assess the accuracy of 3D rendering of the mandibular condylar region obtained from different semi-automatic segmentation methodology. A total of 10 Cone beam computed tomography (CBCT) were selected to perform semi-automatic segmentation of the condyles by using three free-source software (Invesalius, version 3.0.0, Centro de Tecnologia da Informação Renato Archer, Campinas, SP, Brazil; ITK-Snap, version2.2.0; Slicer 3D, version 4.10.2) and one commercially available software Dolphin 3D (Dolphin Imaging, version 11.0, Chatsworth, CA, USA). -
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Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer David Andrew Gutman, Emory University William D. Dunn, Jr., Emory University Jake Cobb, Georgia Institute of Technology Richard M. Stoner, University of California Jayashree Kalpathy-Cramer, Martinos Center for Biomedical Imaging Bradley Erickson, Mayo Clinic Journal Title: Frontiers in Neuroinformatics Volume: Volume 8, Number 53 Publisher: Frontiers | 2014-05-27 Type of Work: Article | Final Publisher PDF Publisher DOI: 10.3389/fninf.2014.00053 Permanent URL: http://pid.emory.edu/ark:/25593/ghkmr Final published version: http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00053/abstract Copyright information: © 2014 Gutman, Dunn, Cobb, Stoner, Kalpathy-Cramer and Erickson. This is an Open Access work distributed under the terms of the Creative Commons Attribution 3.0 Unported License (http://creativecommons.org/licenses/by/3.0/). Accessed September 23, 2021 8:08 AM EDT TECHNOLOGY REPORT ARTICLE published: 27 May 2014 NEUROINFORMATICS doi: 10.3389/fninf.2014.00053 Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer David A. Gutman 1*,WilliamD.DunnJr1,JakeCobb2,RichardM.Stoner3, Jayashree Kalpathy-Cramer 4 and Bradley Erickson 5 1 Department of Biomedical Informatics, Emory University, Atlanta, GA, USA 2 Georgia Institute of Technology, College of Computing, Atlanta, GA, USA 3 Department of Neurosciences, University of California San Diego School of Medicine, La Jolla, CA, USA 4 Harvard-MIT Division of Health Sciences and Technology, Martinos Center for Biomedical Imaging, Charlestown, MA, USA 5 Department of Radiology, Mayo Clinic, Rochester, MN, USA Edited by: Advances in web technologies now allow direct visualization of imaging data sets without Xi Cheng, Lieber Institue for Brain necessitating the download of large file sets or the installation of software.