2454-5422 Medical Informatics
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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. -
A 3D Interactive Multi-Object Segmentation Tool Using Local Robust Statistics Driven Active Contours
A 3D interactive multi-object segmentation tool using local robust statistics driven active contours The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Gao, Yi, Ron Kikinis, Sylvain Bouix, Martha Shenton, and Allen Tannenbaum. 2012. A 3D Interactive Multi-Object Segmentation Tool Using Local Robust Statistics Driven Active Contours. Medical Image Analysis 16, no. 6: 1216–1227. doi:10.1016/j.media.2012.06.002. Published Version doi:10.1016/j.media.2012.06.002 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:28548930 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Med Image Anal. Author manuscript; available in PMC 2013 August 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Med Image Anal. 2012 August ; 16(6): 1216–1227. doi:10.1016/j.media.2012.06.002. A 3D Interactive Multi-object Segmentation Tool using Local Robust Statistics Driven Active Contours Yi Gaoa,*, Ron Kikinisb, Sylvain Bouixa, Martha Shentona, and Allen Tannenbaumc aPsychiatry Neuroimaging Laboratory, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115 bSurgical Planning Laboratory, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115 cDepartments of Electrical and Computer Engineering and Biomedical Engineering, Boston University, Boston, MA 02115 Abstract Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. -
Bio-Formats Documentation Release 4.4.9
Bio-Formats Documentation Release 4.4.9 The Open Microscopy Environment October 15, 2013 CONTENTS I About Bio-Formats 2 1 Why Java? 4 2 Bio-Formats metadata processing 5 3 Help 6 3.1 Reporting a bug ................................................... 6 3.2 Troubleshooting ................................................... 7 4 Bio-Formats versions 9 4.1 Version history .................................................... 9 II User Information 23 5 Using Bio-Formats with ImageJ and Fiji 24 5.1 ImageJ ........................................................ 24 5.2 Fiji .......................................................... 25 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 26 5.4 Installing Bio-Formats in ImageJ .......................................... 26 5.5 Using Bio-Formats to load images into ImageJ ................................... 28 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 32 5.7 Upgrading the Bio-Formats importer for ImageJ to the latest trunk build ...................... 34 6 OMERO 39 7 Image server applications 40 7.1 BISQUE ....................................................... 40 7.2 OME Server ..................................................... 40 8 Libraries and scripting applications 43 8.1 Command line tools ................................................. 43 8.2 FARSIGHT ...................................................... 44 8.3 i3dcore ........................................................ 44 8.4 ImgLib ....................................................... -
An Open-Source Research Platform for Image-Guided Therapy
Int J CARS DOI 10.1007/s11548-015-1292-0 ORIGINAL ARTICLE CustusX: an open-source research platform for image-guided therapy Christian Askeland1,3 · Ole Vegard Solberg1 · Janne Beate Lervik Bakeng1 · Ingerid Reinertsen1 · Geir Arne Tangen1 · Erlend Fagertun Hofstad1 · Daniel Høyer Iversen1,2,3 · Cecilie Våpenstad1,2 · Tormod Selbekk1,3 · Thomas Langø1,3 · Toril A. Nagelhus Hernes2,3 · Håkon Olav Leira2,3 · Geirmund Unsgård2,3 · Frank Lindseth1,2,3 Received: 3 July 2015 / Accepted: 31 August 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Results The validation experiments show a navigation sys- Purpose CustusX is an image-guided therapy (IGT) research tem accuracy of <1.1mm, a frame rate of 20 fps, and latency platform dedicated to intraoperative navigation and ultra- of 285ms for a typical setup. The current platform is exten- sound imaging. In this paper, we present CustusX as a robust, sible, user-friendly and has a streamlined architecture and accurate, and extensible platform with full access to data and quality process. CustusX has successfully been used for algorithms and show examples of application in technologi- IGT research in neurosurgery, laparoscopic surgery, vascular cal and clinical IGT research. surgery, and bronchoscopy. Methods CustusX has been developed continuously for Conclusions CustusX is now a mature research platform more than 15years based on requirements from clinical for intraoperative navigation and ultrasound imaging and is and technological researchers within the framework of a ready for use by the IGT research community. CustusX is well-defined software quality process. The platform was open-source and freely available at http://www.custusx.org. -
Investigating the Practical Use of Computational Fluid Dynamics Simulation of Airflow in the Nasal Cavity and Paranasal Sinuses NOSE Version 1.0 2018-08-30
NOSE Pilot Study Investigating the Practical Use of Computational Fluid Dynamics Simulation of Airflow in the NNOSEasal Cavity and Paranasal Sinuses NOSE Pilot Study Investigating the Practical Use of Computational Fluid Dynamics Simulation of Airflow in the Nasal Cavity and Paranasal Sinuses NOSE Version 1.0 2018-08-30 NOSE Pilot Study Investigating the Practical Use of Computational Fluid Dynamics Simulation Version 1.0 of Airflow in the Nasal Cavity and Paranasal Sinuses NOSE Pilot Study Investigating the Practical Use of Computational Fluid Dynamics Simulation of Airflow in the Nasal Cavity and Paranasal Sinuses Project Number 1000043433 Project Title NOSE Pilot Study Document Reference Investigating the Practical Use of Computational Date 2018-08-30 Title Fluid Dynamics Simulation of Airflow in the Nasal Cavity and Paranasal Sinuses Document Name NOSE_PS_FINAL_v1 Version Draft draft final Restrictions public internal restricted : Distribution Steirische Forschungsförderung Authors Koch Walter, Koch Gerda, Vitiello Massimo, Ortiz Ramiro, Stockklauser Jutta, Benda Odo Abstract The NOSE Pilot study evaluated the technical and scientific environment required for establishing a service portfolio that includes CFD simulation and 3D visualization services for ENT specialists. For this purpose the state-of-the-art of these technologies and their use for upper airways diagnostics were analysed. Keywords Rhinology, Computational Fluid Dynamics, 3D Visualization, Clinical Pathways, Service Center, Knowledge Base Document Revisions Version Date Author(s) Description of Change 1.0 2018-08-30 Koch Walter, Koch Final Version Gerda, Vitiello Massimo, Ortiz NOSERamiro, Stockklauser Jutta, Benda Odo 2018-08-30 Seite 3 / 82 Copyright © AIT ForschungsgesmbH NOSE_PS_FINAL_v1 NOSE Pilot Study Investigating the Practical Use of Computational Fluid Dynamics Simulation Version 1.0 of Airflow in the Nasal Cavity and Paranasal Sinuses Table of Contents Acknowledgments .................................................................................. -
Using Camitk for Rapid Prototyping of Interactive Computer Assisted Medical Intervention Applications*
Using CamiTK for Rapid Prototyping of Interactive Computer Assisted Medical Intervention Applications* Emmanuel Promayon, Céline Fouard, Mathieu Bailet, Aurélien Deram, Gaëlle Fiard, Nikolai Hungr, Vincent Luboz, Yohan Payan, Johan Sarrazin, Nicolas Saubat, Sonia Yuki Selmi, Sandrine Voros, Philippe Cinquin and Jocelyne Troccaz Abstract— Computer Assisted Medical Intervention (CAMI hereafter) is a complex multi-disciplinary field. CAMI research requires the collaboration of experts in several fields as diverse as medicine, computer science, mathematics, instrumentation, signal processing, mechanics, modeling, automatics, optics, etc. CamiTK1 is a modular framework that helps researchers and clinicians to collaborate together in order to prototype CAMI applications by regrouping the knowledge and expertise from each discipline. It is an open-source, cross-platform generic and modular tool written in C++ which can handle medical images, surgical navigation, biomedicals simulations and robot control. This paper presents the Computer Assisted Medical Intervention ToolKit (CamiTK) and how it is used in various applications in our research team. Figure 1. Using CamiTK in the CAMI perception – I. INTRODUCTION decision – action loop. The field of CAMI emerged about 30 years ago from the A) Related Work converging evolution of medicine, physics, materials, Numerous programming frameworks exist, generally electronics, computer science and robotics. CAMI aims at focusing on one or two fields of CAMI. For example, some of providing tools that allow the clinician to use multi-modal the most popular free and open-source libraries or data in a rational and quantitative way in order to plan, applications for scientific visualization [2] are Vtk2, simulate and accurately and safely execute mini-invasive Paraview2, VolView2, as well as proprietary software such as medical interventions. -
India's National Digital Health Mission
CSD Working Paper Series: Towards a New Indian Model of Information and Communications Technology-Led Growth and Development India’s National Digital Health Mission ICT India Working Paper #36 Nirupam Bajpai and Manisha Wadhwa October 2020 CSD Working Paper Series – India’s National Digital Health Mission Abstract India is using Information and Communication Technologies (ICTs) to leapfrog economic development in key sectors: health, education, infrastructure, finance, agriculture, manufacturing, and perhaps most important, governance. In doing so, India is increasing Internet penetration by increasing Internet subscribers and digital literacy. These have acted as the key drivers for the Indian Government to envision digitalization in its various sectors including health care. The Government of India laid emphasis on digitalization in India’s healthcare sector in its National Health Policy, 2017. The National Digital Health Blueprint, 2019 recognized the need to put together a National Digital Health Mission (NDHM) which can act as the foundation on which national digital health ecosystem can be built. On the nation’s 74th Independence Day, the Government of India embarked on its journey to achieve Universal Health Coverage by launching the National Digital Health Mission. NDHM intends to create a holistic and comprehensive digital health ecosystem that will lay the foundation of a strong public digital infrastructure, digitally empower individuals, patients, doctors, health facilities, and help streamline the delivery of healthcare services and related information. However, it is important to emphasize that the success of NDHM is dependent on its adoption by the centre and states, by public and private entities and by individuals and decision makers. -
Bio-Formats Documentation Release 5.2.2
Bio-Formats Documentation Release 5.2.2 The Open Microscopy Environment September 12, 2016 CONTENTS I About Bio-Formats 2 1 Help 4 2 Bio-Formats versions 5 3 Why Java? 6 4 Bio-Formats metadata processing 7 4.1 Reporting a bug ................................................... 7 4.2 Version history .................................................... 8 II User Information 38 5 Using Bio-Formats with ImageJ and Fiji 39 5.1 ImageJ overview ................................................... 39 5.2 Fiji overview ..................................................... 41 5.3 Bio-Formats features in ImageJ and Fiji ....................................... 42 5.4 Installing Bio-Formats in ImageJ .......................................... 42 5.5 Using Bio-Formats to load images into ImageJ ................................... 44 5.6 Managing memory in ImageJ/Fiji using Bio-Formats ................................ 48 6 Command line tools 51 6.1 Command line tools introduction .......................................... 51 6.2 Displaying images and metadata ........................................... 52 6.3 Converting a file to different format ......................................... 54 6.4 Validating XML in an OME-TIFF .......................................... 56 6.5 Editing XML in an OME-TIFF ........................................... 57 6.6 List formats by domain ................................................ 58 6.7 List supported file formats .............................................. 58 6.8 Display file in ImageJ ............................................... -
Evaluation of DICOM Viewer Software for Workflow Integration in Clinical Trials
Evaluation of DICOM Viewer Software for Workflow Integration in Clinical Trials Daniel Haak1*, Charles-E. Page, Klaus Kabino, Thomas M. Deserno Department of Medical Informatics, Uniklinik RWTH Aachen, 52057 Aachen, Germany ABSTRACT The digital imaging and communications in medicine (DICOM) protocol is nowadays the leading standard for capture, exchange and storage of image data in medical applications. A broad range of commercial, free, and open source software tools supporting a variety of DICOM functionality exists. However, different from patient’s care in hospital, DICOM has not yet arrived in electronic data capture systems (EDCS) for clinical trials. Due to missing integration, even just the visualization of patient’s image data in electronic case report forms (eCRFs) is impossible. Four increasing levels for integration of DICOM components into EDCS are conceivable, raising functionality but also demands on interfaces with each level. Hence, in this paper, a comprehensive evaluation of 27 DICOM viewer software projects is performed, investigating viewing functionality as well as interfaces for integration. Concerning general, integration, and viewing requirements the survey involves the criteria (i) license, (ii) support, (iii) platform, (iv) interfaces, (v) two- dimensional (2D) and (vi) three-dimensional (3D) image viewing functionality. Optimal viewers are suggested for applications in clinical trials for 3D imaging, hospital communication, and workflow. Focusing on open source solutions, the viewers ImageJ and MicroView are superior for 3D visualization, whereas GingkoCADx is advantageous for hospital integration. Concerning workflow optimization in multi-centered clinical trials, we suggest the open source viewer Weasis. Covering most use cases, an EDCS and PACS interconnection with Weasis is suggested. -
Kitware Source Issue 21
SOFTWARE DEVELOPER’S QUARTERLY Issue 21 • April 2012 Editor’s Note ........................................................................... 1 PARAVIEW 3.14 RELEASED In late February, Kitware and the ParaView team released Recent Releases ..................................................................... 1 ParaView 3.14. This release features usability enhancements, improvements to the Plugin framework, new panels, and ParaView in Immersive Environments .................................. 3 more than 100 other resolved issues. Teaching Open Source .......................................................... 4 ParaView 3.14 features a redesigned Find Data dialog and Color Editor. The updated Find Data dialog makes it possible ParaView Query Selection Framework................................. 7 to use complex queries to select elements, including combin- ing multiple test cases with Boolean operations. The Color Ginkgo CADx: Open Source DICOM CADx Environment .... 8 Editor, used to edit lookup tables or color tables for scalar mapping, now enables independent editing of the color and Code Review, Topic Branches and VTK ................................. 9 opacity functions. Video Analysis on Business Intelligence, ParaView’s charting capabilities have been extended with a Studies in Computational Intelligence ............................... 11 new scatter plot matrix view and the ability to visualize mul- tiple dimensions of data in one compact form. This improved The Visible Patient .............................................................. -
A Survey of Medical Image Processing Tools
See discussions, stats, and author profiles for this publication at: http://www.researchgate.net/publication/282610419 A Survey of Medical Image Processing Tools CONFERENCE PAPER · AUGUST 2015 DOI: 10.13140/RG.2.1.3364.4241 2 AUTHORS, INCLUDING: Siau-Chuin Liew Universiti Malaysia Pahang 24 PUBLICATIONS 30 CITATIONS SEE PROFILE Available from: Siau-Chuin Liew Retrieved on: 07 October 2015 provided by UMP Institutional Repository View metadata, citation and similar papers at core.ac.uk CORE brought to you by A Survey of Medical Image Processing Tools Lay-Khoon Lee Siau-Chuin Liew 1Faculty of Computer Systems and Software Engineering; 2Faculty of Computer Systems and Software Engineering; Universiti Malaysia Pahang, Universiti Malaysia Pahang, 26300 Gambang, Pahang, Malaysia 26300 Gambang, Pahang, Malaysia Abstract—A precise analysis of medical image is an important registration, segmentation, visualization, reconstruction, stage in the contouring phase throughout radiotherapy simulation and diffusion preparation. Medical images are mostly used as radiographic techniques in diagnosis, clinical studies and treatment planning. Medical image processing tool are also similarly as important. With a medical image processing tool, it is possible to speed up and enhance the operation of the analysis of the medical image. This paper describes medical image processing software tool which attempts to secure the same kind of programmability advantage for exploring applications of the pipelined processors. These tools simulate complete systems consisting of several of the proposed processing components, in a configuration described by a graphical schematic diagram. In this paper, fifteen different medical image processing tools will be compared in several aspects. The main objective of the comparison is to gather and analysis on the tool in order to recommend users of different operating systems on what type of medical image tools to be used when analysing different types of imaging. -
Proceedings of the 12Th Health Informatics in Africa Conference HELINA’ 19
Proceedings of the 12th Health Informatics in Africa Conference HELINA’ 19 PART I Case Studies, Experience Papers and Work in Progress From Evidence to Practice: Te implementation of digital health interventions in Africa for achievement of Universal Health Coverage Editors: Nicky Mostert, Ulrich Kemloh © 2019 HELINA and JHIA. This is an Open Access article published online by JHIA and distributed under the terms of the Creative Commons Attribution Non- Commercial License. ISSN: 2197-6902 ISBN: 978-3-9816261-9-3 Publisher Koegni eHealth, Innovation for Development e.V. Germany D-22071 Hamburg Germany www.koegni-ehealth.org E-mail: [email protected] iii Table of Contents Editorial to the HELINA 2019 proceedings vii Nicky Mostert Work in Progress Assessing How Health Data Systems Support Data Use in the Tanzanian Health System 1 Bigten Kikoba, Felix Sukums, Zabron Abel, Nima Shidende, Yasinta Kijuu, Silvanus Ilomo and Auson Kisanga Using Predictive Algorithms to Offer Differentiated Healthcare in Community: A Study in Rural 8 Kenya Stephen Odindo, Rohin Onyango, Charles Ogechi , Caroline Mbindyo , Asif Akram , Beatrice Wasunna, Erika Salomon, Maria Ma, Isaac Holeman, Justin Loiseau , Andrew Karlyn Towards development of Heuristic Evaluation Guidelines for a Geriatric Interface on mobile 16 interactive devices in Kenya Njeri Ngaruiya, Daniel Orwa, Peter Waiganjo Fortitudo Telemedicine - A Tool to Mitigate the Healthcare Deficits in a Developing Country? A 24 Work in Progress Okechukwu Mgbemena, Barry Levine, Isaac Sears The effect of knowledge sharing on team effectiveness within neonatal intensive care units through 29 the lens of clinical leadership Olateju Jumoke Ajanaku, Welma Lubbe Case Study and Experience Papers Utility of an Electronic Adverse Drug Reaction Reporting System in Uganda: Design and 36 Validation Julius Mayengo, Josephine Nabukenya Strengthening Government capacity for routine immunization data management using the GEEKS 45 Approach in Nigeria A.B.