Debian Med Integrated Software Environment for All Medical Applications
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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. -
Examples of the Electronic Health Record (EHR)
Examples of the Electronic Health Record (EHR) What is Biomedical & Health Informatics? William Hersh Copyright 2020 Oregon Health & Science University Examples of the EHR • Using the Veterans Health Information Systems and Technology Architecture (VistA) • Why VistA? – State-of-the-art EHR that has transformed healthcare in the Veteran’s Health Administration (VHA) (Perlin, 2006; Byrne, 2010) – Not that pretty, but has all of the modern features of the EHR, e.g., clinical decision support (CDS), computerized provider order entry (CPOE), etc. – Distributed under open-source model, unlike most other vendors who do not even allow screen shots to be shown outside their customers’ institutions • Fascinating story (Allen, 2017), but VistA now being phased out in favor of Cerner EHR adopted by Department of Defense (VA, 2017) – https://www.ehrm.va.gov/ WhatIs5 2 1 Some details about VistA • Server written in M (formerly called MUMPS), accessed via command-line interface – Runs in commercial Intersystems Cache (on many platforms) or open-source GT.M (Linux only) • Client (called CPRS) written in Delphi and providers graphical user interface – Only runs on Windows (just about all versions) WhatIs5 3 Logging on to CPRS, the front end to VistA WhatIs5 4 2 Choosing a patient WhatIs5 5 Cover sheet – overview WhatIs5 6 3 Drilling down to details of a problem WhatIs5 7 Details of an allergy WhatIs5 8 4 Viewing vital signs over time WhatIs5 9 More details on problems WhatIs5 10 5 List of active orders WhatIs5 11 Viewing the patient’s notes WhatIs5 12 -
Istls Information Services to Life Science Internet Bioinformatics Resources Josef Maier [E-Mail: [email protected]] Last Checked August, 17Th, 2011
IStLS Information Services to Life Science Internet Bioinformatics Resources Josef Maier [e-mail: [email protected]] Last checked August, 17th, 2011 IStLS Bioinformatics Resources http://www.istls.de/bioinfolinks.php Courses and lectures Bioinformatics - Online Courses and Tutorials http://www.bioinformatik.de/cgi-bin/browse/Catalog/Research_and_Education/Online_Courses_and_Tutorials/ EMBRACE Network of Excellence http://www.embracegrid.info/page.php EMBNet Quick Guides http://www.embnet.org/node/64 EMBNet Courses http://www.embnet.org/ Sequence Analysis with distributed Resources http://bibiserv.techfak.uni-bielefeld.de/sadr/ Tutorial Protein Structures (EXPASY) SwissModel http://swissmodel.expasy.org/course/course-index.htm CMBI Courses for protein structure http://swift.cmbi.ru.nl/teach/courses/index.html 2Can Support Portal - Bioinformatics educational resource http://www.ebi.ac.uk/2can Bioconductor Workshops http://www.bioconductor.org/workshops/ CBS Bioinformatics Courses http://www.cbs.dtu.dk/courses.php The European School In Bioinformatics (Biosapiens) http://www.biosapiens.info/page.php?page=esb Institutes Centers Networks Bioinformatics Institutes Germany WSI Wilhelm-Schickard-Institut für Informatik - Universitaet Tuebingen http://www.uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department.html WSI Huson - Algorithms in Bioinformatics http://www-ab.informatik.uni-tuebingen.de/welcome.html WSI Prof. Zell - Computer Architecture http://www.ra.cs.uni-tuebingen.de/ WSI Kohlbacher - Div. for Simulation -
A Zahlensysteme
A Zahlensysteme Außer dem Dezimalsystem sind das Dual-,dasOktal- und das Hexadezimalsystem gebräuchlich. Ferner spielt das Binär codierte Dezimalsystem (BCD) bei manchen Anwendungen eine Rolle. Bei diesem sind die einzelnen Dezimalstellen für sich dual dargestellt. Die folgende Tabelle enthält die Werte von 0 bis dezimal 255. Be- quemlichkeitshalber sind auch die zugeordneten ASCII-Zeichen aufgeführt. dezimal dual oktal hex BCD ASCII 0 0 0 0 0 nul 11111soh 2102210stx 3113311etx 4 100 4 4 100 eot 5 101 5 5 101 enq 6 110 6 6 110 ack 7 111 7 7 111 bel 8 1000 10 8 1000 bs 9 1001 11 9 1001 ht 10 1010 12 a 1.0 lf 11 101 13 b 1.1 vt 12 1100 14 c 1.10 ff 13 1101 15 d 1.11 cr 14 1110 16 e 1.100 so 15 1111 17 f 1.101 si 16 10000 20 10 1.110 dle 17 10001 21 11 1.111 dc1 18 10010 22 12 1.1000 dc2 19 10011 23 13 1.1001 dc3 20 10100 24 14 10.0 dc4 21 10101 25 15 10.1 nak 22 10110 26 16 10.10 syn 430 A Zahlensysteme 23 10111 27 17 10.11 etb 24 11000 30 18 10.100 can 25 11001 31 19 10.101 em 26 11010 32 1a 10.110 sub 27 11011 33 1b 10.111 esc 28 11100 34 1c 10.1000 fs 29 11101 35 1d 10.1001 gs 30 11110 36 1e 11.0 rs 31 11111 37 1f 11.1 us 32 100000 40 20 11.10 space 33 100001 41 21 11.11 ! 34 100010 42 22 11.100 ” 35 100011 43 23 11.101 # 36 100100 44 24 11.110 $ 37 100101 45 25 11.111 % 38 100110 46 26 11.1000 & 39 100111 47 27 11.1001 ’ 40 101000 50 28 100.0 ( 41 101001 51 29 100.1 ) 42 101010 52 2a 100.10 * 43 101011 53 2b 100.11 + 44 101100 54 2c 100.100 , 45 101101 55 2d 100.101 - 46 101110 56 2e 100.110 . -
Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria
Original Article Healthc Inform Res. 2019 April;25(2):89-98. https://doi.org/10.4258/hir.2019.25.2.89 pISSN 2093-3681 • eISSN 2093-369X Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria Saptarshi Purkayastha1, Roshini Allam1, Pallavi Maity1, Judy W. Gichoya2 1Department of BioHealth Informatics, Indiana University–Purdue University Indianapolis, Indianapolis, IN, USA 2Dotter Institute, Oregon Health and Science University, Portland, OR, USA Objectives: Open-source Electronic Health Record (EHR) systems have gained importance. The main aim of our research is to guide organizational choice by comparing the features, functionality, and user-facing system performance of the five most popular open-source EHR systems. Methods: We performed qualitative content analysis with a directed approach on recently published literature (2012–2017) to develop an integrated set of criteria to compare the EHR systems. The functional criteria are an integration of the literature, meaningful use criteria, and the Institute of Medicine’s functional requirements of EHR, whereas the user-facing system performance is based on the time required to perform basic tasks within the EHR system. Results: Based on the Alexa web ranking and Google Trends, the five most popular EHR systems at the time of our study were OSHERA VistA, GNU Health, the Open Medical Record System (OpenMRS), Open Electronic Medical Record (OpenEMR), and OpenEHR. We also found the trends in popularity of the EHR systems and the locations where they were more popular than others. OpenEMR met all the 32 functional criteria, OSHERA VistA met 28, OpenMRS met 12 fully and 11 partially, OpenEHR-based EHR met 10 fully and 3 partially, and GNU Health met the least with only 10 criteria fully and 2 partially. -
Debian 1 Debian
Debian 1 Debian Debian Part of the Unix-like family Debian 7.0 (Wheezy) with GNOME 3 Company / developer Debian Project Working state Current Source model Open-source Initial release September 15, 1993 [1] Latest release 7.5 (Wheezy) (April 26, 2014) [±] [2] Latest preview 8.0 (Jessie) (perpetual beta) [±] Available in 73 languages Update method APT (several front-ends available) Package manager dpkg Supported platforms IA-32, x86-64, PowerPC, SPARC, ARM, MIPS, S390 Kernel type Monolithic: Linux, kFreeBSD Micro: Hurd (unofficial) Userland GNU Default user interface GNOME License Free software (mainly GPL). Proprietary software in a non-default area. [3] Official website www.debian.org Debian (/ˈdɛbiən/) is an operating system composed of free software mostly carrying the GNU General Public License, and developed by an Internet collaboration of volunteers aligned with the Debian Project. It is one of the most popular Linux distributions for personal computers and network servers, and has been used as a base for other Linux distributions. Debian 2 Debian was announced in 1993 by Ian Murdock, and the first stable release was made in 1996. The development is carried out by a team of volunteers guided by a project leader and three foundational documents. New distributions are updated continually and the next candidate is released after a time-based freeze. As one of the earliest distributions in Linux's history, Debian was envisioned to be developed openly in the spirit of Linux and GNU. This vision drew the attention and support of the Free Software Foundation, who sponsored the project for the first part of its life. -
A Debian Pure Blend for Astronomy and Astrophysics
The Debian Astro project A Debian Pure Blend for astronomy and astrophysics Ole Streicher [email protected] Zeuthen, 2018-02-13 Ole Streicher (AIP Potsdam) The Debian Astro project Zeuthen, 2018-02-13 1 / 23 Debian GNU/Linux Free Linux based operating system One of the oldest distributions (founded 1993) Free as in \Free Speech" Base: Social Contract; Debian Free Software Guidelines > 50:000 software packages > 1:000 official developers Base for many derivatives: Ubuntu, Mint, ... Current stable version: Debian 9 (Stretch), since June 2017 Ole Streicher (AIP Potsdam) The Debian Astro project Zeuthen, 2018-02-13 2 / 23 The Debian Astro Pure Blend Blended tea: a combination of different kinds of teas to guarantee consistent quality (Wikipedia) Method to organize Debian astronomy packages currently 294 packages, (more in preparation) 19 metapackages Web page, \tasks" pages Handle citations, ASCL entries Completely integrated into Debian (Pure) First release with Debian Stretch (June 2017) Ole Streicher (AIP Potsdam) The Debian Astro project Zeuthen, 2018-02-13 3 / 23 Debian Pure Blends Debian Astro - Astronomy and astrophysics Debian GIS - Geographical Information Systems DebiChem - Chemistry Debian Med - Strong focus on Microbiology NeuroDebian - Neuroscience Debian Science - \Umbrella" blend for sciences Debian Edu - Education of all kind Debian Games, Debian Junior, Debian Multimedia, Hamradio, ... Ole Streicher (AIP Potsdam) The Debian Astro project Zeuthen, 2018-02-13 4 / 23 History of Debian Astro First packages: saoimage (1999), cfitsio -
Open Source Et Gestion De L'information Médicale : Aperçu Des Projets Existants
Open source et gestion de l'information médicale : aperçu des projets existants Ateliers CISP Club 2011 – Alexandre BRULET Open Source : bref historique... 1969 : UNIX (Bell Labs°) 1975 : distribué à des universités pour « fins éducatives » avec les codes sources... 1977 : projet BSD 1984 : projet GNU (R. Stallman) (sources partagées) 1985 : Free Software Fondation (cadre légal – licence GPL) 1989 : licence BSD modifiée (open source) 1991 : noyau GNU/Linux ? OS dérivés (NetBSD, FreeBSD, SunOS ...) 1993 : Slackware 1993 : Debian 1994 : Red Hat > 50 OS dérivés > 100 OS dérivés 1998 : MPL (ex : SUSE) > 50 OS dérivés (Knopix, Ubuntu...) (Mandriva, Fedora ...) 1999 : licence Apache UNESCO 2004 : logiciels libres patrimoine de l'humanité (…) > 35 licences libres recensées sur wikipédia (PHP, Cecil, MIT, CPL, W3C, etc.) Open source : un fonctionnement communautaire ● La « pyramide » Linux : développeurs / 'maintainers' / chefs de projet sys USB net (...) L. Torvalds / A. Morton ● Système de «patchs» : publics, signés, discutés, soumis, (approuvés) ● Versions stables régulières et archivées (mirroirs) ● Système de «paquets» permettant la cohérence des OS ● Mode de fonctionnement repris par la plupart des distributions basées sur Linux ainsi que leurs « filles » : Debian → Ubuntu, Slackware → Zenwalk, RedHat → Fedora, etc. ● Idem pour les logiciels (xfce/gnome/kde, OOo, Gimp, Firefox, etc.) Le monde open source : un immense agrégat de communautés... OS OS OS Projets GNU OS OS OS Noyau OS OS OS Noyau OS OS Projets BSD Programme open source Programme propriétaire Système OS d'exploitation Quid des logiciels médicaux ? Petit tour du monde de l'open source médical à partir d'une liste proposée par Wikipédia. 1. Logiciels médicaux francophones : MedinTux ● Petite communauté depuis 2005 (marseille), licence CeCiLL ● DMI cabinet / hôpital - objectif = ergonomie ● Programmes serveurs et clients, consultation web possible. -
Pipenightdreams Osgcal-Doc Mumudvb Mpg123-Alsa Tbb
pipenightdreams osgcal-doc mumudvb mpg123-alsa tbb-examples libgammu4-dbg gcc-4.1-doc snort-rules-default davical cutmp3 libevolution5.0-cil aspell-am python-gobject-doc openoffice.org-l10n-mn libc6-xen xserver-xorg trophy-data t38modem pioneers-console libnb-platform10-java libgtkglext1-ruby libboost-wave1.39-dev drgenius bfbtester libchromexvmcpro1 isdnutils-xtools ubuntuone-client openoffice.org2-math openoffice.org-l10n-lt lsb-cxx-ia32 kdeartwork-emoticons-kde4 wmpuzzle trafshow python-plplot lx-gdb link-monitor-applet libscm-dev liblog-agent-logger-perl libccrtp-doc libclass-throwable-perl kde-i18n-csb jack-jconv hamradio-menus coinor-libvol-doc msx-emulator bitbake nabi language-pack-gnome-zh libpaperg popularity-contest xracer-tools xfont-nexus opendrim-lmp-baseserver libvorbisfile-ruby liblinebreak-doc libgfcui-2.0-0c2a-dbg libblacs-mpi-dev dict-freedict-spa-eng blender-ogrexml aspell-da x11-apps openoffice.org-l10n-lv openoffice.org-l10n-nl pnmtopng libodbcinstq1 libhsqldb-java-doc libmono-addins-gui0.2-cil sg3-utils linux-backports-modules-alsa-2.6.31-19-generic yorick-yeti-gsl python-pymssql plasma-widget-cpuload mcpp gpsim-lcd cl-csv libhtml-clean-perl asterisk-dbg apt-dater-dbg libgnome-mag1-dev language-pack-gnome-yo python-crypto svn-autoreleasedeb sugar-terminal-activity mii-diag maria-doc libplexus-component-api-java-doc libhugs-hgl-bundled libchipcard-libgwenhywfar47-plugins libghc6-random-dev freefem3d ezmlm cakephp-scripts aspell-ar ara-byte not+sparc openoffice.org-l10n-nn linux-backports-modules-karmic-generic-pae -
Case Studies of Vista Implementation— United States and International
39251_CH09_223_284 11/27/06 5:26 PM Page 223 CHAPTER 9 Case Studies of VistA Implementation— United States and International “VHA’s integrated health information system, including its framework for using performance measures to improve quality, is considered one of the best in the nation.” Institute of Medicine (IOM) Report, “Leadership by Example: Coordinating Government Roles in Improving Health Care Quality, 2002” Introduction The U.S. Department of Veterans Affairs (VA) has developed and imple- mented a comprehensive health information system and EHR system known as VistA, which was built from the ground up with a clinical focus. Many of the commercial off-the-shelf (COTS) health information systems in the private sector today were designed from a financial perspective and now are being reengineered to address medical and clinical informatics requirements. The VistA system is a proven product and can be readily adapted for use in acute care, ambulatory, and long-term care settings. It has been used in public and private healthcare provider organizations across the United States and in a number of international settings. 223 39251_CH09_223_284 11/27/06 5:26 PM Page 224 224 CASE STUDIES OF VISTA IMPLEMENTATION—UNITED STATES AND INTERNATIONAL Table 9-1 VistA Software Modules VistA Software Packages Pharmacy: Inpatient Medications Health Data Systems Pharmacy: Inpatient Medications— Automated Medical Information Exchange Intravenous (IV) (AMIE) Pharmacy: Inpatient Medications— Incident Reporting Unit Dose (UD) Lexicon Utility Pharmacy: -
Impacting the Bioscience Progress by Backporting Software for Bio-Linux
Impacting the bioscience progress by backporting software for Bio-Linux Sasa Paporovic [email protected] v0.9 What is Bio-Linux and what is it good for - also its drawbacks: If someone says to use or to have a Linux this is correct as like it is imprecise. It does not exist a Linux as full functional operating system by itself. What was originally meant by the term Linux was the operating system core[1]. The so called kernel, or in a case of a Linux operating system the Linux kernel. It is originally designed and programmed by Linus Torvalds, who is also today the developer in chef or to say it with his words, he is the “alpha-male” of all developers[2]. Anyway, what we have today are Distributions[3]. It has become common to call them simply “a Linux”. This means that there are organizations out there, mostly private, some funded and some other commercial, which gather all what is needed to design around the Linux kernel a full functional operating system. This targets mostly Software, but also web and service infrastructure. Some of them have a history that is nearly as long as the Linux kernel is alive, like Debian. Some others are younger like Ubuntu and some more others are very young, like Bio-Linux[4]. The last Linux, the Bio-Linux, especially its latest version Bio-Linux 7 we are focusing here[5]. In year 2006 Bio-Linux with the work of Tim Booth[42] and team gives its rising[6] and provide an operating system that was and still specialized in providing a bioinformatic specific software environment for the working needs in this corner of bioscience. -
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 ..............................................................