Open-source software for radiologists: a primer

Open-source software for radiologists: a primer

Clinical Radiology (2007) 62, 120e130 REVIEW Open-source software for radiologists: a primer A.F. Scarsbrook* Department of Radiology, St James’s Un...

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Clinical Radiology (2007) 62, 120e130

REVIEW

Open-source software for radiologists: a primer A.F. Scarsbrook* Department of Radiology, St James’s University Hospital, Leeds Teaching Hospitals NHS Trust, UK Received 19 September 2006; accepted 26 September 2006

There is a wide variety of free (open-source) software available via the Internet which may be of interest to radiologists. This article will explore the use of open-source software in radiology to help streamline academic workflow and improve general efficiency and effectiveness by highlighting a number of the most useful applications currently available. These include really simple syndication applications, e-mail management, spreadsheet, word processing, database and presentation packages, as well as image and video editing software. How to incorporate this software into radiological practice will also be discussed. ª 2006 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Introduction Recent advances in medical imaging have been accompanied by a massive influx of new applications in radiology informatics. Those working in the field of radiology are at the ‘‘coal face’’ of this technological revolution and face a constant challenge of how best to adapt to the dramatic changes and at the same time continue to work productively. The preceding articles in this series have covered various aspects of radiological information technology (IT) and explored the utility of web-based resources in expanding knowledge and improving working practice.1e6 This article will focus on freely available software applications that can help improve academic workflow and facilitate efficient and effective time management. There have been a number of exciting developments in the range of free (open-source) software available via the internet of particular interest to radiologists. First, various applications that harness an emerging and refreshingly simple webbased technology called RSS could be utilized in a variety of ways to improve efficiency and effectiveness within radiology. In addition there * Guarantor and correspondent: A.F. Scarsbrook, Department of Radiology, St James’s University Hospital, Leeds, UK. Tel.: þ44 11320 64047; fax: þ44 11320 64691. E-mail address: [email protected]

is a wide variety of open-source software that provides assistance with anything from organization of e-mails, through database and spreadsheet use, to processing of digital images and movie clips for use in presentations and publications. Much time (and money) can be wasted trying to acquire these resources. This article will explore a selection of the most useful software currently available and illustrate how the applications may be of specific use to radiologists.

Open-source software There is a vast amount of web-based, freely available software, some good, some bad, and some indifferent. Frequently the terms free and open-source software are used interchangeably, which can lead to confusion. There may be a large difference in quality between official open-source software and other non-certified freeware. An authentication mark, ‘‘OSI certified,’’ is only applied to software that is distributed under an open-source licence and meets strict criteria set by the Open Source Initiative (OSI).7 This mark is a recognized and valued symbol, indicating that the software is distributed under a license guaranteeing the right to read, redistribute, modify, and use the software freely. All of the software that will be highlighted in this article conforms to the

0009-9260/$ - see front matter ª 2006 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved. doi:10.1016/j.crad.2006.09.023

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Screenshot from the BBC website showing the typical appearance of RSS feed icons (red arrows).

OSI standard and is freely available for download from the internet and for distribution to colleagues.

Open-source software for radiologists There are many different types of open-source software that are of potential use to radiologists. This article will consider a few of the more interesting applications currently available, including really simple syndication (RSS) software, e-mail management, word processing, spreadsheet, database and presentation applications, photo editing and video editing software. A number of other open-source applications of particular use to radiologists have been discussed in previous articles in this series, and elsewhere, including Digital Imaging and Communication in Medicine (DICOM) viewing software3,8,9 and website development applications.5 Anyone wishing to explore the many other types of software not discussed in this article

could start by visiting the open-source software directory accessible at http://www.osdir.com/. In addition a wide variety of other useful open-source applications have been reviewed elsewhere.10

RSS technology RSS is a promising and rapidly developing webbased tool that is likely to have a major impact on the way information is accessed on the internet in the near future. RSS does not officially stand for anything, though is commonly referred to as ‘‘really simple syndication’’ or ‘‘rich site summary’’. RSS consists of a set of technical standards for sending information over the internet prepared using a specialized text format called extensible mark-up language (XML). Because the internet has become such a vast information resource many radiologists regularly visit a number of websites on a daily basis perhaps

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Figure 2 Screenshot from an example open-source RSS reader d FeedReader d which has been configured to receive feeds from various radiology journals and websites.

to browse general news, to see the latest developments in a particular field, for educational purposes or to answer a specific question. Visiting more than a few websites quickly becomes time-

consuming and is inherently inefficient. Herein lies the beauty of RSS; it is a system where websites that frequently update information generate a special feed consisting of short headlines and summaries

Figure 3 Screenshot from the RSS4Medics.com website, which provides information about RSS technology specifically for Doctors and has links to innumerable medically-orientated RSS feeds.

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of new content with links to the full text. It is impossible to be certain exactly how many websites have RSS feeds but it is well in excess of 50,000, with new ones joining all the time. Many mainstream sites such as the British Broadcasting Corporation (http://www.bbc.co.uk) and other news portals have used RSS technology for a few years and increasingly many medically orientated websites (including a large number of medical journals and PubMed) have followed suit. Most websites providing RSS feeds display a small orange ‘‘RSS’’ or ‘‘XML’’ icon, which you may well have seen and wondered what they were for (Fig. 1). Using RSS can save a lot of time by providing a single point of reference to summarized highlights from many different (self-chosen) websites and journal article abstracts with links to the actual websites if you require more information.

RSS readers In order to be able to receive RSS feeds an application called a RSS reader or aggregator is required. These are fully customizable and monitor specific websites or electronic journals (once you have signed up to their RSS feed) notifying you whenever new content is added. If you think it sounds too complicated fear not because in reality it is really quite simple to download and configure the software. The modicum of effort required in the initial Table 1

set-up facilitates highly efficient review of latest medical data rather than having to spend much more time trawling through several websites. Some RSS readers enable setting of keyword filters so that any new web-content (or journal articles) containing the specific keywords are automatically collated and stored in a folder for future reference.11 The first step is to download and install an RSS reader onto your computer. There are many different types to choose from but it is perhaps wise to start with a fairly basic program because these are generally easier to set-up and use. Good examples include FeedReader (http://www.feedreader.com) (Fig. 2), SharpReader (http://www.sharpreader. net/) or BlogExpress (http://blogexpress.com/) all of which can be downloaded at no cost. A wider selection of RSS readers are discussed at http:// blogspace.com/RSS/readers. Alternatively several of the more popular RSS readers are reviewed and compared elsewhere.12 Web-based RSS readers are also available, which allow access to your RSS feeds from any computer with internet access. This can be useful if you do not have regular access to a single computer or wish to access information whilst attending a conference. A good example of a simple web-based RSS reader is available from Google at http://www.google.com/ reader. If you prefer an open-source application called rss2email can be used to send RSS feeds directly to your e-mail account and can be downloaded from http://rss2email.infogami.com/.

RSS feed details from various journals and radiology-related websites

Electronic journals British Journal of Radiology Journal of Magnetic Resonance Imaging American Journal of Roentgenology Cardiovascular & Interventional Radiology Emergency Radiology European Journal of Nuclear Medicine Journal of Digital Imaging European Radiology Abdominal Imaging Neuroradiology Pediatric Radiology Skeletal Radiology Nuclear Medicine Communications Clinical Nuclear Medicine Australasian Radiology Journal of Computer Assisted Tomography Topics in Magnetic Resonance Imaging Journal of Thoracic Imaging

http://api.ingentaconnect.com/content/bir/bjr/latest?format¼rss http://www3.interscience.wiley.com/rss/journal/10005199 http://www.ajronline.org/rss/current.xml http://www.springerlink.com/content/1432-086X/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1438-1435/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1619-7089/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1618-727X/?sortorder¼asc&export¼rss http://www.springerlink.com/content/hxm64668r446/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1432-0509/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1432-1920/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1432-1998/?sortorder¼asc&export¼rss http://www.springerlink.com/content/1432-2161/?sortorder¼asc&export¼rss http://www.nuclearmedicinecomm.com/pt/re/nucmedcomm/toccurrentrss.xml http://www.nuclearmed.com/pt/re/cnm/toccurrentrss.xml http://www.blackwell-synergy.com/action/showFeed?ai¼vg&jc¼ara&type¼ etoc&feed¼rss http://www.jcat.org/pt/re/jcat/toccurrentrss.xml http://www.topicsinmri.com/pt/re/tmri/toccurrentrss.xml http://www.thoracicimaging.com/pt/re/jti/toccurrentrss.xml

Radiology related websites Sumer’s Radiology Weblog Medscape Radiology Headlines Aunt Minnie News BMJ Careers e Radiology Jobs

http://sumerdoc.blogspot.com/atom.xml http://www.medscape.com/cx/rssfeeds/radiology.xml http://www.auntminnie.com/rss/rss.aspx http://www.bmjcareers.com/rss/265491

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Figure 4 Screenshot from an example open-source e-mail management application d Mozilla Thunderbird d being used to access e-mail from multiple different accounts.

Subscribing to RSS feeds Once you have installed an RSS reader, the next step is to decide what content you want to receive by finding and subscribing to relevant RSS feeds. You can manually enter feed addresses when you come across orange ‘‘RSS’’ icons on your preferred websites by right clicking on the icon and selecting ‘‘copy shortcut’’. Then, after opening the reader application and choosing the option to add a new feed, right-clicking on the mouse allows the selected feed address to be pasted directly into the reader. This method is a bit cumbersome and can be time-consuming. A much more efficient method of acquiring feed addresses for sites of interest is to use a RSS referral website, like Syndic8 (http://www.syndic8.com/), one of a number of online RSS directories, listing thousands of feeds, categorized alphabetically by subject. A particularly useful resource for medical professionals, http://www.rss4doctors.com, contains a comprehensive directory of medically orientated RSS feeds (Fig. 3). The website also includes detailed information about RSS technology, a useful tutorial on how to use FeedReader for beginners, and information about advanced applications for more experienced users. The authors of this website have also designed a search engine

specifically for medical RSS feeds, which is available at http://www.medworm.com. An increasing number of online medical journals now use RSS technology. A particularly helpful website from the National Institute of Health Libraries in the United States lists all of the medical journals currently available electronically and provides RSS feed details for any that use this technology. The resource is freely available at http://nihlibrary.nih.gov/ResearchTools/default. htm?srchType¼OnlineJournals. At present not all radiology journals offer RSS feeds. The American Journal of Roentgenology has embraced RSS and provides citation and abstract information for recent and current issues as feeds. In addition there are individual feeds for the many different subspecialty sections of the journal. Further details are provided at http://www.ajronline.org/rss/. A variety of radiology journals and websites that provide RSS feeds are listed in Table 1.

Other RSS applications Anyone already proficient in RSS reader use may want to explore how the technology can be utilized in other ways. It can be relatively easy to create feeds for your own website or weblog

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Figure 5 Screenshots from an open-source alternative to Microsoft Office d Open Office (a) ‘‘Writer’’ a word processor being used to produce an article for publication (b) ‘‘Calc’’ a spreadsheet being used for a training logbook (c) ‘‘Impress’’ a presentation application being used to prepare a talk for an academic meeting (d) ‘‘Draw’’ a graphic design program being used to create a poster for a radiology conference.

using RSS writing software. This could be of specific use in radiology departments. If everyone in the department was shown how to use an RSS reader and a feed was added to the departmental or hospital website which everyone subscribed to, this would then become an extremely powerful communication tool. For example, this would be an excellent way to update all staff about new guidelines, on-call rotas, etc. If the departmental website feed(s) were included in an online RSS directory, the potential audience would be greatly widened and this could be used to disseminate important research findings, details about forthcoming meetings, and promotion of new service developments. With the major developments in IT occurring throughout the medical world it seems likely that RSS may become a more efficient and effective method of communication than either e-mail or conventional mail. A forward-thinking group of radiologists from the Department of Radiology at the Johns Hopkins University in Baltimore, USA, have described their use of RSS technology to distribute educational audio broadcasts on various aspects of cross-sectional imaging via the Internet.13 Detailed discussion of

the processes involved in writing and publishing RSS feeds is beyond the scope of this article but further information is available elsewhere.13,14

The future prospects of RSS in radiology There is a paucity of research in this exciting and rapidly expanding area, however, a thought provoking article on the potential future uses of RSS technology within radiology by David Kelton, a radiology resident at the University of Toronto, is available on the Internet.15 This discusses wideranging possibilities, including incorporation of RSS into medical research to facilitate automatic updating of databases whenever imaging studies have been completed on trial patients and when new content of specific interest has been added to their electronic patient records (EPRs). Similarly specific keywords in radiology reports, e.g. adrenocortical carcinoma, could be set to trigger an RSS feed to clinical trial groups wishing to recruit specific patients into studies of new treatments or interventions. Another important potential use of RSS technology is in radiology education

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Figure 6 Screenshot from an example open-source image editor suitable for less experienced users d IrfanViewd being used to edit a coronal image from an abdominal MR investigation.

whereby trainees could flag on-call images they were uncertain about, and instead of having to manually retrieve the final report after senior review, a RSS feed to the updated report could automatically be sent to their reader with the links to relevant pathological and surgical reports (assuming an EPR is in place). Finally, the article explores the utility of RSS technology in radiology quality control. Instead of annual auditing, RSS could enable continuous review of performance statistics, e.g. mammography recall rates or biopsy results. Clearly there is huge potential for RSS technology within both our field and more widely throughout medical practice. The real beauty is that such simple technology can be so effective. How things will develop is uncertain but it is hoped that this article may encourage readers to raise the profile of RSS within the radiological community and stimulate research into the vast potential it has to offer.

E-mail management software E-mail has become an everyday reality and a major form of communication between professionals.

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Increasingly individuals may have numerous e-mail addresses with at the very least a departmental e-mail and a separate personal address. Frequently many also choose to have at least one other webbased e-mail account that can accessed from the Internet whilst away from home or work. It is inherently more efficient to be able to access all of these accounts from a single source and one commonly used option is an e-mail management application such as Microsoft Outlook. There is an excellent open-source alternative called Mozilla Thunderbird (Fig. 4) which has several potential advantages and can be downloaded from http://www.mozilla.com/thunderbird.16 The software is completely free and because it is opensource the programming code can be (and is) viewed and changed by anyone, unlike proprietary e-mail software from companies such as Microsoft or AOL. The major advantage of this is that any faults or security weaknesses are quickly spotted by independent programmers and the software is rapidly updated by developers. Not only is Thunderbird a very secure e-mail client it also has a sophisticated spam filter that learns from you and after some initial training reliably filters most junk mail without filing legitimate e-mail as spam, which can be an irritating problem with many other e-mail applications. All incoming mail is indexed and there is a powerful search tool that scans all e-mail accounts and makes it very easy to handle large amounts of mail and quickly find the previous e-mail you are looking for. In addition, there is an integrated RSS reader. Another useful feature is the ability to run Thunderbird from removable storage media such as a USB stick enabling you to take your mailbox with you wherever you go. The software is easy to use and compatible with other e-mail management software so that when it is first used all of your old messages and addresses can be easily imported. Tutorials and a variety of tips on using the application are available elsewhere.17

Open office d a free alternative to Microsoft Office Many radiologists are familiar with and no doubt frequently use the Microsoft Office application suite, which includes Word, Access, Excel and PowerPoint. There is an excellent open-source alternative that is as at least as good and has several additional useful features. The latest version of the software, called Open Office is available for download from http://download. openoffice.org/. The application suite includes

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Figure 7 Screenshot from an example open-source image editor suitable for more experienced users d GNU Image Manipulation Program (‘‘The Gimp’’) d being used to edit a chest radiograph.

a word processor (Writer, Fig. 5a), a spreadsheet (Calc, Fig. 5b), a presentation package (Impress, Fig. 5c), a database (Base) and a graphics design program (Draw, Fig. 5d) which can be used to create posters. All of the applications are easy to use and have a very similar user interface to their Microsoft equivalents. Open Office is particularly versatile and allows any file created using Microsoft software to be opened and edited. Likewise any file created using Open Office software can be saved in Microsoft format. Another excellent feature is the ability to save any file in portable data format (PDF), which can then be viewed by anyone using freely available Adobe Acrobat Reader software. This allows sharing of read-only versions of presentations or documents with colleagues. Similarly presentations and drawings can be saved in Macromedia Flash format, which is rapidly becoming a preferred file format for electronic presentations at a number of radiology scientific meetings, e.g., European Congress of Radiology, Radiological Society of North America and the American Roentgen Ray Society. Saving files as Flash documents also simplifies the process of

integrating presentations into a departmental website. The potential uses of Flash technology within Radiology have been explored elsewhere.18,19 Those interested in learning more about Flash and its use in electronic presentations should visit http://www.flashgeek.com/ which is a web portal with lots of useful information and tutorials. There is an active, online Open Office forum group that is an excellent source of further information and support and is available at http:// www.8daysaweek.co.uk. In addition several tutorials on all of the Open Office applications are freely available at http://www.openoffice-support.net. For more advanced users a variety of useful add-ins to extend the software capabilities can be downloaded from http://www.ooomacros.org/user.php.

Open-source image editing software A previous article in this series reviewed the use of image editing software by radiologists and suggested a number of sources of additional information in this area.3 There are a variety of freely

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Figure 8 Screenshot from an example open-source video editing application d Microsoft Movie Maker 2 d being used to adapt digital movie clips from a PET-CT investigation before use in teaching.

available applications that can be used for image editing.20 Two packages are of particular interest to radiologists because of the range of features offered and the similarity of the user interface with other commonly used commercial software such as Adobe Photoshop. First, IrfanView (Fig. 6) is an image editing application that can be downloaded from http:// www.irfanview.com/. This compact but deceptively powerful application supports multiple image and video file formats and is relatively simple to use. There are a number of plugs-ins that can be downloaded from the same website, which extend the functionality of the software. One of these allows the application to read DICOM files, which is not possible with other image editing software. There is an online IrfanView forum group, which is a good source of further information accessible at http:// www.irfanview-online.com. In addition there are a number of helpful tutorials on various aspects of IrfanView provided at http://www.indeavors.com/ resources/tutorials.htm. IrfanView can be used to automatically convert several images, a feature which may be of particular use to radiologists wanting to quickly edit stacks of cross-sectional images for example.21 The second application is a very powerful piece of software with many advanced functions, including

image animation, called GNU Image Manipulation Program (or GIMP for short; Fig. 7). It can be downloaded from http://www.gimp.org/downloads/. The software requires some commitment to master but has a lot to offer and will reward readers who are prepared to experiment with it. A number of tutorials are available at http://www.gimp.org/ tutorials/. In addition there is a free online GIMP encyclopaedia (wiki) available at http://wiki.gimp. org/gimp/.

Open-source video editing software With the technological advances that have occurred in cross-sectional and functional imaging radiologists are frequently confronted with hundreds of images. As a result movie clips of selected imaging studies are increasingly being used in teaching and presentations at academic meetings. An excellent series of articles for radiologists on how to manipulate movie clips for incorporation into electronic presentations or for online publication are available elsewhere.22,23 These articles describe the use of commercial software to edit video clips. There are a number of opensource applications that could be used as a free alternative.24

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another and can also be used to reduce video file size by applying various different codecs is available at http://www.freedownloadscenter.com/Utilities/ Text_Editors_A-G/SC_Free_Video_Converter.html (Fig. 9). The compatibility issues affecting use of video files in electronic presentations are described in more detail in an informative article by Yam et al.25

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Figure 9 Screenshot from an example open-source application for reducing the size of and converting video files to different formats d SC Video Converter.

Perhaps the best option is Microsoft Movie Maker 2 (Fig. 8) a video editing package that is bundled in the software included with all new Windows computers. Alternatively it is available from http://www.microsoft.com/windowsxp/downloads/ updates/moviemaker2.mspx. The application is relatively simple to use for video editing and files can then be saved in a variety of different formats including Windows Media Video (WMV) and Audio Video Interleave (AVI). A free online textbook on Movie Maker 2 is available at http://www.papajohn. org/ for those interested in using the application. There may be compatibility issues when using different video file formats in electronic presentations. Video file size is dramatically reduced by using a codec, a digital algorithm used to compress and decompress movie files. There are a wide variety of different codecs in use and problems sometimes arise when a presentation containing a compressed video clip is displayed on a computer (e.g., at a conference) without the necessary codec installed. A detailed description of codec technology is beyond the scope of this article. The vast majority of codecs are freely available for download from the web and a useful website lists them all, http://www.free-codecs.com/. A bundle of the most commonly used codecs can be downloaded from http://www.free-codecs.com/download/K_Lite_Codec_Pack.htm and kept with your presentation on portable media for installation onto any computer as necessary to avoid this problem. Compatibility issues sometimes also arise because of the type of video file format used. A useful and easy to use open-source application allows conversion of video files from one type to

Radiologists face a constant battle to stay upto-date and adapt to the great technological developments that are occurring in our field. A variety of freely available open-source software can be used to help streamline academic workflow and facilitate more efficient and effective practice. This article has explored a variety of the more useful, currently available applications which should be of specific interest to radiologists.

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14. Eisenzopf J. Making headlines with RSS d using rich site summaries to draw new visitors. Available at http:// www.webtechniques.com/archives/2000/02/eisenzopf/ [accessed 2nd September 2006]. 15. Kelton D. RSS in radiology and medicine. Available at http://opennorthvc.com/?p¼7 [accessed 2nd September 2006]. 16. Al-Ubaydli M. Software solutions. BMJ Careers 2006;333:16. 17. Tschabitscher H. Top 10 most popular Mozilla Thunderbird tips, tricks and tutorials. Available at http://email.about. com/od/mozillathunderbirdtips/tp/et_popular_tips.htm [accessed 5th September 2006]. 18. Yam CS. Using Macromedia Flash for electronic presentations: a new alternative. AJR Am J Roentgenol 2006;187: W209e17. 19. Yam CS. A solution for using dynamic data sets in electronic presentations. AJR Am J Roentgenol 2006;187: 218e26.

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20. Chastain S. Top 8 free photo editors for Windows. Available at http://graphicssoft.about.com/cs/imageediting/tp/ freephotoedw.htm [accessed 18th September 2006]. 21. Mysticmusings.typepad.com Website. IrfanView d batch convert and rename tutorial. Available at http://mystic musings.typepad.com/photos/tutorials_ivw_batchconren/ index.html [accessed 18th September 2006]. 22. Yam CS, Kruskal J, Larson M. Using movie clips in PowerPoint presentations: part 2, movie editing. AJR Am J Roentgenol 2005;185:1371e6. 23. Yam CS. Preparation of digital movie clips for online journal publication. AJR Am J Roentgenol 2006;187:W93eW102. 24. About.com Website. Best free video editing software. Available at http://desktopvideo.about.com/od/softwarereviews/ ss/bestfreesw2_ro.htm [accessed 18th September 2006]. 25. Yam CS, Kruskal J, Larson M. Using movie clips in PowerPoint presentations: part 1, compatibility issues. AJR Am J Roentgenol 2005;185:1074e8.