@article {1304, title = {iBEX: Modular Open-Source Software for Digital Radiography.}, journal = {J Digit Imaging}, volume = {33}, year = {2020}, month = {2020 06}, pages = {708-721}, abstract = {

A device-independent software package, named iBEX, is developed to accelerate the research and development efforts for X-ray imaging setups such as chest radiography, linear and multidirectional tomography, and dental and skeletal radiography. Its extension mechanism makes the software adaptable for a wide range of digital X-ray imaging hardware combinations and provides capabilities for researchers to develop image processing plug-ins. Independent of the X-ray sensor technology, iBEX could integrate with heterogeneous communication channels of digital detectors. iBEX is a freeware option for preclinical and early clinical testing of radiography devices. It provides tools to calibrate the device, integrate to health information infrastructure, acquire image, store studies on local storage, and send them to Picture Archiving and Communication System (PACS). iBEX is a unique open-source project bringing X-ray imaging devices{\textquoteright} software into the scope of the open-source community to reduce the X-ray scanners{\textquoteright} research effort, potentially increase the image quality, and cut down the production and testing costs of radiography devices.

}, keywords = {Humans, Image Processing, Computer-Assisted, Radiographic Image Enhancement, Radiology Information Systems, Software, Tomography, X-Ray Computed}, issn = {1618-727X}, doi = {10.1007/s10278-019-00304-1}, author = {Brusan, Altay and Durmaz, F Ayta{\c c} and Yaman, Alper and {\"O}zt{\"u}rk, Cengizhan} } @article {1271, title = {The impact of PEPFAR transition on HIV service delivery at health facilities in Uganda.}, journal = {PLoS One}, volume = {14}, year = {2019}, month = {2019}, pages = {e0223426}, abstract = {

BACKGROUND: Since 2004, the President{\textquoteright}s Emergency Plan for AIDS Relief (PEPFAR) has played a large role in Uganda{\textquoteright}s HIV/AIDS response. To better target resources to high burden regions and facilities, PEPFAR planned to withdraw from 29\% of previously-supported health facilities in Uganda between 2015 and 2017.

METHODS: We conducted a cross-sectional survey of 226 PEPFAR-supported health facilities in Uganda in mid-2017. The survey gathered information on availability, perceived quality, and access to HIV services before and after transition. We compare responses for facilities transitioned to those maintained on PEPFAR, accounting for survey design. We also extracted data from DHIS2 for the period October 2013-December 2017 on the number of HIV tests and counseling (HTC), number of patients on antiretroviral therapy (Current on ART), and retention on first-line ART (Retention) at 12 months. Using mixed effect models, we compare trends in service volume around the transition period.

RESULTS: There were 206 facilities that reported transition and 20 that reported maintenance on PEPFAR. Some facilities reporting transition may have been in a gap between implementing partners. The median transition date was September 2016, nine months prior to the survey. Transition facilities were more likely to discontinue HIV outreach following transition (51.6\% vs. 1.4\%, p<0.001) and to report declines in HIV care access (43.5\% vs. 3.1\%, p<0.001) and quality (35.6\% vs. 0\%, p<0.001). However, transition facilities did not differ in their trends in HIV service volume relative to maintenance facilities.

CONCLUSIONS: Transition from PEPFAR resulted in facilities reporting worsening patient access and service quality for HIV care, but there is insufficient evidence to suggest negative impacts on volume of HIV services. Facility respondents{\textquoteright} perceptions about access and quality may be overly pessimistic, or they may signal forthcoming impacts. Unrelated to transition, declining retention on ART in Uganda is a cause for concern.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0223426}, author = {Wilhelm, Jess Alan and Qiu, Mary and Paina, Ligia and Colantuoni, Elizabeth and Mukuru, Moses and Ssengooba, Freddie and Bennett, Sara} } @article {1135, title = {Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals.}, journal = {BMJ Glob Health}, volume = {1}, year = {2016}, month = {2016 May 24}, pages = {e000028}, abstract = {

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya. We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals{\textquoteright} paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network. In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians{\textquoteright} initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning. We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.

}, issn = {2059-7908}, doi = {10.1136/bmjgh-2016-000028}, author = {Tuti, Timothy and Bitok, Michael and Malla, Lucas and Paton, Chris and Muinga, Naomi and Gathara, David and Gachau, Susan and Mbevi, George and Nyachiro, Wycliffe and Ogero, Morris and Julius, Thomas and Irimu, Grace and English, Mike} } @article {1131, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.}, journal = {Med Image Anal}, year = {2016}, month = {2016 Jul 7}, abstract = {

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.

}, issn = {1361-8423}, doi = {10.1016/j.media.2016.06.035}, author = {Kapur, Tina and Pieper, Steve and Fedorov, Andriy and Fillion-Robin, J-C and Halle, Michael and O{\textquoteright}Donnell, Lauren and Lasso, Andras and Ungi, Tamas and Pinter, Csaba and Finet, Julien and Pujol, Sonia and Jagadeesan, Jayender and Tokuda, Junichi and Norton, Isaiah and Estepar, Raul San Jose and Gering, David and Aerts, Hugo J W L and Jakab, Marianna and Hata, Nobuhiko and Ibanez, Luiz and Blezek, Daniel and Miller, Jim and Aylward, Stephen and Grimson, W Eric L and Fichtinger, Gabor and Wells, William M and Lorensen, William E and Schroeder, Will and Kikinis, Ron} } @article {1133, title = {Integrating Heterogeneous Biomedical Data for Cancer Research: the CARPEM infrastructure.}, journal = {Appl Clin Inform}, volume = {7}, year = {2016}, month = {2016}, pages = {260-74}, abstract = {

Cancer research involves numerous disciplines. The multiplicity of data sources and their heterogeneous nature render the integration and the exploration of the data more and more complex. Translational research platforms are a promising way to assist scientists in these tasks. In this article, we identify a set of scientific and technical principles needed to build a translational research platform compatible with ethical requirements, data protection and data-integration problems. We describe the solution adopted by the CARPEM cancer research program to design and deploy a platform able to integrate retrospective, prospective, and day-to-day care data. We designed a three-layer architecture composed of a data collection layer, a data integration layer and a data access layer. We leverage a set of open-source resources including i2b2 and tranSMART.

}, issn = {1869-0327}, doi = {10.4338/ACI-2015-09-RA-0125}, author = {Rance, Bastien and Canuel, Vincent and Countouris, Hector and Laurent-Puig, Pierre and Burgun, Anita} } @article {1279, title = {Identifying patients with asthma in primary care electronic medical record systems Chart analysis-based electronic algorithm validation study.}, journal = {Can Fam Physician}, volume = {61}, year = {2015}, month = {2015 Oct}, pages = {e474-83}, abstract = {

OBJECTIVE: To develop and test a variety of electronic medical record (EMR) search algorithms to allow clinicians to accurately identify their patients with asthma in order to enable improved care.

DESIGN: A retrospective chart analysis identified 5 relevant unique EMR information fields (electronic disease registry, cumulative patient profile, billing diagnostic code, medications, and chart notes); asthma-related search terms were designated for each field. The accuracy of each term was tested for its ability to identify the asthma patients among all patients whose charts were reviewed. Increasingly sophisticated search algorithms were then designed and evaluated by serially combining individual searches with Boolean operators.

SETTING: Two large academic primary care clinics in Hamilton, Ont.

PARTICIPANTS: Charts for 600 randomly selected patients aged 16 years and older identified in an initial EMR search as likely having asthma (n = 150), chronic obstructive pulmonary disease (n = 150), other respiratory conditions (n = 150), or nonrespiratory conditions (n = 150) were reviewed until 100 patients per category were identified (or until all available names were exhausted). A total of 398 charts were reviewed in full and included.

MAIN OUTCOME MEASURES: Sensitivity and specificity of each search for asthma diagnosis (against the reference standard of a physician chart review-based diagnosis).

RESULTS: Two physicians reviewed the charts identified in the initial EMR search using a standardized data collection form and ascribed the following diagnoses in 398 patients: 112 (28.1\%) had asthma, 81 (20.4\%) had chronic obstructive pulmonary disease, 104 (26.1\%) had other respiratory conditions, and 101 (25.4\%) had nonrespiratory conditions. Concordance between reviewers in chart abstraction diagnosis was high (κ = 0.89, 95\% CI 0.80 to 0.97). Overall, the algorithm searching for patients who had asthma in their cumulative patient profiles or for whom an asthma billing code had been used was the most accurate (sensitivity of 90.2\%, 95\% CI 87.3\% to 93.1\%; specificity of 83.9\%, 95\% CI 80.3\% to 87.5\%).

CONCLUSION: Usable, practical search algorithms that accurately identify patients with asthma in existing EMRs are presented. Clinicians can apply 1 of these algorithms to generate asthma registries for targeted quality improvement initiatives and outcome measurements. This methodology can be emulated for other diseases.

}, keywords = {Adult, Aged, Algorithms, Asthma, Data Accuracy, electronic health records, Female, Humans, Male, Middle Aged, Ontario, Primary Health Care, Pulmonary Disease, Chronic Obstructive, Registries, Retrospective Studies, Sensitivity and Specificity}, issn = {1715-5258}, author = {Xi, Nancy and Wallace, Rebecca and Agarwal, Gina and Chan, David and Gershon, Andrea and Gupta, Samir} } @article {970, title = {The ImageJ ecosystem: An open platform for biomedical image analysis.}, journal = {Mol Reprod Dev}, year = {2015}, month = {2015 Jul 7}, abstract = {

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software{\textquoteright}s extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. Mol. Reprod. Dev. 2015. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, issn = {1098-2795}, doi = {10.1002/mrd.22489}, author = {Schindelin, Johannes and Rueden, Curtis T and Hiner, Mark C and Eliceiri, Kevin W} } @article {977, title = {Implementation, reliability, and feasibility test of an Open-Source PACS.}, journal = {Radiol Med}, year = {2015}, month = {2015 Jun 19}, abstract = {

PURPOSE: To implement a hardware and software system able to perform the major functions of an Open-Source PACS, and to analyze it in a simulated real-world environment.

MATERIALS AND METHODS: A small home network was implemented, and the Open-Source operating system Ubuntu 11.10 was installed in a laptop containing the Dcm4chee suite with the software devices needed.

RESULTS: The Open-Source PACS implemented is compatible with Linux OS, Microsoft OS, and Mac OS X; furthermore, it was used with operating systems that guarantee the operation in portable devices (smartphone, tablet) Android and iOS.

CONCLUSIONS: An OSS PACS is useful for making tutorials and workshops on post-processing techniques for educational and training purposes.

}, issn = {1826-6983}, doi = {10.1007/s11547-015-0560-y}, author = {Valeri, Gianluca and Zuccaccia, Matteo and Badaloni, Andrea and Ciriaci, Damiano and La Riccia, Luigi and Mazzoni, Giovanni and Maggi, Stefania and Giovagnoni, Andrea} } @article {997, title = {Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.}, journal = {J Am Med Inform Assoc}, year = {2015}, month = {2015 Jun 10}, abstract = {

OBJECTIVE: To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice.

MATERIALS AND METHODS: The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals{\textquoteright} pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals.

RESULTS: In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use.

CONCLUSION: A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research.

}, issn = {1527-974X}, doi = {10.1093/jamia/ocv028}, author = {Tuti, Timothy and Bitok, Michael and Paton, Chris and Makone, Boniface and Malla, Lucas and Muinga, Naomi and Gathara, David and English, Mike} } @article {1292, title = {Innovative Technological Approach to Ebola Virus Disease Outbreak Response in Nigeria Using the Open Data Kit and Form Hub Technology.}, journal = {PLoS One}, volume = {10}, year = {2015}, month = {2015}, pages = {e0131000}, abstract = {

The recent outbreak of Ebola Virus Disease (EVD) in West Africa has ravaged many lives. Effective containment of this outbreak relies on prompt and effective coordination and communication across various interventions; early detection and response being critical to successful control. The use of information and communications technology (ICT) in active surveillance has proved to be effective but its use in Ebola outbreak response has been limited. Due to the need for timeliness in reporting and communication for early discovery of new EVD cases and promptness in response; it became imperative to empower the response team members with technologies and solutions which would enable smooth and rapid data flow. The Open Data Kit and Form Hub technology were used in combination with the Dashboard technology and ArcGIS mapping for follow up of contacts, identification of cases, case investigation and management and also for strategic planning during the response. A remarkable improvement was recorded in the reporting of daily follow-up of contacts after the deployment of the integrated real time technology. The turnaround time between identification of symptomatic contacts and evacuation to the isolation facility and also for receipt of laboratory results was reduced and informed decisions could be taken by all concerned. Accountability in contact tracing was ensured by the use of a GPS enabled device. The use of innovative technologies in the response of the EVD outbreak in Nigeria contributed significantly to the prompt control of the outbreak and containment of the disease by providing a valuable platform for early warning and guiding early actions.

}, keywords = {Disease Outbreaks, Ebolavirus, Epidemiological Monitoring, Female, Hemorrhagic Fever, Ebola, Humans, Male, Medical Informatics, Nigeria}, issn = {1932-6203}, doi = {10.1371/journal.pone.0131000}, author = {Tom-Aba, Daniel and Olaleye, Adeniyi and Olayinka, Adebola Tolulope and Nguku, Patrick and Waziri, Ndadilnasiya and Adewuyi, Peter and Adeoye, Olawunmi and Oladele, Saliu and Adeseye, Aderonke and Oguntimehin, Olukayode and Shuaib, Faisal} } @article {1003, title = {Innovative approaches to clinical data management in resource limited settings using open-source technologies.}, journal = {PLoS Negl Trop Dis}, volume = {8}, year = {2014}, month = {2014 Sep}, pages = {e3134}, issn = {1935-2735}, doi = {10.1371/journal.pntd.0003134}, author = {Omollo, Raymond and Ochieng, Michael and Mutinda, Brian and Omollo, Truphosa and Owiti, Rhoda and Okeyo, Seth and Wasunna, Monique and Edwards, Tansy} } @article {1011, title = {Informatics lessons from using a novel immunization information system.}, journal = {Stud Health Technol Inform}, volume = {192}, year = {2013}, month = {2013}, pages = {589-93}, abstract = {

In the 1990s, NewYork-Presbyterian Hospital began developing a comprehensive, standards-based immunization information system. The system, known as EzVac, has been operational since 1998 and now includes information on 2 million immunizations administered to more than 260,000 individuals. The system exchanges data with multiple electronic health records, a public health immunization registry, and a standalone personal health record. EzVac modules have recently been incorporated into the OpenMRS application and are being used to enhance immunization efforts in developing nations. We report on our experience with developing and using the EzVac system for 1) clinical care, both in local and global settings, 2) public health reporting, 3) consumer engagement, and 4) clinical and informatics research. We emphasize the advantages of using health IT standards to facilitate immunization information exchange in each of these domains.

}, keywords = {electronic health records, Health Information Management, Immunization, Internet, Medical Record Linkage, New York, Registries, Software}, issn = {0926-9630}, author = {Vawdrey, David K and Natarajan, Karthik and Kanter, Andrew S and Hripcsak, George and Kuperman, Gilad J and Stockwell, Melissa S} } @article {900, title = {Innovative low-cost telemonitoring: A versatile system using generic hardware, open source software and free data brokering services}, journal = {Health Care and Informatics Review Online}, volume = {17}, year = {2013}, pages = {2{\textendash}10}, abstract = {Improving access to vital medical information by telemonitoring has been shown to improve patient health, prevent admissions and shorten hospital length of stay [1,2]. Telemonitoring systems are costly and not in widespread use. This paper investigates the feasibility of creating a low-cost, versatile telemonitoring system through the use of generic hardware, open source software (OSS) and free data brokering services, by creating a working prototype. A low-cost, user friendly, widely available system could address the barriers that prevent widespread uptake of telemonitoring in healthcare.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84877107346\&partnerID=40\&md5=eb58b3030333d55f7624d0b54cabe051}, author = {Kok, K.a}, editor = {Lang, D.b} } @article {892, title = {Integration of advanced 3D SPECT modeling into the open-source STIR framework}, journal = {Medical Physics}, volume = {40}, year = {2013}, pages = {092502}, keywords = {C++ language, image reconstruction, medical image processing, object-oriented programming, public domain software, single photon emission computed tomography, software libraries, software packages}, doi = {10.1118/1.4816676}, url = {http://link.aip.org/link/?MPH/40/092502/1}, author = {Berta Marti Fuster and Carles Falcon and Charalampos Tsoumpas and Lefteris Livieratos and Pablo Aguiar and Albert Cot and Domenec Ros and Kris Thielemans} } @article {864, title = {Integration of PACS and CAD systems using DICOMDIR and open-source tools}, year = {2013}, pages = {86740V-86740V-6}, abstract = {The advancements of the last 30 years have made picture archiving and communication system (PACS) an indispensable technology to improve the delivery and management of clinical imaging services. Similarly, the maturation of algorithms and computer aided detection (CAD) systems has enhanced the interpretation and diagnosis of radiographical images. However, the lack of integration between the two systems inhibits the rate of development and application of these recent innovations in reaching the clinical users of PACS. We aim to enhance the clinical efficiency of CAD systems by developing an accessible, fully automated, user-friendly, and integrated linkage of CAD and PACS systems. This is the first integration initiative to take advantage of DICOMDIR file and its ability to index DICOM files, allowing images outside of PACS to be viewed within PACS. In this demonstration, the CAD system evaluates CT chest exams to detect lesions in the ribs and produces whole rib map images, screenshots, and detection report. A script executes the rib CAD system and creates a DICOMDIR file using {\quotedblbase}DCMTK", an open-source DICOM toolkit. We evaluated our system on thirty 5mm slice thickness and thirty 2mm slice thickness image studies and demonstrated a time saving efficiency of 93s{\textpm}14s and 221s{\textpm}17s per exam, respectively, compared to the current non-integrated workflow of using CAD systems. The advantages of this system are that it is easy to implement, requires no additional workstation and training, and allows CAD results to be viewed in PACS without disrupting radiology workflow, while maintaining the independence of both technologies. {\textcopyright} (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).}, doi = {10.1117/12.2001560}, url = {+ http://dx.doi.org/10.1117/12.2001560}, author = {Huang, Jiaxin and Ling, Alexander and Summers, Ronald M. and Yao, Jianhua} } @article {933, title = {International data-sharing for radiotherapy research: An open-source based infrastructure for multicentric clinical data mining.}, journal = {Radiother Oncol}, year = {2013}, month = {2013 Dec 2}, abstract = {

Extensive, multifactorial data sharing is a crucial prerequisite for current and future (radiotherapy) research. However, the cost, time and effort to achieve this are often a roadblock. We present an open-source based data-sharing infrastructure between two radiotherapy departments, allowing seamless exchange of de-identified, automatically translated clinical and biomedical treatment data.

}, issn = {1879-0887}, doi = {10.1016/j.radonc.2013.11.001}, author = {Roelofs, Erik and Dekker, Andr{\'e} and Meldolesi, Elisa and van Stiphout, Ruud G P M and Valentini, Vincenzo and Lambin, Philippe} } @conference {811, title = {Implementing a Personal Health Record Cloud Platform Using Ciphertext-Policy Attribute-Based Encryption}, booktitle = {Intelligent Networking and Collaborative Systems (INCoS), 2012 4th International Conference on}, year = {2012}, month = {sept.}, abstract = {Work on designing and implementing a patient-centric, personal health record cloud platform based on open-source Indivo X system. We adopt cipher text-policy attribute-based encryption to provide privacy protection and fine-grained access control.}, doi = {10.1109/iNCoS.2012.65}, author = {Wang, Changji and Liu, Xuan and Li, Wentao} } @article {805, title = {The Importance of Using Open Source Technologies and Common Standards for Interoperability within eHealth: Perspectives from the Millennium Villages Project}, journal = {Advances in Health Care Management}, volume = {Advances in Health Care Management}, year = {2012}, pages = {189{\textendash}204}, abstract = {Purpose {\textendash} The purpose of this chapter is to illustrate the importance of using open source technologies and common standards for interoperability when implementing eHealth systems, and to illustrate this through case studies, where possible. Design/methodology/approach {\textendash} The sources used to inform this chapter draw from the implementation and evaluation of the eHealth Program in the context of the Millennium Villages Project (MVP). Findings {\textendash} As the eHealth Team was tasked to deploy an eHealth architecture, the Millennium Villages Global-Network (MVG-Net), across all 14 of the MVP sites in sub-Saharan Africa, the team not only recognized the need for standards and uniformity but also realized that context would be an important factor. Therefore, the team decided to utilize open source solutions. Practical implications {\textendash} The MVP implementation of MVG-Net provides a model for those looking to implement informatics solutions across disciplines and countries. Furthermore, there are valuable lessons learned that the eHealth community can benefit from. Originality/value {\textendash} By sharing lessons learned and developing an accessible, open source eHealth platform, we believe that we can more efficiently and rapidly achieve the health-related and collaborative Millennium Development Goals.}, issn = {978-1-78052-858-8}, doi = {10.1108/S1474-8231(2012)0000012013}, author = {Andrew S. Kanter, Rob Borland, Mourice Barasa, Casey Iiams-Hauser, Olivia Velez, Nadi Nina Kaonga, Matt Berg} } @article {796, title = {Improving quality and use of data through data-use workshops: Zanzibar, United Republic of Tanzania.}, journal = {Bull World Health Organ}, volume = {90}, year = {2012}, month = {2012 May 1}, pages = {379-84}, abstract = {PROBLEM: In Zanzibar, United Republic of Tanzania, as in many developing countries, health managers lack faith in the national Health Management Information System (HMIS). The establishment of parallel data collection systems generates a vicious cycle: national health data are used little because they are of poor quality, and their relative lack of use, in turn, makes their quality remain poor. APPROACH: An action research approach was applied to strengthen the use of information and improve data quality in Zanzibar. The underlying premise was that encouraging use in small incremental steps could help to break the vicious cycle and improve the HMIS. LOCAL SETTING: To test the hypothesis at the national and district levels a project to strengthen the HMIS was established in Zanzibar. The project included quarterly data-use workshops during which district staff assessed their own routine data and critiqued their colleagues{\textquoteright} data. RELEVANT CHANGES: The data-use workshops generated inputs that were used by District Health Information Software developers to improve the tool. The HMIS, which initially covered only primary care outpatients and antenatal care, eventually grew to encompass all major health programmes and district and referral hospitals. The workshops directly contributed to improvements in data coverage, data set quality and rationalization, and local use of target indicators. LESSONS LEARNT: Data-use workshops with active engagement of data users themselves can improve health information systems overall and enhance staff capacity for information use, presentation and analysis for decision-making.}, issn = {1564-0604}, doi = {10.2471/BLT.11.099580}, author = {Braa, J{\o}rn and Heywood, Arthur and Sahay, Sundeep} } @article {905, title = {Informatics in radiology: An open-source and open-access cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder}, journal = {Radiographics}, volume = {32}, year = {2012}, pages = {1223{\textendash}1232}, abstract = {In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and Image Markup (AIM), a project supported by the National Cancer Institute{\textquoteright}s cancer Biomedical Informatics Grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible. {\textcopyright} RSNA, 2012.}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84863860787\&partnerID=40\&md5=154429b57f255f957ea8a13055866456}, author = {Mongkolwat, P.a and Channin, D.S.b and Kleper, V.a and Rubin, D.L.c} } @article {793, title = {Integrating clinical practice and public health surveillance using electronic medical record systems.}, journal = {Am J Prev Med}, volume = {42}, year = {2012}, month = {2012 Jun}, pages = {S154-62}, abstract = {Electronic medical record (EMR) systems have rich potential to improve integration between primary care and the public health system at the point of care. EMRs make it possible for clinicians to contribute timely, clinically detailed surveillance data to public health practitioners without changing their existing workflows or incurring extra work. New surveillance systems can extract raw data from providers{\textquoteright} EMRs, analyze them for conditions of public health interest, and automatically communicate results to health departments. The current paper describes a model EMR-based public health surveillance platform called Electronic Medical Record Support for Public Health (ESP). The ESP platform provides live, automated surveillance for notifiable diseases, influenza-like illness, and diabetes prevalence, care, and complications. Results are automatically transmitted to state health departments.}, issn = {1873-2607}, doi = {10.1016/j.amepre.2012.04.005}, author = {Klompas, Michael and McVetta, Jason and Lazarus, Ross and Eggleston, Emma and Haney, Gillian and Kruskal, Benjamin A and Yih, W Katherine and Daly, Patricia and Oppedisano, Paul and Beagan, Brianne and Lee, Michael and Kirby, Chaim and Heisey-Grove, Dawn and DeMaria, Alfred and Platt, Richard} } @article {801, title = {Integration of the Image-Guided Surgery Toolkit (IGSTK) into the Medical Imaging Interaction Toolkit (MITK).}, journal = {J Digit Imaging}, year = {2012}, month = {2012 Apr 26}, abstract = {The development cycle of an image-guided surgery navigation system is too long to meet current clinical needs. This paper presents an integrated system developed by the integration of two open-source software (IGSTK and MITK) to shorten the development cycle of the image-guided surgery navigation system and save human resources simultaneously. An image-guided surgery navigation system was established by connecting the two aforementioned open-source software libraries. It used the Medical Imaging Interaction Toolkit (MITK) as a framework providing image processing tools for the image-guided surgery navigation system of medical imaging software with a high degree of interaction and used the Image-Guided Surgery Toolkit (IGSTK) as a library that provided the basic components of the system for location, tracking, and registration. The electromagnetic tracking device was used to measure the real-time position of surgical tools and fiducials attached to the patient{\textquoteright}s anatomy. IGSTK was integrated into MITK; at the same time, the compatibility and the stability of this system were emphasized. Experiments showed that an integrated system of the image-guided surgery navigation system could be developed in 2~months. The integration of IGSTK into MITK is feasible. Several techniques for 3D reconstruction, geometric analysis, mesh generation, and surface data analysis for medical image analysis of MITK can connect with the techniques for location, tracking, and registration of IGSTK. This integration of advanced modalities can decrease software development time and emphasize the precision, safety, and robustness of the image-guided surgery navigation system.}, issn = {1618-727X}, doi = {10.1007/s10278-012-9477-3}, author = {Lu, Tong and Liang, Ping and Wu, Wen-Bo and Xue, Jin and Lei, Cheng-Long and Li, Yin-Yan and Sun, Yun-Na and Liu, Fang-Yi} } @conference {838, title = {Interactive Electromechanical Model of the Heart for Patient-Specific Therapy Planning and Training using SOFA}, booktitle = {VPH 2012}, year = {2012}, address = {Londres, United Kingdom}, abstract = {The contributions of this work are twofold. First, we developed an electrophysiological training simulator in SOFA which tackles the interactive issue in the context of cardiac arrhythmias. Coupled with this electrophysiology, we developed a mechanical model of the heart that can be personalized from MRI datasets. Our simulations are based on the SOFA platform. SOFA is an open-source framework targeted at real-time simulation with an emphasis on medical simulation, mainly developed at Inria. A large choice of efficient solvers, hyperelastic or viscous material laws are already implemented in SOFA. Moreover, it enables interactivity during the simulation (pacing, surgery planning, ...) and gives a good trade-off between accuracy and computational efficiency.}, url = {http://hal.inria.fr/hal-00751537}, author = {Talbot, Hugo and Marchesseau, St{\'e}phanie and Duriez, Christian and Courtecuisse, Hadrien and Relan, Jatin and Sermesant, Maxime and Cotin, St{\'e}phane and Delingette, Herv{\'e}} } @article {867, title = {Impact of caBIG on the European cancer community.}, journal = {Ecancermedicalscience}, volume = {5}, year = {2011}, month = {2011}, pages = {225}, abstract = {

The cancer Biomedical Informatics Grid (caBIG) was launched in 2003 by the US National Cancer Institute with the aim of connecting research teams through the use of shared infrastructure and software to collect, analyse and share data. It was an ambitious project, and the issue it aimed to address was huge and far-reaching. With such developments as the mapping of the human genome and the advancement of new technologies for the analysis of genes and proteins, cancer researchers have never produced so much complex data, nor have they understood so much about cancer on a molecular level. This new {\textquoteright}molecular understanding{\textquoteright} of cancer, according to the caBIG 2007 {\textquoteright}Pilot Report{\textquoteright}[1], leads to molecular or {\textquoteright}personalised{\textquoteright} medicine being the way forward in cancer research and treatment, and connects basic research to clinical care in an unprecedented way. But the former {\textquoteright}silo-like{\textquoteright} nature of research does not lend itself to this brave new world of molecular medicine-individual labs and institutes working in isolation, "in effect, as cottage industries, each collecting and interpreting data using a unique language of their own"[2] will not advance cancer research as it should be advanced. The solution proposed by the NCI in caBIG was to produce an integrated informatics grid ({\textquoteright}caGrid{\textquoteright}) to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks.caBIG is primarily a US-based endeavour, and though the tools are openly available for users worldwide, it is in US NCI-funded cancer centres that they have been actively introduced and promoted with the eventual hope, according to the pilot report, of being able to do the same worldwide. caBIG also has a collaboration in place with the UK organisation NCRI to exchange technologies and research data. The European Association for Cancer Research, a member association for cancer researchers, conducted an online survey in January 2011 to identify the penetration of the ambitious caBIG project into European laboratories. The survey was sent to 6396 researchers based in Europe, with 764 respondents, a total response rate of 11.94\%.

}, issn = {1754-6605}, doi = {10.3332/ecancer.2011.225}, author = {Warden, R} } @article {642, title = {Implementation of an open source provider organization registry service.}, journal = {Studies in health technology and informatics}, volume = {169}, year = {2011}, month = {2011}, pages = {265-9}, abstract = {Healthcare Information Exchange Networks (HIEN) enables the exchange of medical information between different institutions. One of the biggest problems running a HIEN is the unique identification of the care providers. The provider and organisation registry service (PORS) has to provide a unique identifier for care providers. The concept and the implementation of PORS will be described in this article. Finally the PORS implementation will be compared with the Integrating the Healthcare Enterprise (IHE) profile for a Healthcare Provider Directory (HPD).}, issn = {0926-9630}, author = {Birkle, Markus and Schneider, Benjamin and Beck, Tobias and Deuster, Thomas and Fischer, Markus and Flatow, Florian and Heinrich, Robert and Kapp, Christian and Riemer, Jasmin and Simon, Michael and Bergh, Bj{\"o}rn} } @article {594, title = {Implementation of the Zambia electronic perinatal record system for comprehensive prenatal and delivery care.}, journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics}, volume = {113}, year = {2011}, month = {2011 May}, pages = {131-6}, abstract = {OBJECTIVE: To characterize prenatal and delivery care in an urban African setting. METHODS: The Zambia Electronic Perinatal Record System (ZEPRS) was implemented to record demographic characteristics, past medical and obstetric history, prenatal care, and delivery and newborn care for pregnant women across 25 facilities in the Lusaka public health sector. RESULTS: From June 1, 2007, to January 31, 2010, 115552 pregnant women had prenatal and delivery information recorded in ZEPRS. Median gestation age at first prenatal visit was 23weeks (interquartile range [IQR] 19-26). Syphilis screening was documented in 95663 (83\%) pregnancies: 2449 (2.6\%) women tested positive, of whom 1589 (64.9\%) were treated appropriately. 111108 (96\%) women agreed to HIV testing, of whom 22\% were diagnosed with HIV. Overall, 112813 (98\%) of recorded pregnancies resulted in a live birth, and 2739 (2\%) in a stillbirth. The median gestational age was 38weeks (IQR 35-40) at delivery; the median birth weight of newborns was 3000g (IQR 2700-3300g). CONCLUSION: The results demonstrate the feasibility of using a comprehensive electronic medical record in an urban African setting, and highlight its important role in ongoing efforts to improve clinical care.}, issn = {1879-3479}, author = {Chi, Benjamin H and Vwalika, Bellington and Killam, William P and Wamalume, Chibesa and Giganti, Mark J and Mbewe, Reuben and Stringer, Elizabeth M and Chintu, Namwinga T and Putta, Nande B and Liu, Katherine C and Chibwesha, Carla J and Rouse, Dwight J and Stringer, Jeffrey S A} } @article {538, title = {Integration of 3D anatomical data obtained by CT imaging and 3D optical scanning for Computer Aided Implant Surgery.}, journal = {BMC medical imaging}, volume = {11}, year = {2011}, month = {2011 Feb 21}, pages = {5}, abstract = {ABSTRACT: BACKGROUND: A precise placement of dental implants is a crucial step to optimize both prosthetic aspects and functional constraints. In this context, the use of virtual guiding systems has been recognized as a fundamental tool to control the ideal implant position. In particular, complex periodontal surgeries can be performed using preoperative planning based on CT data. The critical point of the procedure relies on the lack of accuracy in transferring CT planning information to surgical field through custom-made stereo-lithographic surgical guides. METHODS: In this work, a novel methodology is proposed for monitoring loss of accuracy in transferring CT dental information into periodontal surgical field. The methodology is based on integrating 3D data of anatomical (impression and cast) and preoperative (radiographic template) models, obtained by both CT and optical scanning processes. RESULTS: A clinical case, relative to a fully edentulous jaw patient, has been used as test case to assess the accuracy of the various steps concurring in manufacturing surgical guides. In particular, a surgical guide has been designed to place implants in the bone structure of the patient. The analysis of the results has allowed the clinician to monitor all the errors, which have been occurring step by step manufacturing the physical templates. CONCLUSIONS: The use of an optical scanner, which has a higher resolution and accuracy than CT scanning, has demonstrated to be a valid support to control the precision of the various physical models adopted and to point out possible error sources. A case study regarding a fully edentulous patient has confirmed the feasibility of the proposed methodology.}, issn = {1471-2342}, author = {Frisardi, Gianni and Chessa, Giacomo and Barone, Sandro and Paoli, Alessandro and Razionale, Armando and Frisardi, Flavio} } @conference {MEJIA:2011:INRIA-00567598:1, title = {Invasive composition for the evolution of a health information system}, booktitle = {Variability \& Composition (VariComp)}, year = {2011}, note = {{ACM} 978-1-4503-0646-1/11/03 {D}.: {S}oftware/{D}.3: {PROGRAMMING} {LANGUAGES}/{D}.3.3: {L}anguage {C}onstructs and {F}eatures}, month = {03}, address = {Pernambuco Brazil}, abstract = {{I}n this paper we show that some of the evolution tasks in {O}pen{MRS}, a health information system, may require the invasive modification of interfaces and implementations in order to offer an appropriate modularization. {W}e introduce a new composition framework in {J}ava that supports the definition of expressive pattern-based invasive compositions. {F}ur thermore, we show that the composition framework allows us to concisely define an evolution scenario of {O}pen{MRS} that supports the consolidation of patient data from differ- ent remote instances.}, keywords = {Aspect-oriented programming, Distributed systems, Health information systems, Invasive software composition}, url = {http://hal.inria.fr/inria-00567598/PDF/mejia-sudholt-benavides_varicomp-AOSD2011.pdf}, author = {Mejia, Ismael and S{\"u}dholt, Mario and Benavides Navarro, Luis Daniel} } @article {20663194, title = {ImmunoRatio: a publicly available web application for quantitative image analysis of estrogen receptor (ER), progesterone receptor (PR), and Ki-67.}, journal = {Breast cancer research : BCR}, volume = {12}, year = {2010}, month = {2010 Jul 27}, pages = {R56}, abstract = {ABSTRACT: INTRODUCTION: Accurate assessment of estrogen receptor (ER), progesterone receptor (PR), and Ki-67 is essential in the histopathologic diagnostics of breast cancer. Commercially available image analysis systems are usually bundled with dedicated analysis hardware and, to our knowledge, no easily installable, free software for immunostained slide scoring has been described. In this study, we describe a free, Internet-based web application for quantitative image analysis of ER, PR, and Ki-67 immunohistochemistry in breast cancer tissue sections. METHODS: The application, named ImmunoRatio, calculates the percentage of positively stained nuclear area (labeling index) by using a color deconvolution algorithm for separating the staining components (diaminobenzidine and hematoxylin) and adaptive thresholding for nuclear area segmentation. ImmunoRatio was calibrated using cell counts defined visually as the gold standard (training set, n=50). Validation was done using a separate set of 50 ER, PR, and Ki-67 stained slides (test set, n=50). In addition, Ki-67 labeling indexes determined by ImmunoRatio were studied for their prognostic value in a retrospective cohort of 123 breast cancer patients. RESULTS: The labeling indexes by calibrated ImmunoRatio analyses correlated well with those defined visually in the test set (correlation coefficient r=0.98). Using the median Ki-67 labeling index (20\%) as a cutoff, a hazard ratio of 2.2 was obtained in the survival analysis (n=123, P=0.01). ImmunoRatio was shown to adapt to various staining protocols, microscope setups, digital camera models, and image acquisition settings. The application can be used directly with web browsers running on modern operating systems (e.g., Microsoft Windows, Linux distributions, and Mac OS). No software downloads or installations are required. ImmunoRatio is open source software, and the web application is publicly accessible on our website. CONCLUSIONS: We anticipate that free web applications, such as ImmunoRatio, will make the quantitative image analysis of ER, PR, and Ki-67 easy and straightforward in the diagnostic assessment of breast cancer specimens.}, author = {Tuominen, Vilppu J and Ruotoistenmaki, Sanna and Viitanen, Arttu and Jumppanen, Mervi and Isola, Jorma} } @article {541, title = {Implementing medical information systems in developing countries, what works and what doesn{\textquoteright}t.}, journal = {AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium}, volume = {2010}, year = {2010}, month = {2010}, pages = {232-6}, abstract = {Global Health Informatics is an emerging field, as demonstrated by several substantial and widely used electronic medical record (EMR) systems along with the emergence of mobile based or"mhealth" systems. We describe here many of the practical lessons we have learned from implementing systems in a wide range of challenging environments over the last decade. Some requirements, like data backups, skilled staff and local leadership are universally important. Others, such as limited power, poor network access and distributed populations, require different designs and strategies in resource poor environments.}, issn = {1942-597X}, author = {Fraser, Hamish S F and Blaya, Joaquin} } @article {1014, title = {Implementing OpenMRS for patient monitoring in an HIV/AIDS care and treatment program in rural Mozambique.}, journal = {Stud Health Technol Inform}, volume = {160}, year = {2010}, month = {2010}, pages = {411-5}, abstract = {

We have adopted the Open Medical Record System (OpenMRS) framework to implement an electronic patient monitoring system for an HIV care and treatment program in Mozambique. The program provides technical assistance to the Ministry of Health supporting the scale up of integrated HIV care and support services in health facilities in rural resource limited settings. The implementation is in use for adult and pediatric programs, with ongoing roll-out to cover all supported sites. We describe early experiences in adapting the system to the program needs, addressing infrastructure challenges, creating a regional support team, training data entry staff, migrating a legacy database, deployment, and current use. We find that OpenMRS offers excellent prospects for in-country development of health information systems, even in severely resource limited settings. However, it also requires considerable organizational infrastructure investment and technical capacity building to ensure continued local support.

}, keywords = {Database Management Systems, Delivery of Health Care, electronic health records, HIV Infections, Information Storage and Retrieval, Medical Record Linkage, Mozambique, Population Surveillance, Rural Health Services}, issn = {0926-9630}, author = {Manders, Eric-Jan and Jos{\'e}, Eurico and Solis, Manuel and Burlison, Janeen and Nhampossa, Jos{\'e} Leopoldo and Moon, Troy} } @proceedings {512, title = {Indivo X: Developing a Fully Substitutable Personally Controlled Health Record Platform}, year = {2010}, month = {11/2010}, abstract = {To support a rich ecosystem of third-party applications around a personally controlled health record (PCHR), we have redesigned Indivo, the original PCHR, as a web- based platform with feature-level substitutability. Core to this new release is the Indivo X Application Program- ming Interface (API), the contract between the PCHR platform and the end-user apps. Using rapid iterative de- velopment to build a minimal feature set from real-world requirements, the resulting Indivo X API, now in public stable beta, is enabling developers, including third-party contributors, to quickly create and integrate novel fea- tures into patients{\textquoteright} online records, ultimately building a fully customizable experience for diverse patient needs.}, url = {http://proceedings.amia.org/127eoo}, author = {Adida, Ben and Sanyal, Arjun and Zabak, Steve and Kohane, Isaac S. and Mandl, Kenneth D} } @article {20044607, title = {Image analysis of breast cancer immunohistochemistry-stained sections using ImageJ: an RGB-based model.}, journal = {Anticancer research}, volume = {29}, year = {2009}, month = {2009 Dec}, pages = {4995-8}, abstract = {BACKGROUND: Image analysis of tissue sections using RGB image profiling is a modern accepted technique. MATERIALS AND METHODS: A new method of RGB analysis, using the freeware ImageJ, is presented which can be applied to sections with either nuclear or cytoplasmic staining. The step-by-step process is presented and the method is tested using breast cancer specimens immunostained for CK-19 and estrogen receptors. RESULTS: This image analysis easily discriminates CK-19 and estrogen receptor positivity in prepared breast cancer specimens. The method is easy to perform, without the need for previous image transformations. CONCLUSION: Compared to previous methods, this method proved more accurate in estimating the actual colours that an observer recognizes as positive after immunostaining. Further studies are needed to evaluate whether this method is efficient enough to be applied in clinical practice.}, author = {Vrekoussis, T and Chaniotis, V and Navrozoglou, I and Dousias, V and Pavlakis, K and Stathopoulos, E N and Zoras, O} } @article {870, title = {Infrastructure for a learning health care system: CaBIG.}, journal = {Health Aff (Millwood)}, volume = {28}, year = {2009}, month = {2009 May-Jun}, pages = {923-4; author reply 924-5}, keywords = {Cooperative Behavior, Delivery of Health Care, Diffusion of Innovation, Humans, Medical Informatics Applications, Medical Informatics Computing, National Cancer Institute (U.S.), United States, United States Food and Drug Administration}, issn = {1544-5208}, doi = {10.1377/hlthaff.28.3.923-a}, author = {Buetow, Kenneth H and Niederhuber, John} } @article {19439392, title = {Interactive segmentation framework of the Medical Imaging Interaction Toolkit.}, journal = {Computer methods and programs in biomedicine}, volume = {96}, year = {2009}, month = {2009 Oct}, pages = {72-83}, abstract = {Interactive methods are indispensable for real world applications of segmentation in medicine, at least to allow for convenient and fast verification and correction of automated techniques. Besides traditional interactive tasks such as adding or removing parts of a segmentation, adjustment of contours or the placement of seed points, the relatively recent Graph Cut and Random Walker segmentation methods demonstrate an interest in advanced interactive strategies for segmentation. Though the value of toolkits and extensible applications is generally accepted for the development of new segmentation algorithms, the topic of interactive segmentation applications is rarely addressed by current toolkits and applications. In this paper, we present the extension of the Medical Imaging Interaction Toolkit (MITK) with a framework for the development of interactive applications for image segmentation. The framework provides a clear structure for the development of new applications and offers a plugin mechanism to easily extend existing applications with additional segmentation tools. In addition, the framework supports shape-based interpolation and multi-level undo/redo of modifications to binary images. To demonstrate the value of the framework, we also present a free, open-source application named InteractiveSegmentation for manual segmentation of medical images (including 3D+t), which is built based on the extended MITK framework. The application includes several features to effectively support manual segmentation, which are not found in comparable freely available applications. InteractiveSegmentation is fully developed and successfully and regularly used in several projects. Using the plugin mechanism, the application enables developers of new algorithms to begin algorithmic work more quickly.}, author = {Maleike, D and Nolden, M and Meinzer, H-P and Wolf, I} } @article {19068935, title = {Implementation of the Veterans Health Administration VistA clinical information system around the world.}, journal = {Healthcare quarterly (Toronto, Ont.)}, volume = {11}, year = {2008}, month = {2008}, pages = {83-9}, abstract = {The success story of the Veterans Health Administration (VHA) within the US Department of Veterans Affairs has been well documented and is generally well known. What is generally not known is that the VHA{\textquoteright}s clinical information system, known as VistA, and the computerized patient record system clinical user interface front end have been successfully transported and implemented to a number of non-VHA healthcare organizations across the United States. Moreover, VistA software modules have been installed, or are being considered for installation, in healthcare institutions around the world in countries such as Mexico, Finland, Jordan, Germany, Nigeria, Egypt, Malaysia, India, Brazil, Pakistan and Samoa.}, author = {Protti, Denis and Groen, Peter} } @article {18276143, title = {iPath: interactive exploration of biochemical pathways and networks.}, journal = {Trends in biochemical sciences}, volume = {33}, year = {2008}, month = {2008 Mar}, pages = {101-3}, abstract = {iPath is an open-access online tool (http://pathways.embl.de) for visualizing and analyzing metabolic pathways. An interactive viewer provides straightforward navigation through various pathways and enables easy access to the underlying chemicals and enzymes. Customized pathway maps can be generated and annotated using various external data. For example, by merging human genome data with two important gut commensals, iPath can pinpoint the complementarity of the host-symbiont metabolic capacities.}, author = {Letunic, Ivica and Yamada, Takuji and Kanehisa, Minoru and Bork, Peer} } @article {802, title = {The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.}, journal = {J Digit Imaging}, volume = {20 Suppl 1}, year = {2007}, month = {2007 Nov}, pages = {21-33}, abstract = {This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers{\textquoteright} mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.}, keywords = {Computer Systems, Data Display, Database Management Systems, Humans, Information Dissemination, Information Storage and Retrieval, Safety, Software, Software Design, Software Validation, Surgery, Computer-Assisted, Systems Integration, User-Computer Interface}, issn = {0897-1889}, doi = {10.1007/s10278-007-9054-3}, author = {Enquobahrie, Andinet and Cheng, Patrick and Gary, Kevin and Ibanez, Luis and Gobbi, David and Lindseth, Frank and Yaniv, Ziv and Aylward, Stephen and Jomier, Julien and Cleary, Kevin} } @article {17850667, title = {Indivo: a personally controlled health record for health information exchange and communication.}, journal = {BMC medical informatics and decision making}, volume = {7}, year = {2007}, month = {2007}, pages = {25}, abstract = {BACKGROUND: Personally controlled health records (PCHRs), a subset of personal health records (PHRs), enable a patient to assemble, maintain and manage a secure copy of his or her medical data. Indivo (formerly PING) is an open source, open standards PCHR with an open application programming interface (API). RESULTS: We describe how the PCHR platform can provide standard building blocks for networked PHR applications. Indivo allows the ready integration of diverse sources of medical data under a patient{\textquoteright}s control through the use of standards-based communication protocols and APIs for connecting PCHRs to existing and future health information systems. CONCLUSION: The strict and transparent personal control model is designed to encourage widespread participation by patients, healthcare providers and institutions, thus creating the ecosystem for development of innovative, consumer-focused healthcare applications.}, url = {http://www.biomedcentral.com/1472-6947/7/25/}, author = {Mandl, Kenneth D and Simons, William W and Crawford, William C R and Abbett, Jonathan M} } @article {16284146, title = {Informatics in radiology (infoRAD): an open source framework for modification and communication of DICOM objects.}, journal = {Radiographics : a review publication of the Radiological Society of North America, Inc}, volume = {25}, year = {2005}, month = {2005 Nov-Dec}, pages = {1709-21}, abstract = {A configurable framework has been developed that can receive, modify, and export images in different picture archiving and communication system scenarios. The framework has three main components: a receiver for Digital Imaging and Communications in Medicine (DICOM) objects, a processing pipeline to apply one or more modifications to these objects, and one or more senders to send the processed objects to predefined addresses. The toolbox programming was implemented as an open source project in Java. The processing pipeline uses the concept of configurable plug-ins. One plug-in is user programmable by means of extensible stylesheet language files and allows conversion of DICOM objects to extensible markup language documents or other file types. Input and output channels are the DICOM Storage service, DICOM compact disks-read-only memory (CD-ROMs), and the local file system. The toolbox has been successfully applied to different clinical scenarios, including the correction of DICOM objects from non-Integrating the Healthcare Enterprise (IHE) conform modalities, pseudonaming of DICOM images, and use of the IHE Portable Data for Imaging profile with import and export of CD-ROMs. The toolbox has proved reliability in the clinical routine. Because of the open programming interfaces, the functionality can easily be adapted to future applications.}, author = {Hackl{\"a}nder, Thomas and Martin, Jens and Kleber, Klaus} } @article {16257947, title = {Information technology as a tool to improve the quality of American Indian health care.}, journal = {American journal of public health}, volume = {95}, year = {2005}, month = {2005 Dec}, pages = {2173-9}, abstract = {The American Indian/Alaska Native population experiences a disproportionate burden of disease across a spectrum of conditions. While the recent National Healthcare Disparities Report highlighted differences in quality of care among racial and ethnic groups, there was only very limited information available for American Indians. The Indian Health Service (IHS) is currently enhancing its information systems to improve the measurement of health care quality as well as to support quality improvement initiatives. We summarize current knowledge regarding health care quality for American Indians, highlighting the variation in reported measures in the existing literature. We then discuss how the IHS is using information systems to produce standardized performance measures and present future directions for improving American Indian health care quality.}, author = {Sequist, Thomas D and Cullen, Theresa and Ayanian, John Z} } @article {15923755, title = {iPath - a Telemedicine Platform to Support Health Providers in Low Resource Settings.}, journal = {Studies in health technology and informatics}, volume = {114}, year = {2005}, month = {2005}, pages = {11-7}, abstract = {In many developing countries there is an acute shortage of medical specialists. The specialists and services that are available are usually concentrated in cities and health workers in rural health care, who serve most of the population, are isolated from specialist support [1]. Besides, the few remaining specialist are often isolated from colleagues. With the recent development in information and communication technologies, new option for telemedicine and generally for sharing knowledge at a distance are becoming increasingly accessible to health workers also in developing countries. Since 2001 the Department of Pathology in Basel, Switzerland is operating an Internet based telemedicine platform to assist health workers in developing countries. Over 1800 consultation have been performed since. This paper will give an introduction to iPath - the telemedicine platform developed for this project - and analyse two case studies: a teledermatology project from South Africa and a telepathology project from Solomon Islands.}, author = {Brauchli, K and O{\textquoteright}mahony, D and Banach, L and Oberholzer, M} } @article {16375782, title = {The iPath telemedicine platform.}, journal = {Journal of telemedicine and telecare}, volume = {11 Suppl 2}, year = {2005}, month = {2005}, pages = {S3-7}, abstract = {An early, point-to-point telepathology system at the University of Basel developed into an open-source, Internet-based platform for telemedicine in 2001. The Internet Pathology Suite (iPath) is a Web-based telepathology platform that permits the online presentation and discussion of cases within user groups. It also allows realtime telemicroscopy across firewalls. After four years, the telepathology network has over 700 active users. More than 6,300 cases with a total of about 39,000 images have been diagnosed. The diagnostic workload of all these cases is not exclusively handled by the Department of Pathology in Basel, but by a growing number of independent groups who also use the server simply as a case repository. What started as a small project for hospitals in Switzerland has become a global network.}, author = {Brauchli, Kurt and Oberholzer, Martin} } @article {11522765, title = {An integrated software suite for surface-based analyses of cerebral cortex.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {8}, year = {2001}, month = {2001 Sep-Oct}, pages = {443-59}, abstract = {The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, SureFit (Surface Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret (Computerized Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, SuMS (Surface Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.}, author = {Van Essen, D C and Drury, H A and Dickson, J and Harwell, J and Hanlon, D and Anderson, C H} }