Open Source software in medical informatics--why,how and what

'Open Source' is a 20-40 year old approach to licensing and distributing software that has recently burst into public view. Against conventional wisdom this approach has been wildly successful in the general software market--probably because the openness lets programmers the world over obtain, critique, use, and build upon the source code without licensing fees. Linux, a UNIX-like operating system, is the best known success. But computer scientists at the University of California, Berkeley began the tradition of software sharing in the mid 1970s with BSD UNIX and distributed the major internet network protocols as source code without a fee. Medical informatics has its own history of Open Source distribution: Massachusetts General's COSTAR and the Veterans Administration's VISTA software have been distributed as source code at no cost for decades. Bioinformatics, our sister field, has embraced the Open Source movement and developed rich libraries of open-source software. Open Source has now gained a tiny foothold in health care (OSCAR GEHR, OpenEMed). Medical informatics researchers and funding agencies should support and nurture this movement. In a world where open-source modules were integrated into operational health care systems, informatics researchers would have real world niches into which they could engraft and test their software inventions. This could produce a burst of innovation that would help solve the many problems of the health care system. We at the Regenstrief Institute are doing our part by moving all of our development to the open-source model.     

Clinical software development for the Web: lessons learned from the BOADICEA project

ABSTRACT: BACKGROUND: In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. RESULTS: We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had >1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. CONCLUSIONS: We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.     

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages.     

Integration of the Image-Guided Surgery Toolkit (IGSTK) into the Medical Imaging Interaction Toolkit (MITK)

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’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.     

AnatomySketch: An Extensible Open-Source Software Platform for Medical Image Analysis Algorithm Development

The development of medical image analysis algorithm is a complex process including the multiple sub-steps of model training, data visualization, human–computer interaction and graphical user interface (GUI) construction. To accelerate the development process, algorithm developers need a software tool to assist with all the sub-steps so that they can focus on the core function implementation. Especially, for the development of deep learning (DL) algorithms, a software tool supporting training data annotation and GUI construction is highly desired. In this work, we constructed AnatomySketch, an extensible open-source software platform with a friendly GUI and a flexible plugin interface for integrating user-developed algorithm modules. Through the plugin interface, algorithm developers can quickly create a GUI-based software prototype for clinical validation. AnatomySketch supports image annotation using the stylus and multi-touch screen. It also provides efficient tools to facilitate the collaboration between human experts and artificial intelligent (AI) algorithms. We demonstrate four exemplar applications including customized MRI image diagnosis, interactive lung lobe segmentation, human-AI collaborated spine disc segmentation and Annotation-by-iterative-Deep-Learning (AID) for DL model training. Using AnatomySketch, the gap between laboratory prototyping and clinical testing is bridged and the development of MIA algorithms is accelerated. The software is opened at https://github.com/DlutMedimgGroup/AnatomySketch-Software.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10278-022-00660-5.     

Open Source Software Projects of the caBIG™ In Vivo Imaging Workspace Software Special Interest Group

The Cancer Bioinformatics Grid (caBIG?) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG? In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.     

Benchmarking the performance of a low-cost magnetic resonance control system at multiple sites in the open MaRCoS community

Purpose: To describe the current properties and capabilities of an open-source hardware and software package that is being developed by many sites internationally with the aim of providing an inexpensive yet flexible platform for low-cost MRI. Methods: This article describes three different setups from 50 to 360 mT in different settings, all of which used the MaRCoS console for acquiring data, and different types of software interface (custom-built GUI or Pulseq overlay) to acquire it. Results: Images are presented both from phantoms and in vivo from healthy volunteers to demonstrate the image quality that can be obtained from the MaRCoS hardware/software interfaced to different low-field magnets. Conclusions: The results presented here show that a number of different sequences commonly used in the clinic can be programmed into an open-source system relatively quickly and easily, and can produce good quality images even at this early stage of development. Both the hardware and software will continue to develop, and it is an aim of this article to encourage other groups to join this international consortium.     

Quantitative Computed Tomography (QCT) as a Radiology Reporting Tool by Using Optical Character Recognition (OCR) and Macro Program

The objectives are (1) to introduce a new concept of making a quantitative computed tomography (QCT) reporting system by using optical character recognition (OCR) and macro program and (2) to illustrate the practical usages of the QCT reporting system in radiology reading environment. This reporting system was created as a development tool by using an open-source OCR software and an open-source macro program. The main module was designed for OCR to report QCT images in radiology reading process. The principal processes are as follows: (1) to save a QCT report as a graphic file, (2) to recognize the characters from an image as a text, (3) to extract the T scores from the text, (4) to perform error correction, (5) to reformat the values into QCT radiology reporting template, and (6) to paste the reports into the electronic medical record (EMR) or picture archiving and communicating system (PACS). The accuracy test of OCR was performed on randomly selected QCTs. QCT as a radiology reporting tool successfully acted as OCR of QCT. The diagnosis of normal, osteopenia, or osteoporosis is also determined. Error correction of OCR is done with AutoHotkey-coded module. The results of T scores of femoral neck and lumbar vertebrae had an accuracy of 100 and 95.4 %, respectively. A convenient QCT reporting system could be established by utilizing open-source OCR software and open-source macro program. This method can be easily adapted for other QCT applications and PACS/EMR.     

General Consumer Communication Tools for Improved Image Management and Communication in Medicine

We elected to explore new technologies emerging on the general consumer market that can improve and facilitate image and data communication in medical and clinical environment. These new technologies developed for communication and storage of data can improve the user convenience and facilitate the communication and transport of images and related data beyond the usual limits and restrictions of a traditional picture archiving and communication systems (PACS) network. We specifically tested and implemented three new technologies provided on Apple computer platforms. (1) We adopted the iPod, a MP3 portable player with a hard disk storage, to easily and quickly move large number of DICOM images. (2) We adopted iChat, a videoconference and instant-messaging software, to transmit DICOM images in real time to a distant computer for conferencing teleradiology. (3) Finally, we developed a direct secure interface to use the iDisk service, a file-sharing service based on the WebDAV technology, to send and share DICOM files between distant computers. These three technologies were integrated in a new open-source image navigation and display software called OsiriX allowing for manipulation and communication of multimodality and multidimensional DICOM image data sets. This software is freely available as an open-source project at . Our experience showed that the implementation of these technologies allowed us to significantly enhance the existing PACS with valuable new features without any additional investment or the need for complex extensions of our infrastructure. The added features such as teleradiology, secure and convenient image and data communication, and the use of external data storage services open the gate to a much broader extension of our imaging infrastructure to the outside world.     

GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data

Investigation of causal interactions within brain networks using Granger causality analysis (GCA) is a key challenge in studying neural activity on the basis of functional magnetic resonance imaging (fMRI). The article describes an open-source software toolbox GMAC (Granger multivariate autoregressive connectivity) implementing multivariate spectral GCA. Available features are: fMRI data importing/exporting, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions have been integrated into a user-friendly graphical interface developed in the Matlab environment, easily accessible to both technical and clinical users.     

Operationalization of the UFuRT methodology for usability analysis in the clinical research data management domain

Data management software applications specifically designed for the clinical research environment are increasingly available from commercial vendors and open-source communities, however, general-purpose spreadsheets remain widely employed in clinical research data management (CRDM). The suitability of spreadsheets for this use is controversial, and no formal comparative usability evaluations have been performed. We report on an application of the UFuRT (user, function, representation, and task (analyses) methodology to create a domain-specific process for usability evaluation. We demonstrate this process in an evaluation of differences in usability between a spreadsheet program (Microsoft® Excel) and a commercially available clinical research data management system (Phase Forward Clintrial?). Through this domain-specific operationalization of UFuRT methodology, we successfully identified usability differences and quantified task and cost differences, while differentiating these from socio-technical aspects. UFuRT can be generalized to other domains.     

Single-Center Experience Implementing the LOINC-RSNA Radiology Playbook for Adult Abdomen/Pelvis CT and MR Procedures Using a Semi-Automated Method

The LOINC-RSNA Radiology Playbook represents the future direction of standardization for radiology procedure names. We developed a software solution (“RadMatch”) utilizing Python 2.7 and FuzzyWuzzy, an open-source fuzzy string matching algorithm created by SeatGeek, to implement the LOINC-RSNA Radiology Playbook for adult abdomen and pelvis CT and MR procedures performed at our institution. Execution of this semi-automated method resulted in the assignment of appropriate LOINC numbers to 86% of local CT procedures. For local MR procedures, appropriate LOINC numbers were assigned to 75% of these procedures whereas 12.5% of local MR procedures could only be partially mapped. For the standardized local procedures, only 63% of CT and 71% of MR procedures had corresponding RadLex Playbook identifier (RPID) codes in the LOINC-RSNA Radiology Playbook, which limited the utility of RPID codes. RadMatch is a semi-automated open-source software tool that can assist radiology departments seeking to standardize their radiology procedures via implementation of the LOINC-RSNA Radiology Playbook.     

Biodegradable Conduit Small Gap Tubulization for Peripheral Nerve Mutilation: A Substitute for Traditional Epineurial Neurorrhaphy

Nerve regeneration and re-innervation are usually difficult after peripheral nerve injury. Epineurium neurorrhaphy to recover the nerve continuity is the traditional choice of peripheral nerve mutilation without nerve defects, whereas the functional recovery remains quite unsatisfactory. Based on previous research in SD rats and Rhesus Monkeys, a multiple centers clinical trial about biodegradable conduit small gap tubulization for peripheral nerve mutilation to substitute traditional epineurial neurorrhaphy was carried out. Herein, the authors reviewed the literature that focused on peripheral nerve injury and possible clinical application, and confirmed the clinical possibilities of biodegradable conduit small gap tubulization to substitute traditional epineurial neurorrhaphy for peripheral nerve mutilation. The biodegradable conduit small gap tubulization to substitute traditional epineurial neurorrhaphy for peripheral nerve mutilation may be a revolutionary innovation in peripheral nerve injury and repair field.     

SimVascular: An Open Source Pipeline for Cardiovascular Simulation

Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.     

@Note: A workbench for Biomedical Text Mining

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists’ needs is crucial to solve real-world problems and promote further research.We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation.@Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.     

多叶光栅控制软件的设计与实现

目的:多叶光栅作为三维适形放射治疗计划和调强放射治疗计划精确快速地实施的重要设备之一,被广泛应用于肿瘤放射治疗。为精确快速地控制多叶光栅,本文对多叶光栅的控制软件进行设计和实现。方法:本文首先概要介绍该软件的整体功能,共包括治疗模块、校验模块、参数模块和串口模块,并重点介绍串口模块和检验模块。串口模块使用串口通信技术,将光栅叶片位置数据和控制数据转换为串口数据并发送到底层电路中,控制多叶光栅,保证多叶光栅控制软件和底层电路的顺畅通信。校验模块根据实际测量的等中心面叶片位置数据,建立等中心面叶片位置数据和叶片实际位置数据转换关系,得到叶片实际运动位置对应的等中心面运动位置,保证叶片在等中心面上的移动精度。结果:本软件已在VC平台下编程实现,参考某厂商多叶光栅产品注册检验报告进行测试。测量结果显示多项指标均小于1.0 mm。结论:本软件能够精确快速的控制多叶光栅,满足临床要求。     

Fixation offset facilitates saccades and manual reaching for single but not multiple target displays

Turning off a fixation point, typically for 200 ms, before the onset of a peripheral target substantially reduces saccadic reaction times. This facilitatory effect generated by an inserted temporal gap between fixation offset and the target appearance is called the “gap” effect [J Opt Soc Am 57:1030–1033, 1967]. We show that the gap reduces the initial latency of both saccades and manual pointing in single and multiple target displays. Yet, in multiple target displays, the gap increased the movement duration because eye or hand movements were frequently misdirected toward distractors so that the trajectory had to be corrected. Thus, in spite of the shortened latency, the total time for trial completion was not shortened in multiple target displays, whereas it was reduced in single target displays. This selective gap effect for a single target was not restricted to goal-directed motor tasks because perceptual discrimination tasks, where no motor response is required, also demonstrated the gap effect only for single target displays. Our results suggest that the gap may facilitate attentional disengagement, but it does not help target selection in motor and perceptual discrimination tasks, where the allocation of attention to the target is required.     

The intraoperative gap difference (flexion gap minus extension gap) is altered by insertion of the trial femoral component

A Tensor/Balancer device has been recently developed in order to assess soft tissue balancing in total knee arthroplasty (TKA) under more physiological conditions. This device allows us to measure the joint gap with a trial femoral component in place with the patella reduced. The purpose of this study was to clarify whether the placement of the component changes the intraoperative gap difference (flexion gap distance minus extension gap distance). We prospectively investigated the extension (0°) and flexion (90°) gaps in 73 posterior-stabilized TKAs under 30 lb of joint distraction force. Then, we compared the gap difference with and without the trial femoral component in place. Our results showed that the intraoperative gap difference with the trial femoral component in place was larger than the intraoperative gap difference without the trial component (p=0.00003; with the trial component: mean 4.7 mm (standard deviation (SD): 3.0mm); without the trial component: mean 2.7 mm (SD: 3.3mm)). We consider that the change in gap difference with or without femoral component was caused by a relative difference in the elasticity and/or tightness of the soft tissue in extension versus flexion. Surgeons should be aware of this effect of the femoral component when considering intraoperative soft tissue balancing which leads to postoperative stability of the knee joint consequently.