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.     

动态三维CT处理软件OsiriX在颌面部骨折个性化重建中的应用

背景：充分地解读应用影像学数据信息,对于提高临床诊疗效率、降低患者辐射暴露并提高效费比具有重要意义。 目的：利用OsiriX软件对螺旋CT扫描容积数据进行基于颌面部骨折病例的个体化重建与临床动态观测分析,通过与传统影像判读手段对比,评估新型影像处理平台在口腔颌面外科临床诊疗中的应用效能。 方法：选取口腔颌面部骨折病例进行螺旋CT检查,所得数据在专业Dicom处理软件OsiriX平台进行三维可视化模型重建,进行重建前损伤评估、重建方案设计及重建后复位效果评估,并与传统影像学检查判读结果进行对比。 结果与结论：通过OsiriX平台快速建立动态三维可视化模型,直观了解创伤程度,进行相关实时测量,针对性制定重建治疗方案。重建过程中同期对手术入路、术野显露范围进行对比,提高重建效率。重建后复查可有效对比评估治疗效果。提示该类软件在重建前分析及重建设计模拟方面具有独特优势,人机界面友好,操作方便,提高了医患交流效果。     

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.     

The iPad Tablet Computer for Mobile On-Call Radiology Diagnosis? Auditing Discrepancy in CT and MRI Reporting

Tablet computers such as the iPad, which have a large format, improved graphic display resolution and a touch screen interface, may have an advantage compared to existing mobile devices such as smartphones and laptops for viewing radiological images. We assessed their potential for emergency radiology teleconsultation by reviewing multi-image CT and MRI studies on iPad tablet computers compared to Picture Archival and Communication Systems (PACS) workstations. Annonymised DICOM images of 79 CT and nine MRI studies comprising a range of common on-call conditions, reported on full-featured diagnostic PACS workstation by one Reporting Radiologist, were transferred from PACS to three iPad tablet computers running OsiriX HD v 2.02 DICOM software and viewed independently by three reviewing radiologists. Structured documentation was made of major findings (primary diagnosis or other clinically important findings), minor findings (incidental findings), and user feedback. Two hundred and sixty four readings (88 studies read by three reviewing radiologists) were compared, with 3.4 % (nine of 264) major discrepancies and 5.6 % (15 of 264) minor discrepancies. All reviewing radiologists reported favorable user experience but noted issues with software stability and limitations of image manipulation tools. Our results suggest that emergency conditions commonly encountered on CT and MRI can be diagnosed using tablet computers with good agreement with dedicated PACS workstations. Shortcomings in software and application design should be addressed if the potential of tablet computers for mobile teleradiology is to be fully realized.     

Using Keynote to Present Radiology Images

Numerous articles have offered instructions for working with advanced radiology images in Microsoft PowerPoint (Redmond, WA); however, no articles have detailed instructions to do the same on alternative presentation software. Apple Macintosh (Cupertino, CA) computers are gaining popularity with many radiologists, due in part to the availability of a powerful, free, open-source Digital Imaging and Communications in Medicine (DICOM) viewing and manipulating software OsiriX (). Apple’s own presentation software, Keynote, is particularly effective in dealing with medical images and cine clips. This article demonstrates how to use Apple’s Keynote software to present radiology images and scrollable image stacks, without third-party add-on software. The article also illustrates how to compress media files and protect patient information in Keynote presentations. Lastly, it addresses the steps to converting between PowerPoint and Keynote file formats. Apple’s Keynote software enables quick and efficient addition of multiple static images or scrollable image stacks, compression of media files, and removal of patient information. These functions can be accomplished by inexperienced users with no software modifications.     

Accuracy and Reliability of Length Measurements on Three-Dimensional Computed Tomography Using Open-Source OsiriX Software

There is a growing interest in three-dimensional computed tomography (3D-CT) as a research tool for the study of bone, joint anatomy, and kinematics. However, when CT data are processed and handled manually using image processing programs to yield 3D image and coordinate value, systematic and random errors should be validated. We evaluated the accuracy and reliability of length measurement on CT with OsiriX software. 3D-CT scans were made of 14 frozen pig knees with five transosseous holes in the metaphyseal portion of femur. The lengths between tunnel orifices were measured using Mitutoyo Digimatic digital calipers to establish the gold standard, and with the OsiriX program in 3D multi-planar reformatting mode for comparison. All measurements were recorded by a principal (replicate 1, trial 1) and a secondary observer (replicate 2, trial 1) and were repeated once by each observer (trial 2). The mean differences between OsiriX and real measurements were less than 0.1 mm in both replicates, and maximum differences were less than 0.3 mm. There were no significant differences between the replicates and real measurements (p=0.544 and 0.622 for replicates 1 and 2, respectively). The intraclass correlation coefficients (ICC) were very high between trials and between replicates (ICC=0.998 and 0.999, respectively). For kinematic analysis of the knees, length measurements on 3D-CT using OsiriX program can be used as alternatives to real measurements with less than 0.3-mm accuracy and very high reliability.     

MRIdb: Medical Image Management for Biobank Research

Clinical picture archiving and communications systems provide convenient, efficient access to digital medical images from multiple modalities but can prove challenging to deploy, configure and use. MRIdb is a self-contained image database, particularly suited to the storage and management of magnetic resonance imaging data sets for population phenotyping. It integrates a mature image archival system with an intuitive web-based user interface that provides visualisation and export functionality. In addition, utilities for auditing, data migration and system monitoring are included in a virtual machine image that is easily deployed with minimal configuration. The result is a freely available turnkey solution, designed to support epidemiological and imaging genetics research. It allows the management of patient data sets in a secure, scalable manner without requiring the installation of any bespoke software on end users’ workstations. MRIdb is an open-source software, available for download at http://www3.imperial.ac.uk/bioinfsupport/resources/software/mridb.     

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.     

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.     

Survey of Non-Rigid Registration Tools in Medicine

We catalogue available software solutions for non-rigid image registration to support scientists in selecting suitable tools for specific medical registration purposes. Registration tools were identified using non-systematic search in Pubmed, Web of Science, IEEE Xplore® Digital Library, Google Scholar, and through references in identified sources (n?=?22). Exclusions are due to unavailability or inappropriateness. The remaining (n?=?18) tools were classified by (i) access and technology, (ii) interfaces and application, (iii) living community, (iv) supported file formats, and (v) types of registration methodologies emphasizing the similarity measures implemented. Out of the 18 tools, (i) 12 are open source, 8 are released under a permissive free license, which imposes the least restrictions on the use and further development of the tool, 8 provide graphical processing unit (GPU) support; (ii) 7 are built on software platforms, 5 were developed for brain image registration; (iii) 6 are under active development but only 3 have had their last update in 2015 or 2016; (iv) 16 support the Analyze format, while 7 file formats can be read with only one of the tools; and (v) 6 provide multiple registration methods and 6 provide landmark-based registration methods. Based on open source, licensing, GPU support, active community, several file formats, algorithms, and similarity measures, the tools Elastics and Plastimatch are chosen for the platform ITK and without platform requirements, respectively. Researchers in medical image analysis already have a large choice of registration tools freely available. However, the most recently published algorithms may not be included in the tools, yet.     

数字化全景齿科成像系统中医学图像处理软件的开发

目的开发一套数字化全景齿科成像系统专用的图像处理软件。方法借助DCMTK开发包和OpenGL开发包,用VC＋＋语言编程实现。结果本软件不但具有医学图像的显示、几何变换、平滑、锐化、窗宽窗位调节、图像测量等功能,而且具有二维图像的立体显示及三维图形的旋转功能。结论通过实验验证,本软件是一套运行稳定、相对完整的图像处理软件,可成功用于数字化全景齿科成像系统中。     

User-friendly image processing software tools: general purpose features and application to the correlation of PET-CT brain images

An interactive software package, performing some useful general purpose image processing operations and being used as a tool for the problem of the anatomical correlation of PET brain images, is under development. The software is developed as a comprehensive tool with a graphic user-interface allowing the display of the processed images through the use of a variety of colormaps. The implemented routines perform a lot of processing operations on the images: a) Local image processing, i.e. smoothing and sharpening, contours extraction, interactive expansion, shrinking and thresholding of the gray scale, histogram equalization. b) ROI handling, i.e., ROI drawing and computing, transformation of an image to a ROI, ROI editing. c) Additional operators include frequency space image processing such as FFT.     

Characterizing the Discussion of Antibiotics in the Twittersphere: What is the Bigger Picture?

Background

User content posted through Twitter has been used for biosurveillance, to characterize public perception of health-related topics, and as a means of distributing information to the general public. Most of the existing work surrounding Twitter and health care has shown Twitter to be an effective medium for these problems but more could be done to provide finer and more efficient access to all pertinent data. Given the diversity of user-generated content, small samples or summary presentations of the data arguably omit a large part of the virtual discussion taking place in the Twittersphere. Still, managing, processing, and querying large amounts of Twitter data is not a trivial task. This work describes tools and techniques capable of handling larger sets of Twitter data and demonstrates their use with the issue of antibiotics.

Objective

This work has two principle objectives: (1) to provide an open-source means to efficiently explore all collected tweets and query health-related topics on Twitter, specifically, questions such as what users are saying and how messages are spread, and (2) to characterize the larger discourse taking place on Twitter with respect to antibiotics.

Methods

Open-source software suites Hadoop, Flume, and Hive were used to collect and query a large number of Twitter posts. To classify tweets by topic, a deep network classifier was trained using a limited number of manually classified tweets. The particular machine learning approach used also allowed the use of a large number of unclassified tweets to increase performance.

Results

Query-based analysis of the collected tweets revealed that a large number of users contributed to the online discussion and that a frequent topic mentioned was resistance. A number of prominent events related to antibiotics led to a number of spikes in activity but these were short in duration. The category-based classifier developed was able to correctly classify 70% of manually labeled tweets (using a 10-fold cross validation procedure and 9 classes). The classifier also performed well when evaluated on a per category basis.

Conclusions

Using existing tools such as Hive, Flume, Hadoop, and machine learning techniques, it is possible to construct tools and workflows to collect and query large amounts of Twitter data to characterize the larger discussion taking place on Twitter with respect to a particular health-related topic. Furthermore, using newer machine learning techniques and a limited number of manually labeled tweets, an entire body of collected tweets can be classified to indicate what topics are driving the virtual, online discussion. The resulting classifier can also be used to efficiently explore collected tweets by category and search for messages of interest or exemplary content.     

Multidimensional Analysis: A Management Tool for Monitoring HIPAA Compliance and Departmental Performance

Most RIS and PACS systems include extensive auditing capabilities as part of their security model, but inspecting those audit logs to obtain useful information can be a daunting task. Manual analysis of audit trails, though cumbersome, is often resorted to because of the difficulty to construct queries to extract complex information from the audit logs. The approach proposed by the authors uses standard off-the-shelf multidimensional analysis software tools to assist the PACS/RIS administrator and/or security officer in analyzing those audit logs to identify and scrutinize suspicious events. Large amounts of data can be quickly reviewed and graphical analysis tools help explore system utilization. While additional efforts are required to fully satisfy the demands of the ever-increasing security and confidentiality pressures, multidimensional analysis tools are a practical step toward actually using the information that is already being captured in the systems audit logs. In addition, once the work is performed to capture and manipulate the audit logs into a viable format for the multidimensional analysis tool, it is relatively easy to extend the system to incorporate other pertinent data, thereby enabling the ongoing analysis of other aspects of the departments workflow.     

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.     

A general software package for the handling of medical images.

PICS (portable imaging computer software), is a software system designed for handling and processing a variety of types of medical image. It has been designed to satisfy the following criteria: (a) the software should be portable between different items of hardware with minimal alteration; (b) there should be a simple operator interface to enable use by inexperienced users, while avoiding the need for experienced users to be directed through tedious menu trees; (c) the programming environment should enable simple integration of new data handling protocols. To meet these requirements the software was written in FORTRAN using structured subroutine organization. The software has basic image handling and processing facilities and contains a comprehensive set of nuclear medicine clinical protocols. Other facilities include alignment of images from different modalities with display of superimposed images and ability to handle, analyse and display three-dimensional data sets. Data transfer programs have been written to capture data from gamma camera, CT, MRI, ultrasound and radiographs by converting the images to a common data format. The system provides a hospital with a central digital image handling resource, enabling investigation of the value of digital image processing in potential clinical applications.     

Internet Image Viewer (iiV)

Background

Visualizing 3-dimensional (3-D) datasets is an important part of modern neuroimaging research. Many tools address this problem; however, they often fail to address specific needs and flexibility, such as the ability to work with different data formats, to control how and what data are displayed, to interact with values, and to undo mistakes.

Results

iiV, an interactive software program for displaying 3-D brain images, is described. This tool was programmed to solve basic problems in 3-D data visualization. It is written in Java so it is extensible, is platform independent, and can display images within web pages. iiV displays 3-D images as 2-dimensional (2-D) slices with each slice being an independent object with independent features such as location, zoom, colors, labels, etc. Feature manipulation becomes easier by having a full set of editing capabilities including the following: undo or redo changes; drag, copy, delete and paste objects; and save objects with their features to a file for future editing. It can read multiple standard positron emission tomography (PET) and magnetic resonance imaging (MRI) file formats like ECAT, ECAT7, ANALYZE, NIfTI-1 and DICOM. We present sample applications to illustrate some of the features and capabilities.

Conclusion

iiV is an image display tool with many useful features. It is highly extensible, platform independent, and web-compatible. This report summarizes its features and applications, while illustrating iiV's usefulness to the biomedical imaging community.