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At least 1,153 records · Page 64Linked to original sources
PubMed1993

Tool box-based cardiac volumes: visualization and quantitation by computed tomography.

Volumetric image display and analysis techniques have been under development to support x-ray computed tomographic (CT) imaging of the heart and lungs since the mid 1970s when investigators began to understand the image analysis requirements for the Dynamic Spatial Reconstructor. With the spread of Imatron's C-100 scanners (Imatron, South San Francisco, CA) around the world along with the development of slower helical scanners that generate volumetric information, there is an increased interest in the use of volume visualization and analysis tools to study the cardiopulmonary system. An historic overview of the development of such volume visualization for x-ray CT scanning is given along with a discussion of techniques for data acquisition, volumetric display, and image quantitation. We further show throughout the discussion how the integration of tools into a comprehensive image display and analysis software package (the tool box) enhances the utility of the individual tools. An example of such a tool box is given in a discussion of an X Windows-based package dubbed VIDA.

Cardiac Volume↗
PubMedDate not supplied

Comparison of commercially available genetic algorithms: gas as variable selection tool.

Many commercially available software programs claim similar efficiency and accuracy as variable selection tools. Genetic algorithms are commonly used variable selection methods where most relevant variables can be differentiated from 'less important' variables using evolutionary computing techniques. However, different vendors offer several algorithms, and the puzzling question is: which one is the appropriate method of choice? In this study, several genetic algorithm tools (e.g. GFA from Cerius2, QuaSAR-Evolution from MOE and Partek's genetic algorithm) were compared. Stepwise multiple linear regression models were generated using the most relevant variables identified by the above genetic algorithms. This procedure led to the successful generation of Quantitative Structure activity Relationship (QSAR) models for (a) proprietary datasets and (b) the Selwood dataset.

Algorithms↗
PubMed2000

A whole-body registration-free navigation system for image-guided surgery and interventional radiology.

RATIONALE AND OBJECTIVES: To develop and test an image-guided navigation system in which the base of reference is taken from the imaging modality, here, a helical CT scanner. METHODS: An optical digitizer together with a calibration device is used to measure the transformation matrix between the digitizer reference system and a CT reference system. During intervention, it tracks radiological and surgical tools with tool references. A specific software visually integrates the current tool position with the corresponding image information. In vitro accuracy tests were performed. RESULTS: With helical CT, freehand positioning accuracy was 1.9 +/- 1.1 mm (mean +/- SD) in vitro (n = 718). CONCLUSIONS: The navigation system developed by the authors appears to be feasible for radiological interventions as well as for minimally invasive surgery. It is not limited to a certain procedure, can be used in every region of the body, and is functional after imaging. Intraprocedural scans can be integrated immediately.

Equipment Design↗
PubMedDate not supplied

A review guide for computer assisted testing software.

This article describes a tool that delineates guidelines for critiquing computer software programs designed to create test banks, develop tests, administer tests to examinees, and/or provide analysis of performance of items, tests, and/or examinees. The tool identifies features that are unique to computer applications in educational testing, including principles of measurement and evaluation, criteria that are not included in available forms for the review of educational software.

Education, Nursing↗
PubMed2005

Establishing a Web-based DICOM teaching file authoring tool using open-source public software.

Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.

Computer Communication Networks↗
PubMed1999

Beyond anatomy: MR imaging as a molecular diagnostic tool.

Technical advances in software and hardware make MR imaging competitive with CAT scanning as an anatomic imaging tool. Although anatomic relationships remain important, increased understanding of cell structure and function is rapidly moving us toward diagnosis and treatment at the cellular level. By virtue of its reliance on nuclear magnetic spin moment, MR imaging is responsive to real time physico-chemical characteristics of cells and tissues being imaged. This intrinsic advantage of MR imaging is being rapidly developed through the use of targeted imaging agents and magnetic resonance spectroscopy. Imaging agents that target specific cell populations have been prepared by using monoclonal antibodies, liposomes, and short peptides bound to chelates containing paramagnetic atoms. Using magnetic resonance spectroscopy, the chemical composition of tumors can be analyzed and compared with normal tissues in vivo and in vitro. Areas of possible clinical usefulness for magnetic spectral analysis include: (1) in vitro or in vivo characterization of lesions as benign or malignant, (2) differentiation between in situ and invasive carcinomas, (3) determination of responsiveness to specific chemotherapeutic regimens before their institution, (4) study of in vivo drug metabolism by neoplasms, and (5) assessment of response to therapy and of residual disease at the completion of therapy. Early experiences in these parallel fields show great promise, with widespread clinical applications expected in the near future.

Antibodies, Monoclonal↗
PubMed2001

Use of the AIDA diabetes simulation software--www.2aida.org--as an interactive educational tool for teaching student nurses.

In previous "Diabetes Information Technology & WebWatch" columns, various user experiences with an interactive educational virtual diabetes patient simulator, called AIDA, have been documented. The simulator is available free of charge from www.2aida.org on the Web. In the 5+ years since the program was first made available on the Internet, over 125,000 people have visited the AIDA Website and over 27,000 copies of the program have been downloaded, gratis. User comments that have been received about the program have highlighted some of the many and varied ways in which a range of people have been applying the diabetes simulations in their own particular situations and practices. Inevitably, up to now, a great deal of attention has focused on use of the program by individuals with diabetes and their relatives, as well as by health-care professionals such as diabetologists/endocrinologists, diabetes educators, and primary care physicians (general practitioners [GPs]). However, an important group of health-carers involved in the provision of day-to-day care for many people with diabetes are nurses. The current "Diabetes Information Technology & WebWatch" column overviews a workshop held in June 2001 in Italy to gain experience with application of the AIDA diabetes simulation approach as a teaching tool for student nurses. Feedback obtained from participants attending the workshop was generally very positive, with the student nurses reporting the simulation approach to be both of interest and of use. Further workshops involving other health-care students and professionals-in particular, medical students and qualified nurses-are planned.

Computer Simulation↗
PubMed2004

Base-By-Base: single nucleotide-level analysis of whole viral genome alignments.

BACKGROUND: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. RESULTS: A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. CONCLUSION: Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine.

Base Composition↗
PubMed2003

[Development of an on-line course on medication administration].

The study describes the development of an on-line course on medication administration. The World Wide Web Course Tools (WebCT) that was used is software that provides various tools for supervisors and access to a number of environments for students who have a password. The course material is presented in a series of websites which are sub-divided into eight illustrated topics concerning medication administration routes, in addition to questions for knowledge assessment. A sample of undergraduate students at the University of São Paulo at Ribeirão Preto College of Nursing has positively evaluated the course. It is now intended to be included as curricular course in the undergraduate program as an additional resource for student learning.

Drug Administration Routes↗
PubMed2003

[The software QSR Nvivo 2.0 in qualitative data analysis: a tool for health and human sciences researches].

The QSR Nvivo 2.0 is one of the latest versions of qualitative data analysis software package. Taking on board our experience as QSR Nvivo 2.0 users we describe here the software's most important tools. The QSR Nvivo 2.0 was used to facilitate the qualitative analysis of data gathered in a Health and Education research. Considering the shortage of published materials about the issue, which suggests a lack of knowledge about the program in our context, our aim is to show how the QSR Nvivo 2.0 can assist qualitative data analysis.

Data Collection↗
PubMed1996

Maxsim, software for the analysis of multiple axonal arbors and their simulated activation.

In order to analyze the structural organization of complex axonal arbors reconstructed from histological serial sections, and to investigate the functional implications of their geometrical properties, we developed software providing the following facilities: (1) direct importation of data files generated by a commercially available 3-D light-microscopic reconstruction system, including routine procedures for identification and correction of data acquisition errors; (2) real-time 3-D rotations of the arbors in the stack of serial sections; (3) multiple interactive display modes; (4) possibility of modifying diameter and/or connectivity of different branches; (5) simulation of the invasion of the arbor by a single action potential initiated at any chosen point, and visualization of spatio-temporal profiles of activation; (6) extraction of quantitative data converted to standard file formats compatible with available mathematical software. All these tools can be applied to single or multiple axons, individually or simultaneously. The software, called Maxsim, is a highly flexible C-written program running on graphical workstations using the UNIX operating system and X-Window environment.

Animals↗
PubMed2000

A new research program in medical image data processing.

The National Library of Medicine, in partnership with the National Institute for Dental and Craniofacial Research, the National Eye Institute, the National Science Foundation, the National Institute for Deafness and Other Communication Disorders, and the National Cancer Institute, has founded a software consortium to support the creation of a public resource in high-dimension data processing tools. The initial emphasis of this effort is to provide public software tools in 3D segmentation and deformable and rigid registration, capable of analyzing the head-and-neck anatomy of the Visible Human Project data. The eventual goal is for the consortium to provide the cornerstone of a self-sustaining software community in 3D, 4D and higher dimensional data analysis. The consortium is committed to open-source code, public software including open interfaces supporting connections to a broad range of visualization and graphic user interface platforms.

Anatomy, Cross-Sectional↗
PubMed2004

OntologyTraverser: an R package for GO analysis.

UNLABELLED: Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser--an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool. AVAILABILITY: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible. CONTACT: cashaw@bcm.tmc.edu

Algorithms↗
PubMed2006

CreateTarget and Analyze This!: new software assisting imaging mass spectrometry on Bruker Reflex IV and Ultraflex II instruments.

Two new software programs are presented which enable matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI-IMS) on Bruker Reflex and Ultraflex instruments. The first program, CreateTarget, creates a high density raster with the dimensions of the tissue section, and converts these parameters into a virtual target plate file that can be imported in the normal mass spectrometer control software. Following automated spectrum acquisition, the second program, Analyze This!, converts the array of spectra into an Analyze 7.5 image format that can be read by image analysis software. These two tools are sufficient to allow IMS, and offer a valid alternative to commercially available software. CreateTarget and Analyze This! are available free of charge.

Animals↗
PubMed2004

Bioinformatics software resources.

This review looks at internet archives, repositories and lists for obtaining popular and useful biology and bioinformatics software. Resources include collections of free software, services for the collaborative development of new programs, software news media and catalogues of links to bioinformatics software and web tools. Problems with such resources arise from needs for continued curator effort to collect and update these, combined with less than optimal community support, funding and collaboration. Despite some problems, the available software repositories provide needed public access to many tools that are a foundation for analyses in bioscience research efforts.

Algorithms↗