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At least 289 records · Page 16Linked to original sources

PubMed1995

Three dimensional planning target volumes: a model and a software tool.

PURPOSE: Three dimensional (3D) target volumes are an essential component of conformal therapy because the goal is to shape the treatment volume to the target volume. The planning target volume (PTV) is defined by ICRU 50 as the clinical target volume (CTV) plus a margin to ensure that the CTV receives the prescribed dose. The margin must include all interfractional and intrafractional treatment variations. This paper describes a software tool that automatically generates 3D PTVs from CTVs for lung cancers and immobile head and neck cancers. METHODS AND MATERIALS: Values for the interfractional and intrafractional treatment variations were determined by a literature review and by targeted interviews with physicians. The software tool is written in Common LISP and conforms to the specifications for shareable software of the Radiotherapy Treatment Planning Tools Collaborative Working Group. RESULTS: The tool is a rule-based expert system in which the inputs are the CTV contours, critical structure contours, and qualitative information about the specific patient. The output is PTV contours, which are a cylindrical expansion of the CTV. A model for creating PTVs from CTVs is embedded in the tool. The interfractional variation of setup uncertainty and the intrafractional variations of movement of the CTV (e.g., respiration) and patient motion are included in the model. Measured data for the component variations is consistent with modeling the components as independent samples from 3D Gaussian distributions. The components are combined using multivariate normal statistics to yield the cylindrical expansion factors. Rules are used to represent the values of the components for certain patient conditions (e.g., setup uncertainty for a head and neck patient immobilized in a mask). The tool uses a rule interpreter to combine qualitative information about a specific patient with rules representing the value of the components and to enter the appropriate component values for that patient into the cylindrical expansion formula. CONCLUSION: The portable software tool allows the rapid, consistent, and automatic generation of 3D PTVs from CTVs.

Head and Neck Neoplasms↗

PubMedDate not supplied

Approaching the millennium: perinatal problems and software solutions.

Strategic planning for rational development of perinatal computing capabilities for the year 2000 should be driven by anticipated trends in (1) the health care business, (2) computer technology and (3) medicine, as well as (4) the needs of perinatal practitioners. In the USA, health care is the fastest growing segment of the economy. This will produce increasing attention from hardware and software developers, and vendors, and will lead to a proliferation of computing platforms, operating systems and specific medical application software. Desktop computers, already capable of 20 million instructions per second (MIPS) with massive storage capacities, will continue to evolve and fall in price. Increasingly, perinatologists will develop software packages to facilitate patient care in their own environments. All of these trends will lead to severe fragmentation in medical computing. Simultaneously, however, the need for integrated institutional computer-based data access for quality assurance and fiscal and operations management will increase. Perinatal care will be more regionalized, complex and rigorous with new clinical trial- and effectiveness research-based interventions, as well as molecular diagnosis and therapy. To practice appropriately, clinicians will need to be familiar with computer capabilities. Having been exposed to computer-aided instruction (CAI) at the undergraduate and postgraduate levels, they will except on-line access to detailed and accurate patient information with linkage to laboratory, radiology and other medical databases, as well as to reference databases, such as Medlines and the Oxford Database of Perinatal Trials. Artificial intelligence (AI) software may support perinatal decision making; computerized professional and facility billing will be available.

Forecasting↗

PubMed1991

Software and hardware integration of a microprogrammable state machine for NMR imaging.

We have integrated a commercially available microprogrammable state machine (Tecmag PULSkit) for use as a magnetic resonance pulse programmer. Providing the capability for active research environment imaging protocols, it features timing resolution of 100 nsec, ten 16-bit loop counters, and individually addressable look-up tables. This integration involved hardware and software integration with a VAX 11/750 at several levels. Hardware: Each of the three gradient channels employs three digital-to-analog converters (DACs). An 8-bit, 4-quadrant, multiplying DAC generates the gradient waveform shape. A 12-bit DAC generates the multiplying DAC scaling voltage, controlling gradient amplitude and sign. A third 12-bit DAC produces a gradient offset (shim) voltage. An eddy current compensation network is present for each gradient channel. Software: The software design philosophy was to create a flexible interface (interactive window environment), while not constraining complex manipulation of the hardware (direct use of the pulse-sequence compiler primitives and microprogramming). The software levels include (a) pulse-sequence microprogramming, (b) pulse-sequence compiler, (c) interactive parameter specification, and (d) canned pulse-sequence microcode library.

Computer Systems↗

PubMedDate not supplied

Computer-assisted neurosurgery system: Wayne State University hardware and software configuration.

Computer-assisted neurosurgery uses the latest technological advancements in imaging, computers, mechanics, and electronics to improve the accuracy and reduce the invasiveness and risk of neurosurgical procedures. We describe the Wayne State University, Detroit, Michigan, computer-assisted neurosurgical system with the emphasis on software and discuss the theory guiding the development of this system and its application in real-time position tracking systems. Our system consists of the Neurological Surgery Planning System (NSPS) software which we developed at our medical center and three types of position tracking systems: the Zamorano-Dujovny (Z-D) are digitizer for frame-based procedures, an articulated arm, and an infrared-based digitizer for frameless procedures. The NSPS software is designed to offer neurosurgeons a safe and accurate method to approach intracranial lesions by preoperatively planning a surgical trajectory. Software consisting of the most advanced technologies in computer vision, computer imaging/graphics, and stereotactic numeric analysis forms the core of the system. Capabilities for correlating data from imaging studies to facilitate image reconstruction, image mapping, and three-dimensional (3D) visualization of target volumes enable the neurosurgeon to simulate surgical procedures into a preoperative protocol to be used during surgery, both to follow the preplanned trajectory and to track the position of surgical instruments in real-time on the computer monitor. The tracking systems position and orient the surgical instruments relative to the patient's head. With these devices, the display of the surgical instruments together with the virtual images create an excellent intraoperative tool.

Algorithms↗

PubMed1994

Results with new software for plateletpheresis systems.

New software for the cell separators A 201 and CS 3000 Plus have been developed by Baxter. Fresenius recently offered a single needle option for the AS 104 device. The results of separation are described with respect to total platelet yield, efficiency and cell contamination of the platelet concentrate (PC). Two software programs were evaluated in both the A 201 (version 5.12 and 5.13) and AS 104 cell separators (version 4560 with different separation parameters according to protocol IV and V). With software version 5.12, the A 201 collected 2.0 +/- 0.9 x 10(11) platelets in 200 mL plasma whereas 2.3 +/- 0.7 x 10(11) platelets could be harvested with version 5.13. The separation efficiencies were 32.1 +/- 11.6 and 34.7 +/- 10.7%, respectively. The leucocyte contamination was 5.6 +/- 4.6 x 10(8) with software version 5.12 and 4.9 +/- 7.6 x 10(8) with the 5.13 version. With the CS 3000 Plus cell separator, 2.9 +/- 0.8 x 10(11) platelets (efficiency 38.4 +/- 8.2%) could be harvested in 208 +/- 2 mL plasma. The white blood cell contamination was extremely low (1.4 +/- 3.2 x 10(6). There was a high separation efficacy with the Fresenius single needle procedure of 59.1 +/- 10.6% (protocol IV) and 58.7 +/- 7.3% (protocol V), respectively. The total number of platelets sampled in 338 +/- 21 mL plasma was 3.1 +/- 0.8 x 10(11) in protocol IV.(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation Studies as Topic↗

PubMed2005

Protecting youth online: family use of filtering and blocking software.

OBJECTIVE: This paper explores the characteristics associated with decisions to adopt or discontinue the use of filtering software, including a critical analysis of some explanations about why it is used or not used in households with children and adolescents. METHOD: This study consisted of a national telephone survey of households in the United States with youth (10 and 17 years) who use the Internet regularly. Interviews were completed with one youth in the appropriate age group and a parent or caretaker. RESULTS: Thirty-three percent of parents reported using filtering or blocking software, with an additional 5% having discontinued its use within the past year. Parents were more likely to adopt filtering software if they had younger children (10--15 years), a high level of concern about exposure to sexual material on the Internet, more extensive knowledge of what their child did online, low trust in the child's ability to use the Internet responsibly, and if the child used America Online (AOL). Using the Internet for school assignments was associated with not having filtering software. CONCLUSION: Findings suggest the need for (1) evaluation research of filter programs used in a real family context and (2) the development of a variety of strategies to prevent exposure to inappropriate material for youth of different ages.

Adolescent↗

PubMed2005

The reengineering of a software system for glaucoma analysis.

Glaucoma is a destructive eye disease that causes blindness in individuals displaying little or no symptoms. There is no cure as yet though there are treatments that can arrest its effects or slow its development. The earlier the disease is detected, the more likely the treatment will be successful; however early detection of the disease can be difficult. This highlights the importance of ophthalmologists having access to tools that can assist in accurately diagnosing glaucoma and other retinal diseases as early as possible. The stereo optic disc analyser (SODA) software package is a tool intended to be used by ophthalmologists, to aid in the accurate detection of retinal diseases. SODA will use stereoscopy and three-dimensional image analysis to assist in accurately detecting changes in the retina, caused by diseases such as glaucoma. This paper will focus on the reengineering and redesign of the SODA software package to overcome the shortcomings inherent in its prototype implementation and develop a package that can be commercialised. Software Engineering principles and the software development lifecycle, along with principles of object-orientation and usability, have been used to establish a framework for SODA, improve its accuracy, enhance its usability and to redevelop the product into an implementation that can later be commercialised.

Color↗

PubMed2007

Open-source software for radiologists: a primer.

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

Computer Graphics↗

PubMed2005

Using software agents to preserve individual health data confidentiality in micro-scale geographical analyses.

Confidentiality constraints often preclude the release of disaggregate data about individuals, which limits the types and accuracy of the results of geographical health analyses that could be done. Access to individually geocoded (disaggregate) data often involves lengthy and cumbersome procedures through review boards and committees for approval (and sometimes is not possible). Moreover, current data confidentiality-preserving solutions compatible with fine-level spatial analyses either lack flexibility or yield less than optimal results (because of confidentiality-preserving changes they introduce to disaggregate data), or both. In this paper, we present a simulation case study to illustrate how some analyses cannot be (or will suffer if) done on aggregate data. We then quickly review some existing data confidentiality-preserving techniques, and move on to explore a solution based on software agents with the potential of providing flexible, controlled (software-only) access to unmodified confidential disaggregate data and returning only results that do not expose any person-identifiable details. The solution is thus appropriate for micro-scale geographical analyses where no person-identifiable details are required in the final results (i.e., only aggregate results are needed). Our proposed software agent technique also enables post-coordinated analyses to be designed and carried out on the confidential database(s), as needed, compared to a more conventional solution based on the Web Services model that would only support a rigid, pre-coordinated (pre-determined) and rather limited set of analyses. The paper also provides an exploratory discussion of mobility, security, and trust issues associated with software agents, as well as possible directions/solutions to address these issues, including the use of virtual organizations. Successful partnerships between stakeholder organizations, proper collaboration agreements, clear policies, and unambiguous interpretations of laws and regulations are also much needed to support and ensure the success of any technological solution.

Computer Security↗

PubMed2006

Novel fast semi-automated software to segment cartilage for knee MR acquisitions.

OBJECTIVE: Validation of a new fast software technique to segment the cartilage on knee magnetic resonance (MR) acquisitions. Large studies of knee osteoarthritis (OA) will require fast and reproducible methods to quantify cartilage changes for knee MR data. In this report we document and measure the reproducibility and reader time of a software-based technique to quantify the volume and thickness of articular cartilage on knee MR images. METHODS: The software was tested on a set of duplicate sagittal three-dimensional (3D) dual echo steady state (DESS) acquisitions from 15 (8 OA, 7 normal) subjects. The repositioning, inter-reader, and intra-reader reproducibility of the cartilage volume (VC) and thickness (ThC) were measured independently as well as the reader time for each cartilage plate. The root-mean square coefficient of variation (RMSCoV) was used as metric to quantify the reproducibility of VC and mean ThC. RESULTS: The repositioning RMSCoV was as follows: VC=2.0% and ThC=1.2% (femur), VC=2.9% and ThC=1.6% (medial tibial plateau), VC=5.5% and ThC=2.4% (lateral tibial plateau), and VC=4.6% and ThC=2.3% (patella). RMSCoV values were higher for the inter-reader reproducibility (VC: 2.5-8.6%) (ThC: 1.9-5.2%) and lower for the intra-reader reproducibility (VC: 1.6-2.5%) (ThC: 1.2-1.9%). The method required an average of 75.4min per knee. CONCLUSIONS: We have documented a fast reproducible semi-automated software method to segment articular cartilage on knee MR acquisitions.

Cartilage, Articular↗

PubMed2004

A graphical user interface for automatic image registration software designed for radiotherapy treatment planning.

Medical imaging forms a vital component of radiotherapy treatment planning and its evaluation. The integration of the useful data obtained from multiple imaging modalities for radiotherapy planning is achieved by image registration softwares. In radiotherapy planning systems, normally the computed tomography (CT) slices are kept as a standard upon which other modality images (magnetic resonance imaging [MRI], single photon emission computed tomography [SPECT], positron emission tomography [PET], etc.) are aligned--automatically or interactively. Following validation of successful registration, they are resampled and reformatted, as per the requirements. This paper defines the minimum requirements of automatic image registration software for 3-dimensional (3D) radiotherapy planning and describes the implementation of a suitable graphical user interface developed in Visual Basic (version 5). The automatic image registration (AIR) routines freely available from Dr. Roger P. Woods, UCLA, (USA) were used in this software. This software could be easily implemented and was easy to use for image processing suitable for radiotherapy planning systems.

Algorithms↗

PubMed2005

Comparison of fMRI motion correction software tools.

Motion correction of fMRI data is a widely used step prior to data analysis. In this study, a comparison of the motion correction tools provided by several leading fMRI analysis software packages was performed, including AFNI, AIR, BrainVoyager, FSL, and SPM2. Comparisons were performed using data from typical human studies as well as phantom data. The identical reconstruction, preprocessing, and analysis steps were used on every data set, except that motion correction was performed using various configurations from each software package. Each package was studied using default parameters, as well as parameters optimized for speed and accuracy. Forty subjects performed a Go/No-go task (an event-related design that investigates inhibitory motor response) and an N-back task (a block-design paradigm investigating working memory). The human data were analyzed by extracting a set of general linear model (GLM)-derived activation results and comparing the effect of motion correction on thresholded activation cluster size and maximum t value. In addition, a series of simulated phantom data sets were created with known activation locations, magnitudes, and realistic motion. Results from the phantom data indicate that AFNI and SPM2 yield the most accurate motion estimation parameters, while AFNI's interpolation algorithm introduces the least smoothing. AFNI is also the fastest of the packages tested. However, these advantages did not produce noticeably better activation results in motion-corrected data from typical human fMRI experiments. Although differences in performance between packages were apparent in the human data, no single software package produced dramatically better results than the others. The "accurate" parameters showed virtually no improvement in cluster t values compared to the standard parameters. While the "fast" parameters did not result in a substantial increase in speed, they did not degrade the cluster results very much either. The phantom and human data indicate that motion correction can be a valuable step in the data processing chain, yielding improvements of up to 20% in the magnitude and up to 100% in the cluster size of detected activations, but the choice of software package does not substantially affect this improvement.

Algorithms↗

PubMed2006

The GIS-based SafeAirView software for the concentration assessment of radioactive pollutants after an accidental release.

The European Commission Joint Research Centre (JRC) in Ispra (Italy) has long been running nuclear installations for research purposes. The Nuclear Decommissioning and Facilities Management Unit (NDFM) is responsible for the surveillance of radioactivity levels in nuclear emergency conditions. The NDFM Unit has commissioned the implementation of a specifically developed decision support system, which can be used for quick emergency evaluation in the case of hypothetical accident and for emergency exercises. The requisites were to be a user-friendly software, able to quickly calculate and display values of air and ground radioactive contamination in the complex area around JRC, following an accidental release of radioactive substances from a JRC nuclear research installation. The developed software, named "SafeAirView", is an advanced implementation of GIS technology applied to an existing MS-DOS mode dispersion model, SAFE_AIR (Simulation of Air pollution From Emissions_Above Inhomogeneous Regions). SAFE_AIR is a numerical model which simulates transport, diffusion, and deposition of airborne pollutants emitted in the low atmosphere above complex orography at both local and regional scale, under non-stationary and inhomogeneous emission and meteorological conditions. SafeAirView makes use of user-friendly MS-Windows type interface which drives the dispersion model by a sequential and continuous input-output process, allowing a real time simulation. The GIS environment allows a direct interaction with the territory elements in which the simulation takes place, using data for the JRC Ispra region represented in geo-referenced cartography. Furthermore it offers the possibility to relate concentrations with population distribution and other geo-referenced maps, in a geographic view. Output concentration and deposition patterns can be plotted and/or exported. In spite of the selected specific databases, the SafeAirView software architecture is a general structure, therefore the decision support system could be easily modified to be applied in a region different from the JRC one. Beside the description of SafeAirView, the present paper presents a statistical evaluation of the software, which has considered three well known tracer experiments: Copenhagen, Indianapolis and Kincaid. The data sets related to these experiments are all included in the so called Model Validation Kit.

Data Interpretation, Statistical↗

PubMedDate not supplied

Personal computer software evaluation in interactive generation of pig liver three-dimensional anatomical images.

The efficiency of software for a personal computer in the interactive generation of three-dimensional (3D) images from computer tomography was studied in six pig livers after hepatic resection and catheterization of the hepatic and portal veins. After perfusion the livers were submitted to computed tomography angiography, volumetric measurement by water displacement, and production of an acrylic model of the veins by the injection and corrosion method, by which the lengths of the hepatic and portal veins were measured. From the angiogram, the software generated a 3D image that allowed measurement of the vein lengths. The identified branches of the hepatic and portal veins were correlated with the hepatic sectors and segments, respectively. The virtual measures from the 3D images were compared with the real measures. There were no significant differences between the topography and the vessel length. The mean difference between the volumes calculated from software and those measured by water displacement corresponded to 1.2%, and between the vessel lengths, 0.2%. In conclusion, the software for personal computer (named LIVER3D) is efficient, allowing interactive inspection of 3D images. All virtual measurements of liver vessel length and partial/total liver volume were similar to the actual ones.

Animals↗

PubMed2001

Validation of a chromatography data analysis software.

The performance of chromatography data analysis software packages is of cardinal importance when the precision and the accuracy of a chromatographic system are evaluated. Users cannot rely on a procedure generating chromatographic data of known accuracy. Holistic approaches cannot always be entirely trusted. We propose a new method consisting in validating a data analysis package against computer generated chromatograms of exactly known characteristics by feeding these chromatograms into the vendor supplied software and comparing the results supplied by the software and the exact answers. We simulated symmetrical and tailing chromatograms and processed these signals with the Agilent Technologies (formerly Hewlett-Packard) ChemStation software. The noise profile (i.e. the power spectrum of the baseline) was determined for a HPLC UV detector prior to the calculations, and chromatograms of different signal-to-noise ratios were used for the analysis. For every chromatogram, we simulated 25 replicates with identical signal-to-noise ratios but different noise sequences. In this manner, both the random and the systematic errors of the retention data and peak shape characteristics can be evaluated. When analyzing tailing peaks, we simulated the effects of extra-column band broadening and those of column overload. Our calculations show that the general performance of the data analysis system studied is excellent. The contribution of the random error originating from the data analysis procedure is in most cases negligible compared to the repeatability of the chromatographic measurement itself.

Chromatography, High Pressure Liquid↗

PubMed2001

Software and internet resources for capillary electrophoresis and micellar electrokinetic capillary chromatography.

The purpose of the contribution is to show how software and the internet have changed the way in which we carry out research, and what additional possibilities these new resources and tools provide. The internet and e-mail broaden our horizon for cooperation. There are no borders for information exchange: our library is a virtual one, electronic databases are at our fingertips. E-mail discussion groups provide an electronic community of CE users. Such forums have provided a basis for worldwide scientific cooperation amongst scientists; the present contribution is only one of several examples. Estimation software provides us with estimates of component properties in those cases where this information is not available from literature or from experiments (an estimated value is better than no value). Several examples will illustrate the use of estimation software in capillary zone electrophoresis and micellar electrokinetic capillary chromatography. Simulation software presents visualization of experimental results to be expected, both as a training tool and as the first step in method development. Other simulations yield valuable insights into phenomena that are not readily accessible experimentally for reasons of size or time-scale.

Chromatography, Micellar Electrokinetic Capillary↗

PubMed1998

SAAM II: Simulation, Analysis, and Modeling Software for tracer and pharmacokinetic studies.

Kinetic analysis and integrated systems modeling have contributed substantially to our understanding of the physiology and pathophysiology of metabolic systems and the distribution and clearance of drugs in humans and animals. In recent years, many researchers have become aware of the usefulness of these techniques in the experimental design. With this has come the recognition that the discipline of kinetic analysis requires its own expertise. The expertise can impact experimental design in many ways, from the collaborative and service activities in which individuals interact in formal ways to the development of software tools to aid in kinetic analysis. The purpose of this report is to describe one such software tool, Simulation, Analysis, and Modeling Software II (SAAM II). In the first part, we describe in general how the user can take advantage of the capabilities of the software system, and in the second part, we give three specific examples using multicompartmental models found in lipoprotein (apolipoprotein B [apoB] kinetics) and diabetes (glucose minimal model) research.

Algorithms↗

PubMed2006

An introduction to BioArray Software Environment.

BioArray Software Environment (BASE) is a web-based software package for storing, searching, and analyzing locally generated microarray data and information surrounding microarray production. The workflow begins in sample management and, optionally, microtiter plate tracking and ends in visualization and analysis of entire experiments. The relative ease with which new analysis plug-ins can be added has given rise to a plethora of third-party tools, and the licensing terms (GNU GPL) encourage local modifications of the software. This introduction to BASE describes the basics of working with the software, both in general and in more detail for the various parts. It also provides some hints about more advanced usage and a section on what is needed to set up your own BASE server. The information is current as of BASE version 1.2.17b, which was released on November 6, 2005.

Animals↗