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PubMed1994

Integrated software tools for the evaluation of radiotherapy treatment plans.

PURPOSE: This article announces the availability of a convenient and useful software environment for the evaluation of three-dimensional (3D) radiotherapy treatment plans. MATERIALS AND METHODS: Using standards such as American National Standards for Information Systems C and the X Window System allowed us to bring the computation and display of dose-volume histograms, dose statistics, tumor control probabilities, normal tissue complication probabilities, and a figure of merit together under one user interface. These plan evaluation tools are not stand alone, but must interact with a 3D radiation therapy planning system to obtain the required dose matrices and patient anatomical contours. Installation of the software involves a programmer who writes a software bridge between the radiation therapy planning system and the tools, thereby providing access to local data files. This design strategy confines portability issues to one area of the software. RESULTS: Access to the other tools is through the Graphical Plan Evaluation Tool (GPET). GPET coordinates the use of each of the tools and provides graphical facilities for display of their results. Importantly, GPET assures that the displayed results of each tool have been computed with the same input specifications for all treatment plans being compared. For added convenience, the user can rearrange the resultant data to be reviewed in various ways on the video screen. The software design also allows incorporation of customized algorithms and input data for computing tumor control probability and normal tissue complication probabilities, since those currently available are controversial. CONCLUSION: The Graphical Plan Evaluation Tool unifies the simultaneous computation for several analytical tools and graphical display of their results. Within the constraints of the X Window System environment, this assemblage of software tools provides a portable, flexible, and convenient method for the quantitative evaluation of several radiotherapy treatment plans.

Dose-Response Relationship, Radiation↗

PubMed2006

A new software tool for removing, storing, and adding abnormalities to medical images for perception research studies.

RATIONALE AND OBJECTIVES: Image perception studies have been difficult to perform using clinical images because of the problems associated with obtaining proven abnormalities and appropriate normal controls. The objective of this research was to develop and evaluate interactive software that allows the seamless removal, archiving and insertion of abnormal areas from computed tomography (CT) lung image sets for use in image perception research. MATERIALS AND METHODS: The software tools for removing, archiving, and adding lesions are described in detail. The efficacy of the software to remove abnormal areas of lung CT studies was evaluated by having radiologists select the one altered image from a display of four. The software for adding lesions was evaluated by having radiologists classify displayed CT slices with lesions as real or artificial along with their confidence level. RESULTS: Observers could not reliably detect when images had been altered by the software. In the lesion-removal experiment, the observers correctly identified the altered display in only 15.8 +/- 2.8 of 56 sets. In the lesion-add experiment, the observers correctly identified the artificially placed lesions in 38.2 +/- 3.9 of 77 sets. The frequency distribution of the correct responses did not differ from that expected from chance selection. CONCLUSIONS: The results from both of these experiments demonstrate that radiologists could not distinguish between original and altered images. We conclude that this software can be used with volumetric CT lung images for creating normal control and target data sets for medical image perception research.

Humans↗

PubMed2005

Dolphin Imaging Software: an analysis of the accuracy of cephalometric digitization and orthognathic prediction.

The purpose of this study was to examine and compare the reproducibility and reliability of digitization using Dolphin Imaging Software (Version 8.0) with traditional manual techniques. In addition, orthognathic prediction was compared with actual outcomes. Sixty lateral cephalograms were evaluated by two methods: manual tracing and indirect digitization using Dolphin Imaging Software (Version 8.0). Method error (reliability) using duplicate measurements for each method, and comparison of both techniques (reproducibility), were investigated using alternative statistical methods, Bland and Altman (1986) and Lin's Correlation of Concordance (1989). Each technique was significantly reliable at the 95% level (method error). Comparing the standard deviations of the differences, manual tracing proving more reliable for SNA (1.36 degrees manually, 2.07 degrees digitally), SNB (1.19 degrees and 1.69 degrees ), SNMx (1.39 degrees and 2.66 degrees ), and MxMd (1.77 degrees and 2.26 degrees ), and Dolphin digital tracing more reliable for UIMx (3.49 degrees digitally and 3.97 degrees manually) and LIMd (2.90 degrees and 3.04 degrees ). However, systematic error in the software's calculation of LAFH% resulted in measurements 4% larger than manual techniques, a difference which is clinically significant. Comparison of actual outcome and software generated prediction for 26 orthognathic cases demonstrated clinically significant differences for all measurements (rhoc 0.32 for ANB to 0.91 for LIMd; P<0.05). The investigation revealed the impact of radiographic magnification when used in an uncalibrated system. These findings indicate that Version 8.0 of Dolphin Imaging Software needs to be re-assessed for software errors that may result in clinically significant miscalculations, and to facilitate compensation of radiographic magnification when using linear measurements.

Cephalometry↗

PubMed2002

Simple and inexpensive software designed for the evaluation of color.

PURPOSE: To report on new software that was specially designed to evaluate color. METHODS: Software development and observational case report. Each pixel on a computer screen is composed of three colors: red, green, and blue (RGB). Our software analyzes the intensity of each RGB component in a specific area chosen by the user. To test our software, we evaluated the color level of the irises of a subject, which became darker as a side effect of Xalatan (latanoprost; Pharmacia Corporation, Peapack, New Jersey) eyedrops. RESULT: We successfully expressed the level of the color of the iris by number. CONCLUSION: This software measures the color of a lesion and thereby provides an objective evaluation of color. The software we developed is downloadable, without cost, from http://www.isao.com.

Antihypertensive Agents↗

PubMed2002

NEUROFIT: software for fitting Hodgkin-Huxley models to voltage-clamp data.

I introduce publicly available software for accurate fitting of Hodgkin-Huxley models to voltage-clamp data. I describe the model and non-linear fitting procedure employed by the software and compare its results with the usual method of fitting such models using potassium A-current data from a pyloric dilator cell of the lobster Panulirus interruptus and sodium current data from an electrocyte cell of the electric fish Sternopygus macrurus. The set of parameter values for the model determined by this software yield current traces that are substantially closer to the observed data than those determined from the usual fitting method. This improvement is due to the fact that the software fits all of the parameters simultaneously utilizing all of the data rather than fitting steady-state and time constant parameters disjointly using peak currents and portions of the rising and falling phases. I analyze the convergence properties of the software's fitting algorithm using simulated data showing that accurate parameter values are obtained for most of the parameters using any reasonable initial values. The software also incorporates a linear pre-estimation procedure to help in determining reasonable initial values for the full non-linear algorithm. I illustrate and discuss some of the inadequacies of voltage-clamp data.

Algorithms↗

PubMed2003

Comparison of available benchmark dose softwares and models using trichloroethylene as a model substance.

By using trichloroethylene as a model substance the U.S. EPA benchmark dose software was compared to the software by Crump and the software by Kalliomaa. Dose-response and dose-effect data on the liver, kidneys, central nervous system (CNS), and tumours were selected for the evaluation. Based on the present study the U.S. EPA software is preferable to the other softwares for dichotomous data. A wider range in benchmark doses was often observed for dichotomous data when the numbers of dose levels were limited. The log-logistic model in most cases gave the best fit when ranking the dichotomous models. In addition, the log-logistic model often implied a more conservative benchmark dose. For continuous data it was more difficult to find a model describing the data. The softwares by Kalliomaa and by the U.S. EPA offered the best opportunities for benchmark dose modelling of continuous data. Flexible models, like the Hill- and the Mult model, are needed for S-shaped continuous data but these models demand more dose levels in order to describe the data. Since the number of dose levels are important for model selection study design is important and should be further evaluated.

Benchmarking↗

PubMed2001

Comparison of two software versions for assessment of body-composition analysis by DXA.

OBJECTIVE: To compare two software versions provided by Lunar CO: for assessment of body composition analysis by DXA. RESEARCH METHODS AND PROCEDURES: Soft-tissue phantoms for lean tissue (water) and fat tissue (methanol) were repeatedly scanned using DXA machines (DPX-L; Lunar CO., Madison, WI) and analyzed using software version 1.33 and the updated year 2000-compatible version 1.35. For the intersoftware comparison, the phantoms were scanned 10 times (each scan was analyzed once) with both software versions using all three scanning modes (slow, medium, and fast) for a total of 60 scans and analyses. For the intermachine comparison, the same phantoms were scanned three times (each scan was analyzed once) with a second machine from the same manufacturer using all three scanning modes and version 1.35 only. Percentage of fat was the variable of interest. RESULTS: For version 1.33, fat was 9.9 +/- 0.4%, 10.0 +/- 0.5%, and 11.0 +/- 0.5% (mean +/- SD) for the lean-tissue phantom and 50.8 +/- 0.3%, 50.9 +/- 0.5%, and 51.1 +/- 0.6% for the fat-tissue phantom using the slow, medium, and fast scanning modes, respectively. For version 1.35, the respective fat values were 9.8 +/- 0.7%, 9.9 +/- 0.4%, and 10.3 +/- 0.7%, and 50.6 +/- 0.5%, 50.9 +/- 0.6%, and 50.8 +/- 0.8%, respectively. For the lean-tissue phantom, the estimation of percentage of fat was significantly (p < 0.05) affected by scanning mode but not by software version. For the fat-tissue phantom, the estimation of percentage of fat was not affected by either scanning mode or software version. The use of version 1.35 did not effect intermachine variability. DISCUSSION: Versions 1.33 and 1.35 of the Lunar body composition software appear to be comparable. Soft-tissue phantoms, such as the ones described in this paper, may be useful in monitoring the reproducibility of body composition analyses within and between DXA machines, particularly in longitudinal studies.

Absorptiometry, Photon↗

PubMed2006

Improving the accuracy of BRCA1/2 mutation prediction: validation of the novel country-customized IC software.

Inherited mutations of the BRCA1/2 genes confer a significantly increased risk for breast and/or ovarian cancer development. Several models were elaborated to help genetic counsellors in selecting individuals with high probability of being mutation carriers. The IC software, a country-customized version of the Brcapro model, was recently shown to be particularly accurate in the prediction of carrier probability status in the Italian population. Here, we used our independent series of 70 breast/ovarian cancer families to analyze the performances of the IC software and compare it to widely used models, such as Brcapro and the Myriad mutation prevalence tables. Analysis of the areas under the receiver operator characteristics (ROC) curves indicated that overall the models performed well. However, the IC software and Myriad tables were more efficient in predicting mutated cases, showing a higher sensitivity (94 and 88%, respectively) and negative predictive value (NPV, 94 and 92%, respectively) compared to Brcapro (sensitivity 71 and NPV 83%). IC software also appeared particularly accurate in the identification of families belonging the low mutation risk group (<10%). Finally, most Brcapro failures occurred in the hereditary breast cancer (HBC) family subset, and in 75% of the cases, the IC software corrected them. Our data suggest that the country-customized implementation operated on the Brcapro software generated a more accurate tool for the prediction of BRCA1/2 gene mutation. Whether the IC or other country-customized models might improve BRCA1/2 mutation prediction also in non-Italian families needs to be further explored.

BRCA1 Protein↗

PubMedDate not supplied

New software for lens retro-illumination digital image analysis.

PURPOSE: To describe functions of new software for cataract assessment and compare its validity with that of the Nidek EAS-1000 software (Nidek, Japan). METHODS: A new Microsoft Windows 3.1/95 (Microsoft, USA) compliant software, Retroillumination Image Analysis (RIA), has been developed. The cataract reading is based on the contrasts in illumination between the opaque and transparent areas of the lens. Image loading, pupil detection and image analyses are automated. Differentiation between the different cataract types (cortical/posterior subscapsular) and other opacities is possible. RESULTS: The program was tested on 233 Nidek EAS-1000 images. In all, 148 eyes had clear media or cortical cuneiform cataract, 37 also had confounding opacities and 48 had no confounding opacities but pupils were unevenly illuminated. The results of analysis with both Nidek EAS-1000 and RIA software were compared against clinical Wilmer grading. The correlation of cortical opacity size in Nidek EAS-1000 3.01c and RIA software, respectively, were 0.50* and 0.57* for whole data set, 0.54* and 0.55* for subgroup with no confounders or artefacts, 0.54* and 0.66* for subgroup with artefacts, 0.27 (P < 0.105) and 0.65* for subgroup with confounders (*P < 0.001). CONCLUSION: The RIA software significantly improves the accuracy of cataract measurement in lens images with uneven pupil illumination or confounding opacities. Automation of (i) image loading, (ii) pupil detection and (iii) defining of the opacity area increases the efficiency of digital eye photography, eliminates human errors and speeds assessment.

Cataract↗

PubMed2004

[Software-assisted CT-postprocessing of the carotid arteries].

PURPOSE: A software assistant for automatic evaluation of CT-angiograms (CTA) was developed. It should enable the visualization of the vessel lumen and the quantitative evaluation of a stenosis. CTA examinations of patients with suspected carotid artery stenoses were used for the evaluation of the software assistant. MATERIALS AND METHODS: Twelve Patients with suspected high-grade stenosis of the carotid arteries underwent a CTA examination using a multislice CT scanner. The data were analyzed and evaluated using the new software assistant. The results were compared with the data of digital subtraction angiography (DSA) of these patients. RESULTS: The time of digital postprocessing with the new software-assistant took about six minutes on average. Contour extraction of the vessel, MIP and curved MPR (c-MPR) and orthogonal cross-sectional images of the vessels were calculated, followed by an automatic quantification of stenosis by the use of the c-MPR. A good correlation was found between CTA and DSA data regarding the stenosis grade (r = 0.82). Furthermore, some information could be provided about the plaque morphology. CONCLUSION: The software-assisted detection and analysis of carotid artery stenosis with the new developed program is possible within a justifiable time. DSA- and CTA-data did not show a significant difference in stenosis grading. Further development of software tools could lead to a better characterization of plaque morphology.

Carotid Arteries↗

PubMed2004

[A software program for quantitative analysis of alveolar oxygen partial pressure (p(A)O(2)) with oxygen-sensitive (3)He-MRI].

PURPOSE: To develop a software tool for quantitative analysis of alveolar oxygen partial pressure (p(A)O(2)) as well as its time course during apnea. MATERIAL AND METHODS: T (1)-relaxation times of hyperpolarized (3)He are reduced by paramagnetic oxygen rendering (3)He-MRI sensitive to oxygen and thus allowing the assessment of the local oxygen partial pressure in the pulmonary airspaces. Oxygen-related relaxation and loss of polarization by RF-excitation can be discriminated by acquiring two image series with varying interscan delay and/or flip angles. Software was developed to calculate the p(A)O(2) and the decay rate in user-defined regions of interest (ROIs) automatically. Moreover, parameter maps can be calculated. In addition to the analysis of 2-dimensional data sets, the software allows the evaluation of 3-dimensional measurements for the first time. Artifacts due to lung motion were reduced by implementing a motion correction algorithm. RESULTS: The software was successfully applied to data sets from healthy volunteers and from patients with various lung diseases. The parameter maps demonstrated a more homogeneous distribution of p(A)O(2) for the volunteers than for the patients. A regional increase in p(A)O(2) was found in a few patients. CONCLUSION: The described software allows the absolute quantification of p(A)O(2) as well as its variation over time. In the future, therefore, the software may gain importance for detecting mismatches between ventilation and perfusion, e. g., in patients with pulmonary embolism or chronic obstructive lung diseases.

Adult↗

PubMed2000

A methodology for the development of software agent based interoperable telemedicine systems: a tele-electrocardiography perspective.

Telemedicine involves the integration of information, human-machine, and healthcare technologies. Because different modalities of patient care require applications running on heterogeneous computing environment, software interoperability is a major issue in telemedicine. Software agent technology provides a range of promising techniques to solve this problem. This article discusses the development of a methodology for the design of interoperable telemedicine systems (illustrated with a tele-electrocardiography application). Software interoperability between different applications can be modeled at different levels of abstraction such as physical interoperability, data-type interoperability, specification-level interoperability, and semantic interoperability. Software agents address the issue of software interoperability at semantic level. A popular object-oriented software development methodology - unified modeling language (UML) - has been used for this development. This research has demonstrated the feasibility of the development of agent-based interoperable telemedicine systems. More research is needed before widespread deployment of such systems can take place.

Computer Systems↗

PubMed2003

Research use of the AIDA www.2aida.org diabetes software simulation program: a review-part 1. decision support testing and neural network training.

The purpose of this two-part review is to overview research use of the AIDA diabetes software simulator. AIDA is a diabetes computer program that permits the interactive simulation of plasma insulin and blood glucose profiles for teaching, demonstration, and self-learning purposes. It has been made freely available, without charge, on the Internet as a noncommercial contribution to continuing diabetes education. Since its launch in 1996 over 300,000 visits have been logged at the main AIDA Website-www.2aida.org-and over 60,000 copies of the AIDA program have been downloaded free-of-charge. This review describes research projects and ventures, undertaken for the most part by other research workers in the diabetes computing field, that have made use of the freeware AIDA software. Relevant research work was identified in three main ways: (i) by personal (e-mail/written) communications from researchers, (ii) via the ISI Web of Science citation database to identify published articles that referred to AIDA-related papers, and (iii) via searches on the Internet. In a number of cases research students who had sought advice about AIDA, and diabetes computing in general, provided copies of their research dissertations/theses upon the completion of their projects. The two reviews highlight some of the many and varied research projects that have made use of the AIDA diabetes simulation software to date. A wide variety of diabetes computing topics have been addressed. In Part 1 of the review, these range from testing decision support prototypes to training artificial neural networks. In Part 2 of the review, issues surrounding dietary assessments, developing new diabetes models, and performance monitoring of closed-loop insulin delivery devices are considered. Overall, research projects making use of AIDA have been identified in Australia, Italy, South Korea, the United Kingdom, and the United States. These reviews confirm an unexpected but useful benefit of distributing medical software, like AIDA, for free via the Internet-demonstrating how it is possible to have a synergistic benefit with other researchers-facilitating their own research projects in related medical fields. The reviews highlight a variety of these projects that have benefited from the free availability of the AIDA diabetes software simulator. In a number of cases these other research projects simply would not have been possible without unrestricted access to the AIDA software and/or technical descriptions of its workings. In addition, some specific common themes begin to emerge from the research ventures that have been reviewed. These include the use of simulated blood glucose data from the AIDA program for preliminary computerlab-based testing of other decision support prototypes. Issues surrounding such use of simulated data for separate prototype testing are discussed further in Part 2 of the review.

Computer Simulation↗

PubMed2004

British Diabetic Association review of the AIDA v4 diabetes software simulator program.

AIDA is a diabetes-computing program freely available from www.2aida.org on the Web. The software is intended to serve as an educational support tool, and can be used by anyone who has an interest in diabetes, whether they be patients, relatives, health-care professionals, or students. In 1996, during the beta-testing phase of the AIDA v4 project, the British Diabetic Association (BDA)-now called Diabetes UK-was approached and offered the AIDA software by the author, without charge, as a noncommercial contribution to continuing diabetes education. The BDA undertook their own independent assessment of the program, which involved distributing AIDA to a panel of potential end-users (health-care professionals and patients). Comments were solicited regarding the utility, clarity, and perceived safety of the software from users outside the BDA, as well as from various internal assessors. As a result of the feedback, a decision was taken by the BDA to offer AIDA to health-care professionals through the BDA's health-care professional brochure. One thousand copies of the software were produced on diskette, and 1,000 copies of the BDA's version of the program's user guide-printed as a small book-were made available for distribution by post. In this Diabetes Information Technology & WebWatch column an overview is given of the anonymous feedback provided to the BDA by some of the external evaluators. Looking back, nearly 8 years after the launch of AIDA, it is interesting to review some of the comments received and compare these with what has actually happened with the software. To date over 400,000 visits have been logged at the AIDA Web pages, and over 80,000 copies of the program have been downloaded free-of-charge. It is highlighted that this widespread downloading of, and interest in, the AIDA software seems to largely have been fuelled by the program's free availability on the Internet. The use of the World Wide Web to enhance the distribution of other medical (diabetes) programs is highlighted.

Computer Simulation↗

PubMed1997

Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the humanp53gene, the humanhprtgene and both the rodent transgeniclacIandlacZlocus. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web (WWW). Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage.ht ml . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu . There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site-a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

PubMed1998

Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents.

We have created databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ loci. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers with Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. One method of obtaining the databases and software is via the World Wide Web. Open the following home page with a Web Browser: http://sunsite.unc.edu/dnam/mainpage. html . Alternatively, the databases and programs are available via public FTP from: anonymous@sunsite.unc.edu. There is no password required to enter the system. The databases and software are found beneath the subdirectory: pub/academic/biology/dna-mutations. Two other programs are available at the site, a program for comparison of mutational spectra and a program for entry of mutational data into a relational database.

Animals↗

PubMed1992

Validation of respiratory mechanics software in microprocessor-controlled ventilators.

BACKGROUND AND METHODS: Several microprocessor-controlled ventilators, available for clinical use, contain optional computer software programs capable of performing near-instantaneous determinations of airway resistance and lung compliance. This study was undertaken to determine the validity of the measurements for airway resistance and lung compliance obtained by the software packages on three microprocessor-controlled ventilators. Three ventilator models were studied. An artificial ventilator-patient circuit was constructed using a test lung and an endotracheal tube. Airway pressure and gas flow curves were recorded using conventional means. Static lung compliance and airway resistance were calculated using standard equations, while automated measurements were obtained from the ventilators. The following parameters were then varied to simulate a wide variety of clinical situations: tidal volume, peak inspiratory flow rate, respiratory rate, endotracheal tube, and test lung compliance. RESULTS: Automated measurements were highly correlated with values obtained manually (resistance: Puritan-Bennett 7200a r2 = .94, Bear 5 r2 = .98, Veolar r2 = .96; compliance: 7200a r2 = .93, Bear 5 r2 = .97, Veolar r2 = .97). Calculated limits of agreement between the two methods demonstrate that although not in absolute agreement, the software-determined values for airway resistance and lung compliance differed from the manually derived values in a ventilator-specific, predictable fashion. CONCLUSIONS: The correlation and agreement demonstrated between values of airway resistance and lung compliance measured by the respiratory mechanics software packages and those values derived manually suggest that these software packages may be useful for measuring trends, as well as responding to treatment in the clinical setting. These results apply only to the controlled, mechanical ventilation mode. Further studies are indicated to validate this software in patients capable of generating spontaneous breaths.

Airway Resistance↗

PubMedDate not supplied

Software quality assurance and system safety.

The medical field is faced with the increasing sophistication of software-controlled medical equipment. Clinical engineers must understand and become familiar with these sophisticated software-driven medical devices and stand-alone medical software programs in order to evaluate their suitability for the desired purpose. They must be able to assess the nature of the software, its potential and its risks. Numerous aspects of software development and safety must be considered when developing and/or evaluating such software devices and programs.

Biomedical Engineering↗