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At least 415 records · Page 23Linked to original sources

PubMed2006

Software package for integrated data processing for internal dose assessment in nuclear medicine (SPRIND).

PURPOSE: Internal radiation dose calculations are normally carried out using the Medical Internal Radiation Dose (MIRD) schema. This requires residence times of radiopharmaceutical activity and S-values for all organs of interest. Residence times can be obtained by quantitative nuclear imaging modalities. For dealing with S-values, the freeware packages MIRDOSE and, more recently, OLINDA/EXM are available. However, these software packages do not calculate residence times from image data. METHODS AND RESULTS: For this purpose, we developed an IDL-based software package for integrated data processing for internal dose assessment in nuclear medicine (SPRIND). SPRIND allows reading and viewing of planar whole-body scintigrams. Organ and background regions of interest (ROIs) can be drawn and are automatically mirrored from the anterior to the posterior view. ROI statistics are used to obtain anterior-posterior averaged counts for each organ, corrected for background activity and attenuation. Residence times for each organ are calculated based on effective decay. The total body biological half-time is calculated for use in the voiding bladder model. Red bone marrow absorbed dose can be calculated using bone regions in the scintigrams or by a blood-derived method. Finally, the results are written to a file in MIRDOSE-OLINDA/EXM format. Using scintigrams in DICOM, the complete analysis is gamma camera vendor independent, and can be performed on any computer using an IDL virtual machine. CONCLUSION: SPRIND is an easy-to-use software package for radiation dose assessment studies. It has made these studies less time consuming and less error prone.

Algorithms↗

PubMed2001

Managing predefined templates and macros for a departmental speech recognition system using common software.

The authors have developed a networked database system to create, store, and manage predefined radiology report definitions. This was prompted by complete departmental conversion to a computer speech recognition system (SRS) for clinical reporting. The software complements and extends the capabilities of the SRS, and 2 systems are integrated by means of a simple text file format and import/export functions within each program. This report describes the functional requirements, design considerations, and implementation details of the structured report management software. The database and its interface are designed to allow all radiologists and division managers to define and update template structures relevant to their practice areas. Two key conceptual extensions supported by the template management system are the addition of a template type construct and allowing individual radiologists to dynamically share common organ system or modality-specific templates. In addition, the template manager software enables specifying predefined report structures that can be triggered at the time of dictation from printed lists of barcodes. Initial experience using the program in a regional, multisite, academic radiology practice has been positive.

Computer Peripherals↗

PubMedDate not supplied

Some software requirements for a PACS: lessons from experiences in clinical routine.

In the Department of Radiology of the University of Graz a PACS which includes CT-scanners as modalities was installed. Parts (communication and archiving) of this PACS are used in routine work. Summarizing our experiences from routine work we discuss a minimal set of software requirements that a PACS must meet to allow a fast and non-problematic operation concerning communication and archiving. Most of the functionality of the PACS is provided by software processes which are running automatically in the background. These processes convert images into the ACR-Nema format, submit data in the image database and so on. If a process does not work correctly or crashes, it may happen that examinations are only partially or even not archived. If the user recognises a malfunction too late the troubles spread over the whole system and great time delays or loss of data may occur. Examples of such malfunctions are software crashes, interruptions of the connection between 2 processes or a hardware crash. A PACS that is used in routine work should conform to a set of requirements like autonomous supervising of the single processes, automatical elimination of malfunctions, communication with the user and others. Then the PACS will operate without problems and safely. An intelligent process-structure which conforms to these requirements will be discussed.

Radiology Information Systems↗

PubMed1994

Health care professional workstation: software system construction using DSSA scenario-based engineering process.

This paper describes a new method for the evolutionary determination of user requirements and system specifications called scenario-based engineering process (SEP). Health care professional workstations are critical components of large scale health care system architectures. We suggest that domain-specific software architectures (DSSAs) be used to specify standard interfaces and protocols for reusable software components throughout those architectures, including workstations. We encourage the use of engineering principles and abstraction mechanisms. Engineering principles are flexible guidelines, adaptable to particular situations. Abstraction mechanisms are simplifications for management of complexity. We recommend object-oriented design principles, graphical structural specifications, and formal components' behavioral specifications. We give an ambulatory care scenario and associated models to demonstrate SEP. The scenario uses health care terminology and gives patients' and health care providers' system views. Our goal is to have a threefold benefit. (i) Scenario view abstractions provide consistent interdisciplinary communications. (ii) Hierarchical object-oriented structures provide useful abstractions for reuse, understandability, and long term evolution. (iii) SEP and health care DSSA integration into computer aided software engineering (CASE) environments. These environments should support rapid construction and certification of individualized systems, from reuse libraries.

Computer Systems↗

PubMed1990

Tapetool: a software tool for importing image data from image acquisition computers to image processing computers.

Currently, the image distribution gap between image acquisition computers and image processing computers is bridged through magnetic tapes. The tape formats used by the manufacturers of the image acquisition computers are idiosyncratic and fairly complex. A general purpose window based software tool is herein described, which frees the clinical and research sectors of the responsibility of understanding and decoding these complex formats in order to import image databases from acquisition computers to image processing computers. This software tool provides a cornerstone for developing image processing software for diagnostic, therapeutic and surgical planning purposes.

Algorithms↗

PubMed2005

Automated water analyser computer supported system (AWACSS) Part I: Project objectives, basic technology, immunoassay development, software design and networking.

A novel analytical system AWACSS (automated water analyser computer-supported system) based on immunochemical technology has been developed that can measure several organic pollutants at low nanogram per litre level in a single few-minutes analysis without any prior sample pre-concentration nor pre-treatment steps. Having in mind actual needs of water-sector managers related to the implementation of the Drinking Water Directive (DWD) (98/83/EC, 1998) and Water Framework Directive WFD (2000/60/EC, 2000), drinking, ground, surface, and waste waters were major media used for the evaluation of the system performance. The instrument was equipped with remote control and surveillance facilities. The system's software allows for the internet-based networking between the measurement and control stations, global management, trend analysis, and early-warning applications. The experience of water laboratories has been utilised at the design of the instrument's hardware and software in order to make the system rugged and user-friendly. Several market surveys were conducted during the project to assess the applicability of the final system. A web-based AWACSS database was created for automated evaluation and storage of the obtained data in a format compatible with major databases of environmental organic pollutants in Europe. This first part article gives the reader an overview of the aims and scope of the AWACSS project as well as details about basic technology, immunoassays, software, and networking developed and utilised within the research project. The second part article reports on the system performance, first real sample measurements, and an international collaborative trial (inter-laboratory tests) to compare the biosensor with conventional anayltical methods.

Algorithms↗

PubMed1999

Building quantitative stereology data files with scion image, a public domain image processing and analysis software.

Two-dimensional data obtained from a histological cross-section of a tissue can be utilized to obtain three-dimensional information by the methods of quantitative stereology. The resulting quantitative information is useful in both experimental studies and whole-animal investigations for regulatory and safety purposes. Quantitative stereologic analysis requires considerable data collection and calculation and is thus practical only through the use of computer hardware and software. We have previously reported the development of a program, STEREO, which compiles data from carcinogenesis experiments, recording information from tissue sections for the estimation of the number of altered hepatic foci (AHF) per liver and the volume fraction of AHF in liver on a three-dimensional basis. The data file itself was built by measuring tissue and focal transections through a slide-reading process that involved the manual use of a digitizer. In order to increase the speed and efficiency of the analytical process, we have integrated the STEREO program with a public domain software, Scion Image. This software integration involves two portions: the building macros and the interface. Macros for quantitative stereology used in Scion Image were written to customize and simplify the measurement and to generate data needed for building each of the data files. An interface program, BuildFi.exe, was developed to receive data generated from Scion Image and to align sequential tissue plots from up to four serial sections stained with different markers. As a result, the user can store data on a disk in the format of the STEREO data files. By combining STEREO with Scion Image, the slide-reading process is simplified and can be performed automatically. It has proven to be more objective, time saving, and efficient than all earlier versions.

Animals↗

PubMed2003

Software for image registration: algorithms, accuracy, efficacy.

Image registration is finding increased clinical use both in aiding diagnosis and guiding therapy. There are numerous algorithms for registration, which all involve maximizing a measure of similarity between a transformed floating image and a fixed reference image. The choice of the similarity measure depends, to some extent, on the application. Methods based on the use of the joint intensity histogram have become popular because of their flexibility and robustness. A distinction is made between rigid-body and non-rigid transformations. The latter are needed for inter-subject registration or intra-subject registration in cases where the region of the body of interest is not considered rigid. Non-rigid transformation is normally achieved using a global model of the deformation but can also be defined by a set of locally rigid transformations, each constrained to a small block in the image. There is scope for further research on the incorporation of appropriate constraints, especially for the application of non-rigid transformations to nuclear medicine studies. Most of the initial practical concerns regarding image registration have been overcome and there is increasing availability of commercial software. There are several approaches to the validation of registration software, with validation of non-rigid algorithms being particularly difficult. Studies have demonstrated the accuracy on the order of half a pixel for both intra- and inter-modality registration (typically 2 to 3 mm). Although hardware-based registration has now become possible by using dual-modality instruments, software-based registration will continue to play an important role in nuclear medicine.

Algorithms↗

PubMed1994

BIOESTIM: software for automatic design of estimators in bioprocess engineering.

This paper describes BIOESTIM, a software package devoted to on-line estimation in bioprocess engineering. BIOESTIM enables bioengineers automatically to design state and parameter estimators from a minimal knowledge of the process kinetics. Such estimators allow development of software sensors capable of coping with the lack of reliable instrumentation suited to real-time monitoring. The estimator building procedure through BIOESTIM starts up from a dynamical material balance model of the bioprocess. This model, supplied by the user, is next completed by other information with no requirement for numerical values: the user has only to specify available measurements, coupled reactions and the known yield coefficients. On the base of this knowledge, BIOESTIM proceeds to symbolic algebraic manipulations on the model in order to study estimation possibilities and check identifiability of yield coefficients. When the design of an estimator is possible, the corresponding equations are automatically generated. Moreover, these estimators are stored in a user-specified file which is automatically interfaced with a specialized simulation software including data treatment and numerical integration packages. Thus, the user can simulate the estimator performances under various operational conditions using available experimental measurements. A typical example dealing with microbial growth and biosynthesis reactions is given in order to illustrate the main functional capabilities of BIOESTIM. BIOESTIM has been designed and written in a modular fashion. The module dealing with estimators design makes use of symbolic computation; it is written in Mathematica and runs on every computer on which this language is available.

Algorithms↗

PubMed1994

Identifying correct bacteriological vocabulary: software to look up RKC codes and statements.

A program has been written to help identify the correct RKC codes (Rogosa, Krichevsky and Colwell, 1986) for describing microbiological attributes. Terms, which may be complete words, parts of words, or numbers, can be typed into the computer. A search is made of the set of about 13,800 RKC codes and statements that describe them. Statements that contain the search terms are displayed in a scrolling window so that the required statement(s) can be identified. A list of selected RKC statements can be built up in a second window for subsequent use by other software packages. The program called RKCLIST runs under the MS-DOS operating system. The software routines used to create RKCLIST have been written so that they can be incorporated into other software packages that make use of the RKC coding scheme.

Bacteria↗

PubMed1988

BCE: a tool for software integration.

The integration of software into special-purpose systems (e.g. for gene sequence analysis) can be a difficult task. We describe a general-purpose software integration tool, the BCE program, that facilitates assembly of VAX-based software into application systems and provides an easy-to-use, intuitive user interface. We describe the use of BCE to integrate a heterogeneous collection of sequence analysis tools. Many BCE design features are generally applicable and can be implemented in other language or hardware environments.

Algorithms↗

PubMed2004

SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data.

BACKGROUND: Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles. RESULTS: We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation. CONCLUSIONS: SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments.

Chromosome Mapping↗

PubMed2004

ArrayD: a general purpose software for microarray design.

BACKGROUND: Microarray is a high-throughput technology to study expression of thousands of genes in parallel. A critical aspect of microarray production is the design aimed at space optimization while maximizing the number of gene probes and their replicates to be spotted. RESULTS: We have developed a software called 'ArrayD' that offers various alternative design solutions for an array given a set of user requirements. The user feeds the following inputs: type of source plates to be used, number of gene probes to be printed, number of replicates and number of pins to be used for printing. The solutions are stored in a text file. The choice of a design solution to be used will be governed by the spotting chemistry to be used and the accuracy of the robot. CONCLUSIONS: ArrayD is a software for standard cartesian robots. The software aids users in preparing a judicious and elegant design. ArrayD is universally applicable and is available at http://www.igib.res.in/scientists/arrayd/arrayd.html.

Computational Biology↗

PubMed2004

Pegasys: software for executing and integrating analyses of biological sequences.

BACKGROUND: We present Pegasys--a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. RESULTS: The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. CONCLUSIONS: The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at http://bioinformatics.ubc.ca/pegasys/.

Computational Biology↗

PubMed2006

[Assessment of whole body PET/MRI fusion imaging using automated software: usefulness of partial body fusion].

PURPOSE: In this study, we created a whole body fusion image of PET and MRI using automated software for fusion imaging, and assessed the accuracy of the software. MATERIALS AND METHODS: Twenty patients with abnormal FDG-PET findings underwent whole body MRI. Images from both modalities were automatically fused in two ways using software (Fusion Viewer, Nihon Medi-Physics Co., Ltd., Nishinomiya, Japan) with a registration algorithm based on maximum mutual information. One was to create a whole body fusion image at once, named whole body fusion (WBF). The other was to create fusion images of the head and body separately, named partial body fusion (PBF). Two radiologists measured the misregistration between PET and MRI in the fusion images at nine landmarks (brain, cervical spine, chest, heart, liver, right kidney, left kidney, vertebra, base of bladder). RESULTS: When fusion images were created using WBF at once, misregistration was observed in the head and neck area in approximately half of the cases, whereas almost no misregistration was observed in the body. When fusion images were created using PBF, the misregistration in the head and neck areas was significantly smaller than in those using WBF, and misregistration in the body was very small. CONCLUSION: The PBF technique that creates highly accurate whole body PET/MRI fusion images is easy to use and may provide clinically useful information.

Adult↗

PubMedDate not supplied

Engineering in software testing: statistical testing based on a usage model applied to medical device development.

When a population is too large for exhaustive study, as is the case for all possible uses of a software system, a statistically correct sample must be drawn as a basis for inferences about the population. A Markov chain usage model is an engineering formalism that represents the population of possible uses for which a product is to be tested. In statistical testing of software based on a Markov chain usage model, the rich body of analytical results available for Markov chains provides numerous insights that can be used in both product development and test planing. A usage model is based on specifications rather than code, so insights that result from model building can inform product decisions in the early stages of a project when the opportunity to prevent problems is the greatest. Statistical testing based on a usage model provides a sound scientific basis for quantifying the reliability of software.

Equipment Safety↗

PubMed2000

DbMap: improving database interoperability issues in medical software using a simple, Java-Xml based solution.

In medical software development, the use of databases plays a central role. However, most of the databases have heterogeneous encoding and data models. To deal with these variations in the application code directly is error-prone and reduces the potential reuse of the produced software. Several approaches to overcome these limitations have been proposed in the medical database literature, which will be presented. We present a simple solution, based on a Java library, and a central Metadata description file in XML. This development approach presents several benefits in software design and development cycles, the main one being the simplicity in maintenance.

Databases as Topic↗

PubMed2002

SYNCHRONUS: a reusable software module for temporal integration.

Querying time-stamped data in clinical databases is an essential step in the actuation of many decision-support rules. Since previous methods of temporal data management are not readily transferable among legacy databases, developers must create de novo querying methods that allow temporal integration of a decision-support program and existing database. In this paper, we outline four software-engineering principles that support a general, reusable approach to temporal integration. We then describe the design and implementation of SYNCHRONUS, a software module that advances our prior work on temporal querying. We show how this module satisfies the four principles for the task of temporal integration. SYNCHRONUS can help developers to overcome the software-engineering burden of temporal model heterogeneity within decision-support architectures.

Algorithms↗