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PubMed1992

Portable image-manipulation software: what is the extra development cost?

A hospital-wide picture archiving and communication system (PACS) project is currently under development at the University Hospital of Geneva. The visualization and manipulation of images provided by different imaging modalities constitutes one of the most challenging component of a PACS. It was necessary to provide this visualization software on a number of types of workstations because of the varying requirements imposed by the range of clinical uses it must serve. The user interface must be the same, independent of the underlying workstation. In addition to a standard set of image-manipulation and processing tools, there is a need for more specific clinical tools that can be easily adapted to specific medical requirements. To achieve this goal, it was elected to develop a modular and portable software called OSIRIS. This software is available on two different operating systems (the UNIX standard X-11/OSF-Motif based workstations and the Macintosh family) and can be easily ported to other systems. The extra effort required to design such software in a modular and portable way was worthwhile because it resulted in a platform that can be easily expanded and adapted to a variety of specific clinical applications. Its portability allows users to benefit from the rapidly evolving workstation technology and to adapt the performance to suit their needs.

Costs and Cost Analysis↗

PubMed1989

Software engineering education in medical informatics.

Requirements and approaches of Software Engineering education in the field of Medical Informatics are described with respect to the impact of (1) experiences characterizing the "software misery", (2) status and tendencies in software methodology, and (3) educational status and needs in computer science education influenced by the controversy "theoretical versus practical education". Special attention is directed toward the growing importance of analysis, design methods, and techniques in the professional spectrum of Medical Informatics, the relevance of general principles of systems engineering in health care, the potential of non-procedural programming paradigms, and the intersection of Artificial Intelligence and education. Realizations of and experiences with programs in the field of Software Engineering are reported with respect to special requirements in Medical Informatics.

Artificial Intelligence↗

PubMed1991

[Electronic data processing in the hospital: current status, options, "branch packets", customer-specific software and users' needs].

Data management in hospitals used to be the data management of the hospital-management in the last 15 years, not however the data management the doctors performed. The acceptance for electronic means slowly rising more software is used in the clinics today but still by the doctors privately. Software specialists have registered the growing market available for their products. That is why the danger to accept even unusuable software rises every day, as unexperienced software-beginners as doctors mostly are often relied on offers without being told about their dignity and usefulness.

Electronic Data Processing↗

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↗

PubMed1992

Software suite for image archiving and retrieval.

The efficient operation of a clinical picture archiving and communication system (PACS) requires a fully functional image archive. The archive should not only be able to store and retrieve images reliably but should also work in concert with software that optimizes the flow of image-related information throughout the PACS. The authors devised a software suite that serves to improve the flow and content of information and the integrity of the data. The software was developed by translating the functions performed by a conventional film library. Types of transactions possible with this system include scheduling, canceling, rescheduling, and prestaging examinations; changing demographic information; merging patient information; and generating reports. The authors believe such a software suite is essential for a clinically useful PACS.

Data Display↗

PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗

PubMed1990

[Mental health in software engineers. I. Frequency of mental complaints, physical complaints and psychiatric disorders].

This study examined the physical complaints, mental complaints and psychiatric disorders in software engineers. Subjects were 101 male software engineers. They were evaluated by a semistructured interview. Psychiatric diagnosis was based on DSM-III (Diagnostic and Statistical Manual of Mental Disorders, third edition). The results are summarized as follows: 1) Physical complaints were observed in 68% of the subjects with 25% of the subjects complaining of physical ill-health. This study showed that 12% of the subjects had hypertension, 12%, gastritis or gastro-duodenal ulcer, 14%, allergic disease, and 19% miscellaneous diseases. 2) Of the subjects 62% had mental complaints and 31% mental ill-health. Depressive symptom was the most frequent mental complaint with 32% of the subjects diagnosed as DSM-III. The common diagnoses were adjustment disorders (19%), major affective disorders (6%), psychological factors affecting physical condition (5%) and dysthymic disorder (3%). Only one subject sought professional help from a psychiatrist for relief of mental complaints. The data suggest the severity of mental ill health in software engineers, but methodological limitations preclude a firm conclusion at this time. Further studies should be made on the mental health state in software engineers.

Adult↗

PubMedDate not supplied

Specialized PC software package for creation of computer systems supporting partial diagnostics based on numerical results of medical examinations.

Computer scientists creating computer systems supporting partial diagnostics based on numerical results of medical examinations always follow a similar method. Why not algorithmize this procedure? This was the main reason for preparation of the specialized PC software presented in the paper. The software is addressed to clinicians-scientists and enables such users to create by themselves (with no need of programming) practically useful computer systems for differential diagnosis of chosen diseases. These generated systems are assigned to an end-user, i.e. any physician interested in a partial diagnosis of the considered type. They perform classification of patients on the basis of numerical results of the examinations selected for the training databases. The software is based on a statistical approach; multi-dimensional variance analysis and discriminant analysis methods have been used. The pilot version of the software (experimentally implemented in a Warsaw clinic) and an outline of planned work are presented.

Algorithms↗

PubMed1992

FDA regulation of biomedical software.

A major problem faced by biomedical software developers and users is the complexity of the regulatory regimes confronting them. Of particular concern is whether, and to what extent, they are regulated by the Food and Drug Administration (FDA) and the consequences of such regulation. Producers, distributors, and users of biomedical software often are unaware that FDA regulates many of these products as medical devices. Developers, vendors, distributors, or users of such software are subject to significant civil and criminal liability for noncompliance. This article explains the current regulatory requirements imposed on computer software developers and users by FDA, biomedical and some proactive strategies for avoiding adverse enforcement.

Documentation↗

PubMedDate not supplied

Noviceware: a model for learning the software development process.

Students and nursing faculty without formal computer science training can collaborate within an independent study structure to assist the student in gaining experience with the fundamentals of software development. The systems development life cycle approach provides an essential map to structure such independent studies. This article describes the development within an academic setting of a computerized research management system. The software builds a database of research case demographic data and data from a 65-item tool used in scoring videotapes of caregiver-infant interactions. For students and faculty contemplating similar projects, recommendations about planning software development experiences and securing hardware, software, and expert resources are provided.

Algorithms↗

PubMed1991

Record linkage strategies: Part II. Portable software and deterministic matching.

Software to perform record linkage should have several characteristics: (1) portability in being able to function with researchers' current arrangement of computer systems and languages, (2) flexibility in handling different linkage strategies, and (3) low cost in both computer time and researchers' efforts. A linkage package (LINKS) is described which satisfies these criteria; LINKS provides tools for both deterministic and probabilistic linkage as well as test modules for assessing data quality and structure. Because each linkage project is different, the modular nature of the software allows for better control of the programming process and development of unique strategies. Since the user provides the weights and decision rules, he may modify data between steps and/or develop extra steps to supplement the basic modules. In two information-rich linkage projects involving California AIDS data, LINKS identified mortality using deterministic approaches and permitted comparisons with other software and strategies. Flexible software and a deterministic approach would have eliminated the expensive key entry used to add full names and social security numbers as additional identifiers to one of the California data files.

Acquired Immunodeficiency Syndrome↗

PubMed1991

A software system for interactive and quantitative visualization of multidimensional biomedical images.

A comprehensive software system called ANALYZE has been developed which permits detailed investigation and evaluation of 3-D biomedical images. The software can be used with any 2-D or 3-D imaging modality, including x-ray computed tomography, radionuclide emission tomography, ultrasound tomography, magnetic resonance imaging and both light and electron microscopy. The package is unique in its synergistic integration of fully interactive modules for direct display, manipulation and measurement of multidimensional image data. Several original algorithms are included which improve image display efficiency and quality. One of the most versatile and powerful algorithms is interactive volume rendering, which is optimized to be fast without compromising image quality. An important advantage of this technique is to display 3-D images directly from the original data and to provide on-the-fly combinations of selected image transformations and/or volume set operations (union, intersection, difference, etc.). The inclusion of a variety of interactive editing and quantitative mensuration tools significantly extends the usefulness of the software. Any curvilinear path or region-of-interest can be manually specified and/or automatically segmented for numerical determination and statistical analyses of distances, areas, volumes, shapes, densities and textures. ANALYZE is written entirely in "C" and runs on several standard UNIX workstations. It is being used in a variety of applications by over 40 institutions around the world, and has been licensed by Mayo to several imaging companies. The software architecture permits systematic enhancements and upgrades which has fostered development of a readily expandable package. ANALYZE comprises a powerful "visualization workshop" for rapid prototyping of specific application packages, including applications to interactive surgery simulation and radiation treatment planning. ANALYZE offers the potential to accurately and reproducibly examine, from images, the structure and function of any cell, tissue, limb, organ or organ system of the body, much like a surgeon or pathologist might do in real life, but entirely non-invasively, without pain or destruction of tissue. These capabilities promise exciting new insights into the basic processes of life, and major advances in health care delivery through improved diagnosis and treatment of disease.

Computer Graphics↗

PubMed1990

Hospital users rate software applications. 1990 SDR vendor awards of excellence.

Not all software packages are made the same; some do their jobs better than others. Which software is most popular among hospitals? The 1990 SDR Vendor Awards of Excellence is an attempt to answer that question. For the awards, Shared Data Research (SDR), Hudson, OH, asked hospital software users to nominate companies that produce the best-performing software.

Attitude of Health Personnel↗

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↗

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↗

PubMed1992

Computer assisted data collection for stereology: rationale and description of point counting stereology (PCS) software.

The paper describes microcomputer software for point counting stereology. Stereology includes a collection of statistical methods that quantify the images of light and transmission electron microscopy. The methods use test grids placed over images to collect raw data, which includes counts of points, intersections, transections, and profiles. In turn, the counts are included in stereological equations that give estimates of compartmental volumes, surfaces, lengths, or numbers. These parameters describe the composition of a structure in three-dimensional space. The PCS (point counting stereology) System Software III serves as a data collection, storage, and management tool. Users set up point counting protocols without programming, enter data by pressing predefined function (MS-DOS) or alphabetic keys (UNIX), store data in files, select files for analysis, and calculate results as stereological densities. The latest version of the PCS software includes a new user interface and is designed as a research "front end" that can feed data either into the calculation tools of a stereology tutorial (Bolender, 1992, this issue) or into the analysis routines of quantitative morphology databases (Bolender and Bluhm, 1992).

Animals↗

PubMed1989

Fitting heteroscedastic regression models to individual pharmacokinetic data using standard statistical software.

In the analysis of individual pharmacokinetic data by nonlinear regression it is important to allow for possible heterogeneity of variance in the response. Two common methods of doing this are weighted least squares with appropriate weights or data transformation using a suitable transform. With either approach it is appealing to let the data determine the appropriate choice of weighting scheme or transformation. This article describes two methods of doing this which are easy to compute using standard statistical software. The first method is a generalized least squares scheme for the case where the variance is assumed proportional to an unknown power of the mean. The second involves applying a power transformation to both sides of the regression equation. It is shown that both techniques may be implemented using only nonlinear regression routines. Sample code is provided for their implementation using the SAS software package. However, the proposed methods are feasible using any software package that incorporates a nonlinear least squares routine, and are thus well suited to routine use.

Humans↗