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PubMed1999

Comparison of adult and paediatric spine and whole body software for the Lunar dual energy X-ray absorptiometer.

Simple phantoms were devised to compare the performance of adult (software 3.64) and paediatric (software 3.8 g) spine and whole body software developed for the Lunar dual energy X-ray absorptiometer. Rectangular slabs of aluminium with high (1.18 g cm-2) and low (0.57 g cm-2) density were used to represent bone mineral. For spine measurements, the phantoms were scanned in water at depths of 5-20 cm. For whole body measurements, the phantoms were scanned with known amounts of oil and water to represent fat and lean tissue. This simulated tissue depths of 5.5-19.7 cm and body composition ranging from 14-29% fat. There were systematic differences in spine and whole body bone mineral content (BMC), bone area (BA) and bone mineral density (BMD) measurements and also between adult and paediatric software versions. The magnitude and direction of these differences were dependent on BMD of the phantom and tissue depth. Similar systematic differences were observed in vivo when volunteers were scanned using adult and paediatric software. Paediatric software enabled measurements to be made at low tissue depths. The weights of fat, lean and total soft tissue measured by the adult and paediatric whole body software were similar to the values calculated from the known composition of the phantom. Precision estimates for all softwares were excellent. In conclusion, paediatric software should improve bone mineral measurements of children but the discrepancies between adult and paediatric softwares may cause problems in longitudinal studies of skeletal growth and when compiling reference data from infancy through to adulthood.

Absorptiometry, Photon↗

PubMed2005

A surgical simulator for planning and performing repair of cleft lips.

UNLABELLED: The objective of this project was to develop a computer-based surgical simulation system for planning and performing cleft lip repair. This system allows the user to interact with a virtual patient to perform the traditional steps of cleft-lip repair (rotation-advancement technique). MATERIALS AND METHODS: The system interfaces to force-feedback (haptic) devices to track the user's motion and provide feedback during the procedure, while performing real-time soft-tissue simulation. An 11-day-old unilateral cleft lip, alveolus and palate patient was previously CT scanned for ancillary diagnostic purposes using standard imaging protocols and 1mm slices. High-resolution 3D meshes were automatically generated from this data using the ROVE software developed in-house. The resulting 3D meshes of bone and soft tissue were instilled with physical properties of soft tissues for purposes of simulation. Once these preprocessing steps were completed, the patient's bone and soft tissue data are presented on the computer screen in stereo and the user can freely view, rotate, and otherwise interact with the patient's data in real time. The user is prompted to select anatomical landmarks on the patient's data for preoperative planning purposes, then their locations are compared against that of a 'gold standard' and a score, derived from their deviation from that standard and time required, is generated. The user can then move a haptic stylus and guide the motion of the virtual cutting tool. The soft tissues can thus be incised using this virtual cutting tool, moved using virtual forceps, and fused in order to perform any of the major procedures for cleft lip repair. Real-time soft tissue deformation of the mesh realistically simulates normal tissues and haptic-rate (>1 kHz) force-feedback is provided. The surgical result of the procedure can then be immediately visualized and the entire training process can be repeated at will. A short evaluation study was also performed. Two groups (non-medical and plastic surgery residents) of six persons each performed the anatomical marking task of the simulator four times. RESULTS: Results showed that the plastic surgery residents scored consistently better than the persons without medical background. Every person's score increased with practice, and the length of time needed to complete the 11 markings decreased. The data was compiled and showed which specific markers consistently took users the longest to identify as well as which locations were hardest to accurately mark. CONCLUSION: These findings suggest that the simulator is a valuable training tool, giving residents a way to practice anatomical identification for cleft lip surgery without the risks associated with training on a live patient. Educators can also use the simulator to examine which markers are consistently problematic, and modify their training to address these needs.

Cleft Lip↗

PubMed1995

Contour resolution of the EyeSys Corneal Analysis System.

We investigated the accuracy of a conventional videokeratography instrument (Corneal Analysis System, EyeSys Laboratories) to measure contour information using specialized software developed by the manufacturer. Seven calibrated spheres were measured and the results tabulated. A contour resolution for all spheres for all reflected rings was found to be +/- 0.0047 mm, representing a 95% confidence interval. This level of resolution is high enough to obtain clinical value from using the EyeSys instrument as a contour measuring device.

Cornea↗

PubMed1994

User metaphors for health care professional workstations.

The problem encountered by health care professionals and software developers has been a lack of demonstrable visions (prototypes) for Computer-based Patient Record (CPR) and Clinical Information System (CIS) applications. This deficiency has resulted in a quest for and consideration of models, metaphors, and mind maps for the Healthcare Professional Workstation (HPW)--the access mechanism for the CPR and the CIS. The familiar physician desktop and traditional paper-based metaphors are not adequate for all aspects of clinical information processes. In the clinical care environment, the flowsheet is a transporting metaphor because many different applications and tasks can be 'transported' into the flowsheet. 3D Rooms, Gopher and Genes are familiar and transporting metaphors to be exploited for HPWs. Using transporting metaphors for HPW software emphasizes commonality and de-emphasizes diversity. Each model and metaphor has an associated mind map. Only the mental model, mental metaphor or mind map for HPW software is important. Metaphors communicate real-world analogies, and communication is at the core of what defines usability. A mind map facilitates communication by building a model in the user's mind. The barriers to HPWs are not technical; they are related to economics, ownership of patient information, liability and information standards.

Computer Systems↗

PubMed1987

The expert teaching system: a new method for learning rhinoplasty using interactive computer graphics.

We have developed software that employs interactive computer graphics to simulate the surgical experience of rhinoplasty by allowing the surgeon to experiment within a model of nasal behavior. For any of three preoperative noses, the surgeon can choose and see the effects of dorsal resection, modification of nasal spine or caudal septum, alar cartilage resection, osteotomy, alar wedge resection, and a variety of nasal grafts. The available choices and views total nearly 3000 images, or approximately 200 different surgical solutions. The surgeon can get textual analysis at any time or see accelerated healing to the projected nasal appearance at 1 year. We believe that the ability to experiment without risk, to safely learn the biological laws governing nasal behavior, should augment the development of surgical judgement in rhinoplasty.

Computer Graphics↗

PubMed1995

Design and implementation of an electronic point-of-contact oncology clinical record.

An electronic point-of-contact narrative clinical record was developed and implemented in a multidisciplinary regional cancer center with an annual new caseload of 1,200. Design principles included (1) natural clinician-intuitive interface with pen, touch, and sound input options; (2) structure and processes enabling direct input of both clinician-reported and patient-reported data; (3) embedding of decision support and practice guidelines directly into the interface; (4) incorporation of automated cancer staging algorithms; (5) automatic production of consultation and progress notes, limiting transcription requirements to sound fields; (6) outcomes--focused report formats; and (7) integrated billing and activity reporting. The system was implemented in Windows, both on a local area network and on mobile devices. Evaluation parameters included feasibility, acceptance, performance, cost of hardware and software development and/or customization, cost of system maintenance, and comparison of net clinician time for encounter documentation relative to a paper-based standard. Feasibility, acceptance, and cost-effectiveness were established.

Decision Making, Computer-Assisted↗

PubMed1996

Selecting managed care information systems.

A decade ago, a handful of managed care information systems occupied a relatively minor niche in the healthcare information system industry. Today, dozens of small software development firms are experiencing explosive expansion and are being courted by larger vendors for partnership or acquisition. When selecting an information system capable of meeting the demands of managed care providers, financial managers should consider carefully the types of systems that are available, their price ranges, their modules, and the type of vendor selling the systems.

Clinical Medicine↗

PubMed1997

Ultrasound contrast agents. Examples of blood pool agents.

PURPOSE: The concept of contrast agents has been extended to ultrasonography (US) almost 30 years ago. Due to technical limitations, the development of US contrast agents (USCA) was slow until the last decade. The ideal USCA should be nontoxic, i.v. injectable, capable to cross the pulmonary capillary bed after a peripheral injection, and be stable enough to achieve enhancement for the total duration of the examination. It should provide not only Doppler but also B-mode enhancement, at a reasonable cost. The efficacy of the most advanced USCA has been reviewed. RESULTS AND CONCLUSION: Doppler examinations improved in cases of deep or small vessels, vessels with low or slow flow, or vessels studied with a bad insonation angle. USCA also enhanced detection of flow within normal and abnormal vessels, including tumor and stenotic vessels. Ischemic areas were better delineated. Specific settings and software developed by US equipment manufacturers and US sequences (such as second harmonic imaging or transient imaging) prefigured the necessary adaptation of US units to the new potentials of USCA. Second harmonic properties will improve detection of smaller vessels including neovascularization associated with tumors. Targeting possibilities will increase the efficacy of USCA, and allow specific delivery of active drugs such as anticoagulants or cytotoxic compounds. New generations of USCA appear very promising, and are becoming part of the US future.

Contrast Media↗

PubMed1996

Real-time 3D dose calculation and display: a tool for plan optimization.

PURPOSE: Both human and computer optimization of treatment plans have advantages; humans are much better at global pattern recognition, and computers are much better at detailed calculations. A major impediment to human optimization of treatment plans by manipulation of beam parameters is the long time required for feedback to the operator on the effectiveness of a change in beam parameters. Our goal was to create a real-time dose calculation and display system that provides the planner with immediate (fraction of a second) feedback with displays of three-dimensional (3D) isodose surfaces, digitally reconstructed radiographs (DRRs), dose-volume histograms, and/or a figure of merit (FOM) (i.e., a single value plan score function). This will allow the experienced treatment planner to optimize a plan by adjusting beam parameters based on a direct indication of plan effectiveness, the FOM value, and to use 3D display of target, critical organs, DRRs, and isodose contours to guide changes aimed at improving the FOM value. METHODS AND MATERIALS: We use computer platforms that contain easily utilized parallel processors and very tight coupling between calculation and display. We ported code running on a network of two workstations and an array of transputers to a single multiprocessor workstation. Our current high-performance graphics workstation contains four 150-MHz processors that can be readily used in a shared-memory multithreaded calculation. RESULTS: When a 10 x 10-cm beam is moved, using an 8-mm dose grid, the full 3D dose matrix is recalculated using a Bentley-Milan-type dose calculation algorithm, and the 3D dose surface display is then updated, all in < 0.1s. A 64 x 64-pixel DRR calculation can be performed in < 0.1 s. Other features, such as automated aperture calculation, are still required to make real-time feedback practical for clinical use. CONCLUSION: We demonstrate that real-time plan optimization using general purpose multiprocessor workstations is a practical goal. Parallel processing technology provides this capability for 3D planning systems, and when combined with objective plan ranking algorithms should prove effective for optimizing 3D conformal radiation therapy. Compared to our earlier transputer work, multiprocessor workstations are more easily programmed, making software development costs more reasonable compared with uniprocessor development costs. How the dose calculation is partitioned into parallel tasks on a multiprocessor work station can make a significant difference in performance. Shared-memory multiprocessor workstations are our first choice for future work, because they require minimum programming effort and continue to be driven to higher performance by competition in the workstation arena.

Computer Graphics↗

PubMed1994

Image analysis software for the detection of preneoplastic and early neoplastic lesions.

Preneoplastic lesions are usually small, and often appear as foci of atypical cells that blend into the surrounding normal tissue without producing a detectable tumor mass. Since these lesions seldom provide adequate tissue for biochemical studies, their detection often depends upon subtle distinctions in cytologic features. Image analysis permits pathologists to obtain quantitative measurements on cytologic and histologic preparations, so that visual impressions can be augmented by quantitative morphometry. Preneoplastic lesions have well-described morphometric features relating to nuclear area, texture, or shape. It is now feasible for every pathology department to capture images of pathologic material with equipment costing less than the price of a microscope. Captured image files can be analyzed using commercial software or software developed in several U.S. government agencies and made freely available to the public. Image analysis has been shown to improve the detection of preneoplastic cells. Recent improvements in the resolution of captured images, in the algorithms that measure preneoplastic descriptors, and in the ease and speed of transmission of images between laboratories, should increase our ability to detect and treat preneoplastic lesions.

Carcinoma in Situ↗

PubMed2005

Tilt and rotation correction of acetabular version on pelvic radiographs.

Anteroposterior pelvic radiographs are the gold standard of imaging for mechanical hip problems. However, correct interpretation is difficult because the projected morphologic features of the acetabulum and nearly all routinely used hip parameters depend on individual pelvic position, which can vary considerably during acquisition. We developed software that recreates the projected acetabular rim and the measured hip parameters as if obtained in a standardized orientation. The vertical and horizontal distances between two easy identifiable points were used as indicators of tilt and rotation. These points were the middle of the sacrococcygeal joint and the middle of the upper border of the symphyseal gap. Calibration of the indicators was achieved by means of serial pelvic radiographs of 20 cadaver pelves. Validation of tilt indicator in 100 patients and a theoretical error analysis revealed that for accurate tilt prediction an additional one-time lateral radiograph of the pelvis is mandatory. The computer-assisted method allows standardized evaluation of anatomic morphologic differences of femoral coverage (dysplasia, retroversion), making their clinical relevance for development of early osteoarthritis more valuable.

Acetabulum↗

PubMed2006

The Ultrasonix 500RP: a commercial ultrasound research interface.

Unlike researchers in magnetic resonance imaging who have considerable access to high level tools and to data at a very basic level on their scanners, those involved with ultrasound have found little in the way of meaningful and widespread access to even the most basic echo signals in their clinical systems. Interest has emerged, however, in ultrasound research interfaces on commercial scanners to provide access to raw ultrasound data and control of basic research functions. This paper describes initial experience gained on one such ultrasound system. The Ultrasonix 500RP system provides research access to the data at multiple points in the signal processing chain and allows control over most imaging parameters. The Ultrasonix system allows for three methods of research control. One is implemented along with the standard clinical imaging software using "mouseover" screens on the periphery of the application window. These screens are configured by the user to display various signal processing variables, which can be modified in real time. Second, the system can be controlled via a user-written remote control client application interacting through the clinical exam software. Lastly, the user can write a complete application which initializes the basic ultrasound module but need not use the Ultrasonix clinical exam software. All of the modes can be done locally on the scanner itself or via a network, and are based on software developed in C++ with libraries supplied with the scanner. Two examples are presented in this paper from the evaluation of the system in "real world" applications. Measurements of absolute backscatter coefficients and attenuation coefficients versus frequency are shown and elastograms utilizing spatial compounding are described.

Biomedical Research↗

PubMed1991

The design of a user interface for a ventilator-management advisor.

The lack of user acceptance for many medical decision-support systems should force medical software developers to rethink strategies for user interaction with decision-support programs. Participatory design is an emerging method for the development for computer applications that emphasizes user involvement in both the design and implementation phases. We have applied participatory design to the development of a user interface for VentPlan, an application that assists physicians in the management of artificial respiration of critically ill patients. In this paper, we present a case history of the participatory design process and describe the resulting interface for the VentPlan program. As a result of applying participatory design ideas, we gained insight as to how to implement VentPlan more effectively.

Critical Care↗

PubMed2001

The Virtual Cell: a software environment for computational cell biology.

The newly emerging field of computational cell biology requires software tools that address the needs of a broad community of scientists. Cell biological processes are controlled by an interacting set of biochemical and electrophysiological events that are distributed within complex cellular structures. Computational modeling is familiar to researchers in fields such as molecular structure, neurobiology and metabolic pathway engineering, and is rapidly emerging in the area of gene expression. Although some of these established modeling approaches can be adapted to address problems of interest to cell biologists, relatively few software development efforts have been directed at the field as a whole. The Virtual Cell is a computational environment designed for cell biologists as well as for mathematical biologists and bioengineers. It serves to aid the construction of cell biological models and the generation of simulations from them. The system enables the formulation of both compartmental and spatial models, the latter with either idealized or experimentally derived geometries of one, two or three dimensions.

Biology↗

PubMed2006

SEBINI: Software Environment for BIological Network Inference.

UNLABELLED: The Software Environment for BIological Network Inference (SEBINI) has been created to provide an interactive environment for the deployment and evaluation of algorithms used to reconstruct the structure of biological regulatory and interaction networks. SEBINI can be used to compare and train network inference methods on artificial networks and simulated gene expression perturbation data. It also allows the analysis within the same framework of experimental high-throughput expression data using the suite of (trained) inference methods; hence SEBINI should be useful to software developers wishing to evaluate, compare, refine or combine inference techniques, and to bioinformaticians analyzing experimental data. SEBINI provides a platform that aids in more accurate reconstruction of biological networks, with less effort, in less time. AVAILABILITY: A demonstration website is located at https://www.emsl.pnl.gov/NIT/NIT.html. The Java source code and PostgreSQL database schema are available freely for non-commercial use.

Algorithms↗

PubMedDate not supplied

Bsoft: image and molecular processing in electron microscopy.

Software for the processing of electron micrographs in structural biology suffers from incompatibility between different packages, poor definition and choice of conventions, and a lack of coherence in software development. The solution lies in adopting a common philosophy of interaction and conventions between the packages. To understand the choices required to have such common interfaces, I am developing a package called "Bsoft." Its foundations lie in the variety of different image file formats used in electron microscopy-a continually frustrating experience to the user and programmer alike. In Bsoft, this problem is greatly diminished by support for many different formats (including MRC, SPIDER, IMAGIC, SUPRIM, and PIF) and by separating algorithmic issues from image format-specific issues. In addition, I implemented a generalized functionality for reading the tag-base STAR (self-defining text archiving and retrieval) parameter file format as a mechanism to exchanging parameters between different packages. Bsoft is written in highly portable code (tested on several Unix systems and under VMS) and offers a continually growing range of image processing functionality, such as Fourier transformation, cross-correlation, and interpolation. Finally, prerequisites for software collaboration are explored, which include agreements on information exchange and conventions, and tests to evaluate compatibility between packages.

Computer Systems↗

PubMedDate not supplied

A computerized purchase order management system.

Order processing and parts issuing are within the scope of an inventory management system and, as such, it was logical to incorporate the Purchase Order Management Menu into the biomedical engineering inventory management system. The Purchase Order Management function was implemented using the services of a biomedical engineering technician who is a staff member. Software development time (two months) was the only resource that was necessary to incorporate this function into the inventory system. This function, implemented on a PC, provided locally functions that had not been available on the mainframe-based hospital purchasing system. These functions directly addressed the needs of the users, who in this case are the staff members of the department of biomedical engineering at University Hospital, Stony Brook, New York.

Computer Systems↗

PubMed2006

Accuracy of dental digitizers.

UNLABELLED: The need for proper validation and verification methodology for CAD/CAM systems is imminent. CAD/CAM systems consisting of an optical impression system, design software and a fabrication machine have to perform to a certain level, whereby manufacturers need to prove the effectiveness of the system as a whole. However, especially when dental surface digitization devices are used as open, stand-alone applications in dental outsourcing, a reliable standard test for comparison is necessary. PURPOSE: This study evaluates a proposed test method to be used to quantify "digitizing quality" with respect to accuracy and reproducibility of two dental surface digitization devices. Comparability of the characteristics should be ensured. METHOD: Two laser light section scanners: DentaScope II and D200 were evaluated by means of the 'Sphere Test', that involves repeated measurements of a precision ball (radius: 6mm) according to a pre-defined protocol. The surface information was received as unmatched, overlapping point clouds and statistically processed with a newly developed software package. The standard deviation of all points as well as a measure for undercutting the equator were determined. RESULTS: The standard deviation for the radius for D and S were 7.7 (+/-0.8) and 13.9 (+/-1.0) microm respectively. The equator undercut elevations were -2.0 degrees and -0.25 degrees for scanner D and S respectively. CONCLUSION: Scanner D had a significantly higher accuracy than S (p<0.05), corresponding with the smaller pixel distance of the sensor. Both devices show adequate accuracy and reproducibility and have an adequate ability to detect the equator. The test is also suitable for calibration purposes.

Computer-Aided Design↗