Why and how is soft copy reading possible in clinical practice? (1/561)

The properties of the human visual system (HVS) relevant to the diagnostic process are described after a brief introduction on the general problems and advantages of using soft copy for primary radiology interpretations. At various spatial and temporal frequencies the contrast sensitivity defines the spatial resolution of the eye-brain system and the sensitivity to flicker. The adaptation to the displayed radiological scene and the ambient illumination determine the dynamic range for the operation of the HVS. Although image display devices are determined mainly by state-of-the-art technology, analysis of the HVS may suggest technical characteristics for electronic displays that will help to optimize the display to the operation of the HVS. These include display size, spatial resolution, contrast resolution, luminance range, and noise, from which further consequences for the technical components of a monitor follow. It is emphasized that routine monitor quality control must be available in clinical practice. These image quality measures must be simple enough to be applied as part of the daily routine. These test instructions might also serve as elements of technical acceptance and constancy tests.  (+info)

Image processing strategies in picture archiving and communication systems. (2/561)

An image processing strategy is presented that assures very similar soft-copy presentation on diagnostic workstations of a picture archiving and communication system (PACS) over the lifetime of an image file and simultaneously provides efficient work-flow. The strategy is based on rigid partitioning of image processing into application- and display-device-specific processing. Application-specific processing is optimized for a reference display system. A description of this system is attached to the file header of the application-specifically processed image which is stored in the PACS. Every diagnostic display system automatically reproduces the image quality for which the application-specific processing was optimized by adjusting its properties by display-system-specific processing so that the system becomes effectively equal to the reference display system.  (+info)

3D angiography. Clinical interest. First applications in interventional neuroradiology. (3/561)

3D angiography is a true technical revolution that allows improvement in the quality and safety of diagnostic and endovascular treatment procedures. 3D angiography images are obtained by reconstruction of a rotational angiography acquisition done on a C-arm (GE Medical Systems) spinning at 40 degrees per second. The carotid or vertebral selective injection of a total of 15 ml of non-ionic contrast media at 3 ml/sec over 5 seconds allows the selection of the "arterial phase". Four hundred sixty 3D angiographic studies were performed from December 1996 to September 1998 on 260 patients and have been analyzed in MIP (Maximum Intensity Projection) and SSD (Shaded Surface Display) views. The exploration of intracranial aneurysms is simplified and only requires, for each vascular axis, a biplane PA and Lateral run followed by a single rotational angiography run. The 3D angiography image is available on the workstation's screen (Advantage Workstation 3.1, GE Medical Systems) in less than 10 minutes after the acquisition of the rotational run. It therefore allows one to analyze, during the intervention, the aneurysm's angioarchitecture, in particular the neck, and select the best therapeutic technique. When endovascular treatment is the best indication, 3D angiography allows one to define the optimal angle of view and accurately select the microcoils dimensions. 3D angiography replaces the multiple oblique views that used to be required to analyze the complex aneurysms and therefore allows a reduction of the total contrast medium quantity, the patient X-ray dose and the length of the intervention time which is a safety factor. Also, in particular for complex cases, it brings additional elements complementing the results of standard 2D DSA and rotational angiograms. In the cervical vascular pathology, 3D angiography allows for a better assessment of the stenosis level and of dissection lesions. Our current research activities focus on the matching without stereotactic frame between 3D X-ray angiography and volumetric MR acquisition, which should allow us to improve the treatment of intracerebral arterio-venous malformations (AVMs).  (+info)

Imagene: an integrated computer environment for sequence annotation and analysis. (4/561)

MOTIVATION: To be fully and efficiently exploited, data coming from sequencing projects together with specific sequence analysis tools need to be integrated within reliable data management systems. Systems designed to manage genome data and analysis tend to give a greater importance either to the data storage or to the methodological aspect, but lack a complete integration of both components. RESULTS: This paper presents a co-operative computer environment (called Imagenetrade mark) dedicated to genomic sequence analysis and annotation. Imagene has been developed by using an object-based model. Thanks to this representation, the user can directly manipulate familiar data objects through icons or lists. Imagene also incorporates a solving engine in order to manage analysis tasks. A global task is solved by successive divisions into smaller sub-tasks. During program execution, these sub-tasks are graphically displayed to the user and may be further re-started at any point after task completion. In this sense, Imagene is more transparent to the user than a traditional menu-driven package. Imagene also provides a user interface to display, on the same screen, the results produced by several tasks, together with the capability to annotate these results easily. In its current form, Imagene has been designed particularly for use in microbial sequencing projects. AVAILABILITY: Imagene best runs on SGI (Irix 6.3 or higher) workstations. It is distributed free of charge on a CD-ROM, but requires some Ilog licensed software to run. Some modules also require separate license agreements. Please contact the authors for specific academic conditions and other Unix platforms. CONTACT: imagene home page: http://wwwabi.snv.jussieu.fr/imagene  (+info)

Stem Trace: an interactive visual tool for comparative RNA structure analysis. (5/561)

MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations.  (+info)

RNA movies: visualizing RNA secondary structure spaces. (6/561)

MOTIVATION: RNA Movies is a system for the visualization of RNA secondary structure spaces. Its input is a script consisting of primary and secondary structure information. From this script, the system fully automatically generates animated graphical structure representations. In this way, it creates the impression of an RNA molecule exploring its own two-dimensional structure space. RESULTS: RNA Movies has been used to generate animations of a switching structure in the spliced leader RNA of Leptomonas collosoma and sequential foldings of potato spindle tuber viroid transcripts. AVAILABILITY: Demonstrations of the animations mentioned in this paper can be viewed on our Bioinformatics web server under the following address: http://BiBiServ.TechFak.Uni-Bielefeld. DE/rnamovies/. The RNA Movies software is available upon request from the authors.  (+info)

E-CELL: software environment for whole-cell simulation. (7/561)

MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.  (+info)

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. (8/561)

SUMMARY: BAliBASE is a database of manually refined multiple sequence alignments categorized by core blocks of conservation sequence length, similarity, and the presence of insertions and N/C-terminal extensions. AVAILABILITY: From http://www-igbmc. u-strasbg.fr/BioInfo/BAliBASE/index.html  (+info)