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At least 469 records · Page 26Linked to original sources
PubMed1998

Digital images in dermatology and the Dermatology Online Atlas on the World Wide Web.

The digital revolution opens new ways of storing, retrieving and distributing images. The informativeness of digital images of dermatological conditions as compared to conventional photographs and slides has proven to be statistically similar; in many cases, digital images may even substitute for dermatologic physical examination. Current developments in high-speed, high-capacity international networks and the growing popularity of the World Wide Web are converging in ways that have great potential for enhancing access to biomedical information, including medical images. However, lack of metainformation and indexing services specialised in retrieving images makes finding images--as opposed to textual information--on the Web difficult. To provide an image collection and entry point into dermatological resources on the World Wide Web, we have developed an image database (Dermatological OnlIne Atlas--DOIA). The database, which is freely available on the Internet at http://dermis.net, contains about 3,000 clinical images covering more than 600 dermatological diagnoses. It is designed for worldwide use; international submissions are encouraged. It serves as a teaching tool for medical students, doctors and patients, assists professional users by being an easy gateway to other databases such as MEDLINE, PDQ, and OMIM and serves as a platform for conducting research by means of administering Internet surveys to users. We conclude that an online image atlas has multiple educational, clinical, and research applications.

Anatomy, Artistic↗
PubMed2006

A high-resolution anatomical rat atlas.

This paper reports the availability of a high-resolution atlas of the adult rat. The atlas is composed of 9475 cryosectional images captured in 4600 x 2580 x 24-bit TIFF format, constructed using serial cryosection-milling techniques. Cryosection images were segmented, labelled and reconstructed into three-dimensional (3D) computerized models. These images, 3D models, technical details, relevant software and further information are available at our website, http://vchibp.vicp.net/vch/mice/.

Animals↗
PubMed2002

Surface-based atlases of cerebellar cortex in the human, macaque, and mouse.

This study describes surface reconstructions and associated flat maps that represent the highly convoluted shape of cerebellar cortex in three species: human, macaque, and mouse. The reconstructions were based on high-resolution structural MRI data obtained from other laboratories. The surface areas determined for the fiducial reconstructions are about 600 cm(2) for the human, 60 cm(2) for the macaque, and 0.8 cm(2) for the mouse. As expected from the ribbon-like pattern of cerebellar folding, the cerebellar flat maps are elongated along the axis parallel to the midline. However, the degree of elongation varies markedly across species. The macaque flat map is many times longer than its mean width, whereas the mouse flat map is only slightly elongated and the human map is intermediate in its aspect ratio. These cerebellar atlases, along with associated software for visualization and for mapping experimental data onto the atlas, are freely available to the neuroscience community (see http:/brainmap.wustl.edu).

Animals↗
PubMed2005

An introduction to the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas.

This article gives a short overview of the development and characteristics of the OMERACT rheumatoid arthritis MRI scoring system (RAMRIS), followed by an introduction to the use of the EULAR-OMERACT rheumatoid arthritis MRI reference image atlas. With this atlas, MRIs of wrist and metacarpophalangeal joints of patients with rheumatoid arthritis can be scored for synovitis, bone oedema, and bone erosion, guided by standard reference images.

Arthritis, Rheumatoid↗
PubMed2005

Does increasing the grades of the knee osteoarthritis line drawing atlas alter its clinimetric properties?

OBJECTIVES: To (a) develop further logically derived line drawing atlases (LDAs) for grading radiographic knee osteoarthritis (OA); and (b) determine which is superior using metrological criteria. METHODS: A series of LDAs (-3 to +3, -4 to +4, and -5 to +5) were produced by (a) incorporating additional grades for osteophyte and joint space width (JSW) above the 0-3 pilot LDA, over an equivalent range of disease; and (b) adding negative grades for JSW. 121 sets of bilateral knee radiographs (standing, anteroposterior plus flexed skyline), plus serial views of 68 tibiofemoral joints (TFJs) and 36 patellofemoral joints were scored twice by one observer for each LDA. Minimum JSW of 50 radiograph sets was directly measured and awarded a categorical grade dependent upon the boundaries of each LDA grade. Time taken to grade 30 randomly selected knee radiograph sets was measured. RESULTS: Intraobserver reproducibility was similar for all LDAs, (weighted kappa: JSW = 0.85-0.87; osteophyte = 0.77-0.79), with no deterioration with increasing grades. Criterion validity favoured the -5 to +5 LDA, which was also quickest to use. All atlases showed similar responsiveness (standardised response mean: medial TFJ JSW = 0.78-0.83; medial femoral osteophyte = 0.61-0.73), with most sites compromised by small sample size, little change in score, and high variation between subjects. CONCLUSIONS: A set of LDAs was created illustrating the full range of normality/abnormality likely to be encountered in a community study of knee pain or OA. Despite superior validity and equivalent reproducibility, improved responsiveness of the -5 to +5 LDA was not confirmed.

Humans↗
PubMed2004

A digital atlas of breast histopathology: an application of web based virtual microscopy.

AIMS: To develop an educationally useful atlas of breast histopathology, using advanced web based virtual microscopy technology. METHODS: By using a robotic microscope and software adopted and modified from the aerial and satellite imaging industry, a virtual microscopy system was developed that allows fully automated slide scanning and image distribution via the internet. More than 150 slides were scanned at high resolution with an oil immersion x 40 objective (numerical aperture, 1.3) and archived on an image server residing in a high speed university network. RESULTS: A publicly available website was constructed, http://www.webmicroscope.net/breastatlas, which features a comprehensive virtual slide atlas of breast histopathology according to the World Health Organisation 2003 classification. Users can view any part of an entire specimen at any magnification within a standard web browser. The virtual slides are supplemented with concise textual descriptions, but can also be viewed without diagnostic information for self assessment of histopathology skills. CONCLUSIONS: Using the technology described here, it is feasible to develop clinically and educationally useful virtual microscopy applications. Web based virtual microscopy will probably become widely used at all levels in pathology teaching.

Breast↗
PubMed2003

Fiber tract-based atlas of human white matter anatomy.

Two- and three-dimensional (3D) white matter atlases were created on the basis of high-spatial-resolution diffusion tensor magnetic resonance (MR) imaging and 3D tract reconstruction. The 3D trajectories of 17 prominent white matter tracts could be reconstructed and depicted. Tracts were superimposed on coregistered anatomic MR images to parcel the white matter. These parcellation maps were then compared with coregistered diffusion tensor imaging color maps to assign visible structures. The results showed (a). which anatomic structures can be identified on diffusion tensor images and (b). where these anatomic units are located at each section level and orientation. The atlas may prove useful for educational and clinical purposes.

Adult↗
PubMed1998

The incidence and dimensions of the retroarticular canal of the atlas vertebra.

The retroarticular canal has been implicated in compression of the vertebral artery, where it passes over the posterior arch of the atlas vertebra, during extreme rotational movements of the head and neck. The incidence of this retroarticular canal is not known in the South African population. The aim of the present study was to record the incidence and the dimensions of the retroarticular canal in South African white and black adults, aged 20-80 years. In a total of 1,354 atlas vertebrae, 9.8% of sides (264 left and/or right sides) were classified as having complete retroarticular canals, of which 11.7% (31 sides) were right-only, 24.6% (65 sides) left-only and 31.8% (84 left plus right sides) bilateral canals. This incidence did not increase with age and was lower in whites than blacks, with white males having the lowest and white and black females alike having the highest incidence of the canal. Measurements of the retroarticular canal showed that there was no difference between left and right sides. However, the superoinferior diameter was significantly less than the anteroposterior diameter, in all but the right canals in the white female subgroup. This difference in the dimensions of the retroarticular canal will decrease the cross-sectional area of the space available for the vertebral artery passing through it and may compromise blood flow in the vessel.

Adult↗
PubMed2003

Variability in position of the subthalamic nucleus targeted by magnetic resonance imaging and microelectrode recordings as compared to atlas co-ordinates.

BACKGROUND: Traditional methods for localisation of target nuclei for deep brain stimulation (DBS) have used brain atlas co-ordinates for initial targeting. It is now possible to visualise the subthalamic nucleus (STN) on magnetic resonance imaging (MRI) and determine the individual variability of its position. METHODS: The present study was performed in patients undergoing STN DBS for Parkinson's disease. The STN was directly targeted from axially obtained MRI and verified with microelectrode recordings. Postoperatively, the most effective contact was identified for each patient, and its position was calculated. RESULTS: Fifty electrodes were inserted in 25 patients. The target position varied considerably in relation to the mid-commissural point. The mean effective contact position lies just dorsal to the location of the STN in a standard brain atlas. CONCLUSION: The STN varies in position, and can be accurately targeted from MRI alone.

Adult↗
PubMed1992

Magnetic resonance imaging and anatomic atlas mapping for thalamotomy.

A computerized anatomic atlas mapping technique has been developed and used to determine target sites for stereotactic thalamotomies. The digitized stereotactic atlases of Schaltenbrand and Bailey, Van Buren and Borke, and Schaltenbrand and Wahren are used in conjunction with an associated electrophysiological data base to determine the intended target site on MR images of the diencephalon. This mapping technique uses the 'Brierley and Beck' proportional hypothesis for thalamic nuclear determination. Target site determination by this method was found to be very accurate, and frequently the mere placement of the probe in the target site resulted in tremor cessation.

Brain Mapping↗
PubMed1997

Computerized brain atlas in functional neurosurgery.

Computerized brain atlas is a new application area in the practical use of stereotactic neurosurgery. Our approach provides a solution for the straightforward definition of a coordinate system (CA-CP), localization of the selected target point, trepanation points and trajectory transformation of the stereotactic electrode or canula for functional neurosurgery. These problems were solved by comparison of CT, MR and the Schaltenbrand-Wahren atlas. Our original software package integrates all modalities into one system.

Brain↗
PubMed1991

A brain atlas of the northern fulmar (Fulmarus glacialis) in stereotaxic coordinates.

The brain of a procellariiform bird, the Northern Fulmar (Fulmarus glacialis), is presented in the form of a stereotaxic atlas. The Northern Fulmar is especially interesting because both field and laboratory evidence support olfaction as one of its major sensory systems. The nasal cavity and olfactory bulb of most procellariiforms are among the largest of all avian orders; the central olfactory pathways may be more extensive as well. A brain atlas of the Northern Fulmar, a relatively accessible procellariiform species on which several studies have already been done, can provide reference for research both on neural mechanisms underlying olfaction and on comparative neuroanatomical data within Aves and between avian and nonavian groups.

Animals↗
PubMed2006

Implementation of talairach atlas based automated brain segmentation for radiation therapy dosimetry.

Radiotherapy for brain cancer inevitably results in irradiation of uninvolved brain. While it has been demonstrated that irradiation of the brain can result in cognitive deficits, dose-volume relationships are not well established. There is little work correlating a particular cognitive deficit with dose received by the region of the brain responsible for the specific cognitive function. One obstacle to such studies is that identification of brain anatomy is both labor intensive and dependent on the individual performing the segmentation. Automatic segmentation has the potential to be both efficient and consistent. Brains2 is a software package developed by the University of Iowa for MRI volumetric studies. It utilizes MR images, the Talairach atlas, and an artificial neural network (ANN) to segment brain images into substructures in a standardized manner. We have developed a software package, Brains2DICOM, that converts the regions of interest identified by Brains2 into a DICOM radiotherapy structure set. The structure set can be imported into a treatment planning system for dosimetry. We demonstrated the utility of Brains2DICOM using a test case, a 34-year-old man with diffuse astrocytoma treated with three-dimensional conformal radiotherapy. Brains2 successfully applied the Talairach atlas to identify the right and left frontal, parietal, temporal, occipital, subcortical, and cerebellum regions. Brains2 was not successful in applying the ANN to identify small structures, such as the hippocampus and caudate. Further work is necessary to revise the ANN or to develop new methods for identification of small structures in the presence of disease and radiation induced changes. The segmented regions-of-interest were transferred to our commercial treatment planning system using DICOM and dose-volume histograms were constructed. This method will facilitate the acquisition of data necessary for the development of normal tissue complication probability (NTCP) models that assess the probability of cognitive complications secondary to radiotherapy for intracranial and head and neck neoplasms.

Adult↗
PubMed2003

Congruence of tissue expression profiles from Gene Expression Atlas, SAGEmap and TissueInfo databases.

BACKGROUND: Extracting biological knowledge from large amounts of gene expression information deposited in public databases is a major challenge of the postgenomic era. Additional insights may be derived by data integration and cross-platform comparisons of expression profiles. However, database meta-analysis is complicated by differences in experimental technologies, data post-processing, database formats, and inconsistent gene and sample annotation. RESULTS: We have analysed expression profiles from three public databases: Gene Expression Atlas, SAGEmap and TissueInfo. These are repositories of oligonucleotide microarray, Serial Analysis of Gene Expression and Expressed Sequence Tag human gene expression data respectively. We devised a method, Preferential Expression Measure, to identify genes that are significantly over- or under-expressed in any given tissue. We examined intra- and inter-database consistency of Preferential Expression Measures. There was good correlation between replicate experiments of oligonucleotide microarray data, but there was less coherence in expression profiles as measured by Serial Analysis of Gene Expression and Expressed Sequence Tag counts. We investigated inter-database correlations for six tissue categories, for which data were present in the three databases. Significant positive correlations were found for brain, prostate and vascular endothelium but not for ovary, kidney, and pancreas. CONCLUSION: We show that data from Gene Expression Atlas, SAGEmap and TissueInfo can be integrated using the UniGene gene index, and that expression profiles correlate relatively well when large numbers of tags are available or when tissue cellular composition is simple. Finally, in the case of brain, we demonstrate that when PEM values show good correlation, predictions of tissue-specific expression based on integrated data are very accurate.

Brain↗
PubMed2005

GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.

BACKGROUND: Macrophages play an integral role in the host immune system, bridging innate and adaptive immunity. As such, they are finely attuned to extracellular and intracellular stimuli and respond by rapidly initiating multiple signalling cascades with diverse effector functions. The macrophage cell is therefore an experimentally and clinically amenable biological system for the mapping of biological pathways. The goal of the macrophage expression atlas is to systematically investigate the pathway biology and interaction network of macrophages challenged with a variety of insults, in particular via infection and activation with key inflammatory mediators. As an important first step towards this we present a single searchable database resource containing high-throughput macrophage gene expression studies. DESCRIPTION: The GPX Macrophage Expression Atlas (GPX-MEA) is an online resource for gene expression based studies of a range of macrophage cell types following treatment with pathogens and immune modulators. GPX-MEA follows the MIAME standard and includes an objective quality score with each experiment. It places special emphasis on rigorously capturing the experimental design and enables the searching of expression data from different microarray experiments. Studies may be queried on the basis of experimental parameters, sample information and quality assessment score. The ability to compare the expression values of individual genes across multiple experiments is provided. In addition, the database offers access to experimental annotation and analysis files and includes experiments and raw data previously unavailable to the research community. CONCLUSION: GPX-MEA is the first example of a quality scored gene expression database focussed on a macrophage cellular system that allows efficient identification of transcriptional patterns. The resource will provide novel insights into the phenotypic response of macrophages to a variety of benign, inflammatory, and pathogen insults. GPX-MEA is available through the GPX website at http://www.gti.ed.ac.uk/GPX.

Animals↗
PubMed1994

Stereotactic gamma-thalamotomy with a computerized brain atlas: technical case report.

Radiosurgical stereotactic thalamotomy was performed in a patient with parkinsonian tremor with a computerized stereotactic brain atlas, which was transformed to fit the patient's thin-sliced magnetic resonance image to select an optimal target in the nucleus ventralis intermedius of the thalamus. The patient's tremor and rigidity disappeared and have not appeared again for more than 1 year since the eighth postoperative month. A method for converting the presurgically planned stereotactic coordinates in the atlas coordinate system to the coordinates in the frame coordinate system is described.

Aged↗
PubMed2026

Development of the zebrafish foveal analogue: a quantitative atlas of high-acuity zone growth and retinal regionalisation.

The vertebrate retina contains specialised regions for high-acuity vision, exemplified by the human fovea and its zebrafish analogue, the high-acuity zone (HAZ). Despite the widespread use of zebrafish to model retinal disease, a stage-resolved quantitative reference describing normal eye, photoreceptor layer (PRL) and lens growth has been lacking. Here, we apply contrast-enhanced micro-computed tomography (micro-CT) to construct the first three-dimensional micro-CT normative atlas of wild-type zebrafish eye development across five larval stages [3, 5, 7, 10 and 18 days post-fertilisation (dpf)], mapping circumferential PRL thickness, eye and lens morphology, and compartment growth rates. Regional PRL thickening within the temporo-ventral region of the expected HAZ emerged by 5 dpf and was sustained by a localised redistribution of growth, persisting and extending towards the optic nerve through 18 dpf. The PRL, lens and eye grew through four phases, alternating between disproportionate PRL expansion and coordinated growth, while the eye remodelled from a nasal-dominant to a temporo-ventral-dominant form. This regional specialisation was protracted relative to gross ocular growth and could proceed independently of it, paralleling the extended postnatal maturation of the human fovea. This atlas provides a quantitative baseline for distinguishing disease-induced changes from normal variation, supporting zebrafish models of foveal hypoplasia and related disorders.

Animals↗
PubMed2006

Mapping heritability and molecular genetic associations with cortical features using probabilistic brain atlases: methods and applications to schizophrenia.

There is an urgent need to decipher the complex nature of genotype-phenotype relationships within the multiple dimensions of brain structure and function that are compromised in neuropsychiatric syndromes such as schizophrenia. Doing so requires sophisticated methodologies to represent population variability in neural traits and to probe their heritable and molecular genetic bases. We have recently developed and applied computational algorithms to map the heritability of, as well as genetic linkage and association to, neural features encoded using brain imaging in the context of three-dimensional (3D), populationbased, statistical brain atlases. One set of algorithms builds on our prior work using classical twin study methods to estimate heritability by fitting biometrical models for additive genetic, unique, and common environmental influences. Another set of algorithms performs regression-based (Haseman-Elston) identical-bydescent linkage analysis and genetic association analysis of DNA polymorphisms in relation to neural traits of interest in the same 3D population-based brain atlas format. We demonstrate these approaches using samples of healthy monozygotic (MZ) and dizygotic (DZ) twin pairs, as well as MZ and DZ twin pairs discordant for schizophrenia, but the methods can be generalized to other classes of relatives and to other diseases. The results confirm prior evidence of genetic influences on gray matter density in frontal brain regions. They also provide converging evidence that the chromosome 1q42 region is relevant to schizophrenia by demonstrating linkage and association of markers of the Transelin-Associated-Factor-X and Disrupted-In- Schizophrenia-1 genes with prefrontal cortical gray matter deficits in twins discordant for schizophrenia.

Algorithms↗