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PubMed2004

Using GIS in government: an overview of the VHA's Healthcare Atlas, FY-2000.

The amount of VA data available for analysis can be overwhelming to individuals who need to translate these data into usable information. The Atlas, using current GIS technology, was funded to provide data in a comprehensive guide. Patients were identified using a disease classification scheme based on Kaiser Permanente methodology and the Clinical Classifications Software (AHRQ). Utilization data were extracted from the Medical SAS Datasets. Cost data were obtained from the HERC. GIS tools were used to create the Atlas. The Atlas overviews the location of VA hospitals; profiles veteran, VA enrollee and patient populations; examines overall utilization; depicts patterns in healthcare use by specific disease cohorts; and examines geographic variations in costs. This product will enhance knowledge of VA's enrolled patient population and their healthcare needs, and provide background information that will improve the formulation of specific research questions to address those needs.

Databases, Factual↗
PubMed1990

Accuracy and precision of the computerized brain atlas programme for localization and quantification in positron emission tomography.

The computerized brain atlas programme (CBA) provides a powerful tool for the anatomical analysis of functional images obtained with positron emission tomography (PET). With a repertoire of simple transformations, the data base of the CBA is first adapted to the anatomy of the subject's brain represented as a set of magnetic resonance (MR) or computed tomography (CT) images. After this, it is possible to spatially standardize (reformat) any set of tomographic images related to the subject, PET images, as well as CT and MR images, by applying the inverse atlas transformations. From these reformatted images, statistical images, such as average images and associated error images corresponding to different groups of subjects, may be produced. In all these images, anatomical structures can be localized using the atlas data base and the functional values can be evaluated quantitatively. The purpose of this study was to determine the spatial and quantitative accuracy and precision of the calculated regional mean values. Therefore, the CBA was applied to regional CBF (rCBF) measurements with [11C]fluoromethane and PET on 26 healthy male volunteers during rest and during three different physiological stimulation tasks. First, the spatial accuracy and precision of the reformation process were determined by measuring the spread of defined anatomical structures in the reformatted MR images of the subjects. Second, the mean global CBF and the mean rCBF in the average PET images were compared with the global CBF and rCBF in the original PET images. Our results demonstrate that the reformation process accurately transformed the individual brains of the subjects into the standard brain anatomy of the CBA. The precision of the reformation process had an SD of approximately 1 mm for the lateral dislocation of midline structures and approximately 2-3 mm for the dislocation of the inner and outer brain surfaces. The quantitative rCBF values of the original PET images were accurately represented in the reformatted PET images. Moreover, this study shows that the application of the CBA improves the analysis of functional PET images: (a) The average PET images had a low background noise [0.4 ml/100 g/min +/- 0.7 (SD)] compared to the mean rCBF changes specifically induced by physiological stimulation. (b) The reformatted PET images had a voxel volume of 10.9 mm3. Owing to this high sampling resolution, it was possible to differentiate the mean rCBF changes in adjacent activated fields such as the left motor hand area from the sensory hand area and the left premotor cortex.(ABSTRACT TRUNCATED AT 400 WORDS)

Adult↗
PubMed2003

A gene expression atlas of the central nervous system based on bacterial artificial chromosomes.

The mammalian central nervous system (CNS) contains a remarkable array of neural cells, each with a complex pattern of connections that together generate perceptions and higher brain functions. Here we describe a large-scale screen to create an atlas of CNS gene expression at the cellular level, and to provide a library of verified bacterial artificial chromosome (BAC) vectors and transgenic mouse lines that offer experimental access to CNS regions, cell classes and pathways. We illustrate the use of this atlas to derive novel insights into gene function in neural cells, and into principal steps of CNS development. The atlas, library of BAC vectors and BAC transgenic mice generated in this screen provide a rich resource that allows a broad array of investigations not previously available to the neuroscience community.

Animals↗
PubMed2006

Genome-wide atlas of gene expression in the adult mouse brain.

Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.

Animals↗
PubMed2006

Towards multimodal atlases of the human brain.

Atlases of the human brain have an important impact on neuroscience. The emergence of ever more sophisticated imaging techniques, brain mapping methods and analytical strategies has the potential to revolutionize the concept of the brain atlas. Atlases can now combine data describing multiple aspects of brain structure or function at different scales from different subjects, yielding a truly integrative and comprehensive description of this organ. These integrative approaches have provided significant impetus for the human brain mapping initiatives, and have important applications in health and disease.

Anatomy, Artistic↗
PubMed2005

An evaluation of a colour food photography atlas as a tool for quantifying food portion size in epidemiological dietary surveys.

OBJECTIVE: To test the validity of a colour food photography atlas for quantifying portion size eaten compared with weighed foods. DESIGN: The colour food photography atlas was prepared by cooking, weighing and taking digital photographs of three portion sizes of 434 foods and beverages typical of the Italian diet. SUBJECTS AND INTERVENTIONS: In all, 448 male and female volunteers aged 6-60 y from a wide variety of social backgrounds completed 9075 assessments of food portions eaten at lunch and dinner in relation to a set of colour food photographs during 8 weeks of investigation. The amounts of foods eaten by individuals in five different cafeterias in Pavia, Northern Italy, were weighed by trained investigators at the time of serving and, within 5-10 min of the end of the meal, each subject was asked to quantify all foods consumed with reference to one of the three food photographs or in terms of virtual portions among those shown in the photographs. RESULTS: Multiple regression analysis shows that weights of portion sizes chosen from the set of photographs are significantly associated (P<0.05) to weights of eaten portions (beta=0.81; R(2)=0.70) and are independent of age, gender and BMI. The differences between mean weights of the portions chosen by individuals from photographs and mean weights of eaten foods are significant for all food categories (P<0.05), except for bread. However, because of the very large number of observations, the mean differences are very small (range: from +23.2 g (+11.2%) for first courses to -1.3 g (-2.7%) for bread). Bland-Altman plots show that first courses limits of agreement are wide because the dispersion is increasing while weights are rising. CONCLUSIONS: The use of a series of three photographs and virtual portion sizes being associated with relatively small errors, our findings support the validity of using this colour food photography atlas as a tool for quantifying food portion size in epidemiological dietary surveys on different age groups of Italian subjects.

Adolescent↗
PubMed2000

The interactive Web-based histology atlas system.

Molecular pathways and mechanisms underlying human cancer are frequently investigated in animal models. Studies to identify and dissect molecular pathways include the discovery of genes and their subsequent analysis in transgenic and 'knock-out' mice. A critical aspect in such investigations is the evaluation of organ integrity and histology upon the alteration or inactivation of specific genes. Results from such studies are usually published in scientific journals. However, due to print space and costs the display of large high quality images is limited. Furthermore, the printed media does not permit an easy comparison of histological images published in different journals and different years. The Internet provides a tool for the timely and inexpensive dissemination of scientific data to the research community. However, its potential for the analysis of histological images has not been explored. Here we present a web-based interactive histology atlas (http://histology.nih.gov) that permits the retrieval of annotated, high-resolution histology images via the Internet. This histology atlas also takes advantage of the interactive nature of the Internet to support the communication between different research groups. As an outline forum this atlas provides the framework to evaluate and understand cancer pathology, and to develop a consensus between veterinary and human pathologists.

Animals↗
PubMed2000

Efficacy and safety of high-dose lisinopril in chronic heart failure patients at high cardiovascular risk, including those with diabetes mellitus. Results from the ATLAS trial.

AIMS: An analysis was designed to determine whether chronic heart failure patients at high cardiovascular risk benefited to the same extent from high-dose lisinopril as the whole ATLAS population. METHODS AND RESULTS: A retrospective analysis was performed on high-risk heart failure patients in the Assessment of Treatment with Lisinopril And Survival (ATLAS) trial (total number of patients 3164) comparing highdose (32.5-35 mg. day(-1)) vs low-dose (2.5-5 mg. day(-1)) lisinopril for a median of 46 months. These high-risk patients included those with hypotension, hyponatraemia, compromised renal function, the elderly and patients with diabetes mellitus at baseline. In the whole study population, high-dose lisinopril led to a trend in risk reduction of all-cause mortality (primary end-point P=0.128) and a significant risk reduction in all-cause mortality plus hospitalization (principal secondary end-point P=0.002). Subgroup analyses were performed for these end-points. There were no consistent interactions between age, baseline sodium, creatinine or potassium values, and treatment effect. Diabetics showed a beneficial response to high-dose therapy that was at least as good as that in non-diabetics. The underlying higher morbidity/mortality rates in diabetics mean that high-dose lisinopril has potential for a larger absolute clinical impact in these patients. CONCLUSION: Long-term high-dose lisinopril was as effective and well-tolerated in high-risk patients, including those with diabetes mellitus, as for the ATLAS study population as a whole.

Aged↗
PubMed1981

Atlas of cancer mortality in the People's Republic of China. An aid for cancer control and research.

A set of maps which display the patterns of cancer mortality in China has been prepared and published by the China Map Press. The 200 page atlas was edited by the National Cancer Control Office of the Ministry of Health and the Nanjing Institute of Geography of the Chinese Academy of Sciences on the basis of a nation-wide cancer mortality survey. The Cancer Institute of the Chinese Academy of Medical Sciences with related Colleges, Universities and Institutes provided the data and took part in the preparation of the atlas, which is published both in Chinese and English. 58 maps and several dozen charts depict, in seven colours, the mortality distribution in this 2392 countries and county-level administrative units of 9 types of cancer common in China--stomach, oesophagus, liver, cervix, lung, colon and rectum, breast, nasopharynx, and leukaemia as well as 5 less common cancers--brain tumours, malignant lymphoma, cancer of the bladder, of the penis, and choriocarcinoma. The Atlas of Cancer Mortality will be an important new aid for cancer control and research in the People's Republic of China.

Adolescent↗
PubMed1994

Use of a computerized brain atlas in magnetoencephalographic activation studies.

A pilot study was carried out to test the feasibility of an adjustable computerized brain atlas, adapted to the individual anatomy for localizing current dipoles by means of magnetoencephalography (MEG). The atlas can be adapted to individual computed tomography (CT) or magnetic resonance (MR) images. Position information is transferred between these imaging methods and MEG using a stereotactic technique. For this purpose, a special non-magnetic helmet was designed to be used together with the ordinary head fixation system. It seems likely that the proposed combination of the brain atlas with MEG, CT and MRI methods will become a powerful tool in exploring different brain functions.

Anatomy, Artistic↗
PubMedDate not supplied

Automatic atlas-based volume estimation of human brain regions from MR images.

OBJECTIVE: MRI offers many opportunities for noninvasive in vivo measurement of structure-function relationships in the human brain. Although automated methods are now available for whole-brain measurements, an efficient and valid automatic method for volume estimation of subregions such as the frontal or temporal lobes is still needed. MATERIALS AND METHODS: We adapted the Talairach atlas to the study of brain subregions. We supplemented the atlas with additional boxes to include the cerebellum. We assigned all the boxes to 1 of 12 regions of interest (ROIs) (frontal, parietal, temporal, and occipital lobes, cerebellum, and subcortical regions on right and left sides of the brain). Using T1-weighted MR scans collected with an SPGR sequence (slice thickness = 1.5 mm), we manually traced these ROIs and produced volume estimates. We then transformed the scans into Talairach space and compared the volumes produced by the two methods ("traced" versus "automatic"). The traced measurements were considered to be the "gold standard" against which the automatic measurements were compared. RESULTS: The automatic method was found to produce measurements that were nearly identical to the traced method. We compared absolute measurements of volume produced by the two methods, as well as the sensitivity and specificity of the automatic method. We also compared the measurements of cerebral blood flow obtained through [15O]H2O PET studies in a sample of nine subjects. Absolute measurements of volume produced by the two methods were very similar, and the sensitivity and specificity of the automatic method were found to be high for all regions. The flow values were also found to be very similar by both methods. CONCLUSION: The automatic atlas-based method for measuring the volume of brain subregions produces results that are similar to manual techniques. The method is rapid, efficient, unbiased, and not subject to the problems of rater drift or potentially poor interrater reliability that plague manual methods. Consequently, this method may be very useful for the study of structure-function relationships in the human brain.

Anatomy, Artistic↗
PubMed2004

The Atlas genome assembly system.

Atlas is a suite of programs developed for assembly of genomes by a "combined approach" that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for dealing with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This "sequence-based" growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects.

Animals↗
PubMed2006

Atlas-driven lung lobe segmentation in volumetric X-ray CT images.

High-resolution X-ray computed tomography (CT) imaging is routinely used for clinical pulmonary applications. Since lung function varies regionally and because pulmonary disease is usually not uniformly distributed in the lungs, it is useful to study the lungs on a lobe-by-lobe basis. Thus, it is important to segment not only the lungs, but the lobar fissures as well. In this paper, we demonstrate the use of an anatomic pulmonary atlas, encoded with a priori information on the pulmonary anatomy, to automatically segment the oblique lobar fissures. Sixteen volumetric CT scans from 16 subjects are used to construct the pulmonary atlas. A ridgeness measure is applied to the original CT images to enhance the fissure contrast. Fissure detection is accomplished in two stages: an initial fissure search and a final fissure search. A fuzzy reasoning system is used in the fissure search to analyze information from three sources: the image intensity, an anatomic smoothness constraint, and the atlas-based search initialization. Our method has been tested on 22 volumetric thin-slice CT scans from 12 subjects, and the results are compared to manual tracings. Averaged across all 22 data sets, the RMS error between the automatically segmented and manually segmented fissures is 1.96 +/- 0.71 mm and the mean of the similarity indices between the manually defined and computer-defined lobe regions is 0.988. The results indicate a strong agreement between the automatic and manual lobe segmentations.

Algorithms↗
PubMed2005

Hypertext atlas of dermatopathology with expert system for epithelial tumors of the skin.

BACKGROUND: Image resolution required for reference histological images is high. Obtaining high-resolution images requires a system, composing large image from individual smaller components. Such systems must thus be capable of automatically taking individual image parts, performing shading compensation and fusion of the image parts into one large image. Distribution of such images over the Internet requires developing a suitable user's interface with access to the image details. METHODS: The ways of creating high-resolution images (virtual slides) and the interface enabling access to image details using Internet browser are described. RESULTS: A collection of about 3200 dermatopathological, mostly histologic images is available at http://www.muni.cz/atlases: Hypertext atlas of dermatopathology. Methods of high-resolution image acquisition were used in digitizing the collection of skin lymphomas (Dermatology Institute, University Hospital, Zurich), which is a part of the atlas. The atlas is continuously maintained and upgraded; the number of contributors is growing.

Dermatology↗
PubMedDate not supplied

A four-dimensional probabilistic atlas of the human brain.

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype- phenotype-behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders.

Adolescent↗
PubMedDate not supplied

The visible man: three-dimensional interactive musculoskeletal anatomic atlas of the lower extremity.

A personal computer-based interactive musculoskeletal anatomic atlas of the lower extremity has been created by using the Visible Human Male data set. A semiautomatic segmentation program was developed by using an intelligent scissors approach and shape-based interpolation, thus considerably reducing the laborious work of the segmentation and labeling process. Manual contour extractions at 3-mm section intervals and shape-based interpolations of intervening sections of the musculoskeletal structures of the lower extremity were performed. For interactive and realistic three-dimensional display, an efficient binary volume rendering method was developed that introduces the concept of shear-warp factorization and applies a newly developed normal calculation technique. Binary volume rendering reconstructs various structures from a series of two-dimensional sections in a few seconds, thus enabling real-time manipulations of the computerized atlas. All of the muscles, tendons, and bones of the lower extremity have been segmented and labeled. The volume-based three-dimensional interactive atlas supports various interactions including rotation, removal, highlighting with artificial colors, arbitrary cutting operation, transparent view, and descriptive knowledge representation. In addition, browsing through the two-dimensional images of transverse, coronal, and sagittal views with labeling and segmentation information is possible.

Anatomy, Cross-Sectional↗
PubMedDate not supplied

Nerves of the thorax: atlas of normal and pathologic findings.

An anatomic and imaging atlas was created to provide detailed information about the six pairs of thoracic nerves (phrenic nerves, vagus nerves, recurrent laryngeal nerves, sympathetic trunks, costal nerves, long thoracic nerves). Serial axial computed tomographic (CT) scans of the normal thorax were obtained and included in the atlas, along with drawings showing the proper location of each nerve relative to adjacent anatomic structures. CT scans obtained in both symptomatic and asymptomatic patients with various thoracic diseases were paired with appropriate drawings and normal CT scans in the atlas. This format was designed to help determine the presence and severity of related disease, including injury from surgery, trauma, or penetrating injury, metastatic disease involvement, and, rarely, primary tumor. Although the nerves of the thorax are rarely identified at cross-sectional imaging, their location can be inferred by localizing easily identified anatomic landmarks. Familiarity with the functional anatomy and clinical significance of the nerves of the thorax is important for the correct interpretation of thoracic images.

Cadaver↗
PubMed2006

Direct anatomical localization of the subthalamic nucleus on CT with comparison to Schaltenbrand-Wahren atlas.

Stimulation of the subthalamic nucleus (STN) has become an accepted treatment for motor symptoms of Parkinson's disease. Generally, localization of the target is based on stereotactic atlas coordinates and magnetic resonance (MR) images. In this paper a method of direct anatomical localization of the STN on computed tomography (CT) images is described and compared with the Schaltenbrand-Wahren atlas. Serial CT scans were obtained at 1.5-mm interval and scan thickness of 3 mm, with the CT gantry and glabella-inion plane of the patient's head vertical. The STN was identified as a dense structure medial to the inner semicircular border of the internal capsule in the subthalamic region. Its visibility was increased by changing the window and level settings on the CT workstation computer. The center of the STN in relationship to the intercommissural line, determined by this technique, was similar to those found on standard atlases.

Adult↗