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At least 109 records · Page 6Linked to original sources
PubMed2003

EMAP and EMAGE: a framework for understanding spatially organized data.

The Edinburgh MouseAtlas Project (EMAP) is a time-series of mouse-embryo volumetric models. The models provide a context-free spatial framework onto which structural interpretations and experimental data can be mapped. This enables collation, comparison, and query of complex spatial patterns with respect to each other and with respect to known or hypothesized structure. The atlas also includes a time-dependent anatomical ontology and mapping between the ontology and the spatial models in the form of delineated anatomical regions or tissues. The models provide a natural, graphical context for browsing and visualizing complex data. The Edinburgh Mouse Atlas Gene-Expression Database (EMAGE) is one of the first applications of the EMAP framework and provides a spatially mapped gene-expression database with associated tools for data mapping, submission, and query. In this article, we describe the underlying principles of the Atlas and the gene-expression database, and provide a practical introduction to the use of the EMAP and EMAGE tools, including use of new techniques for whole body gene-expression data capture and mapping.

Animals↗
PubMed2003

The informatics of a C57BL/6J mouse brain atlas.

The Mouse Atlas Project (MAP) aims to produce a framework for organizing and analyzing the large volumes of neuroscientific data produced by the proliferation of genetically modified animals. Atlases provide an invaluable aid in understanding the impact of genetic manipulations by providing a standard for comparison. We use a digital atlas as the hub of an informatics network, correlating imaging data, such as structural imaging and histology, with text-based data, such as nomenclature, connections, and references. We generated brain volumes using magnetic resonance microscopy (MRM), classical histology, and immunohistochemistry, and registered them into a common and defined coordinate system. Specially designed viewers were developed in order to visualize multiple datasets simultaneously and to coordinate between textual and image data. Researchers can navigate through the brain interchangeably, in either a text-based or image-based representation that automatically updates information as they move. The atlas also allows the independent entry of other types of data, the facile retrieval of information, and the straight-forward display of images. In conjunction with centralized servers, image and text data can be kept current and can decrease the burden on individual researchers' computers. A comprehensive framework that encompasses many forms of information in the context of anatomic imaging holds tremendous promise for producing new insights. The atlas and associated tools can be found at http://www.loni.ucla.edu/MAP.

Anatomy, Artistic↗
PubMed2006

A hybrid approach to shape-based interpolation of stereotactic atlases of the human brain.

Stereotactic human brain atlases, either in print or electronic form, are useful not only in functional neurosurgery, but also in neuroradiology, human brain mapping, and neuroscience education. The existing atlases represent structures on 2D plates taken at variable, often large intervals, which limit their applications. To overcome this problem, we propose a hybrid interpolation approach to build high-resolution brain atlases from the existing ones. In this approach, all section regions of each object are grouped into two types of components: simple and complex. A NURBS-based method is designed for interpolation of the simple components, and a distance map-based method for the complex components. Once all individual objects in the atlas are interpolated, the results are combined hierarchically in a bottom-up manner to produce the interpolation of the entire atlas. In the procedure, different knowledge-based and heuristic strategies are used to preserve various topological relationships. The proposed approach has been validated quantitatively and used for interpolation of two stereotactic brain atlases: the Talairach-Tournoux atlas and Schaltenbrand-Wahren atlas. The interpolations produced are of high resolution and feature high accuracy, 3D consistency, smooth surface, and preserved topology. They potentially open new applications for electronic stereotactic brain atlases, such as atlas reformatting, accurate 3D display, and 3D nonlinear warping against normal and pathological scans. The proposed approach is also potentially useful in other applications, which require interpolation and 3D modeling from sparse and/or variable intersection interval data. An example of 3D modeling of an infarct from MR diffusion images is presented.

Algorithms↗
PubMed2006

Investments in cancer genomics: who benefits and who decides.

The Cancer Genome Atlas--formerly the Human Cancer Genome Project--provides an opportunity for considering how social concerns about resource allocation are interrelated with practical decisions about specific research strategies--part of a continuing convergence between scientific and public evaluations of priorities for biomedical research funding. For example, the manner, order, and extent that The Cancer Genome Atlas selects tumor types and populations to be sampled will determine who benefits most from its findings. Those choices will be determined on the basis of both scientific and social values. By soliciting public involvement and conducting rigorous policy analysis in the design of large scientific projects such as The Cancer Genome Atlas, cancer researchers can help democratize the allocation of scientific resources and foster public confidence in biomedical research.

Atlases as Topic↗
PubMed1997

Healthcare practices vary widely from town to town: regional Dartmouth Atlas.

Healthcare practices in neighboring towns vary as much as 33-fold, according to the Dartmouth Atlas of Health Care analysis of claims and census data. Still unknown is the effect that this variation has on outcomes. The new regional version of the atlas makes it possible to compare care at the local community level and decide what to do about it.

Atlases as Topic↗
PubMed1997

The BRAIN project: an interactive learning tool using desktop virtual reality on personal computers.

The BRAIN-project is an endeavor in using computer aided learning to improve the understanding of the human brain anatomy. The project consists of four parts, each based on modular packages: BRAINIMAGES: Brain atlas consisting of horizontal and frontal brain slices spaced I mm apart enabling the identification of structures and areas of the brain. The software also contains views of the brain's outer surface with all pertinent structures marked. BRAINRADIOLOGY: Visualisation of the brain using CT, MRI and angiography. The different imaging techniques enable the user to explore the brain from several angles and also view the major blood vessels of the brain. NEUROHISTOLOGY: Cells of the brain using histologically stained sections. The program emphasizes the organization of cells in layers and the interaction of different cell types. 3D-BRAIN: Three dimensional reconstructions based on physical slices of a human brain. The reconstructed brain views are made interactive using a simple form of desktop virtual reality: QuickTime VR technology. The user can rotate the different views in all directions producing a 3D effect. The different views are designed to highlight important structures and their organization within the outlined (and semi transparent) brain surface. Contrary to similar applications, the actual three dimensional objects are not based on MRI or CT scans (with comparatively poor resolution), but on tracings made on high resolution images of photographs of actual sections of a postmortem brain. N.B., this approach produces 3D renderings in a more detailed and reliable way. The BRAIN project is designed as a support package for students in preclinical education by supplying additional means for gathering information pertinent to the curriculum. By cross linking, the students can switch from a three dimensional object to a corresponding slice, and then to the relevant histological sample and son on. The software components are based on a modular design enabling easy modification of the various parts and the entire project is designed to run on both Apple Macintosh and MS Windows based PCs.

Anatomy↗