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At least 289 records · Page 16Linked to original sources
PubMed2005

Consequences of large interindividual variability for human brain atlases: converging macroscopical imaging and microscopical neuroanatomy.

In human brain imaging studies, it is common practice to use the Talairach stereotaxic reference system for signifying the convergence of brain function and structure. In nearly all neuroimaging reports, the studied cortical areas are specified further with a Brodmann Area (BA) number. This specification is based upon macroscopic extrapolation from Brodmann's projection maps into the Talairach atlas rather than upon a real microscopic cytoarchitectonic study. In this review we argue that such a specification of Brodmann area(s) via the Talairach atlas is not appropriate. Cytoarchitectonic studies reviewed in this paper show large interindividual differences in 3-D location of primary sensory cortical areas (visual cortex) as well as heteromodal associational areas (prefrontal cortical areas), even after correction for differences in brain size and shape. Thus, the simple use of Brodmann cortical areas derived from the Talairach atlas can lead to erroneous results in the specification of pertinent BA. This in turn can further lead to wrong hypotheses on brain system(s) involved in normal functions or in specific brain disorders. In addition, we will briefly discuss the different 'Brodmann' nomenclatures which are in use for the cerebral cortex.

Adult↗
PubMed1999

A digital three-dimensional atlas of the honeybee antennal lobe based on optical sections acquired by confocal microscopy.

We present a digital atlas of the glomeruli in the antennal lobe of the honeybee, Apis mellifera, accessible to the scientific community via the Internet. The atlas allows the identification of glomeruli in preparations in which the glomeruli can be recognized, be it in sections or in whole-mounts. The high resolution of the anatomical data upon which the atlas is based and its electronic form should prove to be an important tool for anyone involved in the study of the honeybee antennal lobe. Its accessibility via the Internet is a step towards interactive and freely accessible databases of animal brains.

Animals↗
PubMedDate not supplied

An atlas of the deep cerebellar nuclei and subtentorial brainstem of the cat with compensation for skull-size.

The bony tentorium in the cat precludes a stereotaxic approach, in the coronal plane, to widespread areas of the cerebellum and underlying brainstem. To facilitate the application of the stereotaxic method in these areas, an atlas of the subtentorial brainstem was prepared, with plates (30 degrees from the vertical) based on an angle of entry which avoids the tentorium. In addition, a placement error regression function, based on a measure of skull size, was derived to provide atlas coordinate corrections for different brain sizes. The application of this regression function, together with the present atlas plates, can greatly increase placement accuracy.

Animals↗
PubMed2006

Dense deformation field estimation for atlas-based segmentation of pathological MR brain images.

Atlas registration is a recognized paradigm for the automatic segmentation of normal MR brain images. Unfortunately, atlas-based segmentation has been of limited use in presence of large space-occupying lesions. In fact, brain deformations induced by such lesions are added to normal anatomical variability and they may dramatically shift and deform anatomically or functionally important brain structures. In this work, we chose to focus on the problem of inter-subject registration of MR images with large tumors, inducing a significant shift of surrounding anatomical structures. First, a brief survey of the existing methods that have been proposed to deal with this problem is presented. This introduces the discussion about the requirements and desirable properties that we consider necessary to be fulfilled by a registration method in this context: To have a dense and smooth deformation field and a model of lesion growth, to model different deformability for some structures, to introduce more prior knowledge, and to use voxel-based features with a similarity measure robust to intensity differences. In a second part of this work, we propose a new approach that overcomes some of the main limitations of the existing techniques while complying with most of the desired requirements above. Our algorithm combines the mathematical framework for computing a variational flow proposed by Hermosillo et al. [G. Hermosillo, C. Chefd'Hotel, O. Faugeras, A variational approach to multi-modal image matching, Tech. Rep., INRIA (February 2001).] with the radial lesion growth pattern presented by Bach et al. [M. Bach Cuadra, C. Pollo, A. Bardera, O. Cuisenaire, J.-G. Villemure, J.-Ph. Thiran, Atlas-based segmentation of pathological MR brain images using a model of lesion growth, IEEE Trans. Med. Imag. 23 (10) (2004) 1301-1314.]. Results on patients with a meningioma are visually assessed and compared to those obtained with the most similar method from the state-of-the-art.

Brain↗
PubMed2005

An atlas of the inferior colliculus of the gerbil in three dimensions.

An atlas of the inferior colliculus of the gerbil is presented in three dimensions. Sections were cut in the transverse (coronal), horizontal or saggital planes and fit to a common cartesian coordinate grid. The sections used for the atlas were reacted for cytochrome oxidase activity, a functional marker that can be used to distinguish different areas in the brainstem. The atlas can be used for representation, comparison and correlation of neuroanatomical, neurophysiological, neurochemical and other data that can be spatially mapped in the inferior colliculus.

Animals↗
PubMed2004

Optimized prostate biopsy via a statistical atlas of cancer spatial distribution.

A methodology is presented for constructing a statistical atlas of spatial distribution of prostate cancer from a large patient cohort, and it is used for optimizing needle biopsy. An adaptive-focus deformable model is used for the spatial normalization and registration of 100 prostate histological samples, which were provided by the Center for Prostate Disease Research of the US Department of Defense, resulting in a statistical atlas of spatial distribution of prostate cancer. Based on this atlas, a statistical predictive model was developed to optimize the needle biopsy sites, by maximizing the probability of detecting cancer. Experimental results using cross-validation show that the proposed method can detect cancer with a 99% success rate using seven needles, in these samples.

Algorithms↗
PubMed2005

Atlas-guided non-uniform attenuation correction in cerebral 3D PET imaging.

Photon attenuation in tissues is the primary physical degrading factor limiting both visual qualitative interpretation and quantitative analysis capabilities of reconstructed Positron Emission Tomography (PET) images. This study investigates the implementation and applicability of transmission atlas-guided attenuation correction in cerebral 3D PET imaging, thus eliminating the need for acquisition of a measured transmission scan. Patient-specific attenuation map is derived by anatomic standardization through nonlinear warping of a stereotactic transmission template obtained by averaging 11 scans of normal subjects. This template is coregistered to a specially designed tracer-specific 18F-[FDG] template constructed by scanning 17 normal subjects in resting condition during tracer uptake in a dark room. This emission template is first coregistered and spatially normalized to preliminary PET images of subjects corrected for scatter and attenuation using an approximate calculated method. The resulting transformation matrices are recorded and re-applied to the transmission template. The derived attenuation map is then forward projected to generate attenuation correction factors to be used for correcting the subjects' PET data. Twelve cerebral clinical studies are used for evaluation of the developed attenuation correction technique as compared to the standard pre-injection measured transmission-based method used in clinical routine. Statistical Parametric Mapping (SPM2) analysis is used to assess significant differences between images obtained using both techniques. The subjective qualitative assessment shows no significant visual differences between atlas-guided and transmission-based attenuation correction methods. However, the quantitative voxel-based analysis comparing atlas-guided to transmission-based attenuation corrections suggest that regional brain metabolic activity increases significantly bilaterally in the superior frontal and precentral gyri, in addition to the left middle temporal gyrus and the left frontal lobe. Conversely, activity decreases in the corpus callosum in the left parasagittal region. A new non-uniform attenuation correction method is thus proposed, which is suitable for both research and clinical routine applications in 3D brain PET imaging on a transmissionless PET scanner or when a patient-specific transmission scan is not available.

Aged↗
PubMed2005

Probabilistic 3D MRI atlas of the human cerebellar dentate/interposed nuclei.

In a previous study, a three-dimensional (3D) MRI atlas of the human cerebellar nuclei was introduced based on findings in one healthy human subject [Dimitrova, A., Weber, J., Redies, C., Kindsvater, K., Maschke, M., Kolb, F.P., Forsting, M., Diener, H.C., Timmann, D., 2002. MRI atlas of the human cerebellar nuclei. NeuroImage 17, 240-255]. The present MRI investigation was designed to study variability of the anatomy of the dentate/interposed nuclei in a larger group of healthy subjects. Similar to our previous study, iron-induced susceptibility artifacts were used to visualize the cerebellar nuclei as hypointensities on MR images. Data of 63 healthy subjects (27 female, 36 male; mean age 45.3+/-13.4 years, age range 22--71 years) were included. A 3D axial volume of the cerebellum was acquired using a T2*-weighted FLASH sequence on a Siemens Sonata 1.5 T MR scanner. Each volume was registered, re-sampled to 1.00 x 1.00 x 1.00 mm(3) voxel size and spatially normalized into a standard proportional stereotaxic space using SPM99. Dentate/interposed nuclei were traced on axial images and saved as regions of interest using MRIcro-software by two independent examiners. A probabilistic 3D MRI atlas of the cerebellar dentate/interposed nuclei is presented based on findings in all subjects.

Adolescent↗
PubMed2006

Development of a high resolution three-dimensional surgical atlas of the murine head for strains 129S1/SvImJ and C57Bl/6J using magnetic resonance imaging and micro-computed tomography.

The mouse has emerged as a major experimental model system for examining the functional properties of the mammalian CNS; both during development and following CNS injury. Histologic procedures currently used to determine the relative position of structures within the CNS are presently limited in their ability to take full advantage of this system for surgical and morphometric procedures. We present here the first three-dimensional interactive digital atlas of the murine brain and skull for two genetically important strains of mice; 129S1/SvImJ and C57Bl/6J. The final resolution of these digital atlases is 54 micro m(3). These representations of the murine brain and skull, in conjunction with our development of a new, more dynamic master coordinate system, provide improved accuracy with respect to targeting CNS structures during surgery compared with previous systems. The interactive three-dimensional nature of these atlases also provide users with stereotactic information necessary to perform accurate "off-axis" surgical procedures, as is commonly required for experiments such as in vivo micro-electroporation. In addition, three-dimensional analysis of the brain and skull shape in C57Bl, 129Sv, CD1, and additional murine strains, suggests that a stereotactic coordinate system based upon the lambda and rostral confluence of the sinuses at the sagittal midline, provides improved accuracy compared with the traditional lambda-bregma landmark system. These findings demonstrate the utility of developing highly accurate and robust three-dimensional representations of the murine brain and skull, in which experimental outputs can be directly compared using a unified coordinate system. The aim of these studies is to enhance comparative morphometric analyses and stereotactic surgical procedures in mice.

Animals↗
PubMed2000

Simulation of cardiac excitation patterns in a three-dimensional anatomical heart atlas.

Computerized anatomical atlas systems enable interactive investigation of digital body models. Here we present a three-dimensional atlas of the human heart, based on image data provided in the Visible Human Project. This heart atlas consists of multiple kinds of cardiac tissues and offers unlimited possibilities for its visual exploration. A temporal dimension is added to the underlying heart model by simulation of cardiac excitation spreading. For this purpose a second generation cellular automata algorithm is adapted to the excitation kinetics of cardiac tissue. The presented system is shown as a successful method for the visualization-based investigation of cardiac excitation.

Algorithms↗
PubMed1998

A web-accessible digital atlas of the distribution of nitric oxide synthase in the mouse brain.

We have produced a digital atlas of the distribution of nitric oxide synthase (NOS) in the mouse brain as a reference source for our studies on the roles of nitric oxide in brain development and plasticity. NOS was labeled using nicotinamide adenine dinucleotide phosphate diaphorase (NADPHd) histochemistry. In addition, choline acetyltransferase (ChAT) immunocytochemistry was used to identify cholinergic cells because many of the NADPHd positive cells were thought to colocalize acetylcholine. Some sections were also labeled with antibodies to either the neuronal (nNOS) or endothelial (eNOS) isoforms of NOS. Series of sections from 11 C57/BL6 mice were collected and labeled for NADPHd and/or ChAT. We collected two types of data from this material: color digital photographs illustrating the density of cell and fiber labeling, and computer/microscope plots of the locations of all the labeled cells in selected sections. The data can be viewed as either a series of single-section maps produced by combining the plots with the digital images, or as 3-D views derived from the cell plots. The atlas of labeled cell maps, together with selected color photographs and 3-D views, is available for viewing via the World Wide Web (http:@nadph.anatomy.lsumc.edu). Examination of the atlas data has revealed several points about the distribution of NOS throughout the mouse brain. Firstly, different populations of NADPHd-positive neurons can be distinguished by different patterns of staining. In some brain areas neurons are intensely stained by the NADPHd technique where label fills the cell bodies and much of the dendritic trees. In other brain regions labeling is much lighter, is principally confined to the cytoplasm of the cell soma, and extends only a short distance within proximal dendrites. Intense labeling is typical of neurons in the caudate/putamen and mesopontine tegmental nuclei. Most of the labeled neurons in the cortex also stain this way. Lighter, "granular" label is found in many other nuclei, including the medial septum, hippocampus, and cerebellum. In addition to staining pattern, we have also noted that different subpopulations of NOS-neurons can be distinguished on the basis of colocalization with ChAT. Substantial overlap of the distributions of these two substances was observed although very little colocalization was found in most cholinergic cell groups except the mesopontine tegmental nuclei. Other points of interest arising from this project include the apparent lack of NADPHd labeling in the CA1 pyramidal cells of the hippocampus or the Purkinje neurons in the cerebellum. This observation is especially relevant given that synaptic plasticity in these regions is reported to be nitric-oxide dependent.

Animals↗
PubMed1998

Stereotaxic atlas of the telencephalon of the weakly electric fish Gymnotus carapo.

A restraining box for the head and body of the electric fish Gymnotus carapo was constructed and coupled to a micromanipulator, permitting us to prepare an atlas of the telencephalon with stereotaxic parameters. A photograph and a schematic drawing of an animal's head is presented, showing two skin electroreceptors that were used as external landmarks. A sagittal section of the telencephalic structure is also presented, whose vertical bars indicate the frontal planes that compose the atlas. The frontal planes of the atlas consist of serial sections spaced 600 or 500 microns apart in the rostrocaudal axis. Sections mapped with acetylcholinesterase are shown, intercalated with Nissl-stained sections. The acetylcholinesterase sections proved to be useful for the delimitation of certain nuclei and for the exact localization of small fissures and fiber tracts. A brief description of major cytoarchitectural subdivision and connections of the telencephalon is provided.

Acetylcholinesterase↗
PubMed2004

Design and implementation of software for assembly and browsing of 3D brain atlases.

Visualization software for three dimensional digital brain atlases present many challenges in design and implementation. These challenges include the design of an effective human interface, management of large data sets, display speed when slicing the data set for viewing/browsing, and the display of delineated volumes of interest (VOI). We present a software design, implementation and storage architecture that addresses these issues, allowing the user to navigate through a reconstructed volume quickly and smoothly, with an easy-to-use human interface. The software (macostat, for use with Macintosh OS) allows the user to rapidly display slices of the digital atlas at any arbitrary slicing angle, complete with delineated VOIs. The VOIs can be assigned colors of the user's choosing. The entire atlas, or selected portions, may be resliced with slices stored as individual image files, complete with delineations. These delineations may be transferred to corresponding sections of experimental materials using our analysis program (brain). The software may be obtained from the laboratory's web site: http://www.neuroterrain.org

Brain↗
PubMed1981

Horizontal stereotaxic atlas of the albino rat brain.

An atlas of the albino rat brain was prepared in the horizontal plane, extending from the olfactory bulbs through the hind brain. It was drawn to the scale of König and Klippel's rat brain atlas so as to be used in conjunction with their atlas. Corresponding histological sections were also prepared.

Animals↗
PubMedDate not supplied

Computerized brain atlases as decision support systems: a methodological approach.

This paper deals with the development of computerized brain atlases addressing both research and clinical needs. The authors analyze in detail the potential of these systems and discuss the capabilities and limitations of the digital atlases currently being developed around the world. The authors propose to reconsider the concept of a brain atlas, regarding both its content, and the way it has to be used and managed in order to set up more effective cooperation between the user and the system. Particular emphasis is placed on extensibility and reuse issues. which are critical in this rapidly evolving field. These orientations result from both the authors' experience and the analysis of current trends in the field of neuroimaging. The general methodology is illustrated with examples related to computer aided surgical planning.

Artificial Intelligence↗
PubMed2002

A transcriptome atlas of the mouse brain at cellular resolution.

A genome-wide expression atlas of the nervous system at cellular resolution would be a valuable resource for neurobiology, genetics, developmental biology and medicine. Progress in automation of in situ hybridization makes such an atlas possible. Standardized and computerized annotation of expression patterns will be critical for producing a searchable atlas database that can be accessed through the internet.

Animals↗
PubMed2002

Windows on the brain: the emerging role of atlases and databases in neuroscience.

Brain atlases and associated databases have great potential as gateways for navigating, accessing, and visualizing a wide range of neuroscientific data. Recent progress towards realizing this potential includes the establishment of probabilistic atlases, surface-based atlases and associated databases, combined with improvements in visualization capabilities and internet access.

Animals↗
PubMed2003

Characterizing volume and surface deformations in an atlas framework: theory, applications, and implementation.

Given deformations for mapping images or surfaces into an atlas configuration, methods are described for characterizing the mean deformation and deviations from this mean. Jacobian matrices are used to characterize the deformations locally, and the method can be applied to any image warping method for which Jacobian matrices can be computed. The method makes use of the fact that each matrix descriptor of the local deformation required to match an image to the atlas corresponds to a point on a semi-Riemannian manifold. By assuring that the mean matrix lies within this manifold, fundamental geometric properties common to all of the images can be preserved. Local deviations from the mean can be characterized in a euclidean space tangent to the semi-Riemannian manifold at the mean and can be accumulated globally across multiple sampling locations within the atlas to generate a global multivariate characterization of how each image deviates from the mean.

Algorithms↗