The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Claudio V. Mello - One of the best experts on this subject based on the ideXlab platform.

  • ZEBrA: Zebra finch Expression Brain Atlas-A resource for comparative molecular neuroanatomy and Brain evolution studies.
    Journal of Comparative Neurology, 2020
    Co-Authors: Peter V. Lovell, Morgan Wirthlin, Taylor Kaser, Alexa A. Buckner, Julia B. Carleton, Brian R. Snider, Anne Mchugh, Alexander Tolpygo, Partha P. Mitra, Claudio V. Mello
    Abstract:

    An in-depth understanding of the genetics and evolution of Brain function and behavior requires detailed mapping of gene expression in functional Brain circuits across major vertebrate clades. Here we present the Zebra finch Expression Brain Atlas (ZEBrA; www.zebrafinchAtlas.org, RRID: SCR_012988), a web-based resource that maps the expression of genes linked to a broad range of functions onto the Brain of zebra finches. ZEBrA is a first of its kind gene expression Brain Atlas for a bird species, and a first for any sauropsid. ZEBrA's >3,200 high-resolution digital images of in situ hybridized sections for ~650 genes (as of June, 2019) are presented in alignment with an annotated histological Atlas and can be browsed down to cellular resolution. An extensive relational database connects expression patterns to information about gene function, mouse expression patterns and phenotypes, and gene involvement in human diseases and communication disorders. By enabling Brain-wide gene expression assessments in a bird, ZEBrA provides important substrates for comparative neuroanatomy and molecular Brain evolution studies. ZEBrA also provides unique opportunities for linking genetic pathways to vocal learning and motor control circuits, as well as for novel insights into the molecular basis of sex steroids actions, Brain dimorphisms, reproductive and social behaviors, sleep function, and adult neurogenesis, among other fundamental themes. This article is protected by copyright. All rights reserved.

Keigo Hikishima - One of the best experts on this subject based on the ideXlab platform.

  • population averaged standard template Brain Atlas for the common marmoset callithrix jacchus
    NeuroImage, 2011
    Co-Authors: Keigo Hikishima, M M Quallo, Yuki Komaki, Masayuki Yamada, Kenji Kawai, Suketaka Momoshima, Hirotaka James Okano
    Abstract:

    Abstract Advanced magnetic resonance (MR) neuroimaging analysis techniques based on voxel-wise statistics, such as voxel-based morphometry (VBM) and functional MRI, are widely applied to cognitive Brain research in both human subjects and in non-human primates. Recent developments in imaging have enabled the evaluation of smaller animal models with sufficient spatial resolution. The common marmoset (Callithrix jacchus), a small New World primate species, has been widely used in neuroscience research, to which voxel-wise statistics could be extended with a species-specific Brain template. Here, we report, for the first time, a tissue-segmented, population-averaged standard template of the common marmoset Brain. This template was created by using anatomical T1-weighted images from 22 adult marmosets with a high-resolution isotropic voxel size of (0.2 mm)3 at 7-Tesla and DARTEL algorithm in SPM8. Whole Brain templates are available at International Neuroinformatics Japan Node website, http://BrainAtlas.Brain.riken.jp/marmoset/ .

Louis D Collins - One of the best experts on this subject based on the ideXlab platform.

  • Reviewed by:
    2015
    Co-Authors: Citation Nitzsche, Louis D Collins, Stephen Frey, Donald Lobsien, Antje Dreyer, Holger Kirsten, H. Stoffel, Vladimir S. Fonov, Johannes Boltze “a, Citable Link
    Abstract:

    A stereotaxic, population-averaged T1w ovine Brain Atlas including cerebral morphology and tissue volumes (Article begins on next page) The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

  • the creation of a Brain Atlas for image guided neurosurgery using serial histological data
    NeuroImage, 2006
    Co-Authors: Mallar M Chakravarty, Gilles Bertrand, Charles P Hodge, Abbas F Sadikot, Louis D Collins
    Abstract:

    Abstract Digital and print Brain Atlases have been used with success to help in the planning of neurosurgical interventions. In this paper, a technique presented for the creation of a Brain Atlas of the basal ganglia and the thalamus derived from serial histological data. Photographs of coronal histological sections were digitized and anatomical structures were manually segmented. A slice-to-slice nonlinear registration technique was used to correct for spatial distortions introduced into the histological data set at the time of acquisition. Since the histological data were acquired without any anatomical reference (e.g., block-face imaging, post-mortem MRI), this registration technique was optimized to use an error metric which calculates a nonlinear transformation minimizing the mean distance between the segmented contours between adjacent pairs of slices in the data set. A voxel-by-voxel intensity correction field was also estimated for each slice to correct for lighting and staining inhomogeneity. The reconstructed three-dimensional (3D) histological volume can be viewed in transverse and sagittal directions in addition to the original coronal. Nonlinear transformations used to correct for spatial distortions of the histological data were applied to the segmented structure contours. These contours were then tessellated to create three-dimensional geometric objects representing the different anatomic regions in register with the histological volumes. This yields two alternate representations (one histological and one geometric) of the Atlas. To register the Atlas to a standard reference MR volume created from the average of 27 T1-weighted MR volumes, a pseudo-MRI was created by setting the intensity of each anatomical region defined in the geometric Atlas to match the intensity of the corresponding region of the reference MR volume. This allowed the estimation of a 3D nonlinear transformation using a correlation based registration scheme to fit the Atlas to the reference MRI. The result of this procedure is a contiguous 3D histological volume, a set of 3D objects defining the basal ganglia and thalamus, both of which are registered to a standard MRI data set, for use for neurosurgical planning.

  • the creation of a Brain Atlas for image guided neurosurgery using serial histological data
    NeuroImage, 2006
    Co-Authors: Mallar M Chakravarty, Gilles Bertrand, Charles P Hodge, Abbas F Sadikot, Louis D Collins
    Abstract:

    Digital Atlases of the human Brain can help in the specific localization of structures of surgical relevance and interest in Image Guided Neurosurgery (IGNS). This paper outlines one of the steps in the creation of a digital Atlas intended for IGNS, using histological data. The acquisition of histological data can include artefacts such as tearing, shearing, stretching, shrinking, as well as inhomogeneous staining leading to structural inhomogeneities. These inconsistencies are reduced using a non-linear intensity based registration procedure where deformations are defined using a maximized correlation coefficient estimate. The intensity artefacts brought about by inhomogeneous staining are reduced by applying a slice to slice intensity inhomogeneity correction by modelling the intensity mapping between slices as a third order polynomial that is estimated with a Least Trimmed Squared fit. The lateral ventricle was then segmented and to demonstrate increased smoothing along its surface.

Rolf Kotter - One of the best experts on this subject based on the ideXlab platform.

  • the scalable Brain Atlas instant web based access to public Brain Atlases and related content
    Neuroinformatics, 2015
    Co-Authors: Rembrandt Bakker, Paul H E Tiesinga, Rolf Kotter
    Abstract:

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of Brain Atlas templates for different species. Its main component is an Atlas viewer that displays Brain Atlas data as a stack of slices in which stereotaxic coordinates and Brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 Atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of Brain regions. The ambition of SBA is to provide a unified representation of all publicly available Brain Atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in Atlas comparisons, searches, coordinate transformations and interactive displays. Electronic supplementary material The online version of this article (doi:10.1007/s12021-014-9258-x) contains supplementary material, which is available to authorized users.

  • SOFTWARE ORIGINAL ARTICLE The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases
    2015
    Co-Authors: Related Content, Paul H E Tiesinga, T Bakker, Rolf Kotter
    Abstract:

    # The Author(s) 2015. This article is published with open access at Springerlink.com Abstract The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of Brain Atlas templates for different species. Its main compo-nent is an Atlas viewer that displays Brain Atlas data as a stack of slices in which stereotaxic coordinates and Brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 Atlas templates in six species, and plugins to com-pute coordinate transformations, display anatomical connec-tivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of Brain regions. The am-bition of SBA is to provide a unified representation of all publicly available Brain Atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in Atlas comparisons, searches, coordinate transfor-mations and interactive displays

  • the scalable Brain Atlas instant web based access to public Brain Atlases and related content
    arXiv: Neurons and Cognition, 2013
    Co-Authors: Rembrandt Bakker, Paul H E Tiesinga, Rolf Kotter
    Abstract:

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of Brain Atlas templates for different species. Its main component is an Atlas viewer that displays Brain Atlas data as a stack of slices in which stereotaxic coordinates and Brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 Atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of Brain regions. The ambition of SBA is to provide a unified representation of all publicly available Brain Atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in Atlas comparisons, searches, coordinate transformations and interactive displays.

Yasuhisa Nakamura - One of the best experts on this subject based on the ideXlab platform.

  • web accessible digital Brain Atlas of the common marmoset callithrix jacchus
    Neuroscience Research, 2009
    Co-Authors: Hironobu Tokuno, Yoshitomo Umitsu, Ikuko Tanaka, Toshikazu Akazawa, Yasuhisa Nakamura
    Abstract:

    Here we describe a web-accessible digital Brain Atlas of the common marmoset (Callithrix jacchus) at http://marmoset-Brain.org:2008. We prepared the histological sections of the marmoset Brain using various staining techniques. For virtual microscopy, high-resolution digital images of sections were obtained with Aperio Scanscope. The digital images were then converted to Zoomify files (zoomable multiresolution image files). Thereby, we could provide the multiresolution images of the marmoset Brains for fast interactive viewing on the web via the Internet. In addition, we describe an automated method to obtain drawings of Nissl-stained sections.