title: Waxholm Space atlas of the Sprague Dawley rat brain.
abstract: Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces.
authors.affiliation: Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
authors.forename: Eszter A
authors.initials: EA
authors.lastname: Papp
authors.affiliation: Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
authors.forename: Trygve B
authors.initials: TB
authors.lastname: Leergaard
authors.affiliation: Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA.
authors.forename: Evan
authors.initials: E
authors.lastname: Calabrese
authors.affiliation: Center for In Vivo Microscopy, Department of Radiology, Duke University Medical Center, Durham, NC, USA.
authors.forename: G Allan
authors.initials: GA
authors.lastname: Johnson
authors.affiliation: Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway. Electronic address: j.g.bjaalie@medisin.uio.no.
authors.forename: Jan G
authors.initials: JG
authors.lastname: Bjaalie
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology*; D038524:Diffusion Magnetic Resonance Imaging; D066128:Gray Matter / Q000033:anatomy & histology; D007091:Image Processing, Computer-Assisted; D033181:Information Dissemination; D020407:Internet; D008297:Male; D051381:Rats; D017207:Rats, Sprague-Dawley / Q000033:anatomy & histology*; D013116:Spinal Cord / Q000033:anatomy & histology; D066127:White Matter / Q000033:anatomy & histology
keywords: Diffusion tensor imaging; Digital brain atlas; Magnetic resonance imaging; Neuroinformatics; Rat brain template; Segmentation; Sprague Dawley; Waxholm Space
references.citation: Hum Brain Mapp. 2013 Jun;34(6):1306-18
references.pmid: 22287270
references.citation: Neurotherapeutics. 2007 Jul;4(3):316-29
references.pmid: 17599699
references.citation: J Magn Reson Imaging. 2001 Apr;13(4):534-46
references.pmid: 11276097
references.citation: Neuroscience. 2009 Sep 15;162(4):1339-50
references.pmid: 19490934
references.citation: Magn Reson Imaging. 2010 Jan;28(1):146-52
references.pmid: 19608368
references.citation: Neuroimage. 2007 May 15;36(1):64-8
references.pmid: 17433879
references.citation: Neuroimage. 2007 Aug 1;37(1):82-9
references.pmid: 17574443
references.citation: Exp Neurol. 2005 Jan;191(1):77-85
references.pmid: 15589514
references.citation: BMC Bioinformatics. 2010 Dec 22;11:608
references.pmid: 21176225
references.citation: Cereb Cortex. 2005 May;15(5):639-45
references.pmid: 15342433
references.citation: Methods Mol Biol. 2011;711:251-70
references.pmid: 21279606
references.citation: J Magn Reson Imaging. 1991 May-Jun;1(3):301-5
references.pmid: 1802143
references.citation: Neuroimage. 2006 Aug 15;32(2):538-50
references.pmid: 16784876
references.citation: Magn Reson Med. 2013 Nov;70(5):1380-8
references.pmid: 23213043
references.citation: Radiology. 2002 Mar;222(3):789-93
references.pmid: 11867802
references.citation: Prog Neurobiol. 2005 Feb;75(2):143-60
references.pmid: 15784304
references.citation: Physiol Genomics. 2006 Jan 12;24(2):154-62
references.pmid: 16410543
references.citation: Neuroimage. 2007 Sep 1;37(3):683-93
references.pmid: 17627846
references.citation: Neuroimage. 2012 Aug 15;62(2):911-22
references.pmid: 22248580
references.citation: Nature. 2007 Jan 11;445(7124):168-76
references.pmid: 17151600
references.citation: Comput Methods Programs Biomed. 2011 Dec;104(3):e158-77
references.pmid: 21871688
references.citation: Neuroimage. 2011 Jan 1;54(1):80-9
references.pmid: 20656042
references.citation: Front Neuroanat. 2008 Apr 17;2:1
references.pmid: 18958199
references.citation: Nat Rev Neurosci. 2006 Dec;7(12):952-66
references.pmid: 17115077
references.citation: J Neurosci Methods. 1980 Dec;3(2):129-49
references.pmid: 6110810
references.citation: Front Neuroinform. 2011 Apr 08;5:2
references.pmid: 21519393
references.citation: PLoS Comput Biol. 2011 Feb 03;7(2):e1001065
references.pmid: 21304938
references.citation: PLoS One. 2013 Jul 05;8(7):e67334
references.pmid: 23861758
references.citation: Front Neuroinform. 2011 Nov 24;5:26
references.pmid: 22275894
references.citation: Neuroscience. 2005;135(4):1203-15
references.pmid: 16165303
references.citation: Neuroimage. 2011 Oct 15;58(4):975-83
references.pmid: 21749925
references.citation: Electroencephalogr Clin Neurophysiol. 1955 May;7(2):223-42
references.pmid: 13241384
references.citation: Neuroimage. 2010 Apr 1;50(2):465-71
references.pmid: 20034583
references.citation: Neuroimage. 2010 Nov 1;53(2):365-72
references.pmid: 20600960
references.citation: AJNR Am J Neuroradiol. 2008 Apr;29(4):632-41
references.pmid: 18339720
references.citation: J Neurosci Methods. 2003 Oct 30;129(2):105-13
references.pmid: 14511814
references.citation: Neuroimage. 2006 Jul 1;31(3):1116-28
references.pmid: 16545965
references.citation: PLoS One. 2010 Jan 07;5(1):e8595
references.pmid: 20062822
references.citation: Magn Reson Med. 2003 Oct;50(4):743-8
references.pmid: 14523960
references.citation: Neuroimage. 2012 Sep;62(3):1848-56
references.pmid: 22634863