title: Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates.
abstract: BACKGROUND
  Assignment of anatomical reference is a key step in integration of the rapidly expanding collection of rodent brain data. Landmark-based registration facilitates spatial anchoring of diverse types of data not suitable for automated methods operating on voxel-based image information.
  Here we propose a standardized set of anatomical landmarks for registration of whole brain imaging datasets from the mouse and rat brain, and in particular for integration of experimental image data in Waxholm Space (WHS).
  
  
  RESULTS
  Sixteen internal landmarks of the C57BL/6J mouse brain have been reliably identified: by different individuals, independent of their experience in anatomy; across different MRI contrasts (T1, T2, T2(*)) and other modalities (Nissl histology and block-face anatomy); in different specimens; in different slice acquisition angles; and in different image resolutions. We present a registration example between T1-weighted MRI and the mouse WHS template using these landmarks and reaching fairly high accuracy. Landmark positions identified in the mouse WHS template are shared through the Scalable Brain Atlas, accompanied by graphical and textual guidelines for locating each landmark. We identified 14 of the 16 landmarks in the WHS template for the Sprague Dawley rat.
  
  
  METHODS
  This landmark set can withstand substantial differences in acquisition angle, imaging modality, and is less vulnerable to subjectivity.
  
  
  CONCLUSIONS
  This facilitates registration of multimodal 3D brain data to standard coordinate spaces for mouse and rat brain taking a step toward the creation of a common rodent reference system; raising data sharing to a qualitatively higher level.
authors.affiliation: Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University, Fahrstr. 17, 91054 Erlangen, Germany. Electronic address: marina.sergeeva@fau.de.
authors.forename: Marina
authors.initials: M
authors.lastname: Sergejeva
authors.affiliation: Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1105, Blindern, 0317 Oslo, Norway.
authors.forename: Eszter A
authors.initials: EA
authors.lastname: Papp
authors.affiliation: Donders Institute for Brain, Cognition and Behaviour, Radboud University, P.O. Box 9010, 6500 GL Nijmegen, Netherlands; Institute of Neuroscience and Medicine (INM-6), Research Center Jülich, 52425 Jülich, Germany.
authors.forename: Rembrandt
authors.initials: R
authors.lastname: Bakker
authors.affiliation: Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University, Fahrstr. 17, 91054 Erlangen, Germany.
authors.forename: Manuel A
authors.initials: MA
authors.lastname: Gaudnek
authors.affiliation: Brain Research Network (BreNt) and RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamura-Oho
authors.affiliation: Informed Minds, 2100 NE 16th Ave, Wilton Manors, FL 33305, USA.
authors.forename: Jyl
authors.initials: J
authors.lastname: Boline
authors.affiliation: Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, P.O. Box 1105, Blindern, 0317 Oslo, Norway.
authors.forename: Jan G
authors.initials: JG
authors.lastname: Bjaalie
authors.affiliation: Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander University, Fahrstr. 17, 91054 Erlangen, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hess
mesh_terms: D000818:Animals; D001271:Atlases as Topic; D001921:Brain / Q000033:anatomy & histology*; D016208:Databases, Factual; D006652:Histological Techniques; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D008279:Magnetic Resonance Imaging / Q000379:methods*; D008297:Male; D008810:Mice, Inbred C57BL; D017207:Rats, Sprague-Dawley
keywords: Anatomical landmarks; Brain MRI; Landmark-based registration; Mouse; Rat; Waxholm Space