MR Neonatal (P0) Mouse Brain Atlas

Description:

MRM.  Eight mice from two sets of littermates were sacrificed hypothermally within 24 hours after birth. After intracardial perfusion with 10ml of phosphate-buffered saline (PBS) and then 10ml 2% paraformaldehyde (PFA), the animals were decapitated and the heads post-fixed with 2% PFA for 24hr before MR scans. Heads were soaked in 5% ProHance® (paramagnetic MR contrast agent)  for 5 days then immersed in Fomblin® (an embedding medium to limit tissue dehydration) for the MR scans.
T2 weighted 3D spin-echo MRI images were acquired using an 11.7 T BrukerAvance imaging spectrometer with a micro-imaging gradient insert and 20 mm birdcage RF coil (Bruker Instruments). The following data acquisition parameters were used: TR/TE=300ms/6.8ms, 2 averages, FOV=12.8mm x 9mm x 9mm, matrix size= 256x128x128, T=288.1ºK.
Spatial resolution of the obtained images was 70 mm x 50 mm x 70 mm per voxel or 40 mm x 40 mm x 40 mm per voxel. The mice weighed between 1.4 and 1.5 g before being sacrificed. All animals were housed and treated in accordance with the UCLA Animal Research Committee guidelines. 

Nomenclature and Delineations.  Each MR brain image volume was first segmented into olfactory bulbs, cerebrum, diencephalon, midbrain-hindbrain and cerebellum as in Figure 1. The basal ganglia (including only caudate putamen + globus pallidus), mammillary bodies, superior and inferior colliculi, substantia nigra, and white matter tracts anterior commissure (temporal limb) and fimbria of hippocampus, were then labeled. The primary reference for delineation was the adult mouse brain atlas of Paxinos and Franklin (2001). The neuroanatomy at age P0 is similar but not identical to the adult mouse brain. These structures were delineated because their boundaries could be identified clearly in all eight raw MR volumes. Nomenclature for each anatomical label was assigned to the structure best representing the delineation (name of smallest structure including all the painted nuclei ) and was consistent with what was used in a similar adult mouse atlas (MacKenzie-Graham et al. 2004). Since some substructures were unrecognizable, we only labeled regions with clear boundaries in basal ganglia and anterior commissure and indicated which sub-nuclei were included in the parenthesis.

Labeling was done manually using in-house software Duff (Shattuck et al. 2004). This program allows the user to view simultaneously all three orthogonal planes and “paint” on volumes, effectively labeling every voxel. Each label was assigned an intensity value uniquely referencing to the anatomic structures. These anatomical labels are also used for feature-based co-registration.

 

Usage: This atlas volume can be viewed using the Mouse BIRN Atlasing Tool (MBAT) or SHIVA.  See the respective manuals for these programs. 

To get more information about MBAT, see http://www.nbirn.net/downloads/mbat/index.shtm

For more information about SHIVA, see http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=12

Accession Number: TBD

To download the Mouse DTI Atlas, please go to the download form.

Contributors/Authors:
Erh-Fang Lee1, Russell E. Jacobs2, Ivo Dinov1, Alex Leow1, and Arthur W. Toga1

  1. Laboratory of Neuro Imaging, Department of Neurology, University of California, Los Angeles.
  2. Beckman Institute, California Institute of Technology.

Citations:

  • Lee, E.-F., Jacobs, R.E., Dinov, I., Leow, A., and Toga, A.W.  (2005)  Standard Atlas Space for C57BL/6J Neonatal Mouse Brain. Lee EF, Jacobs RE, Dinov I, Leow A, Toga AW. Anat Embryol (Berl)  Nov; 210(4):245-263.
  • Please acknowledge the contributors and the mouse BIRN.

Technical Contacts:
Erh-Fang Lee eflee@ucla.edu

Acknowledgements: This work was supported by the NIBIB research grant R01 EB002172, the NCRR grant U24 RR021760, and the Beckman Institute at Caltech.  Additional support was provided by the NCRR resource grant P41 RR013642 and the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 RR021813 entitled Center for Computational Biology (CCB). Information on the National Centers for Biomedical Computing can be obtained from <http://nihroadmap.nih.gov/bioinformatics>.