Nissl Neonatal (P0) Mouse Brain Atlas

Description:

Preparation of histological volume
Brain slices of 25µm thickness were collected coronally from a C57BL/6J mouse on the first day after birth (P0). These slices were stained, aligned, and warped to a reference MRI volume using the same protocols described in MacKenzie-Graham et al., 2004. The registration procedures employed corrected the slice distortions introduced during sample preparation. The 3D histological volume was reconstructed using 150 registered histological sections 50 µm apart. All animals were housed and treated in accordance with the UCLA Animal Research Committee guidelines.

Labeling anatomical structures
Tissue labeling of the histological image volume was delineated on the images after 2D non-linear distortion were corrected. Labeling was done using BrainSuite2. The delineation was based on coronal sections, aided by consultation of the orthogonal planes. Primary references were the prenatal mouse brain atlases of Jacobowitz et al., 1998 and Schambra et al., 1992.  Because the boundaries of most structures were left undefined in these primary references, delineations were inferred from the cytoarchitectural atlas of adult mouse brain (Paxinos and Franklin, 2001) based on cell arrangement, and relative position to the surrounding structure and 3D morphology.

The nomenclature and abbreviation used were primarily based on Paxinos’ mouse brain atlas, thus remaining consistent with those used in the predefined atlas-based database (MacKenzie-Graham et al., 2004). If the structures in the anatomical database were hard to discriminate in the stained slices, they were labeled as their parent structures based on the hierarchical relations defined in the adult mouse brain (Paxinos and Franklin, 2001) and Brain Architecture Management System (BAMS http://brancusi.usc.edu/bkms). The relationships between anatomical structures were organized hierarchically and modeled using BrainGraph (MacKenzie-Graham et al., 2003).

Registering histological image volume to the standard space

The reconstructed histological brain volume was re-sampled to the standard atlas space with the registration protocol described in Lee et al., 2005. In brief, the histological brain was first co-registered to the MRI-based atlas using a 12-parameter transformation. An anatomical label volume was reconstructed from the delineations based on the defined anatomical hierarchical relations such that it had the same 13 features defined in the low resolution MRI-based atlas. Feature-based warping was then performed by maximizing the mutual information between the anatomical labels of the two brain volumes (Leow et al., 2005). Global registration has been previously validated in Lee et al., 2005.

 

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, Arthur W. Toga1

  1. Laboratory of Neuro Imaging, Department of Neurology, University of California, Los Angeles.

Citations:

  • Lee E-F, Boline J, Yuan H, and Toga AW.  (2007) A digital atlas as a framework for data management and cross-data comparison.  Society for Neuroscience, Abstract #100.11

  • Lee E-F, Jacobs RE, Dinov I, Leow A, and Toga AW.  (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.

  • MacKenzie-Graham A, Lee E-F, Dinov ID, Bota M, Shattuck DW, Ruffins S, Yuan H, Konstantinidis F, Pitiot A, Ding Y, Hu G, Jacobs RE, and Toga AW.  (2004) A Multimodal, Multidimensional Atlas of C57BL/6J Mouse Brain. Journal of Anatomy. 204, 93-102.

  • Please acknowledge the contributors and the mouse BIRN.

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

Acknowledgements: This work was supported by NIH Grant U24 RR021760 to the Mouse Biomedical Informatics Research Network (BIRN, http://www.nbirn.net), which is funded by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH).