Magnetic resonance imaging-based mouse brain atlas and its applications

Manisha Aggarwal, Jiangyang Zhang, Susumu Mori

Research output: Chapter in Book/Report/Conference proceedingChapter


In this chapter, we introduce modern magnetic resonance imaging (MRI)-based mouse brain atlases. Although unable to match the resolution and specificity of their histology-based counterparts, MRI-based mouse brain atlases feature higher anatomical fidelity and can facilitate high-throughput computer-assisted analysis of certain brain phenotypes. This chapter discusses several technical aspects of MRI-based mouse brain atlases, which are important to understand the usefulness as well as limitations of existing atlases. We focus on a novel MRI technique, diffusion tensor imaging (DTI), which provides rich tissue contrasts and is uniquely suited for studying white matter structures and immature mouse brains. The chapter then demonstrates several applications of MRI-based mouse brain atlases in anatomical phenotyping and guiding stereotaxic operations.

Original languageEnglish (US)
Title of host publicationMagnetic Resonance Neuroimaging
Subtitle of host publicationMethods and Protocols
EditorsMichel Modo, Jelte Bulte
Number of pages20
StatePublished - Dec 1 2010

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Mouse brain atlas
  • brain morphology
  • diffusion tensor imaging
  • magnetic resonance imaging

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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