Whole-Brain Microscopy Meets In Vivo Neuroimaging: Techniques, Benefits, and Limitations

Mol Imaging Biol. 2017 Feb;19(1):1-9. doi: 10.1007/s11307-016-0988-z.


Magnetic resonance imaging, positron emission tomography, and optical imaging have emerged as key tools to understand brain function and neurological disorders in preclinical mouse models. They offer the unique advantage of monitoring individual structural and functional changes over time. What remained unsolved until recently was to generate whole-brain microscopy data which can be correlated to the 3D in vivo neuroimaging data. Conventional histological sections are inappropriate especially for neuronal tracing or the unbiased screening for molecular targets through the whole brain. As part of the European Society for Molecular Imaging (ESMI) meeting 2016 in Utrecht, the Netherlands, we addressed this issue in the Molecular Neuroimaging study group meeting. Presentations covered new brain clearing methods, light sheet microscopes for large samples, and automatic registration of microscopy to in vivo imaging data. In this article, we summarize the discussion; give an overview of the novel techniques; and discuss the practical needs, benefits, and limitations.

Keywords: Brain atlas; Brain clearing; Clarity; Image registration; In vivo neuroimaging; Light sheet microscopy; MRI; Pet.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anatomy, Artistic
  • Animals
  • Atlases as Topic
  • Brain / anatomy & histology*
  • Image Processing, Computer-Assisted
  • Microscopy / methods*
  • Neuroimaging / methods*