Molecular Imaging and Biology

, Volume 19, Issue 1, pp 1–9 | Cite as

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

  • Markus Aswendt
  • Martin Schwarz
  • Walid M. Abdelmoula
  • Jouke Dijkstra
  • Stefanie DedeurwaerdereEmail author
Review Article


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.

Key words

In vivo neuroimaging MRI Pet Clarity Brain clearing Light sheet microscopy Image registration Brain atlas 



We wish to thank all participants for the lively discussion during the study group meeting. MA and MS were financially supported by grants from the German Research Foundation DFG (AS464/1-1 and SFB 1089); WA by the Dutch-LSH framework (Cyttron II grant FES0908); and SD by BOF UAntwerpen, the Research Foundation Flanders (FWO) (grant numbers, G.0586.12, G.A009.13N), and the Queen Elisabeth Medical Foundation for Neurosciences.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.


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Copyright information

© World Molecular Imaging Society 2016

Authors and Affiliations

  • Markus Aswendt
    • 1
  • Martin Schwarz
    • 2
  • Walid M. Abdelmoula
    • 3
  • Jouke Dijkstra
    • 3
  • Stefanie Dedeurwaerdere
    • 4
    Email author
  1. 1.In-vivo-NMR LaboratoryMax Planck Institute for Metabolism ResearchCologneGermany
  2. 2.Department of EpileptologyUniversity of BonnBonnGermany
  3. 3.Department of Radiology, Division of Image ProcessingLeiden University Medical CenterLeidenThe Netherlands
  4. 4.Experimental Laboratory Translational Neurosciences and Otolaryngology, Department of Translational NeurosciencesUniversity of AntwerpAntwerpBelgium

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