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Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain

Nature Methods volume 4, pages 331336 (2007) | Download Citation



Visualizing entire neuronal networks for analysis in the intact brain has been impossible up to now. Techniques like computer tomography or magnetic resonance imaging (MRI) do not yield cellular resolution, and mechanical slicing procedures are insufficient to achieve high-resolution reconstructions in three dimensions. Here we present an approach that allows imaging of whole fixed mouse brains. We modified 'ultramicroscopy' by combining it with a special procedure to clear tissue. We show that this new technique allows optical sectioning of fixed mouse brains with cellular resolution and can be used to detect single GFP-labeled neurons in excised mouse hippocampi. We obtained three-dimensional (3D) images of dendritic trees and spines of populations of CA1 neurons in isolated hippocampi. Also in fruit flies and in mouse embryos, we were able to visualize details of the anatomy by imaging autofluorescence. Our method is ideally suited for high-throughput phenotype screening of transgenic mice and thus will benefit the investigation of disease models.

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We thank G. Ryseck for help with initial experiments and S. Espinoza, L. Luo, E. Kramer and C. Wotjak for specimens. This work was supported by grants of the Hertie foundation and the SFB391.

Author information

Author notes

    • Hans-Ulrich Dodt
    • , Nina Jährling
    •  & Klaus Becker

    Present address: Department of Bioelectronics, Institute of Solid State Electronics, Vienna University of Technology, Floragasse 7, 1040 Vienna, Austria.


  1. Max Planck Institute of Psychiatry, Kraepelinstr. 2, 80804 Munich, Germany.

    • Hans-Ulrich Dodt
    • , Ulrich Leischner
    • , Anja Schierloh
    • , Nina Jährling
    • , Christoph Peter Mauch
    • , Jan Michael Deussing
    • , Matthias Eder
    • , Walter Zieglgänsberger
    •  & Klaus Becker
  2. Department of Molecular Neurobiology, Max Planck Institute of Neurobiology, Am Klopferspitz 18, 82152 Martinsried, Germany.

    • Katrin Deininger


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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hans-Ulrich Dodt.

Supplementary information


  1. 1.

    Supplementary Video 1

    whole mouse brain reconstructed from 550 optical sections.

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    Supplementary Video 2

    Granule cells with dendrites in the hippocampus of a thy-1 GFP mouse.

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    Supplementary Video 3

    Excised whole hippocampus.

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    Supplementary Video 4

    Optical sectioning of a whole hippocampus.

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    Supplementary Video 5

    3D-reconstruction and animation of a part of a whole hippocampus.

  6. 6.

    Supplementary Video 6

    3D reconstruction and animation of axonal bundles in the hippocampal alveus and dendritic spines of CA1 pyramidal neurons.

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    Supplementary Video 7

    Primary and secondary barrel field made visible by excitation of autofluorescence in the whole brain of a 10 day old mouse.

  8. 8.

    Supplementary Video 8

    Optical sectioning of a mouse brain imaged by detection of scattered light. Note the appearance of fibre tracts during the movement of the optical sectioning plane through the brain.

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  1. 1.

    Supplementary Methods

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