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Three-Dimensional Computerized Reconstruction from Serial Sections: Cell Populations, Regions, and Whole Brain

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Neuroanatomical Tract-Tracing 3

Abstract

Three-dimensional (3D) reconstruction of data collected from serial sections brings together information that has been separated by sectioning. From 3D reconstructions, shapes of structures and complicated distributions of tissue elements can be analyzed to an extent not possible by inspection of individual sections. This chapter reviews preparatory steps that are needed to produce high-quality series of sections, procedures that are typically used to acquire data from the sections, alignment of the section data, use of global and local coordinate systems for comparison of data across experiments, and useful tools (visualization and others) for extracting information from 3D reconstructions. The examples shown are based on axonal tracing data from the rat cerebro-cerebellar system, made available via The Rodent Brain Workbench (www.rbwb.org).

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Authors and Affiliations

  1. Neural Systems and Graphics Computing Laboratory, Centre for Molecular Biology and Neuroscience, and Department of Anatomy, University of Oslo, N-0317, Oslo, Norway

    Jan G. Bjaalie & Trygve B. Leergaard

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  1. Jan G. Bjaalie
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  2. Trygve B. Leergaard
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Editors and Affiliations

  1. Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA

    Laszlo Zaborszky

  2. Department of Anatomy, Vrije University Medical Center, Amsterdam, The Netherlands

    Floris G. Wouterlood

  3. Neurosciences Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain

    José Luis Lanciego

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Bjaalie, J.G., Leergaard, T.B. (2006). Three-Dimensional Computerized Reconstruction from Serial Sections: Cell Populations, Regions, and Whole Brain. In: Zaborszky, L., Wouterlood, F.G., Lanciego, J.L. (eds) Neuroanatomical Tract-Tracing 3. Springer, Boston, MA . https://doi.org/10.1007/0-387-28942-9_17

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