Encyclopedia of Computational Neuroscience

2015 Edition
| Editors: Dieter Jaeger, Ranu Jung

TREES Toolbox: Code for Neuronal Branching

  • Hermann Cuntz
Reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6675-8_793

Definition

The TREES toolbox is a software package in MATLAB (MathWorks) that provides tools for reconstructing neuronal branching structures from microscopy image stacks and for generating synthetic axonal and dendritic trees. Furthermore, it enables the analysis, visualization, and editing of these trees for which it provides a large set of dedicated MATLAB functions. The TREES toolbox is freely available as open source at www.treestoolbox.org.

Detailed Description

Accurate predictions of neural computation and network connectivity are well known to require detailed morphological representations. In 2010, we launched a freely distributed open-source software package, the TREES toolbox (Cuntz et al. 2010, 2011), written in MATLAB (MathWorks, Natick, MA). This software package introduces a simple general description of neuronal morphology as a graph connecting targets (e.g., synapses) that are distributed in space. The underlying principle is based on the idea that a dendrite connects...
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Notes

Acknowledgements

I thank all users of the TREES toolbox and am grateful for all the feedback I received. I also wish to thank Friedrich Förstner, Alexander Borst, and Michael Häusser for their active role in the development of the software package and for their comments on this manuscript. The development of the TREES toolbox was supported financially by the Max Planck Society, the Wellcome Trust, the Gatsby Charitable Foundation, the Alexander von Humboldt Foundation, and the European Research Council.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck SocietyFrankfurt am MainGermany