[Comp-neuro] Release of the TREES toolbox for MATLAB

Hermann Cuntz h.cuntz at ucl.ac.uk
Mon Aug 16 11:41:06 CEST 2010


Dear colleagues,

We are pleased to announce the release of the TREES toolbox for Matlab, freely available at:

http://www.treestoolbox.org/

The TREES toolbox is a large Matlab (Mathworks, Natick, MA) software package based on the following paper, published recently in PLoS Computational Biology:

"One rule to grow them all: A general theory of neuronal branching and its practical application", PLoS Comput Biol 6(8):e1000877.
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000877

Here we present a reduced but powerful description of neuronal morphology using graph theory, and based on the idea that dendritic and axonal branching optimizes total wiring and conduction distances.

The TREES toolbox provides:

1. Tools to automatically reconstruct neuronal branching from microscopy image stacks (including an extensive user interface) and to generate synthetic axonal and dendritic trees.

2. The basic tools to edit, visualize and analyze dendritic and axonal trees.

3. Methods for quantitatively comparing branching structures between neurons.

4. Tools for exploring how dendritic and axonal branching depends on local optimization of total wiring and conduction distances.

We hope that other groups will benefit from this package and that they will add their own code to the TREES toolbox based on their own specific applications. The code is therefore freely distributed.

Best regards,

Hermann Cuntz, Friedrich Forstner, Alexander Borst, Michael Häusser


Support statement: This work was supported by the Gatsby Charitable Foundation, the Wellcome Trust, the Alexander von Humboldt Foundation, and the Max-Planck Society.

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