Connectionists: Release of the TREES toolbox for MATLAB

[Hermann]

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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