TREES toolbox

the TREES toolbox: edit, generate, visualise and analyse neuronal trees
Updated 28 Sep 2018

More than a century ago, Ramón y Cajal provided a qualitative description of neuronal branching in all its forms and variants. However, even today, few rigorous and useful formalisms are available for a quantitative description of dendritic and axonal morphology.

The TREES toolbox provides:

Tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate synthetic axonal and dendritic trees.

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

Methods for quantitatively comparing branching structures between neurons.

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

This software package is written in Matlab (Mathworks, Natick, MA), the most widely used scientific programming language. 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. When publishing scientific work using this toolbox please cite the paper:

"Cuntz H, Forstner F, Borst A, Häusser M (2010). One rule to grow them all: A general theory of neuronal branching and its practical application. PLoS Comput Biol 6(8): e1000877."

We encourage users of the toolbox to recommend it to their peers (and also to funding and award agencies where appropriate).

Hermann Cuntz, main developer
(see for more details)

This work was generously supported by
the Max Planck Society
the Wellcome Trust
the Gatsby Charitable Foundation
the Alexander von Humboldt Foundation
the European Research Council
the German Research Foundation
the German Federal Ministry of Education and Research

MATLAB Release Compatibility
Created with R2018a
Compatible with R2010a to R2018b
Platform Compatibility
Windows macOS Linux
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