graphtheory

edit

metrics

graphical

construct

electrotonics

IO

asym_tree

branch point asymmetry

asym = asym_tree (intree, v, options)

More than a century ago, Ramón y Cajal verbally described neuronal branching in all its forms and variants. Still, nowadays, very few rigorous and useful descriptive formalisms exist.

Here we attempt to take two steps in one:

1. We start with a simple description of neuronal morphology as a graph and provide the basic tools to edit, visualize and analyze neuronal trees in the basis of this description.


2. Following our own approach, assuming that neuronal branching can largely be expressed by local optimization of total wiring and conduction distances: we provide tools to automatically reconstruct neuronal branching from microscopy image stacks and to generate artificial branched structures.

This software package is written in Matlab (Mathworks, Natick, MA), the most widely used scientific programming language. We hope that other groups can easily add to the TREES toolbox with their own code for their own specific applications. The code is therefore freely distributed. When publishing scientific work using this toolbox please cite the current paper:

"One rule to grow them all: A general theory of neuronal branching and its practical application, Cuntz H, Forstner F, Borst A, Häusser M"

We encourage users of the toolbox software to recommend the toolbox to their peers but also to funding and award agencies.