The TREES Toolbox—Probing the Basis of Axonal and Dendritic Branching
It has now been 100 years since Ramón y Cajal described the remarkable diversity of neuronal branching. Only recently, however, have a number of rigorous formalisms emerged providing an accurate quantitative description of axonal and dendritic morphologies. We have launched a freely distributed open-source software package, the TREES toolbox, written in Matlab(Mathworks, Natick, MA), in order to help to pool together the resources offered by a wide variety of novel approaches to studying dendritic and axonal branching that have recently become available. This package introduces a simple general description of neuronal morphology as a graph and provides the basic tools to edit, visualize and analyze neuronal trees in the basis of this description. We then implement our own approach, assuming that neuronal branching can largely be expressed by local optimization of total wiring and conduction distances. We provide the corresponding modular extendable tools to automatically reconstruct...
KeywordsMorphology Trees Computational neuroanatomy Dendrites Axons Toolbox Matlab
We thank Karl Farrow, Yihwa Kim, Philipp Rautenberg, Martin O’Reilly and Sarah Rieubland for testing parts of the software package; Jan Gründemann for providing the Purkinje cell used in the TREES toolbox logo; Idan Segev, Erik de Schutter and Alanna Watt for helpful discussions.