The TREES toolbox is a software package written in Matlab (Mathworks, Natick, MA) and 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.

The toolbox is introduced and described in this 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.


Dendritica is a package of software tools for studying propagation of action potentials in dendrites, to be used in conjunction with the simulator NEURON. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Häusser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937.

voltage jump method.jpg

The voltage jump method is a method for extracting the time course of synaptic conductances under conditions of inadequate space clamp. The method is described in detail in the following paper: Häusser, M. & Roth, A. (1997). Estimating the time course of the excitatory synaptic conductance in neocortical pyramidal cells using a novel voltage jump method. Journal of Neuroscience 17, 7606-7625.

The paper also describes a method for estimating synaptic charge at electrotonically remote synapses.

IGOR Pro procedure for fitting the equations in the paper to experimental data. 

Download the sit or zip file.

Mathematica notebook for fitting the equations to data. Download the zip file here. 

MathReader, a free program for viewing Mathematica notebooks, is available here.