Figure 1. TREES-to-NEURON (T2N) interface linking compartmental modeling environment NEURON with morphology modeling and analysis tools of Matlab and TREES toolbox.

T2N enables fast and simple incorporation of many diverse morphologies in compartmental simulations facilitating the search for morphologically robust biophysical models. (A) Illustration of T2N workflow. T2N allows for setting up a full compartmental model in Matlab by importing reconstructed or synthetic morphologies (orange; e.g. from NeuroMorpho.org) and by distributing subcellular channel mechanisms (green; mod files generated with NEURON’s NMODL or obtained from databases such as IonChannelGenealogy or Channelpedia). In addition, T2N enables setting up full simulation control by attaching stimulation and recording electrodes and specifying simulation conditions (e.g. stimulation protocols; blue). T2N then automatically produces stereotyped NEURON hoc code, initializes and runs simulations and returns recorded data in a structured output format (red). (B) A comparison of two example results in NEURON and T2N validates T2N simulation output. The orange script shows sample code for visualizing the output. Upper row: somatic voltage trace during a current injection. Lower row: membrane voltage at each dendrite location at a single time point. (C) Examples of using T2N for a simple and fast analysis and visualization of simulation results. (Code for creating the panels is shown in orange; code for the specific labels is omitted).