NeuroBox can use various sources and formats to define either single cells or networks, 1D or 3D geometries. Data can be imported, e.g. from NeuroMorpho.org, in swc-format. For NeuroBox simulations geometry files are then converted to uG4's ugx-geometry file format. See below a list of ways to get or generate geometries. We also offer a repository of cell geometries in ugx format for you to work with.
NeuroMorpho.org is an extensive database hosting anatomically reconstructed cells. Available in swc-format, cells can be imported into NeuroBox for single cell 1D simulations.
NeuGen is a synthetic neuron network generator. Using anatomical fingerprints, NeuGen synthetically grows neurons and integrates them into neural networks.
Cell reconstructions are typically 1D-graph representations or cellular morphology. AnaMorph uses these data from, e.g. NeuroMorpho.org, to generate equivalent 3D surface representations. AnaMorph cells can then be used for full dimensional simulations and coupled to 1D simulations
In order to systematically investigate cellular features, it can be helpful to use parametric geometry design to study the influence of geometric parameters with respect to cellular functions. NeuroBox offers some parametric design tools, such as a synaptic bouton generator or spine/organelle generators.
Find below some single cell and network geometries you can use with NeuroBox.
NETWORKS