Multi-compartment neural circuitry

The SWC format became the quasi-standard for the description of single neuronal cell morphology reconstructions. For the description of larger neural circuits with many neurons and their synaptic connectivity, a new and efficient data format is needed. NeuroHDF describes a multi-compartmental neural circuit, similar to SWC, with points in 3D space (vertices) and their connectivity. Attributes like vertex (skeleton node, connector, root) or edge (presynaptic_to, postsynaptic_to) type or radius are expressed as arrays corresponding to the vertices or edges.

You can use Hdfview to inspect an example NeuroHDF file. The software tool CATMAID for neural circuit reconstruction exports microcircuits in this format. Another emerging standard is libNeuroML.

Useful for neuroscience data types

  • Single cell morphology
  • Neural circuit reconstructions

Tool supporting this specification

  • CATMAID exports neural circuit reconstructions in NeuroHDF