Conversion of NeuroML files into X3D
In NeuroML version 1.7, a simple mapping from MorphML and NetworkML to X3D was introduced. X3D is a standardised language for 3D graphics providing a XML-based follow up to VRML (Virtual Reality Modeling Language). The mapping uses an XSL file to map the XML of a MorphML or NetworkML file to XML in X3D format. To view the X3D, you will need a browser plugin, such as Octaga or Flux Player.
For examples click the X3D link at the bottom of each of these pages:
- MorphML: Layer 2/3 Pyramidal cell (Traub et al 2005)
- MorphML: Detailed Layer 5 Pyramidal Cell (from NEURON demo)
- NetworkML: Spiral network
- Cerebellum: Abstract cerenellar network with Mossy Fibers, granule cells and Purkinje cells
Nov 2010: An update to the X3D mapping (contributed by Aditya Gilra in NCBS, Bangalore) allows visualisation of the full morphology of each cell in the network when the cell morphology and network positions are present for a NeuroML Level 3 file.
The images below show a Layer 5 Pyramidal morphology, and an abstract cerebellar network exported to X3D and visualised using Octaga Player.
Current limitations:
- MorphML files are visualised "lines only"; i.e., diameters of sections or segments are not shown.
- For NetworkML, only instance-based files can be mapped (lists of cells and connections), so no template based representations.