NeuroML Tools and Utilites
Octaga player visualization of pyramidal cell
based on X3D translation of NeuroML document.
X3D support for NeuroML files
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
Current limitations:
- Visualisations are quite slow with greater than a few hundred segments (MorphML) or cells (NetworkML).
- 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).
- All instances in NetworkML files are represented by spheres of the same size and colour.
- Connections are made at the centre of the sphere, ignoring any segment_id.