VolRoverN

VolRoverN

Description

VolRoverN is a software package that offers comprehensive functionality for geometric and electrophysiological neuronal simulation at multiple scales. It produces spatially realistic surface models of neuronal processes, glia, and intracellular organelles from cross-sectional traces. This results in a “forest” of structures. These surface meshes are geometrically accurate and topologically correct. Beyond visualization and a suite of direct geometric quantifications, VolRoverN generates derivative models for sophisticated simulations at multiple scales, such as cable and electrodiffusion models. Functionality includes:

  • 3D reconstruction of neurons from RECONSTRUCT series files
  • 2D and 3D geometry curation and improvement
  • Extra-cellular space (ECS) generation
  • Cable model export to NEURON
  • Electrodiffusion model export to MCell (both surface mesh and tetrahedra)

VolRoverN is an integral part of our Neuromodeling project. It shares components with VolumeRover2 and thus has many shared features.

Download

Mac 10.7 binary: VolRoverN-2.0.6909.dmg
Sample data: VolRoverN-sample.zip
Tutorial: VolRoverN.pdf
Source code:
  * Currently the source code is distributed only for academic use. Users interested in commercial licensing should contact Jitendra Jain.
  * Request academic license
  * Download source

Contact

Contact CVC for more info.

References

  • J. Edwards, E. Daniel, J. Kinney, T. Bartol, T. Sejnowski, K. Harris, D. Johnston, C. Bajaj
    VolRoverN: Automated reconstruction of cellular morphology for multiscale dynamical simulation of neural activity
    Manuscript submitted for publication
  • C. Bajaj, E. Coyle, K. Lin
    Arbitrary topology shape reconstruction from planar cross sections
    Graphical Models and Image Processing 58:524–543
  • J. Edwards, C. Bajaj
    Topologically correct reconstruction of tortuous contour forests
    Computer-Aided Design 43:1296-1306