VolumeRover

VolumeRover

Rover 1 Rover 2 Rover 3 Rover 4
Description VolumeRover (a.k.a VolRover) is interactive multi-purpose image processing software developed at CVC. It can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations.

  • Image Contrast Enhancement
  • Filtering/Noise Reduction
  • Image Segmentation
  • Isocontouring
  • Symmetry Detection (for Virus Maps)
  • Boundary-free Image Skeletonization

VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation.

Download VolumeRover

Video
For more pictures, animations, and interactive viz. of macromolecular structures using Volume Rover, please visit CVC Gallery


Contact developers Joe Rivera or Alex Rand for more info.
References

  • C. Bajaj, S. Goswami, and Q. Zhang
    Detection of Secondary and Supersecondary Structures of Proteins for Cryo-Electron Microscopy
    Journal of Structural Biology, Volume 177, Issue 2, February 2012, Pages 367-381. (pdf)
  • Q. Zhang, R. Bettadapura and C. Bajaj
    Macromolecular Structure Modeling from 3DEM using VOLROVER 2.0
    Accepted in Biopolymers, 2012. (pdf)
  • G. Xu, M. Li, A. Gopinath, C. Bajaj
    Computational Inversion of Electron Tomography Images Using L2-Gradient Flows
    Journal of Computational Mathematics, 29:501-525, 2011. (pdf)
  • Z. Yu, C. Bajaj
    A Fast and Adaptive Algorithm for Image Contrast Enhancement
    Procedings of 2004 IEEE International Conference on Image Processing (ICIP’04), Volume 2, Oct. 24-27 2004, Pages 1001-1004, Singapore.
  • W. Jiang, M. Baker, Q. Wu, C. Bajaj, W. Chiu
    Applications of Bilateral Denoising Filter in Biological Electron Microscopy
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 114-122.
  • S. Park, C. Bajaj, G. Gladish
    Artery-Vein Separation of Human Vasculature from 3D Thoracic CT Angio Scans
    CompIMAGE. Coimbra, Portugal. October 20-21, 2006.
  • M. Baker, Z. Yu, W. Chiu, C. Bajaj
    Automated Segmentation of Molecular Subunits in Electron Cryomicroscopy Density Maps Journal of Structural Biology, 2006, Dec;156(3):432-41.
  • Z. Yu, C. Bajaj
    Automatic Ultrastructure Segmentation of Reconstructed CryoEM Maps of Icosahedral Viruses
    IEEE Transactions on Image Processing: Special Issue on Molecular and Cellular Bioimaging, 2005 Sep;14(9):1324-37.
  • Z. Yu, C. Bajaj
    Anisotropic Vector Diffusion in Image Smoothing
    Proceeding of the 9th IEEE International Conference on Image Processing, vol. 1, pp. 828-831, (Published by IEEE CS Press), Rochester, New York, September 22-25, 2002.
  • Z. Yu, C. Bajaj
    Normalized Gradient Vector Diffusion and Image Segmentation
    Procedings of the 7th European Conference on Computer Vision (LNCS 2352), vol. 3, pp. 517-530, (Published by Springer Press), Copenhagen, Denmark, May 28-31, 2002.
  • Z. Yu, C. Bajaj
    Computational Approaches for Automatic Structural Analysis of Large Bio-molecular Complexes
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, (digital library) 22 June 2007.
  • C. Bajaj, Z. Yu
    Geometric and Signal Processing of Reconstructed 3D Maps of Molecular Complexes
    Handbook of Computational Molecular Biology, Edited by S. Aluru, Chapman & Hal l/CRC Press, Computer and Information Science Series, December 21, 2005, ISBN: 1584884061.
  • C. Bajaj, E. Coyle, K. Lin
    Arbitrary Topology Shape Reconstruction from Planar Cross Sections
    Graphical Models and Image Processing, 58:6, (1996), 524-543.
  • Wilson, Van Gelder, Wilhelms
    Direct Volume Rendering via 3D Textures
    Technical Report UCSC-CRL-94-19. Univ. of Calif. Santa Cruz. 1994
  • Lorensen, Cline
    Marching Cubes: A High Resolution 3D Surface Construction Algorithm
    Proceedings of the 14th annual conference on Computer graphics and interactive techniques
  • C. Bajaj, V.Pascucci, and D.Schikore
    The Contour Spectrum
    Proceedings of the 1997 IEEE Visualization Conference,167-173, October 1997 Phoeniz, Arizona
  • C. Bajaj, M. van Kreveld, R. van Oostrum, V. Pascucci, and D. Schikore
    Contour Trees and Small Seed Sets for Isosurface Generation
    Topological Data Structures for Surfaces, Chap5, pg 71 – 86, 2004 ed. by S. Rana, John Wiley & Sons, Ltd, 2004
  • C. Bajaj, Z. Yu, M. Auer
    Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging
    Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143.