References

References

  • Image Processing Sub-Pipeline

    • Contrast Enhancement
      1. Z. Yu, C. Bajaj
        A Fast and Adaptive Algorithm for Image Contrast Enhancement
        Proceedings of 2004 IEEE International Conference on Image Processing (ICIP’04), Volume 2, Oct. 24-27 2004, Pages 1001-1004, Singapore. (pdf) (ps) (abstract)
      2. H. Pfister, B. Lorenson, C. Bajaj, G. Kindlmann, W. Schroeder, L. Avila, K. Raghu, R. Machiraju, J. Lee
        The Transfer Function Bake-off
        IEEE Computer Graphics and Applications, Volume 21: Issue 3. May/June 2001. Pages 16-22. (pdf)
    • Filtering
      1. 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. (pdf)
    • Classification
      1. S. Park, C. Bajaj
        Feature Selection of 3D Volume Data through Multi-Dimensional Transfer Functions
        Pattern Recognition Letters, 28, 3, pp. 367-374, 2007. (pdf) (abstract)
      2. B. Duerstock, C. Bajaj, R. Borgens
        A Comparative Study of the Quantitative Accuracy of Three-Dimensional Reconstructions of Spinal Cord from Serial Histological Sections
        Journal of Microscopy, 210:2, (2003), 138-148. (pdf)
      3. B. Duerstock, C. Bajaj, V. Pascucci, D. Schikore. K. Lin, R. Borgens
        Advances in three-dimensional reconstruction of the experimental spinal cord injury
        Computerized Medical Imaging and Graphics, Volume 24, Issue 6, November 2000, Pages 389-406. (pdf)
      4. L. Moriarty, B. Duerstock, C. Bajaj, K. Lin, R. Borgens
        Two and Three Dimensional Computer Graphics Evaluation of the Subacute Spinal Cord Injury
        Journal of Neurological Sciences, vol. 155, 121-137 (1998). (pdf)
      5. 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.
    • Segmentation
      1. M. Baker, Z. Yu, W. Chiu, C. Bajaj
        Automated Segmentation of Molecular Subunits in Electron Cryomicroscopy Density Maps
        Journal of Structural Biology, 2006. Accepted. (pdf)
      2. 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. (pdf) (abstract)
      3. Y. Zhu, B. Carragher, R. Glaeser, D. Fellmann, C. Bajaj, M. Bern, F. Mouche, F. Haas, R. Hall, D. Kriegman, S. Ludtke, S. Mallick, P. Penczek, A. Roseman, F. Sigworth, N. Volkmann, C. Potter
        Automatic Particle Selection: Results of a comparative study
        Journal of Structural Biology, Volume 145, 2004, Pages 3-14. (pdf) (abstract)
      4. Z. Yu, C. Bajaj
        Detecting Circular and Rectangular Particles Based on Geometric Feature Detection in Electron Micrographs
        Journal of Structural Biology, Volume 145, 2004, Pages 168-180. (pdf) (abstract)
      5. 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. (pdf)
      6. Z. Yu, C. Bajaj
        A clustering-based method for particle detection in electron micrographs
        Proceedings of the 5th International Conference on Advances in Pattern Recognition(ICAPR’03), pp. 137-140, Calcutta, India, December 2003. (pdf) (abstract)
      7. 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. (pdf)
      8. Z. Yu, C. Bajaj
        Image Segmentation Using Gradient Vector Diffusion and Region Merging
        Proceedings of the 16th International Conference on Pattern Recognition, vol. 2, pp. 941-944, (Published by IEEE CS-Press), Quebec, Canada, August 11-15, 2002. (pdf)
      9. Z. Yu, C. Bajaj
        Normalized Gradient Vector Diffusion and Image Segmentation
        Proceedings 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. (pdf)
      10. 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 & Hall/CRC Press, Computer and Information Science Series, December 21, 2005, ISBN: 1584884061. (pdf) (abstract)
    • Skeletonization
      1. Z. Yu, C. Bajaj
        A Segmentation-Free Approach for Skeletonization of Gray-Scale Images via Anisotropic Vector Diffusion
        Proceedings of 2004 IEEE International Conference on Computer Vision and Pattern Recognition (CVPR’04), Volume 1, Pages 415-420, Washington, DC. (pdf) (abstract)
      2. S. Goswami, T. Dey, C. Bajaj
        Identifying Flat and Tubular Regions of a Shape by Unstable Manifolds
        Proc. 11th ACM Sympos. Solid and Physical Modeling, pp. 27-37, 2006. (pdf) (abstract)
  • Geometry Processing Sub-Pipeline

    • Topological Filtering
      1. C. Bajaj, J. Castrillon-Candas, V. Siddavanahalli, Z. Xu
        Compressed Representations of Macromolecular Structures and Properties
        Structure, Volume 13, Issue 3, March 2005, Pages 463-471. (pdf) (abstract)
      2. C. Bajaj
        Surface Fitting with Implicit Algebraic Surface Patches
        Topics in Surface Modeling, edited by H. Hagen, SIAM Publications, (1992), Chapter 2, 23-52.
    • Geometry Skeletonization
      1. C. Bajaj, S. Goswami
        Secondary and Tertiary Structural Fold Elucidation from 3D EM Maps of Macromolecules
        Proceedings of the Fifth Indian Conference on Computer Vision, Graphics & Image Processing, ICVGIP 2006, LNCS 4338, Springer Verlag, 2006, 264 – 275. (abstract)
      2. C. Bajaj
        Electronic Skeletons: Modeling Skeletal Structures with Piecewise Algebraic Surfaces
        Curves and Surfaces in Computer Vision and Graphics 2: Proceedings of the Symposium on Electronic Imaging Science and Technology, volume 1610, pages 230-237, Boston, MA, 1991. (pdf) (abstract)
    • Geometry Reconstruction from Surface Point-Sets
      1. C. Bajaj, G. Xu
        Data Fitting with Cubic A-splines
        Proceedings: Computer Graphics International, CGI94, Melbourne, Australia, (1994). (pdf) (ps)
      2. F. Bernardini, C. Bajaj, J. Chen, D. Schikore
        Automatic Reconstruction of 3D CAD Models from Digital Scans
        Int. J. on Comp. Geom. and Appl., vol. 9, nos. 4-5, Aug & Oct 1999, pp. 327-369. (pdf) (ps)
    • Linear Meshing
      1. Y. Zhang, C. Bajaj
        Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
        Computer Methods in Applied Mechanics and Engineering, Volume 195, Issues 9-12, 1 February 2006, Pages 942-960. (pdf) (abstract)
      2. Y. Zhang, G. Xu, C. Bajaj
        Quality Meshing of Implicit Solvation Models of Biomolecular Structures
        The special issue of Computer Aided Geometric Design (CAGD) on Applications of Geometric Modeling in the Life Sciences, Volume 23, Issue 6, August 2006, Pages 510-530. (pdf) (abstract)
      3. Y. Zhang, C. Bajaj, B. Sohn
        3D Finite Element Meshing from Imaging Data
        Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194, 48-49, 5083-5106, 2005. (pdf) (abstract)
      4. C. Bajaj
        A Laguerre Voronoi Based Scheme for Meshing Particle Systems
        Japan Journal of Industrial and Applied Mathematics, (JJIAM), vol. 22, No. 2, Pages 167-177, June 2005. (pdf) (abstract)
      5. C. Bajaj, S. Schaefer, J. Warren, G. Xu
        A Subdivision Scheme for Hexahedral Meshes
        The Visual Computer, Vol. 18. Numbers 5-6. Pages 343-356. August 2002. (pdf)
      6. C. Bajaj, E. Coyle, K. Lin
        Tetrahedral Meshes from Planar Cross Sections
        Computer Methods in Applied Mechanics and Engineering, Vol. 179 (1999), pp. 31-52. (pdf) (ps)
      7. C. Bajaj, E. Coyle, K. Lin
        Arbitrary Topology Shape Reconstruction from Planar Cross Sections
        Graphical Models and Image Processing, 58:6, (1996), 524-543. (pdf)
      8. C. Bajaj, T. Dey
        Convex Decomposition of Polyhedra and Robustness
        Siam Journal on Computing, 21, 2, (1992), 339-364. (pdf)
      9. T. Dey, K. Sugihara, C. Bajaj
        Delaunay Triangulations in Three Dimensions with Finite Precision Arithmetic
        Computer Aided Geometric Design, 9:6(1992), 457-470. (pdf)
      10. T. Dey, C. Bajaj, K. Sugihara
        On Good Triangulations in Three Dimensions
        International Journal of Computational Geometry and Applications, 2, 1, (1992), 75-95. (pdf)
      11. C. Bajaj, T. Dey
        Robust Decompositions of Polyhedra
        Proceedings: Ninth Conference on Foundations of Software Technology and Theoretical Computer Science, Lecture Notes in Computer Science, No. 405, Springer-Verlag, (1989), 267-279.
      12. T. Dey, C. Bajaj, K. Sugihara
        On Good Triangulations in Three Dimensions
        Proceedings: The ACM Symposium on Solid Modeling Foundations and CAD/CAM Applications, (1991), 431-441. (pdf)
      13. Y. Zhang, C. Bajaj, G. Xu
        Surface Smoothing and Quality Improvement of Quadrilateral/Hexahedral Meshes with Geometric Flow
        Proceedings of 14th International Meshing Roundtable, pp. 449-468. San Diego, CA. September 11-14, 2005. (pdf)
      14. C. Bajaj
        A Laguerre Voronoi Based Scheme for Meshing Particle Systems
        Proc. of International Symposium on Voronoi Diagrams in Science and Engineering, VD2004, University of Tokyo, Japan, Sep 2004, pp. 115 -122. (pdf) (abstract)
      15. Y. Zhang, C. Bajaj
        Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Imaging Data
        In Proceedings of 13th International Meshing Roundtable, pp. 365-376. Willamsburg, VA. September 19-22, 2004. (pdf)
      16. Y. Zhang, C. Bajaj, B. Sohn
        Adaptive and Quality 3D Meshing from Imaging Data
        Proceedings of 8th ACM Symposium on Solid Modeling and Applications. Pages 286-291. Seattle, WA. June 16-20, 2003. (pdf) (abstract)
      17. C. Bajaj, E. Coyle, K. Lin
        Boundary and 3D Triangular Meshes from Planar Cross Sections
        Proceedings: The Fifth International Meshing Roundtable, Sandia National Lab., Sandia Report SAND96-2301, UC-405, (1996), Pittsburgh, PA, 169-178. (ps)
      18. C. Bajaj, G. Xu
        Adaptive Surfaces Fairing by Geometric Diffusion
        Geometric Modeling: Techniques, Applications, Systems and Tools, 2004, M. Sarfraz(ed), Kluwer Academic Publishers, ISBN: 1-4020-1817-7, Pages 32-49. (pdf) (abstract)
      19. C. Bajaj, G. Xu
        Anisotropic Diffusion of Surfaces and Functions on Surfaces
        ACM Transactions on Graphics, 22, 1, (2003), 4-32. (pdf)
      20. C. Bajaj, G. Xu
        Adaptive fairing of surface meshes by geometric diffusion
        Proceedings of Fifth International Conference on Information Visualisation, 2001. 25-27 July 2001. Page(s):731 – 737. (pdf)
      21. C. Bajaj, G. Xu
        Anisotropic Diffusion of Noisy Surfaces and Noisy Functions on Surfaces
        Proc. of Information Visualization 2001, London, UK, 2001. (pdf)
    • Non-Linear Meshing
      1. Y. Zhang, Y. Bazilevs, S. Goswami, C. Bajaj, T. Hughes
        Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
        Proceedings of 15th International Meshing Roundtable, pp. 73-92. Birmingham, AL. September 17-20, 2006.
      2. C. Bajaj, G. Xu, R. Holt, A. Netravali
        NURBS Approximation of A-splines and A-patches
        International Journal of Computational Geometry and Applications, 13, 5, (2003), 359-389. (pdf)
      3. G. Xu, C. Bajaj, S. Evans
        C1 Modeling with Hybrid Multiple-sided A-patches
        Special issue on Surface and Volume Reconstructions in the International Journal of Foundations of Computer Science, 13, 2, (2002), 261-284. (pdf)
      4. C. Bajaj, G. Xu, R. Holt, A. Netravali
        Hierarchical Multiresolution Reconstruction of Shell Surfaces
        Computer Aided Geometric Design, 19:2(2002), 89-112. (pdf) (ps)
      5. G. Xu, C. Bajaj, H. Huang
        C1 Modeling with A-patches from Rational Trivariate Functions
        Computer Aided Geometric Design, 18:3(2001), 221-243. (pdf) (ps) (abstract)
      6. C. Bajaj, G. Xu
        Regular Algebraic Curve Segments (III) – Applications in Interactive Design and Data Fitting
        Computer Aided Geometric Design, 18:3(2001), 149-173. (pdf) (ps) (abstract)
      7. G. Xu, Q. Pan, C. Bajaj
        Discrete Surface Modelling Using Partial Differential Equations
        Computer Aided Geometric Design, Volume 23/2, pp 125-145, 2006. (pdf) (abstract)
      8. G. Xu, C. Bajaj, W. Xue
        Regular algebraic curve segments (I)-Definitions and characteristics
        Computer Aided Geometric Design, 17:6(2000), 485-501. (pdf) (ps)
      9. G. Xu, C. Bajaj, C. Chu
        Regular Algebraic Curve Segments (II) – Interpolation and Approximation
        Computer Aided Geometric Design, 17:6(2000), 503-519. (pdf) (ps)
      10. C. Bajaj, G. Xu
        A-Splines: Local Interpolation and Approximation Using Gk- Continuous Piecewise Real Algebraic Curves
        Computer Aided Geometric Design, 16:6(1999), 557-578. (pdf) (ps)
      11. C. Bajaj, G. Xu
        Piecewise Rational Approximation of Real Algebraic Curves
        Journal of Computational Mathematics, vol. 15, no. 1, (1997), 55-71. (pdf) (ps)
      12. C. Bajaj, F. Bernardini, G. Xu
        Reconstructing Surfaces and Functions on Surfaces from Unorganized Three-Dimensional Data
        Algorithmica, 19, 1-2, (1997), 243-261. (pdf) (ps)
      13. C. Bajaj, G. Xu
        Spline Approximations of Real Algebraic Surfaces
        Journal of Symbolic Computation, Special Isssue on Parametric Algebraic Curves and Applications, 23, 2-3, (1997), 315 – 333. (pdf) (ps)
      14. C. Bajaj, F. Bernardini, G. Xu
        Automatic Reconstruction of Surfaces and Scalar Fields from 3D Scans
        Proceedings: Computer Graphics (1995), Annual Conference Series, SIGGRAPH 95, ACM SIGGRAPH, 109-118. (pdf) (ps)
      15. C. Bajaj, J. Chen, G. Xu
        Modeling with Cubic A-patches
        ACM Transactions on Graphics, 14:2, (1995), 103-133. (pdf) (ps)
      16. C. Bajaj, G. Xu
        NURBS Approximation of Surface/Surface Intersection Curves
        Advances in Computational Mathematics, 2, 1, (1994), 1-21. (pdf) (ps)
      17. C. Bajaj, T. Dey
        Convex Decomposition of Polyhedra and Robustness
        Siam Journal on Computing, 21, 2, (1992), 339-364. (pdf)
      18. C. Bajaj, I. Ihm
        Smoothing Polyhedra using Implicit Algebraic Splines
        Computer Graphics, 26, 2, (1992), 79-88. Proceedings: 1992 ACM Transactions on Graphics, SIGGRAPH 92, Chicago, Illinois. (pdf)
      19. C. Bajaj, M. Kim
        Convex Hulls of Objects bounded by Algebraic Curves
        Algorithmica, 6, 1, (1990), 533-553. (pdf)
      20. C. Bajaj, J. Bloomenthal, J. Blinn, M. Gascuel, A. Rockwood, B. Wyvill, G. Wyvill
        Introduction to Implicit Surfaces
        Morgan Kaufman Publishers Inc., (1997).
      21. C. Bajaj, S. Goswami, Z. Yu, Y. Zhang, Y. Bazilevs, T. Hughes
        Patient Specific Heart Models from High Resolution CT
        CompIMAGE. Coimbra, Portugal. October 20-21, 2006.
      22. D. Xue, L. Demkowicz, C. Bajaj
        Reconstruction of G1 Surfaces with Biquartic Patches for hp FE Simulations
        In Proceedings of 13th International Meshing Roundtable, pp. 323-332. Willamsburg, VA. September 19-22, 2004. (pdf)
      23. C. Bajaj, H. Lee, R. Merkert, V. Pascucci
        NURBS based B-rep Models from Macromolecules and their Properties
        In Proceedings of Fourth Symposium on Solid Modeling and Applications, Atlanta,Georgia, 1997, C. Hoffmann and W. Bronsvort Eds., ACM Press. pp. 217-228. (pdf) (ps)
      24. F. Bernardini, C. Bajaj, J. Chen, D. Schikore
        Automatic Reconstruction of 3D CAD Models from Digital Scans
        Int. J. on Comp. Geom. and Appl., vol. 9, nos. 4-5, Aug & Oct 1999, pp. 327-369. (pdf) (ps)
      25. C. Bajaj, G. Xu, J. Chen
        Approximation of Polyhedron with C^2 A-Patches
        report on Fourth SIAM Conference on Geometric Design, November 6-9, 1995, Nashville, Tennessee.
      26. C. Bajaj, J. Chen, G. Xu
        Interactive Shape Control and Rapid Display of A-Patches
        Eurographics International Workshop on Implicit Surfaces, Grenoble, France, (1995), 197-215. (pdf) (ps)
      27. C. Bajaj, J. Chen, G. Xu
        Free-Form Surface Design with A-Patches
        Proceedings: Graphics Interface ’94, GI94, Vancouver, Canada, Canadian Information Processing Society (1994), 174-191. (pdf) (ps)
      28. C. Bajaj, A. Royappa
        Triangulation and Display of Rational Parametric Surfaces
        Proceedings: IEEE Visualization ’94 Conference, Washington, DC, edited by R. Bergeron, A. Kaufman, IEEE Computer Society Press, (1994), 69-76. (pdf) (ps)
      29. C. Bajaj, A. Royappa
        Robust Display of Arbitrary Rational Parametric Surfaces
        Curves and Surfaces in Computer Vision and Graphics III
        Proceedings: Symposium on Electronic Imaging Science and Technology, Boston, Massachusetts, vol. 1830, (1992), 70-80.
        (pdf) (abstract)
      30. C. Bajaj
        Geometric Modeling and Quantitative Visualization of Virus Ultrastructure
        Modeling Biology: Structures, Behaviors, Evolution, Edited L. da Fontoura Costa and M. Laublichler, MIT Press, 2005, (to appear). (pdf)
      31. C. Bajaj, S. Evans
        Splines and Geometric Modeling
        CRC Handbook of Discrete and Computational Geometry, edited by J. Goodman and J. O’Rourke, CRC Series, Discrete and Combinatorial Mathematics, (1997), 833-849. (pdf) (ps)
      32. C. Bajaj
        Smooth Shell Construction with Mixed Prism Fat Surfaces
        Brunett, G., Bieri,H., Farin, G. (eds.), Geometric Modeling Computing Supplement, 14, (2001), 19-35. (pdf) (ps)
      33. C. Bajaj
        Implicit Surface Patches
        Introduction to Implicit Surfaces, edited by J. Bloomenthal, Morgan Kaufman Publishers, (1997), 98-125.
      34. C. Bajaj
        Free-Form Modeling with Implicit Surface Patches
        Implicit Surfaces, edited by J. Bloomenthal abd B. Wyvill, Morgan Kaufman Publishers, (1996). (pdf) (ps)
      35. C. Bajaj
        The Emergence of Algebraic Curves and Surfaces in Geometric Design
        Directions in Geometric Computing, edited by R. Martin, Information Geometers Press, United Kingdom (1993), Chapter 1, 1-29.
      36. C. Bajaj
        Geometric Modeling with Algebraic Surfaces
        The Mathematics of Surfaces III, edited by D. Handscomb, Oxford University Press, (1990), Chapter I, 3-48.
        Invited Paper: 3rd IMA, Conference on the Mathematics of Surfaces.
  • Appli