Tech Report

G. Xu, M. Li, A. Gopinath, C. Bajaj
Computational Inversion of Electron Tomography Images Using L2-Gradient Flows
ICES Technical Report TR-10-11, The University of Texas at Austin, 2010 (pdf)

Journal Publications

Q. Zhang, C. Bajaj
Cryo-Electron Microscopy Data Denoising Based on the Generalized Digitized Total Variation Method
Far East Journal of Applied Mathematics, 2010, Accepted for publication, NIHMSID# 187605, PMC Journal in Process (pdf)

W. Zhao, G. Xu, C. Bajaj
An Algebraic Spline Model of Molecular Surfaces for Energetic Computations
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009, Accepted for publication, http://dx.doi.org/10.1145/1236246.1236288, NIHMSID153456, PMC Journal in Process (pdf) (abstract)

C. Bajaj, M. Auer, A. Koster, U. Ziese, N. Volkmann, D-N. Wang, J. Hudspeth
Three-Dimensional Architecture of Hair-Bundle Linkages Revealed by Electron-Microscopic Tomography
Journal of the Association for Research in Otolaryngology, June 2008, 9(2):215-24, http://tinyurl.com/PMC2504599, PMCID: PMC2504599

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, http://tinyurl.com/PMID18989044, PMID: 18989044, PMC Journal in Process (pdf) (abstract)

J. Oden, K. Diller, C.Bajaj, J. Browne, J. Hazle, I. Babuska, J. Bass, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Prudhomme, M. Rylander, R. Stafford, Y. Zhang
Dynamic Data-Driven Finite Element Models for Laser Treatment of Cancer
Journal of Numerical Methods for Partial Differential Equations, 23 (4) 901-922, 2007, doi: 10.1002/num.20251, http://tinyurl.com/NIHMS92557, PMCID: PMC2850081

S. Park, C. Bajaj
Feature Selection of 3D Volume Data through Multi-Dimensional Transfer Functions
Pattern Recognition Letters, 28, 3, pp. 367-374, 2007, doi: 10.1016/j.patrec.2006.04.008, http://tinyurl.com/PMC2743423, PMCID: PMC2743423 (pdf) (abstract)

Y. Zhang, Y. Bazilives, S. Goswami, T. Hughes, C. Bajaj
Patient-Specific Vascular NURBS Modeling for Isogeometric Analysis of Blood Flow
Computer Methods in Applied Mechanics and Engineering (CMAME), 196 (29-30) 2943-2959. 2007, doi: 10.1007/978-3-540-34958-7, NIHMSID 87598, http://tinyurl.com/PMC2839408, PMCID: PMC2839408

C. Bajaj, J. T. Oden, K. R. Diller, J. C. Browne, J. Hazle, I. Babuska, J. Bass, L. Bidaut, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes, S. Prudhomme, R. J. Stafford, Y. Zhang.
Using Cyber-infrastructure for Dynamic Data Driven Laser Treatment of Cancer
Lecture Notes in Computer Science, 2007, 4487: 972-979, doi: 10.1007/978-3-540-72584-8_128, http://tinyurl.com/PMC2743440, PMCID: PMC2743440 (pdf) (abstract)

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, doi: 10.1016/j.jsb.2006.05.013, PMID: 16908194, http://tinyurl.com/PMID16908194, PMC Journal in Process (pdf)

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, doi:10.1016/j.cma.2004.11.026, http://tinyurl.com/PMC2748876, PMCID: PMC2748876 (pdf) (abstract)

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, doi: 10.1109/TIP.2005.852770, http://tinyurl.com/PMID16190468, PMID16190468, PMC Journal in Process

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, doi: 10.1016/j.jsb.2003.09.033, http://tinyurl.com/PMID15065668, PMID15065668, PMC Journal In Process (pdf) (abstract)

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, doi: 10.1016/j.jsb.2003.10.027, http://tinyurl.com/PMID15065684, PMID15065684, PMC Journal In Process (pdf) (abstract)

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, http://tinyurl.com/PMID12753096, PMID12753096, PMC Journal In Process (pdf)

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, doi:10.1016/j.jsb.2003.09.028, http://tinyurl.com/PMID14643214, PMID14643214, PMC Journal In Process (pdf)

C. Bajaj, Z. Yu, M. Auer
Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging
Journal of Structural Biology, Volume 144, Issues 1-2, Oct. 2003, Pages 132-143, doi:10.1016/j.jsb.2003.09.037, http://tinyurl.com/PMID14643216, PMID14643216, PMC Journal In Process (pdf)

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)

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, http://tinyurl.com/PMID11008186, PMID11008186, PMC Journal in Process (pdf)

C. Bajaj, I. Ihm, S. Park
Compression-Based 3D Texture Mapping for Real-Time Rendering
Graphical Models, 62:6, (2000), 391-410. (pdf) (abstract)

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, pp 121-137 (1998), http://tinyurl.com/PMID9562256, PMID: 9562256, PMC Journal in Process). (pdf)

Conference Presentations & Publications

O. Sharma, Q. Zhang, F. Anton, C. Bajaj
Multi-Domain, Higher Order Level Set Scheme for 3D Image Segmentation on the GPU
Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), 2010, NIHMSID# 192191, PMC Journal in Process (pdf)

D. Ress, S. Dhandapani, S. Katyal, and C. Greene, C. Bajaj
Surface-Based Imaging Methods for High-Resolution Functional Magnetic Resonance Imaging
Proceedings of Second Intl. Symposium, CompIMAGE 2010: Computational Modeling of Objects Represented in Images, ed. by R. Barneva, V. Brimkov, H. Hauptman, R. Jorge, J. Tavares. LNCS 6026, Springer Verlag, 2010, p 130-140, NIHMSID# 187599. (pdf)

R. Araiza, M. Averill, G. Keller, S. Starks, C. Bajaj
3-D Image Registration Using Fast Fourier Transform, With Potential Applications To Geoinformatics and Bioinformatics
Proceedings of the International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems IPMU06, Paris, France, July 2-7, 2006, pp. 817-824, NIHMSID193945, PMC Journal in Process (pdf) (ps) (abstract)

S. Park, C. Bajaj, G. Gladish
Artery-Vein Separation of Human Vasculature from 3D Thoracic CT Angio Scans
Proceedings of CompIMAGE 2006, Coimbra, Portugal. October 20-21, 2006, NIHMSID194051, PMC Journal in Process (pdf)

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. (pdf)

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, http://tinyurl.com/PMC2860966, PMCID: PMC2860966 (pdf) (abstract)

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)

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)

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)

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)

S. Park, C. Bajaj, V. Siddavanahalli
Case Study: Interactive Rendering of Adaptive Mesh Refinement Data
Proceedings of IEEE Visualization, Pages 521-524, 2002, Boston, MA. (pdf)

B. Sohn, C. Bajaj, V. Siddavanahalli
Feature Based Volumetric Video Compression for Interactive Playback
Proceedings of IEEE/SIGGRAPH Symposium on Volume Visualization and Graphics, Pages 89-96, 2002, Boston, MA, http://tinyurl.com/PMC2805201, PMCID: PMC2805201 (pdf)

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)

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)

X. Zhang, C. Bajaj, W. Blanke
Scalable Isosurface Visualization of Massive Datasets on COTS-Cluster
Proc. of IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, pp. 51-58, San Diego, CA, 2001. (pdf)

C. Bajaj, I. Ihm, S. Park
Visualization-Specific Compression of Large Volume Data
Proc. of Pacific Graphics, pp. 212-222, 2001, Tokyo, Japan, Oct 2001. (pdf) (ps)

C. Bajaj, I. Ihm, S. Park, D. Song
Compression-Based Ray Casting of Very Large Volume Data in Distributed Environments
HPC-Asia 2000, Pages 720-725, Beijing, China, May 2000. (pdf) (ps)

C. Bajaj, V. Pascucci
Time Critical Isosurface Refinement and Smoothing
Proceedings of the ACM/IEEE Volume Visualization and Graphics Symposium 2000, Salt lake City, Utah, pp. 33- 42. (pdf) (ps)

C. Bajaj, I. Ihm, S. Park
Making 3D Textures Practical
In Proceedings of Pacific Graphics, October 5-7, 1999, Seoul, Korea, Pages 259-268. (pdf) (ps)

C. Bajaj, I. Ihm, G Koo, S. Park
Parallel Ray Casting of Visible Human on Distributed Memory Architectures
In Proceedings of Joint EUROGRAPHICS - IEEE TCVG Symposium on Visualization, May 26-28, 1999, Vienna, Austria. pp. 269-276. (pdf) (ps)

C. Bajaj, V. Pascucci, G. Ribbiolo, D. Schikore
Hypervolume Visualization: A Challenge in Simplicity
Proceeding of the IEEE/ACM 1998 Symposium on Volume Visualization pages 95-102 October 1998, Research Triangle Park, NC. (pdf) (ps) (abstract)

C. Bajaj, V. Pascucci, D. Schikore
Visualization of Scalar Topology for Structural Enhancement
Proceeding of the IEEE Visualization, pages 51-58, October 1998, Research Triangle Park, NC. (pdf) (ps)

C. Bajaj, V. Pascucci, D.Schikore
The Contour Spectrum
Proceedings of the 1997 IEEE Visualization Conference,167-173, October 1997 Phoeniz, Arizona. (pdf)

C. Bajaj, V. Pascucci, D. Schikore
Fast Isocontouring for Improved Interactivity
Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, (1996), San Francisco, CA. Pages: 39-46 (text) 99 (color plate). (pdf) (ps)

C. Bajaj, F. Bernardini, V. Pascucci, D. Schikore
Interrogative Visualization of the Visible Human Datasets
The Visible Human Project Conference, 1996. (ps)

C. Bajaj, M. Fields
The VAIDAK Medical Image Model Reconstruction Toolkit
Proceedings: The 1993 ACM/SIGAPP Symposium on Applied Computing, (1993), Indianapolis, Indiana, ACM Press, 28-35. (pdf) (ps)

Book Chapters

C. Bajaj, A. Gillette, S. Goswami, B. Kwon, and J. Rivera
Complementary Space for Enhanced Uncertainty and Dynamics Visualization
Topological Data Analysis and Visualization: Theory, Algorithms and Applications, ed. by Pascucci, Tricoche, Hagen, Tierny, Springer-Verlag, in publication, 2009, NIHMSID194093, PMC Journal in Process (pdf)

C. Bajaj, S. Goswami
Modeling Cardiovascular Anatomy from Patient-Specific Imaging
Advances in Computational Vision and Medical Image Processing, ed. by Joao Tavares and Renato Jorge, Springer, 2008, Chapter 1, pgs 1-28, NIHMS155076, PMC Journal in Process

C. Bajaj, V. Pascucci, D. Schikore
Accelerated IsoContouring of Scalar Fields
Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998). (pdf) (ps)

C. Bajaj
Visualization Paradigms
Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998). (pdf) (ps)

C. Bajaj
Interactive Visualization of Multidimensional Data
Computer Graphics and Applications, edited by S. Y. Shin, T. Kunii, World Scientific Publishing, (Invited Paper), (1995), 63-77. (pdf) (ps)