Published and Accepted

1. M.E. Sargin, L. Bertelli, B.S. Manjunath and K. Rose,
   "Probabilistic Occlusion Boundary Detection on Spatio-Temporal Lattices"
   12th IEEE International Conference on Computer Vision,, Kyoto, Japan, Oct. 2009.
   
2. Pratim Ghosh, Mehmet Emre Sargin, and B.S. Manjunath,
   "Robust Dynamical Model for Simultaneous Registration and Segmentation in a Variational Framework: A Bayesian Approach"
   12th IEEE International Conference on Computer Vision, Kyoto, Japan, Oct. 2009.
   
3. Pratim Ghosh, Luca Bertelli, Baris Sumengen, and B.S. Manjunath,
   "A Non-Conservative Flow Field for Robust Variational Image Segmentation"
   IEEE Transactions on Image Processing, Sep. 2009.
   
4. Alphan Altinok, Erkan Kiris, Emre Sargin, Leslie Wilson, Stuart C. Feinstein, B.S. Manjunath and Kenneth Rose,
   "Quantification of dynamic behavior of microtubules in living cells using novel computational methods"
   38th Annual Meeting of Society for Neuroscience (SfN), Washington, DC, USA, Nov. 2008.
   Submitted to
   
5. E. Kiris, M. R. Gaylord, D. Ventimiglia, A. Altinok, M.E. Sargin, K. Rose, B.S. Manjunath, M. A. Jordan, L. Wilson and S. C. Feinstein,
   "Effects of tau pseudo-phosphorylation at residues thr231 ser262 ser396 and ser404 upon regulation of microtubule dynamic instability in living cells"
   38th Annual Meeting of Society for Neuroscience (SfN), Washington, DC, USA, Nov. 2008.
   Submitted to
   
6. Elisa Drelie Gelasca, Jiyun Byun, Boguslaw Obara, B.S. Manjunath,
   "Evaluation and Benchmark for Biological Image Segmentation"
   Proc. IEEE International Conference on Image Processing, San Diego, CA, Oct. 2008.
   
7. Nhat Bao Sinh Vu,
   "Image Segmentation with Semantic Priors: A Graph Cut Approach"
   Ph.D. Thesis, University of California, Santa Barbara, Sep. 2008.
   
8. Nhat Vu and B.S. Manjunath,
   "Shape Prior Segmentation of Multiple Objects with Graph Cuts"
   IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Anchorage, Alaska, USA, Jun. 2008.
   
9. M. E. Sargin, A. Altinok, K. Rose and B.S. Manjunath,
   "Deformable Trellis: Open Contour Tracking in Bio-Image Sequences"
   IEEE Int. Conf. on Acoustics, Speech and Signal Processing (ICASSP'08), Las Vegas, USA, Apr. 2008.
   
10. Laura E. Boucheron, Neal R. Harvey, and B. S. Manjunath,
    "On Using Cytoplasm and Stroma Features in Automated Cancer Diagnosis"
    Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA, Jan. 2008.
    
11. Jiyun Byun, DeeAnn Hartung, Stuart Feinstein and B. S. Manjunath,
    "Quantifying Cell Viability in Cultured Cells"
    Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA, Jan. 2008.
    
12. Boguslaw Obara, Michael Veeman, William Smith and B.S. Manjunath,
    "Segmentation and analysis of notochord cells in 3D microscope data"
    Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA, Jan. 2008.
    
13. Boguslaw Obara, Jiyun Byun, Dmitry Fedorov and B. S. Manjunath,
    "Automatic nuclei detection and dataflow in Bisquik system"
    Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA, Jan. 2008.
    
14. Elisa Drelie Gelasca, Jiyun Byun, Boguslaw Obara and B.S. Manjunath,
    "Benchmark for evaluating biological image analysis tools"
    Workshop on Bio-Image Informatics: Biological Imaging, Computer Vision and Data Mining, Santa Barbara, CA, USA, Jan. 2008.
    
15. Laura E. Boucheron, Neal R. Harvey and B.S. Manjunath,
    "A Quantitative Object-Level Metric for Segmentation Performance and Its Application to Cell Nuclei"
    Proc. International Symposium on Visual Computing (ISVC), Lake Tahoe, Nevada/California, pp. 208–219, Nov. 2007.
    
16. A. Altinok, E. Sargin, E. Kiris, L. Wilson, S. C. Feinstein, B.S. Manjunath and K. Rose,
    "Segmenting filamentous biological structures by automated tracing"
    Society for Neuroscience Annual Meeting (SfN), San Diego, CA, Nov. 2007.
    Abstract
    
17. E. Kiris, M. R. Gaylord, J. Reifert, M.E. Sargin, A. Altinok, K. Rose, B.S. Manjunath, M. A. Jordan, L. Wilson and S. C. Feinstein,
    "Effects of combinatorial tau pseudophosphorylation upon microtubule binding assembly andthe regulation of dynamic instability in vitro"
    Society for Neuroscience (SfN), San Diego, CA, USA, Nov. 2007.
    abstract
    
18. Alphan Altinok, B. S. Manjunath and Kenneth Rose,
    "Extracting Dynamic Microtubule Features from Image Sequences"
    Asilomar Conference On Signals, Systems and Computers (ACSSC), Monterey, CA, Nov. 2007.
    Invited paper
    
19. Pratim Ghosh, E. Drelie Gelasca, K.R. Ramakrisnan and B.S. Manjunath,
    "Duplicate Image Detection in Large Scale Databases"
    Book Chapter in Platinum Jubilee Volume, Indian Statistical Institute, Kolkata, Oct. 2007.
    
20. Luca Bertelli and B.S. Manjunath,
    "Edge Preserving Filters Using Geodesic Distances on Weighted Orthogonal Domains"
    Proc. IEEE International Conference on Image Processing 2007 (ICIP07), San Antonio, TX, Sep. 2007.
    
21. M. E. Sargin, A. Altinok, K. Rose and B.S. Manjunath,
    "Tracing Curvilinear Structures in Live Cell Images"
    Proc. IEEE International Conference on Image Processing (ICIP 07), San Antonio, TX, Sep. 2007.
    
22. L. Bertelli, Jiyun Byun and B.S. Manjunath,
    "A Variational Approach to Exploit Prior Information in Object-Background Segregation: Application to Retinal Images"
    Proc. IEEE International Conference on Image Processing (ICIP 07), San Antonio, TX, Sep. 2007.
    
23. Nhat Vu, and Pratim Ghosh and B.S Manjunath,
    "Retina layer segmentation and spatial alignment of antibody expression levels"
    Proc. International Conference on Image Processing (ICIP'07), San Antonio, Texas, Sep. 2007.
    
24. Alphan Altinok, Erkan Kiris, Austin Peck, Stuart Feinstein, Leslie Wilson, B. S. Manjunath and Kenneth Rose,
    "Model based dynamics analysis in live cell microtubule images"
    BMC Cell Biology, BioMed Central, vol. 8, Jul. 2007.
    
25. Laura E. Boucheron, Zhiqiang Bi, Neal R. Harvey, B. S. Manjunath, David L. Rimm,
    "Utility of multispectral imaging for nuclear classification of routine clinical histopathology imagery"
    BMC Cell Biology, BioMed Central, vol. 8, Jul. 2007.
    
26. Jiyun Byun,
    "Quantitative Analysis and Modeling of Confocal Retinal Images"
    Ph.D. Thesis, University of California, Santa Barbara, Jun. 2007.
    
27. M.E. Sargin, A. Altinok, E. Kiris, L. Wilson, S. Feinstein, K. Rose and B.S. Manjunath,
    "Tracing Microtubules in Live Cell Images"
    Proc. IEEE International Symposium on Biomedical Imaging (ISBI'07), Metro Washington DC, USA, Apr. 2007.
    
28. Vebjorn Ljosa and Ambuj K. Singh,
    "APLA: Indexing Arbitrary Probability Distributions"
    Proc. 23rd International Conference on Data Engineering (ICDE), pp. 946-955, Apr. 2007.
    
29. Samuel Frame and S. Rao Jammalamadaka,
    "Generalized Mixture Models, Semi-supervised Learning, and Unknown Class Inference"
    Advances in Data Analysis and Classification, Springer, 2007.
    
30. T. Manna, G. Grenningloh, HP Miller, L. Wilson,
    "Stathmin Family Protein SCG10 Differentially Regulates the Plus and Minus ends Dynamics of Microtubules at Steady State in Vitro: Implications for its role in Neurite Outgrowth"
    Biochemistry, vol. 46, pp. 3543-3552, 2007.
    
31. E. Kiris, M. Massie, A. Altinok, K. Rose, M.A. Jordan, L. Wilson and S.C. Feinstein,
    "Effects of tau pseudophosphorylation at residues ser262 ser396 andser404 upon microtubule binding and assembly in vitro"
    American Society for Cell Biology (ASCB), San Diego, CA, USA, Dec. 2006.
    
32. Vebjorn Ljosa and Ambuj K. Singh,
    "Probabilistic Segmentation and Analysis of Horizontal Cells"
    Proc. 2006 IEEE International Conference on Data Mining (ICDM), pp. 980-985, Dec. 2006.
    
33. E. Kiris, M. Massie, A. Altinok, K. Rose, M.A. Jordan, L. Wilson and S.C. Feinstein,
    "Effects of tau pseudophosphorylation at residues ser262 ser396 andser404 upon microtubule binding and assembly in vitro"
    Society for Neuroscience (SfN), Atlanta, GA, USA, Oct. 2006.
    
34. Luca Bertelli, Baris Sumengen, B.S. Manjunath,
    "Redundancy in All Pairs Fast Marching Method"
    Proc. IEEE International Conference on Image Processing 2006 (ICIP06), Atlanta, GA USA, Oct. 2006.
    
35. Dmitry Fedorov, Baris Sumengen and B. S. Manjunath,
    "Multi-Focus Imaging using Local Focus Estimation and Mosaicking"
    Proc. IEEE International Conference on Image Processing 2006 (ICIP06), Atlanta, GA USA, Oct. 2006.
    
36. J. Byun, M. R. Verardo, N. Vu, D. Fedorov, G. P. Lewis, S. K. Fisher and B. S. Manjunath,
    "Quantifying structural distortions in retinal tissue before and after injury"
    Workshop on Multiscale Biological Imaging, Data Mining & Informatics, Santa Barbara, CA, USA, Sep. 2006.
    
37. Laura E. Boucheron, Neal R. Harvey and B. S. Manjunath,
    "Utility of Multispectral Imaging for Analysis of Routine Clinical Histopathology Imagery"
    Workshop on Multiscale Biological Imaging, Data Mining & Informatics, Santa Barbara, CA, USA, Sep. 2006.
    
38. Dmitry Fedorov, Baris Sumengen and B. S. Manjunath,
    "Mosaicking based framework for local enhancement of bio imagery"
    Workshop on Multiscale Biological Imaging, Data Mining & Informatics, Santa Barbara, CA, USA, Sep. 2006.
    
39. A. Bhattacharya and A. K. Singh,
    "Prediction of Growth Parameters of In Vitro Microtubules in Association with Different Isoforms of Tau"
    Workshop on Multiscale Biological Imaging, Data Mining & Informatics, Santa Barbara, CA, USA, pp. 53-54, Sep. 2006.
    
40. Vebjorn Ljosa and Ambuj K. Singh,
    "Probabilistic segmentation of horizontal cells"
    Workshop on multiscale biological imaging, data mining & informatics, pp. 39-40, Sep. 2006.
    
41. Jiyun Byun, Mark R. Verardo, Baris Sumengen, Geoffrey P. Lewis, B. S. Manjunath and Steven K. Fisher,
    "Automated tool for the detection of cell nuclei in digital microscopic images: Application to retinal images"
    Molecular Vision, http://www.molvis.org/molvis/v12/a107/, vol. 12, pp. 949-960, Aug. 2006.
    
42. Alphan Altinok, Motaz El-Saban, Austin Peck, Leslie Wilson, Stuart Feinstein, B.S Manjunath and Kenneth Rose,
    "Activity Analysis in Microtubule Videos by Mixture of Hidden Markov Models"
    Proc. International Conference on Computer Vision and Pattern Recognition (CVPR), New York, NY, Jun. 2006.
    double-blind review
    
43. Baris Sumengen, Luca Bertelli and B.S. Manjunath,
    "Fast and Adaptive Pairwise Similarities for Graph Cuts-based Image Segmentation"
    Proc. IEEE CVPR Workshop on Perceptual Organization in Computer Vision (POCV), New York City, Jun. 2006.
    double-blind review
    
44. S. K. Fisher, M. R. Verardo, J. Byun, G. P. Lewis, G. Luna, S. Kjellstrom, and P. Sieving,
    "Retinal Changes Following Experimental Retinal Detachment In The Retinoschisin Knockout Mouse"
    Invest Ophthalmol Vision Science 2006;47: Association for Research in Vision and Ophthalmology (ARVO) EAbstract 1538, Fort Lauderdale, Florida, Apr. 2006.
    
45. Motaz El-Saban, Alphan Altinok, Austin Peck, Charles Kenney, Stuart Feinstein, Leslie Wilson, Kenneth Rose and B.S Manjunath,
    "Automated tracking and modeling of microtubule dynamics"
    Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Crystal City, CA, Apr. 2006.
    
46. M.R. Verardo, G.P. Lewis, M. Takeda, K.A. Linberg, U. Wilhelmsson, M. Pekny, D.F. Chen and S.K. Fisher,
    "Lack of Intermediate Filaments in GFAP -/-vim-/- Mice leads to Changes in Mueller Cell Endfeet and Ganglion Cells Following Retinal Detachment"
    Proc. Invest Ophthalmol Vision Science 2006;47: Association for Research in Vision and Ophthalmology (ARVO) E-Abstract 4225, Fort Lauderdale, Florida, USA, Apr. 2006.
    
47. S. K. Fisher, J. Byun, D. Fedorov, N. Vu, B. Sumengen, M. Verardo, G. P. Lewis and B. S. Manjunath,
    "Image Informatics Tools for the analysis of Retinal Images"
    Invest Ophthalmol Vision Science 2006;47: Association for Research in Vision and Ophthalmology (ARVO) E-Abstract 4225, Fort Lauderdale, Florida, USA, Apr. 2006.
    abstract only
    
48. B. S. Manjunath, B. Sumengen, Z. Bi, J. Byun, M. El-Saban, D. Fedorov and N. Vu,
    "Towards Automated Bioimage Analysis: From Features to Semantics"
    Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Crystal City, CA, pp. 255-258, Apr. 2006.
    Invited paper
    
49. J. Byun, N. Vu, B. Sumengen and B. S. Manjunath,
    "Quantitative analysis of immunofluorescent retinal images"
    Proc. IEEE International Symposium on Biomedical Imaging (ISBI), Crystal City, CA, pp. 1268-1271, Apr. 2006.
    
50. Vebjorn Ljosa, Arnab Bhattacharya and Ambuj K. Singh,
    "LB-Index: A Multi-Resolution Index Structure for Images"
    Proc. 22nd International Conference on Data Engineering (ICDE), Apr. 2006.
    To appear. Poster and short paper.
    
51. B. Sumengen and B. S. Manjunath,
    "Graph Partitioning Active Contours (GPAC) for Image Segmentation"
    IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), Apr. 2006.
    
52. Motaz El-Saban,
    "Automated Microtubule Tracking and Analysis"
    Ph.D. Thesis, University of California, Santa Barbara, Mar. 2006.
    
53. Vebjorn Ljosa, Arnab Bhattacharya and Ambuj K. Singh,
    "Indexing Spatially Sensitive Distance Measures Using Multi-Resolution Lower Bounds"
    Proc. 10th International Conference on Extending Database Technology (EDBT), Mar. 2006.
    To appear.
    
54. Tapas Manna, Douglas Thrower, Herbert P. Miller, Patrick Curmi and Leslie Wilson,
    "Stathmin Strongly Increases the Minus End Catastrophe Frequency and Induces Rapid Treadmilling of Bovine Brain Microtubules at Steady State in Vitro"
    The Journal of Biological Chemistry, vol. 281, no. 4, pp. 2071–2078, Jan. 2006.
    
55. Automated Microtubule Tracking and Analysis,
    "A. Altinok, E. Kiris, B.S. Manjunath, L. Wilson, S. C. Feinstein, K. Rose"
    46th Annual Meeting of the American Society for Cell Biology, San Diego, CA, 2006.
    
56. Alphan Altinok, Austin Peck and Kenneth Rose,
    "Computational Methods for Analyzing Patterns in Dynamic"
    Biological Phenomena: An Application to Microtubule Dynamics, 2006.
    
57. Janis M. Bunker, Kathy Kamath, Leslie Wilson, Mary Ann Jordan, and Stuart C. Feinstein,
    "Ftdp-17 Mutations Compromise the Ability of Tau to Regulate Microtubule Dynamics In Cells"
    The Journal of Biological Chemistry, 2006.
    In press
    
58. Arnab Bhattacharya, Vebjorn Ljosa, Jia-Yu Pan, Mark R. Verardo, Hyungjeong Yang, Christos Faloutsos and Ambuj K. Singh,
    "ViVo: Visual vocabulary construction for mining biomedical images"
    Proc. Fifth IEEE International Conference on Data Mining (ICDM), pp. 50-57, Nov. 2005.
    Received one of five "best student paper" awards.
    
59. B. Sumengen and B. S. Manjunath,
    "Category Pruning in Image Databases using Segmentation and Distance Maps"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
    
60. B. Sumengen and B. S. Manjunath,
    "Multi-scale Edge Detection and Image Segmentation"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
    
61. Robert John Coulier,
    "A Storage, Processing, and Retrieval System for Microtubule Tracking Data"
    IEEE Computational Systems Bioinformatics Conference, Stanford University, CA, Aug. 2005.
    
62. Ambuj K. Singh, Arnab Bhattacharya and Vebjorn Ljosa,
    "Current Challenges in Bioimage Database Design"
    Proc. International Workshop on Bioimage Data Mining and Informatics, IEEE Computational Systems Bioinformatics Conference (CSB), pp. 375-379, Aug. 2005.
    Invited talk and abstract.
    
63. B. Sumengen and B. S. Manjunath,
    "Edgeflow-driven Variational Image Segmentation: Theory and Performance Evaluation"
    IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), May. 2005.
    under review
    
64. A. Altinok, A. J. Peck, S. C. Feinstein, L. Wilson, B. S. Manjunath and K. Rose,
    "Automated Motion Detection and Quantitation of Cell Components: Application to Dynamic Populations of Microtubules in Living Cells"
    45th Annual Meeting of the American Society for Cell Biology, San Francisco, CA, 2005.
    
65. Steven K. Fisher, Geoffrey P. Lewis, Kenneth A. Linberg and Mark R. Verardo,
    "Cellular remodeling in mammalian retina: results from studies of experimental retinal detachment"
    Progress in Retinal and Eye Research, vol. 25, pp. 395-431, 2005.
    
66. M.R. Verardo, G.P. Lewis, M. Takeda, K.A. Linberg, B. Wardak and M. Rabena,
    "Retinal Detachment in Mice Deficient in GFAP and Vimentin: Reduced Glial Hypertrophy and Increased Ganglion Cell Remodeling"
    International Symposium on Neural Regeneration, 2005.
    MRV was given a Travel award for the International Symposium on Neural Regeneration, 2005 for this abstract.
    
67. M.R. Verardo, G.P. Lewis, M. Takeda, B.M. Wardak, M.D. Rabena, D.F. Chen, S.K. Fisher,
    "Glial Hypertrophy and Neuronal Remodeling in Mice Deficient in GFAP and Vimentin Following Experimental Retinal Detachment"
    Proc. Invest Ophthalmol Vision Science 2004;45: Association for Research in Vision and Ophthalmology (ARVO) E-Abstract 3000, Fort Lauderdale, Florida, USA, 2005.
    
68. A. Singh, B. S. Manjunath and R. Murphy,
    "Design of a Distributed Database for Bio-Molecular Images"
    ACM SIGMOD Records, New York, NY, USA, vol. 33, no. 3, pp. 65-71, Jun. 2004.
    
69. J. Byun, L. Wang, G. P. Lewis, S. K. Fisher and B.S. Manjunath,
    "Challenges in Bio-Molecular Imaging and Information Discovery: Developing a Searchable, Distributed Retinal Image Database"
    Invest Ophthalmol Vision Science 2004;45: Association for Research in Vision and Ophthalmology (ARVO) E-Abstract 3000, Fort Lauderdale, Florida, USA, Apr. 2004.
    
70. -,
    "-"
    -, -.
    

Technical Reports

71. Vebjorn Ljosa and Ambuj K. Singh,
    "Top-k Spatial Joins of Probabilistic Objects"
    Technical Report, Center for Bio-Image Informatics, University of California, Santa Barbara, 2007.
    Submitted to International Conference on Data Engineering 2008
    
72. S.K. Fisher, M.R. Verardo, J. Byun, G.P. Lewis, G. Luna, S. Kjellstrom and P. Sieving,
    "Reduced glial hypertrophy and increased neuronal reactivity following retinal detachment in mice deficient in GFAP and vimentin."
    Technical Report, Center for Bio-Image Informatics,, University of California, Santa Barbara, 2007.
    
73. Mark R. Verardo, Geoffrey P. Lewis, Jiyun Byun, M. Takeda, Kenneth A. Linberg, U. Wilhelmsson, Milos Pekny, Dong-Feng Chen, Steven K. Fisher.,
    "Reduced glial hypertrophy and increased neuronal reactivity following retinal detachment in mice deficient in GFAP and vimentin."
    Technical Report, Center for Bio-Image Informatics,, University of California, Santa Barbara, 2007.
    
74. V. Singh, A. Bhattacharya, A. K. Singh, C. Banna, G. P. Lewis and S. K. Fisher,
    "QUIP: Querying Significant Patterns from Image Databases"
    Technical Report, Center for Bio-Image Informatics, UCSB, 2007.
    To be submitted to International Conference on Data Engineering (ICDE) 2008
    
75. A. Bhattacharya and S. C. Feinstein and A. LeBoeuf and S. Levy and A. K. Singh and L. Wilson,
    "A General Modeling and Visualization Tool for Comparing Different Members of a Group: Application to Understanding Tau-Mediated Regulation of Microtubule Dynamics"
    Technical Report, Center for Bio-Image Informatics, UCSB, 2007.
    To be submitted to BMC Bioinformatics
    
76. Md. Aleemuddin Siddiqi and S. Rao Jammalamadaka,
    "Analysis of Microtubules using Growth Curve Modeling"
    Technical Report, VRL, ECE, UCSB, Mar. 2006.
    
77. Samuel J. Frame, S. Rao Jammalamadaka,
    "Semi-Supervised Learning and Generalized Mixture Models in the analysis of Retinal Images"
    Technical Report, Center for Bio-Image Informatics, UCSB, Mar. 2006.
    
78. Alphan Altinok, Baris Sumengen, B.S Manjunath and Kenneth Rose,
    "Reducing incidental fluorescence in live cell imaging"
    Technical Report, ECE, UCSB, 2006.
    
79. Zhiqiang Bi and B.S. Manjunath,
    "Analysis Of Confocal Microscope Images From Retina Detachment Experiments Using Texture Bases Features"
    Technical Report, VRL, ECE, UCSB, 2006.
    Submitted to IEEE International Conference on Image Processing 2006 (ICIP06)
    
80. Dmitry Fedorov, Baris Sumengen and B. S. Manjunath,
    "Tile-based framework for local enhancement of bio imagery"
    Technical Report, VRL, ECE, UCSB, Dec. 2005.
    
81. M. A. El Saban and B. S. Manjunath,
    "Spatiotemporal Contour Tracking of Microtubules"
    Technical Report, VRL, ECE, UCSB, Jun. 2005.
    
82. M. A. El Saban and B. S. Manjunath,
    "Tracking curvilinear structures using active contours and application to microtubule videos"
    Technical Report, VRL, ECE, UCSB, Jun. 2005.