Center for Bio-Image Informatics

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Center for Bio-Image Informatics

Tracking Microtubules Using Deformable Trellis

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Accurate tracking of the microtubules is crucial for their dynamic instability analysis. We present a method for microtubule tracking that employs an arc-emission Hidden Markov Model (HMM) [1]. Proposed method is generic in terms of tracking general curvilinear structures/open-contour that can grow, shrink and undergo lateral motion from frame to frame.

 

The algorithm encodes the shape information of the structure in a spatially deformable trellis model that is iteratively modified to account for observations in subsequent frames. As the open contour is determined on the trellis of an HMM, a dynamic programming procedure reduces the computational complexity to linear in the length of the structure (or open-contour). Length changes of the structures are modeled by the addition of appropriate transient and absorbing states to the HMM. 

 

Our results provide experimental evidence for the proposed algorithm's capability to track non-rigid curvilinear objects in challenging environments in terms of noise and clutter.

 

Microtubule tracking results 

 

Output of the proposed algorithm (green) and the ground truth (red).

 

 

[1] M.E. Sargin, A. Altinok, K. Rose, B.S. Manjunath, "Deformable Trellis: Open Contour Tracking in Bio-Image Sequences", IEEE Int. Conf. on Acoustics, Speech and Signal Processing (ICASSP'08), April 2008

 

 

Image Analysis Research

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The Image Analysis Group is concerned with advanced analysis of biological imagery. The main thrust of research is to develop novel techniques for automatically extracting high-level information from the full range of images generated by the biologists. Current research is focused on two main areas of biological research: the effects of retinal detachment and microtubule dynamics. The retina group is working on algorithms for automated cell counting, layer segmentation, texture analysis, and a host of other quantifiers. The microtubule group is working on techniques for tracking microtubules as well as analyzing microtubule dynamics.

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Publications

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Published and Accepted

  1. S. Karthikeyan, Vignesh Jagadeesh, Renuka Shenoy, Miguel Eckstein and B.S. Manjunath,
    "From Where and How to What We See"
    Proc. IEEE International Conference on Computer Vision, Sydney, Dec. 2013.
  2. A. Baddeley, A. Jammalamadaka and G. Nair ,
    "Multitype point process analysis of spines on the dendrite network of a neuron"
    Proc. Journal of Royal Statistical Society, vol. C, Dec. 2013.
  3. Vignesh Jagadeesh, James Anderson, Bryan Jones, Robert Marc, Steven Fisher and B.S. Manjunath,
    "Robust Segmentation based Tracing using an Adaptive Wrapper for Inducing Priors"
    IEEE Transactions on Image Processing, Nov. 2013.
  4. Vignesh Jagadeesh, James Anderson, Bryan Jones, Robert Marc, Steven K Fisher and B.S Manjunath,
    "Synapse Classification and Localization in Electron Micrographs"
    Pattern Recognition Letters, Nov. 2013.
  5. A. Jammalamadaka, S. Banerjee, B.S. Manjunath and K. Kosik,
    "Statistical analysis of dendritic spine distributions in rat hippocampal cultures"
    Proc. BMC Bioinformatics, vol. 14, no. 287, Oct. 2013.
    Highly Accessed Article, http://www.biomedcentral.com/1471-2105/14/287
  6. Diana Delibaltov, Pratim Ghosh, Volkan Rodoplu, Michael Veeman, William Smith and B.S. Manjunath,
    "A Linear Program Formulation for the Segmentation of Ciona Membrane Volumes"
    Proc. International Conference on Medical Image Computing and Computer Assisted Intervention, Sep. 2013.
  7. B.E. Ruttenberg, G. Luna, G.P. Lewis, S.K. Fisher and A.K. Singh,
    "Quantifying spatial relationships from whole retinal images"
    Bioinformatics, vol. 29, no. 7, pp. 940-946, Apr. 2013.
  8. R.H.J. Fick, D. Fedorov, A.H.K. Roeder and B.S. Manjunath,
    "Simultaneous cell tracking and image alignment in 3D CLSM imagery of growing Arabidopsis thaliana sepals"
    Proc. 10th International Symposium on Biomedical Imaging (ISBI), pp. 914-917, Apr. 2013.
  9. Diana Delibaltov, S. Karthikeyan, Vignesh Jagadeesh and B. S. Manjunath,
    "Robust Biological Image Sequence Analysis Using Graph Based Approaches"
    Proc. Asilomar Conference On Signals, Systems and Computers (ACSSC), Monterey, CA, Nov. 2012.
    Invited paper
  10. S. Karthikeyan, Diana Delibaltov, Utkarsh Gaur, Mei Jiang, David Williams and B.S. Manjunath,
    "Unified Probabilistic Framework for Simultaneous Detection and Tracking of Multiple Objects with Application To Bio-Image Sequences"
    International Conference on Image Processing, Oct. 2012.
  11. K. Eliceiri, M. R. Berthold, I. G. Goldberg, L. Ibanez, B. S. Manjunath, M. E. Martone, R. F. Murphy, H. Peng, A. L. Plant, B. Roysam. N. Stuurmann, J. R. Swedlow, P. Tomancak and A. E. Carpenter,
    "Biological imaging software tools"
    Nature Methods, Nature Publishing Group, vol. 9, pp. 697710, Jun. 2012.
  12. Panuakdet Suwannatat, Gabriel Luna, Geoffrey P. Lewis, Steven K. Fisher and Tobias Hollerer,
    "Scalable Interactive Analysis of Retinal Astrocyte Networks"
    Proc. BioVis, 2012.
  13. Robert J. Miller, John Hocevar, Robert P. Stone, Dmitry V. Fedorov,
    "Structure-Forming Corals and Sponges and Their Use as Fish Habitat in Bering Sea Submarine Canyons"
    PLoS ONE, vol. 7, no. 3, 2012.
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033885
  14. S. Karthikeyan, Utkarsh Gaur, B.S. Manjunath, and Scott Grafton,
    "Probabilistic subspace-based learning of shape dynamics modes for multi-view action recognition"
    International Conference on Computer Vision (ICCV) Workshop PERHAPS 2011, Barcelona, Spain, Nov. 2011.
  15. S. Karthikeyan, M.E. Sargin, S. Joshi, B.S. Manjunath and S. Grafton,
    "Generalized subspace based high dimensional density estimation"
    Proc. International Conference on Image Processing, Brussels, Belgium, Sep. 2011.
  16. B. Obara, M. Veeman, J.H. Choi, W. Smith and B.S. Manjunath,
    "Segmentation of ascidian notochord cells in DIC timelapse images "
    Microscopy Research and Technique, vol. 74, no. 8, pp. 727-734, Aug. 2011.
  17. M.E. Sargin, A. Altinok, B.S. Manjunath and K. Rose,
    "Variable Length Open Contour Tracking Using a Deformable Trellis"
    IEEE Transactions on Image Processing, vol. 20, no. 4, pp. 1023-1035, Apr. 2011.
  18. E. Kiris, D. Ventimiglia, M.E. Sargin, M.R. Gaylord, A. Altinok, K. Rose, B.S. Manjunath, M.A. Jordan, L. Wilson and S.C. Feinstein,
    "Combinatorial Tau Pseudophosphorylation"
    The Journal of Biological Chemistry, vol. 286, no. 16, pp. 14257-14270, Apr. 2011.
  19. Luca Bertelli, Shivkumar Chandrasekaran, Frederic Gibou and B.S. Manjunath,
    "On the Length and Area Regularization for Multiphase Level Set Segmentation"
    International Journal on Computer Vision, vol. 90, no. 3, pp. 267-282, Dec. 2010.
  20. Diego Piedrahita, Israel Hernandez, Alejandro Lopez-Tobon, Dmitry Fedorov, Boguslaw Obara, B. S. Manjunath, Ryan L. Boudreau, Beverly Davidson, Frank LaFerla, Juan Carlos Gallego-Gomez, Kenneth S. Kosik, and Gloria Patricia Cardona-Gomez,
    "Silencing of CDK5 Reduces Neurofibrillary Tangles in Transgenic Alzheimer's Mice"
    Journal of Neuroscience, vol. 30, no. 42, pp. 13966-13976, Oct. 2010.
  21. Aruna Jammalamadaka, Swapna Joshi, S. Karthikeyan, B.S. Manjunath,
    "Discriminative Basis Selection using Non-negative Matrix Factorization"
    IEEE International Conference on Pattern Recognition, Aug. 2010.
  22. Pradeep Koulgi, Mehmet Emre Sargin, Kenneth Rose and B. S. Manjunath,
    "Graphical Model-based Tracking of Curvilinear Structures in Bio-image Sequences"
    IEEE International Conference on Pattern Recognition, Aug. 2010.
  23. M.E. Sargin, P. Ghosh, B. S. Manjunath and K. Rose,
    "Object Tracking with Ratio Cycles Using Shape and Appearance Cues"
    IEEE International Conference on Pattern Recognition, pp. 3649-3652, Aug. 2010.
  24. Pratim Ghosh, M.E. Sargin, B.S. Manjunath,
    "Generalized Simultaneous Registration and Segmentation"
    IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 1363-1370, Jun. 2010.
  25. Swapna Joshi, S. Karthikeyan, B. S. Manjunath, Scott Grafton and Kent A. Kiehl,
    "Anatomical Parts-Based Regression Using Non-Negative Matrix Factorization"
    IEEE Computer Society Conference on Computer Vision and Pattern Recognition, pp. 2863-2870, Jun. 2010.
  26. A.H.K. Roeder , V. Chickarmane, A.Cunha, B. Obara, B.S. Manjunath and E.M. Meyerowitz,
    "Variability in the Control of Cell Division Underlies Sepal Epidermal Patterning in Arabidopsis thaliana"
    PLoS Biology, vol. 8, no. 5, pp. e1000367, May. 2010.
  27. Laura E. Boucheron, B. S. Manjunath, and Neal R. Harvey,
    "USE OF IMPERFECTLY SEGMENTED NUCLEI IN THE CLASSIFICATION OF HISTOPATHOLOGY IMAGES OF BREAST CANCER"
    Proc. of IEEE ICASSP, Dallas, Texas, pp. 666-699, Mar. 2010.
  28. Kristian Kvilekval, Dmitry Fedorov, Boguslaw Obara, Ambuj Singh and B.S. Manjunath,
    "Bisque: A Platform for Bioimage Analysis and Management"
    Bioinformatics, vol. 26, no. 4, pp. 544-552, Feb. 2010.
  29. 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, vol. 19, no. 2, pp. 478-490, Feb. 2010.
  30. Elisa Drelie Gelasca, Boguslaw Obara, Dmitry Fedorov, Kristian Kvilekval and B. S. Manjunath,
    "A biosegmentation benchmark for evaluation of bioimage analysis methods"
    BMC Bioinformatics, vol. 10, no. 1, pp. 368, Nov. 2009.
    http://www.biomedcentral.com/1471-2105/10/368
  31. 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.
  32. 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.
  33. B. Gretarsson, J. O'Donovan, S. Bostandjiev and T. Hollerer,
    "WiGis: A Framework for Scalable Web-based Interactive Graph Visualizations"
    Proc. 17th International Symposium on Graph Drawing, Chicago, Il., Sep. 2009.
  34. J. O'Donovan, B. Gretarsson, S. Bostandjiev, T. Hollerer and B. Smyth,
    "A Visual Interface for Social Information Filtering"
    Proc. International Conference on Social Computing, Vancouver, Canada, pp. 7481, Aug. 2009.
  35. 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.
  36. 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.
  37. Elisa Drelie Gelasca, Jiyun Byun, Boguslaw Obara, B.S. Manjunath,
    "Evaluation and Benchmark for Biological Image Segmentation"
    IEEE International Conference on Image Processing, San Diego, CA, pp. 1816-1819, Oct. 2008.
  38. Nhat Bao Sinh Vu,
    "Image Segmentation with Semantic Priors: A Graph Cut Approach"
    Ph.D. Thesis, University of California, Santa Barbara, Sep. 2008.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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
  48. 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
  49. 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
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. Jiyun Byun,
    "Quantitative Analysis and Modeling of Confocal Retinal Images"
    Ph.D. Thesis, University of California, Santa Barbara, Jun. 2007.
  58. 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.
  59. Vebjorn Ljosa and Ambuj K. Singh,
    "APLA: Indexing Arbitrary Probability Distributions"
    Proc. 23rd International Conference on Data Engineering (ICDE), pp. 946-955, Apr. 2007.
  60. Samuel Frame and S. Rao Jammalamadaka,
    "Generalized Mixture Models, Semi-supervised Learning, and Unknown Class Inference"
    Advances in Data Analysis and Classification, Springer, 2007.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. Vebjorn Ljosa and Ambuj K. Singh,
    "Probabilistic segmentation of horizontal cells"
    Workshop on multiscale biological imaging, data mining & informatics, pp. 39-40, Sep. 2006.
  72. 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.
  73. 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
  74. 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
  75. 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.
  76. 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.
  77. 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.
  78. 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
  79. 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
  80. 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.
  81. 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.
  82. 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.
  83. Motaz El-Saban,
    "Automated Microtubule Tracking and Analysis"
    Ph.D. Thesis, University of California, Santa Barbara, Mar. 2006.
  84. 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.
  85. 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.
  86. 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.
  87. Alphan Altinok, Austin Peck and Kenneth Rose,
    "Computational Methods for Analyzing Patterns in Dynamic"
    Biological Phenomena: An Application to Microtubule Dynamics, 2006.
  88. 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
  89. 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.
  90. B. Sumengen and B. S. Manjunath,
    "Category Pruning in Image Databases using Segmentation and Distance Maps"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
  91. B. Sumengen and B. S. Manjunath,
    "Multi-scale Edge Detection and Image Segmentation"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
  92. Robert John Coulier,
    "A Storage, Processing, and Retrieval System for Microtubule Tracking Data"
    IEEE Computational Systems Bioinformatics Conference, Stanford University, CA, Aug. 2005.
  93. 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.
  94. 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
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. 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.
  100. 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.
  101. -,
    "-"
    -, -.
  102. Technical Reports

  103. Nhat Vu, Vignesh Jagadeesh, and B.S.Manjunath,
    "Mutilabel MRFs with Label Adjacency Constraint: Globally Optimal Solutions and Applications"
    Technical Report, VRL, ECE, University of California, Santa Barbara, Jun. 2013.
  104. 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
  105. 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.
  106. 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.
  107. 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
  108. 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
  109. Md. Aleemuddin Siddiqi and S. Rao Jammalamadaka,
    "Analysis of Microtubules using Growth Curve Modeling"
    Technical Report, VRL, ECE, UCSB, Mar. 2006.
  110. 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.
  111. Alphan Altinok, Baris Sumengen, B.S Manjunath and Kenneth Rose,
    "Reducing incidental fluorescence in live cell imaging"
    Technical Report, ECE, UCSB, 2006.
  112. 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)
  113. Dmitry Fedorov, Baris Sumengen and B. S. Manjunath,
    "Tile-based framework for local enhancement of bio imagery"
    Technical Report, VRL, ECE, UCSB, Dec. 2005.
  114. M. A. El Saban and B. S. Manjunath,
    "Spatiotemporal Contour Tracking of Microtubules"
    Technical Report, VRL, ECE, UCSB, Jun. 2005.
  115. 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.
 

Retina Research

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 The Retinal Research Group studies cellular changes that occur following retinal detachment and reattachment. They are also developing new therapies for the treatment of retinal detachment. In this process, they are generating thousands of high quality images of tissue samples in the form of electron micrographs and laser scanning confocal images.

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Project Objective

With the emergence of smart phones and their increasing popularity, we envision a mobile application capable of plant identifi cation from geo-tagged images. The application sends user generated images to the server, and retrieves information about plant taxonomy and habitat. The system uses plant features such as leaf properties, branching structure, and flower attributes, where applicable, as well as location information, to identify the species. The server returns a list of plant species that are closely related based on phenotypical characteristics.

Plant Identification System

Coal Oil Point Reserve

Devereux Slough - Januuary, 24, 2008

The University of California (UC) Natural Reserve System (NRS) manages 37 natural areas representing nearly all the State's major ecosystems in as undisturbed a condition as possible. This reserve system protects California's natural heritage for the public trust and provides protected natural areas for research and teaching to contribute to the understanding and wise management of the Earth and its natural systems. The Coal Oil Point Reserve is one of these re- serves and o ers many opportunities for public and student education as well as research.

The Coal Oil Point Natural Reserve (COPR) consists of 170 acres of protected coastal habitats along the south coast of Santa Barbara County, adjacent to the West Campus of the UCSB. The diversity of habitats and wildlife at the Reserve is striking and some of these species are now rare along the coast. For example, the COPR beach is breeding habitat for the Pacifi c coastal population of the threatened Western Snowy Plover and the endangered California Least Terns. The Belding savanna Sparrow breeds on the pickleweed habitat at Devereux slough. The Reserve has one of the most pristine remnants of Coastal Dune Scrub in Santa Barbara County, and contains a number of rare plant species. Several types of wetlands such as vernal pool, dune swale, salt at and salt marsh are part of the 5% remaining coastal wetland in California. In a short walk, visitors can observe all these habitats and learn why it is important to preserve them.

Easy access to the Reserve's great natural beauty provides an opportunity to foster education and connect people to nature. One way to help to engage people with their local environment is by teaching them to recognize the native plant species. This project will provide a cutting edge tool to help people identify plants. The reserve's 3 mile nature trail contains a number of plants from the coastal scrub community, the most important vegetation, and the one with the fastest decline in coastal California. People love what they know and protect what they love. Thus, by learning the local ora, people will help preserve it.

Plant Itendification Challenges

The difficulty in plant identification comes from the fact that all elements of the plant (flower, leaf, branching structure, etc) give clues that need to be examined in order to identify the plant. Therefore, our system cannot be limited to leaves, like other plant identification systems already existent. Furthermore, the variety of types of leaves and flowers as well as complicated 3-d geometry of the branching structure of leaves and petals poses difficulty. Our system aims at addresses these challenges and taking advantage of as many plant features as possible, 2-d as well as 3-d.

Variety in imaging subjects: whole plant, leaf, branch, flower

Data Collection Process

During the summer of 2010 we started a systematic data collection process (one undergraduate research intern and a graduate student mentor have been involved in this work, supervised by Professor Manjunath and the Director of the COPR). We are collecting data along the trail mentioned in above. Also, the appearance of plants varies greatly throughout the year, so our e fort of data collection will be ongoing work.

Throughout the data collection process, we consider the variety in features from plant to plant as well as leaf to leaf on the same plant, but we assume that the query images only contain mature healthy leaves, and healthy fully blossomed flowers. Also, we do not constrain the user image the plant on a white background, but we do expect a uniform background. We do not consider trees at this point.

As mentioned above, we aim at extracting 2D features, such as leaf geometry, venation structure, as well as 3D features, such as shape of the leaf and branching structure. Ideally, the user should be able to take several pictures from diff erent angles in order to be able to extract the 3D structure. We also consider the possibility of providing the user with a wallet-sized calibration pattern which should be captured in the query images.

We collect data in the following manner. The camera is calibrated using a checkerboard pattern. Images from multiple angles are required for the computation of 3D features. The procedure for multi-pose imaging is illustrated in the figure below The checkerboard pattern and the color calibration patterns are mounted next to the target. Several images from diff erent angles are taken. The calibration information allows us to estimate the relative position of the two cameras in the two poses. The target can be one of the subjects discussed above: leaf, flower, fruit, branch and whole plant.

Data collection process

Plant Identification System

Building the Database

Images are collected as explained above. The imaged subject can be: leaf, flower, branch, fruit, whole plant, or a combination thereof. The subject can be photographed with one view, or with multiple views, depending on whether 2D or 3D features will be extracted. Every image comes with date/time information and GPS coordinates. The data is stored in the BISQUE system which the VRL maintains.

The figure below explains the information that is annotated for every image collected. This information includes, but is not restricted to: genus and species, ecology information (such as habitat, seasonal variations, etc), phenotypical features (age and physical characteristics). Additionally, several maps are available from COPR (geology, habitat, topography and hydrology maps). The information in these maps is extracted using the GPS coordinates and is associated with the plant. Thus, for example, plants belonging to a specific habitat will be marked according to the maps. Also, to aid the image segmentation process, the background type can be specifi ed as natural or artifi cial (such as a white paper). Features that are later extracted using image processing techniques, are also associated with the image, and can later be retrieved for classifi cation.

Database building flow chart

User Query System

The figure below shows the system that we envision once the database is complete. The user takes a picture of a portion of the plant with their smart phone. The image is sent to the server, along with information about date, time and GPS coordinates. Additionally the system asks the user to clarify what portion of the plant is visible (leaf, branch, etc). Optional parameters can also be specifi ed to aid the feature extraction and classifi cation. Such optional parameters include the age of the plant, phenotypical information, the type of background present in the image (natural or arti ficial), as well as certain keywords which can narrow down the classi fication.

Once the information is received on the server, plant features can be extracted and matched with the database. The GPS coordinates are used to pull up information from the geology, habitat, topography and hydrology maps. The time and date are used to extract season information. Speci fic features are extracted using image processing techniques, as described in the figure below. These features are used for classi fication, and the closest plant species, if any, are returned to the user, along with some relevant information.

User Query System

Infrastructure

We are in the process of building the database of geo-tagged images, along the 3 mile nature trail at the Coal Oil Point Reserve. These images include pictures of leaves, branches, flowers, fruit and whole plants. The reservation includes roughly 130 native species, of which about 30 are common. We currently aim at obtaining images of the common species along the trail over all seasons. The images are obtained using a DSLR camera (Canon EOS 7D) together with a GPS device (i- gatU GT-120). The database is incorporated into the Bio-Image Semantic Query User Environment (BISQUE) system that the VRL maintains.

The Bisque is a web-based platform speci fically designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend Bisque with both data model and analysis extensions in order to adapt the system to local needs. Bisque's extensibility stems from two core concepts: flexible metadata facility and an open web-based architecture. Together these empower researchers to create, develop and share novel bioimage analysis. Bisque is web based, cross-platform and open-source. The system is also available as software-as-a-service through the Center of Bioimage Informatics at UCSB.

 

File Exchange Area

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This is a repository of files pertaining to the retina project. In case you want to view or upload files, please do so by clicking on the above link.
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Database Research

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The Database Group is primarily focused on research methods to store, compare and mine biological data. Our current focus is on mining and comparing probabilistic and uncertain data, and content based retrieval of large image data sets.

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