VRL an eye

Information Technology Research on Bio-Molecular Image Database

People

Jiyun Byun, Jelena Tesic, Lei Wang, B.S.Manjunath, Kenneth Rose

Objective

High resolution imaging of molecules and cells will be critical for understanding complex systems such as the nervous system, whether it be for the localization of specific neuron types within a region of the central nervous system, the branching pattern of dendritic trees, or the localization of molecules at the subcellular level. Further, knowing how these distribution patterns and subcellular locations change as a function of time is critical to understanding how cells respond to stress, injury, aging and disease.

Our goal is to provide new imaging and information processing technologies allowing the creation of large, distributed image databases that are searchable based on metadata.

Acknowledgements

This research is supported by a grant from NSF ITR-0331697

See also

Bio Image Informatics Project

Publications

    2014

  1. 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. Series C (Applied Statistics), Feb. 2014.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We develop methods for analysing the spatial pattern of events, classified into several types, that occur on a network of lines. The motivation is the study of small protrusions called ‘spines’ which ..." [more]

  2. 2013

  3. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Eye movement studies have confirmed that overt attention is highly biased towards faces and text regions in images. In this paper we explore a novel problem of predicting face and text regions in imag..." [more]

  4. 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, vol. 22, no. 12, pp. 4952-4963, Dec. 2013.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Segmentation based tracing algorithms detect the extent and borders of an object in a given frame Iz by propagating results from frames I < z < Z. While application specific tracers have been forthcom..." [more]

  5. 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, vol. 43, pp. 17-24, Nov. 2013.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Classification and Detection of biological structures in Electron Micrographs (EM) is a relatively new large scale image analysis problem. The primary challenges are in characterizing diverse visual c..." [more]

  6. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Dendritic spines serve as key computational structures in brain plasticity. Much remains to be learned about their spatial and temporal distribution among neurons. Our aim in this study was to perform..." [more]

  7. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We address the problem of cell segmentation in confocal microscopy membrane volumes of the ascidian Ciona used in the study of morphogenesis. The primary challenges are non-uniform and patchy membrane..." [more]

  8. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "This work addresses the problem of optimally solving Markov Random Fields(MRFs) in which labels obey a certain topology constraint. Utilizing prior information, such as domain knowledge about the appe..." [more]

  9. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "In this research we propose a combined cell matching and image alignment method for tracking cells based on their nuclear locations in 3D fluorescent Confocal Laser Scanning Microscopy (CLSM) image se..." [more]

  10. 2012

  11. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Robust methods for segmentation and tracking are critical for quantitative biology. We give an overview of our recent work on graph based methods for various microscopy image analysis, including traci..." [more]

  12. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We present a detection based tracking algorithm for tracking melanosomes (organelles containing melanin) in time lapse image sequences imaged using bright field microscopy. Due to heavy imaging noise ..." [more]

  13. 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. 697–710, Jun. 2012.
    [abstract] [BibTex]

    Abstract preview: "Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost ..." [more]

  14. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Continental margins are dynamic, heterogeneous settings that can include canyons, seamounts, and banks. Two of the largest canyons in the world, Zhemchug and Pribilof, cut into the edge of the contine..." [more]

  15. 2011

  16. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We propose a human action recognition algorithm by capturing a compact signature of shape dynamics from multi-view videos. First, we compute R transforms and its temporal velocity on action silhouett..." [more]

  17. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Our paper presents a novel high dimensional probability density estimation technique using any dimensionality reduction method. Our method first performs subspace reduction using any matrix factorizat..." [more]

  18. 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.
    [BibTex]
  19. 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.
    [PDF] [BibTex]
  20. 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.
    [BibTex]
  21. 2010

  22. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "In this paper we introduce novel regulariza tion techniques for level set segmentation that target specically the problem of multiphase segmentation. When the multiphase model is used to obtain a part..." [more]

  23. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Alzheimer's disease is a major cause of dementia for which treatments remain unsatisfactory. Cyclin-dependent kinase 5 (CDK5) is a relevant kinase that has been hypothesized to contribute to the tau p..." [more]

  24. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Non-negative matrix factorization (NMF) has proven to be useful in image classification applications such as face recognition. We propose a novel discriminative basis selection method for classificati..." [more]

  25. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Tracking of curvilinear structures is a task of fundamental importance in the quantitative analysis of biological structures such as neurons, blood vessels, retinal interconnects, microtubules, etc. T..." [more]

  26. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We present a method for object tracking over time sequence imagery. The image plane is represented with a 4-connected planar graph where vertices are associated with pixels. On each image, the outer c..." [more]

  27. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Simultaneous registration and segmentation (SRS) provides a powerful framework for tracking an object of interest in an image sequence. The state-of-the-art SRSbased tracking methods assume that the i..." [more]

  28. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Non-negative matrix factorization (NMF) is an excellent tool for unsupervised parts-based learning, but proves to be ineffective when parts of a whole follow a specific pattern. Analyzing such local c..." [more]

  29. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "How growth and proliferation are precisely controlled in organs during development and how the regulation of cell division contributes to the formation of complex cell type patterns are important ques..." [more]

  30. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Many features used in the analysis of pathology imagery are inspired by grading features defined by clinical pathologists as important for diagnosis and characterization. A large majority of these fea..." [more]

  31. 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.
    [abstract] [PDF] [BibTex] See also:

    Abstract preview: "Motivation: Advances in the field of microscopy have brought about the need for better image management and analysis solutions. Novel imaging techniques have created vast stores of images and metadata..." [more]

  32. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We introduce a robust image segmentation method based on a variational formulation using edge flow vectors. We demonstrate the non-conservative nature of this flow field, a feature that helps in a bet..." [more]

  33. 2009

  34. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Background: We present a biosegmentation benchmark that includes infrastructure, datasets with associated ground truth, and validation methods for biological image analysis. The primary motivation for..." [more]

  35. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "In this paper, we present an algorithm for occlusion boundary detection. The main contribution is a probabilistic detection framework defined on spatio-temporal lattices, which enables joint analysis ..." [more]

  36. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We introduce a dynamical model for simultaneous registration and segmentation in a variational framework for image sequences, where the dynamics is incorporated using a Bayesian formulation. A linear ..." [more]

  37. 2008

  38. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Studies of MT dynamic instability in living cells require MT tip tracking, data analysis and calculation of dynamics statistics. Generally, these tasks are performed manually. Investigators manually f..." [more]

  39. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Tau is a neural specific microtubule associated protein that is crucial for the proper development and maintenance of the nervous system. Mechanistically, tau binds directly to microtubules (MT), prom..." [more]

  40. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "This paper describes ongoing work on creating a benchmarking and validation dataset for biological image segmentation. While the primary target is biological images, we believe that the dataset would ..." [more]

  41. Nhat Bao Sinh Vu,
    "Image Segmentation with Semantic Priors: A Graph Cut Approach"
    Ph.D. Thesis, University of California, Santa Barbara, Sep. 2008.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Image segmentation is the partitioning of an image into meaningful regions or pixel groups and is a necessary prerequisite for many higher level computer vision tasks, such as object recognition, scen..." [more]

  42. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We present a new shape prior segmentation method using graph cuts capable of segmenting multiple objects. The shape prior energy is based on a shape distance popular with level set approaches. We also..." [more]

  43. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "This paper presents an open contour tracking method that employs an arc-emission Hidden Markov Model (HMM). The algorithm encodes the shape information of the structure in a spatially deformable trell..." [more]

  44. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "The utility of nuclear features for automated cancer diagnosis has been well established. Use of cytoplasm and stroma features, however, has not been addressed in an computeraided diagnosis system, al..." [more]

  45. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Analyzing cell viability is crucial in understanding the underlying molecular mechanisms of disease. With more than 20 million cases worldwide, Alzheimer's disease (AD) is now the most common neurodeg..." [more]

  46. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "The notochord is an embryonic structure that undergoes dramatic cell shape changes as it itself changes shape from a roughly isodiametric primordium of mesenchymal cells to a long extended rod. Ascidi..." [more]

  47. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Identification of cell nuclei is a fundamental operation,and nuclei centroids are used in a wide gamut of biological and medical analysis. Many methods exist for semi-automated and automated counting ..." [more]

  48. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Biological images are critical components for a detailed understanding of the structure and functioning of cells and proteins. Image processing and analysis tools increasingly play a significant role ..." [more]

  49. 2007

  50. 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.
    VRL ID: 186a, [abstract] [PDF] [BibTex]

    Abstract preview: "We present an object-level metric for segmentation performance which was developed to quantify both over- and under-segmentation errors, as well as to penalize segmentations with larger deviations in ..." [more]

  51. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Currently, biological image analysis generally relies on manual segmentation of objects and subsequent quantification of desired features. In the case of filamentous structures, such as cytoskeletal s..." [more]

  52. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Tau is a neural specific microtubule-associated protein that is crucial for the proper development and maintenance of the nervous system. Mechanistically, tau binds directly to microtubules, promotes ..." [more]

  53. 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
    [abstract] [PDF] [BibTex]

    Abstract preview: "Microtubules (MT) are filamentous cytoskeletal structures composed of tubulin protein subunits. Through their dynamic behaviors, they participate in many essential cellular functions. MT dynamics are ..." [more]

  54. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We propose an image duplicate detection method for identifying modified copies of the same image in a very large database. Modifications that we consider include rotation, scaling and cropping. A comp..." [more]

  55. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We introduce a framework for image enhancement, which smooths images while preserving edge information. Domain (spatial) and range (feature) information are combined in one single measure in a princip..." [more]

  56. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Tracing of curvilinear structures is one of the fundamental tools in the quantitative analysis of biological images, for extracting information about structures such as blood vessels, neurons, microtu..." [more]

  57. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "One of the main challenges in image segmentation is to adapt prior knowledge about the objects/regions that are likely to be present in an image, in order to obtain more precise detection and recognit..." [more]

  58. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "The expression levels of rod opsin and glial fibrillary acidic protein (GFAP) capture important structural changes in the retina during injury and recovery. Quantitatively measuring these expression l..." [more]

  59. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Background: The dynamic growing and shortening behaviors of microtubules are central to the fundamental roles played by microtubules in essentially all eukaryotic cells. Traditionally, microtubule beh..." [more]

  60. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Background: We present an analysis of the utility of multispectral versus standard RGB imagery for routine H&E stained histopathology images, in particular for pixel-level classification of nuclei. Ou..." [more]

  61. Jiyun Byun,
    "Quantitative Analysis and Modeling of Confocal Retinal Images"
    Ph.D. Thesis, University of California, Santa Barbara, Jun. 2007.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Images have become critical components for a detailed understanding of the structure and function of cells and proteins. For example, confocal microscopy images are used to obtain a better understandi..." [more]

  62. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Microtubule (MT) dynamics are traditionally analyzed from time lapse images by manual techniques that are laborious, approximate and often limited. Recently, computer vision techniques have been appli..." [more]

  63. 2006

  64. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "In this paper, we analyze the redundancy in calculating all pairs of geodesic distances on a rectangular grid. Fast marching method is an efficient way to estimate the geodesic distances from a point...." [more]

  65. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We propose an algorithm to generate one multi-focus image from a set of images acquired at different focus settings. First images are registered to avoid misalignment if needed. Then, best focus is es..." [more]

  66. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Quantifying the deformation of retinal tissue after injury is crucial in understanding and characterizing the functional effect of cellular changes. We present a novel method to compute multiple quant..." [more]

  67. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Our paper will present an analysis of the utility of multispectral imagery versus standard RGB imagery for routine H&Estained histopathology imagery, in particular for the classification of histologic..." [more]

  68. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We propose an algorithm to process images using their local information. Each image is tiled with overlapping neighborhoods. Then, each region is enhancement independently. The overlapping tiles are t..." [more]

  69. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Purpose: To develop an automated nuclei detection tool that provides reliable and consistently accurate results for counting cell nuclei. Methods: We propose a simple yet robust method to analyze lar..." [more]

  70. 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
    VRL ID: 155, [abstract] [PDF] [BibTex]

    Abstract preview: "We present an automated method for the tracking and dynamics modeling of microtubules -a major component of the cytoskeleton- which provides researchers with a previously unattainable level of data an..." [more]

  71. 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
    VRL ID: 156, [abstract] [PDF] [BibTex]

    Abstract preview: "We introduce the use of geodesic distances and geodesic radius for calculating pairwise similarities needed in various graph cuts based methods. By using geodesics on an edge strength function we are ..." [more]

  72. 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.
    VRL ID: 152, [abstract] [PDF] [BibTex]

    Abstract preview: "The method of microtubule tracking and dynamics analysis, presented here, improves upon the current means of manual and automated quantification of microtubule behavior. Key contributions are increasi..." [more]

  73. 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
    VRL ID: 154, [abstract] [PDF] [BibTex]

    Abstract preview: "Purpose: To develop software tools that can be used for the enhancement and quantitative analysis of retinal images, and to test these methods on a large retinal image database. Methods: We have asse..." [more]

  74. 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
    VRL ID: 151, [abstract] [PDF] [BibTex]

    Abstract preview: "Recent advances in bio-molecular imaging have afforded biologists a more thorough understanding of cellular functions in complex tissue structures. For example, high resolution fluorescence images of ..." [more]

  75. 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.
    VRL ID: 153, [abstract] [PDF] [BibTex]

    Abstract preview: "We present a novel method to quantitatively analyze confocal microscope images of retinas. We automatically detect nuclei within the outer nuclear layer (ONL) in a retinal image. Based on nuclei detec..." [more]

  76. 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.
    VRL ID: 150, [abstract] [PDF] [BibTex]

    Abstract preview: "In this paper we introduce new type of variational segmentation cost functions and associated active contour methods that are based on pairwise similarities or dissimilarities of the pixels. As a solu..." [more]

  77. Motaz El-Saban,
    "Automated Microtubule Tracking and Analysis"
    Ph.D. Thesis, University of California, Santa Barbara, Mar. 2006.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Microtubules are major components of the cytoskeleton and play an important role in a number of cellular functions such as maintaining cell shape, cell division and transport of various molecules. Abn..." [more]

  78. Alphan Altinok, Baris Sumengen, B.S Manjunath and Kenneth Rose,
    "Reducing incidental fluorescence in live cell imaging"
    Technical Report, ECE, UCSB, 2006.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Fluorescence staining is the prevailing image acquisition technique in cell biology research. A problem of this method is the incidental fluorescence, that is the total fluorescence collected by a cam..." [more]

  79. 2005

  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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We present a simple framework for image enhancement using local image information. The main idea is to divide the image into small tiles and individually enhance each of these tiles. Enhanced tiles ar..." [more]

  81. B. Sumengen and B. S. Manjunath,
    "Category Pruning in Image Databases using Segmentation and Distance Maps"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
    VRL ID: 147, [abstract] [PDF] [BibTex]

    Abstract preview: "A novel framework for pruning a category of images is proposed in this paper. We assume no prior information about the contents or semantics of the images. Our framework discovers consistencies and kn..." [more]

  82. B. Sumengen and B. S. Manjunath,
    "Multi-scale Edge Detection and Image Segmentation"
    Proc. European Signal Processing Conference (EUSIPCO), Sep. 2005.
    VRL ID: 146, [abstract] [PDF] [BibTex]

    Abstract preview: "In this paper, we propose a novel multi-scale edge detection and vector field design scheme. We show that using multiscale techniques edge detection and segmentation quality on natural images can be i..." [more]

  83. M. A. El Saban and B. S. Manjunath,
    "Spatiotemporal Contour Tracking of Microtubules"
    Technical Report, VRL, ECE, UCSB, Jun. 2005.
    [abstract] [PDF] [BibTex]

    Abstract preview: "Microtubules (MTs), one of three major cytoskeletal components, serve numerous critical functions in cells. Mechanistically, MTs are not static polymers; rather, they can be very dynamic and their pre..." [more]

  84. 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.
    [abstract] [PDF] [BibTex]

    Abstract preview: "We present a novel active contour-based tracking algorithm for highly deformable and fast moving curvilinear structures. We propose to use line features as external forces for the active contour for t..." [more]

  85. 2004

  86. 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.
    VRL ID: 133, [abstract] [PDF] [BibTex]

    Abstract preview: "Information technology research has played a significant role in the genomics revolution over the past decade, from aiding with large-scale sequence assembly to automating gene identification to effic..." [more]

  87. 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.
    VRL ID: 129, [abstract] [PDF] [BibTex]

    Abstract preview: "PURPOSE. To develop a digital library of immunofluorescence images of vertebrate retina. The long-term objective is to provide new imaging and information processing technologies allowing the creation..." [more]