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.
2008
- 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.
[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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
2007
- 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.
[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]
- 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
[BibTex]
- 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
[BibTex]
- 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
[BibTex]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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.
[BibTex]
- 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]
- 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]
- 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]
2006
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
2005
- 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]
- 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]
- 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]
- 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]
- 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]
2004
- 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]
- 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]
