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An Automated Three-Dimensional Detection and Segmentation Method for Touching Cells by Integrating Concave Points Clustering and Random Walker Algorithm

Yong He, Yunlong Meng, Hui Gong, Shangbin Chen, Bin Zhang, Wenxiang Ding, Qingming Luo, Anan Li, Wang Zhan
2014 PLoS ONE  
As presented herein, we have developed an automated threedimensional detection and segmentation method applied to the Nissl staining data, with the following two key steps: 1) concave points clustering  ...  to determine the seed points of touching cells; and 2) random walker segmentation to obtain cell contours.  ...  Acknowledgments The author would like to thank Xiaoquan Yang, Cheng Yan and Jingpeng Wu for their helpful comments, suggestions and careful reading of the manuscript.  ... 
doi:10.1371/journal.pone.0104437 pmid:25111442 pmcid:PMC4128780 fatcat:ojkwlupzhbgmxagz2vu6fcaxi4

Coupled edge profile active contours for red blood cell flow analysis

I. Ersoy, F. Bunyak, J. M. Higgins, K. Palaniappan
2012 2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)  
RBCs have varying annular and disk like morphologies, and are often clustered into clumps that are difficult to segment using watershed-based methods.  ...  Physiological properties of blood flow at the microvasculature scale can be measured by tracking the movement and density of red blood cells (RBCs).  ...  Fig. 1 : 1 Seed detection using iterative voting. a) iterative voting kernel, b) radial directions, c) vote surface after 2nd iteration, d) detected centers (seeds) overlayed on the original cell cluster  ... 
doi:10.1109/isbi.2012.6235656 dblp:conf/isbi/ErsoyBHP12 fatcat:zgeqpi4yefhbpf57vgacarmrpi

A Fast, Automatic Segmentation Algorithm for Locating and Delineating Touching Cell Boundaries in Imaged Histopathology

X. Qi, F. Xing, D. J. Foran, L. Yang
2012 Methods of Information in Medicine  
The segmentation algorithm subsequently performs a quick, voting based seed detection.  ...  Finally, the contour of each cell is obtained using a repulsive level set deformable model using the seeds generated in the previous step.  ...  Acknowledgments This research was funded, in part, by grants from the National Institutes of Health through contract 5R01CA156386-06 from the National Cancer Institute; and contracts 5R01LM009239-04 and  ... 
doi:10.3414/me11-02-0015 pmid:22526139 pmcid:PMC3650677 fatcat:7hqnvwbthvc6hbziep5o3snpxm

Segmentation of heterogeneous blob objects through voting and level set formulation

Hang Chang, Qing Yang, Bahram Parvin
2007 Pattern Recognition Letters  
In this paper, voting, Voronoi tessellation, and level set methods are combined to delineate blob-like structures.  ...  The paper concludes with the application of the proposed method to a dataset produced from cell based fluorescence assays and stellar data.  ...  Other segmentation methods have focused on clustering (Shi and Malik, 2000) based on local similarity measures and perceptual grouping of local features (Medi-oni et al., 2000) .  ... 
doi:10.1016/j.patrec.2007.05.008 pmid:19774202 pmcid:PMC2747325 fatcat:tymijh7pojbqfdsb5nlyfgemxq

Robust Segmentation of Overlapping Cells in Histopathology Specimens Using Parallel Seed Detection and Repulsive Level Set

Xin Qi, Fuyong Xing, D. J. Foran, Lin Yang
2012 IEEE Transactions on Biomedical Engineering  
Next, the contour of each cell is obtained using a level set algorithm based on an interactive model. We compared the experimental results with those reported in the most current literature.  ...  The method was systematically tested on 234 image patches exhibiting dense overlap and containing more than 2200 cells.  ...  Acknowledgments This research was funded, in part, by grants from the NIH through contract 9R01CA156386-05A1 from the National Cancer Institute and contracts 5R01LM009239-03 and 3R01LM009239-03S2 from  ... 
doi:10.1109/tbme.2011.2179298 pmid:22167559 pmcid:PMC3655778 fatcat:xtjfrpvjrzh2fhbrqr6u2ydklu

Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images

Can Fahrettin Koyuncu, Rengul Cetin-Atalay, Cigdem Gunduz-Demir
2018 Cytometry Part A  
In response to these issues, this article introduces a new nucleus segmentation method that relies on using gradient information not at the pixel level but at the object level.  ...  a merging algorithm, in which the edge-objects vote for subregion pairs along their orientations and the pairs are iteratively merged if they get sufficient votes from multiple orientations.  ...  Gradient-based methods identify individual nuclei in a cluster relying on the fact that nucleus contours have high contrast differences.  ... 
doi:10.1002/cyto.a.23594 pmid:30211975 fatcat:ohbdyzn7azhqtn7srcvrzs3fky

Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation

Can Fahrettin Koyuncu, Ece Akhan, Tulin Ersahin, Rengul Cetin-Atalay, Cigdem Gunduz-Demir
2016 Cytometry Part A  
The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system.  ...  In each iteration, the proposed algorithm defines a set of candidates using a particular h value and selects the markers from those candidates provided that they fulfill the size requirement.  ...  The other two are model-based segmentation algorithms. The iterative voting method (10) gets image pixels iteratively voted along the radial and tangential directions to determine nucleus centers.  ... 
doi:10.1002/cyto.a.22824 pmid:26945784 fatcat:lvgnxud5vnhujb2525yijgvv3m

Segmentation of Three Dimensional Cell Culture Models from a Single Focal Plane [chapter]

Hang Chang, Bahram Parvin
2006 Lecture Notes in Computer Science  
The paper concludes with the application of the proposed method to a dataset of experimental data demonstrating a stable solution when iterative radial voting and level set methods are used synergistically  ...  These colonies are first delineated from background using the level set method.  ...  This local neighborhood is further partitioned based on its intensity distribution using the level set methods. Organization of the paper is as follows. Section 2 summarized previous methods.  ... 
doi:10.1007/11919629_59 fatcat:jcrbg3veyzhm3nwgonbd4e5z3u

Clustering initiated multiphase active contours and robust separation of nuclei groups for tissue segmentation

Adel Hafiane, Filiz Bunyak, Kannappan Palaniappan
2008 Pattern Recognition (ICPR), Proceedings of the International Conference on  
We describe a novel approach for tissue segmentation using fuzzy spatial clustering, vector-based multiphase level set active contours and nuclei detection using an iterative kernel voting scheme that  ...  It requires sophisticated algorithms for image segmentation, tissue architecture characterization, global texture feature extraction, and high-dimensional clustering and classification algorithms.  ...  The algorithm described in this section is based on a recent Hough transform-like approach for detecting centers of individual cell nuclei based on the segmented nucleus clusters (see previous section)  ... 
doi:10.1109/icpr.2008.4761744 pmid:35695882 pmcid:PMC9186214 dblp:conf/icpr/HafianeBP08 fatcat:lhhxevziqvdwzef3stixzwtive

Coupled segmentation of nuclear and membrane-bound macromolecules through voting and multiphase level set

Hang Chang, Quan Wen, Bahram Parvin
2015 Pattern Recognition  
, where clumps of nuclei are segmented through a delaunay triangulation approach, and (iii) assign membrane-bound macromolecules to individual cells through an application of multi-phase geodesic level-set  ...  Segmentation of these membrane proteins on a cell-by-cell basis enables the quantitative assessment of localization for comparative analysis.  ...  DE-AC02-05CH11231 with the University of California.  ... 
doi:10.1016/j.patcog.2014.10.005 pmid:25530633 pmcid:PMC4269261 fatcat:dkaprkvcyza4nmfsvn6sz2jne4

QUANTITATIVE REPRESENTATION OF THREE-DIMENSIONAL CELL CULTURE MODELS

Hang Chang, Catherine Park, Bahram Parvin
2007 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
The paper concludes with the application of the proposed method to a set of experimental data demonstrating a stable solution when iterative radial voting and level set methods are used synergistically  ...  These colonies are first delineated from the background using the level set method.  ...  This local neighborhood is further partitioned based on its intensity distribution using level set methods.  ... 
doi:10.1109/isbi.2007.356795 dblp:conf/isbi/ChangPP07 fatcat:uyuk6qvqrfe4leztt3qvfmerv4

PERCEPTUAL GROUPING OF MEMBRANE SIGNALS IN CELL-BASED ASSAYS

H. Chang, K. Andarawewa, J. Han, M. Barcellos-Hoff, B. Parvin
2007 2007 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
This paper introduces an iterative voting method for inferring the membrane signal as it relates to continuity.  ...  A unique aspect of this technique is in the topography of the voting kernel, which is refined and reoriented iteratively.  ...  Update the voting direction: Compute the Hessian of the voted landscape and construct an orientation map based on Equation 2. 5.  ... 
doi:10.1109/isbi.2007.356906 dblp:conf/isbi/ChangAHBP07 fatcat:clxjeuz5k5bbxlcbv7fcsanpcy

Robust Nucleus/Cell Detection and Segmentation in Digital Pathology and Microscopy Images: A Comprehensive Review

Fuyong Xing, Lin Yang
2016 IEEE Reviews in Biomedical Engineering  
In addition, we discuss the challenges for the current methods and the potential future work of nucleus/cell detection and segmentation.  ...  In the past few decades, many efforts have been devoted to automated nucleus/cell detection and segmentation.  ...  [233] have proposed a fast coupled level set method based on the four color theorem to segment cells in phase-contrast microscopy images, and another efficient level set method is reported in [192]  ... 
doi:10.1109/rbme.2016.2515127 pmid:26742143 pmcid:PMC5233461 fatcat:hx5ldvsppvgzxk6rdiok7siyvi

Multiscale iterative voting for differential analysis of stress response for 2D and 3D cell culture models

J. HAN, H. CHANG, Q. YANG, G. FONTENAY, T. GROESSER, M. HELEN BARCELLOS-HOFF, B. PARVIN
2010 Journal of Microscopy  
The main issues are the volume of data, overlapping subcellular compartments and variation in scale or size of subcompartments of interest, which lead to ambiguities for quantitative analysis on a cell-by-cell  ...  We address these ambiguities through a series of geometric operations that constrain the problem through iterative voting and decomposition strategies.  ...  In Li et al. (2007) , a method based on regularization of the gradient vector flow is proposed.  ... 
doi:10.1111/j.1365-2818.2010.03442.x pmid:21118235 fatcat:f5tmhnypxngy5prvw5wcxb4wa4

Iterative Voting for Inference of Structural Saliency and Characterization of Subcellular Events

Bahram Parvin, Qing Yang, Ju Han, Hang Chang, Bjorn Rydberg, Mary Helen Barcellos-Hoff
2007 IEEE Transactions on Image Processing  
This paper introduces the iterative voting method, which uses oriented kernels for inferring saliency as it relates to symmetry.  ...  Iterative voting has been implemented in both 2-D and 3-D for multi image analysis.  ...  Examples of iterative methods include the level set method [13] and the regularized centroid transform (RCT) [23] , which iteratively transport boundary points to the local center of mass.  ... 
doi:10.1109/tip.2007.891154 pmid:17357723 fatcat:5r6cu5gtcjdw7f6phbl53b2omm
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