Robust segmentation of overlapping cells in histopathology specimens using parallel seed detection and repulsive level set

IEEE Transactions on Biomedical Engineering

Volumn 59, Issue 3, 2012, Pages 754-765

  Qi, Xin ^a   Xing, Fuyong ^b   Foran, David J ^a   Yang, Lin ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

Level set; mean shift; parallel computing; seed detection; segmentation

Indexed keywords

AUTOMATED IMAGE ANALYSIS; AUTOMATED SEGMENTATION; BLOOD SMEARS; BREAST CANCER; DETECTION ALGORITHM; EARLY DETECTION; GRAPHIC PROCESSING UNITS; HUMAN EXPERT; IMAGE PATCHES; INTERACTIVE MODELS; LEVEL SET; LEVEL SET ALGORITHM; MEAN SHIFT; NOVEL ALGORITHM; OVERLAPPING CELLS; PARALLEL VERSION; PARALLELIZATIONS; RGB CAMERAS; ROBUST SEGMENTATION; SEGMENTATION ALGORITHMS; SINGLE PATH; TISSUE MICROARRAYS; TOUCHING CELLS;

ALGORITHMS; AUTOMATION; CELLS; IMAGE SEGMENTATION; PARALLEL ARCHITECTURES; PARALLEL PROCESSING SYSTEMS; SEED; TISSUE;

CYTOLOGY;

HEMATOXYLIN;

ALGORITHM; ARTICLE; BLOOD SMEAR; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; PROCEDURES CONCERNING CELLS; TISSUE MICROARRAY;

ALGORITHMS; BREAST NEOPLASMS; EARLY DIAGNOSIS; FEMALE; HISTOLOGICAL TECHNIQUES; HUMANS; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MICROARRAY ANALYSIS; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; STAINING AND LABELING;

EID: 84863170133     PISSN: 00189294     EISSN: 15582531     Source Type: Journal    
DOI: 10.1109/TBME.2011.2179298     Document Type: Article

References (45)

1. A. Jemal, R. Siegel, E. Ward, Y. Hao, J. Xu, and M. J. Thun, "Cancer statistics: 2010," CA Cancer J. Clin., vol. 60, no. 5, pp. 277-300, 2010.
2. J. Kononen, L. Bubendorf, A. Kallionimeni, M. Barlund, P. Schraml, S. Leighton, J. Torhorst,M. J.Mihatsch,G. Sauter, and O. P. Kallionimeni, "Tissue microarrays for high-throughput molecular profiling of tumor specimens," Nature Med., vol. 4, pp. 844-847, 1998. (Pubitemid 28331029)
3. D. L. Rimm, R. L. Camp, L. A. Charette, J. Costa, D. A. Olsen, and M. Reiss, "Tissue microarray: A new technology for amplification of tissue resources," Cancer J., vol. 7, pp. 24-31, 2001.
4. R. L. Camp, L. A. Charette, andD. L. Rimm, "Validation of tissuemicroarray technology in breast carcinoma," Lab. Invest., vol. 80, pp. 1943-1949, 2000. (Pubitemid 32012762)
5. O. P. Kallioniemi, U. Wagner, J. Kononen, and G. Sauter, "Tissue microarray technology for high-throughput molecular profiling of cancer," Human Mol. Genet., vol. 10, pp. 657-662, 2001. (Pubitemid 32331572)
6. R. L. Parker, D. G. Huntsman, D. W. Lesack, J. B. Cupples, D. R. Grant, M. Akbari, and C. B. Gilks, "Assessment of interlaboratory variation in the immunohistochemical determination of estrogen receptor status using a breast cancer tissuemicroarray," Amer. J. Clin. Pathol., vol. 117, pp. 723-728, 2002. (Pubitemid 34457006)
7. D. M. A. El-Rehim, G. Ball, S. E. Pinder, E. Rakha, C. Paish, J. F. R. Robertson, D. Macmillan, R. W. Blamey, and I. O. Ellis, "Highthroughput protein expression analysis using tissuemicroarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses," Int. J. Cancer, vol. 116, pp. 340-350, 2005. (Pubitemid 40993329)
8. M. V. Iorio, M. Ferracin, C. Liu, A. Veronese, R. Spizzo, E. M. S. Sabbioni, M. Pedriali, M. Fabbri, M. Campiglio, S. Menard, J. P. Palazzo, A. Rosenberg, P. Musiani, S. Volinia, I. Nenci, G. A. Calin, P. Querzoli, M. Negrini, and C. M. Croce, "Microrna gene expression deregulation in human breast cancer," Cancer Res., vol. 65, pp. 7065-7070, 2005. (Pubitemid 41161233)
9. A. Afework, M. D. Beynon, F. Bustamante, S. Cho, A. Demarzo, R. Ferreira, R. Miller, M. Silberman, J. Saltz, A. Sussman, and H.Tsang, "Digital dynamic telepathology-The virtual microscope," in Proc. Amer. Med. Informat. Assoc., 1998, pp. 912-916.
10. B. Molnar, L. Berczi, C. Diczhazy, A. Tagscherer, S. V. Varga, B. Szende,and Z. Tulassay, "Digital slide and virtualmicroscopy based on routine and telepathology evaluation of routine gastrointestinal biopsy specimens," J. Clin. Pathol., vol. 56, pp. 433-438, 2003. (Pubitemid 36724211)
11. M. Lundin, J. Lundin, and J. Isola, "A digital atlas of breast histopathology: An application of web based virtual microscopy," J. Clin. Pathol., vol. 57, pp. 1288-1291, 2004. (Pubitemid 39611514)
12. M. Datar,D. Padfield, and H.Cline, "Color and texture based segmentation of molecular pathology images using HSOMs," in Proc. IEEE Int. Symp. Biomed. Imag., 2008, pp. 292-295.
13. T. Amaral, S. McKenna, K. Robertson, and A. Thompson, "Classification of breast-tissuemicroarry spots using colour and local invariants," in Proc. IEEE Int. Symp. Biomed. Imag., 2008, pp. 999-1002.
14. A. Hafiane, F. Bunyak, and K. Palaniappan, "Evaluation of level set-based histology image segmentation using geometric region criteria," in Proc. IEEE Int. Symp. Biomed. Imag., 2009, pp. 1-4.
15. X. Zhou, K. Y. Liu, N. Bradley, N. Perrimon, and S. T. Wong, "Towards automated cellular image segmentation for RNAi genome-wide screening,"in Proc.Med. Image Comput. Comput. Assist. Intervent., 2005, pp. 885-892. (Pubitemid 43828333)
16. R. Rodríquez, T. E. Alarcón, and O. Pacheco, "A new strategy to obtain robust markers for blood vessels segmentation by using the watersheds method," Comput. Biol. Med., vol. 35, no. 8, pp. 665-686, 2005. (Pubitemid 41206727)
17. C. Wahlby, J. Lindblad, M. Vondrus, E. Bengtsson, and L. Bjorkesten, "Algorithms for cytoplasm segmentation of fluorescence labelled cells," Anal. Cell. Pathol., vol. 24, pp. 101-111, 2002. (Pubitemid 35340818)
18. G. Lin, M. K. Chawla, K. Olson, J. F. Guzowski, C. A. Barnes, and B. Roysam, "Hierarchical, model-basedmerging of multiple fragments for improved three-dimensional segmentation of nuclei," Cytometry, vol. 63, pp. 20-33, 2005. (Pubitemid 40194276)
19. W.Yu,H.Lee, S. Hariharan,W.Y. Bu, and S. Ahmed, "Quantitative neurite outgrowth measurement based on image segmentation with topological dependence," Cytometry, vol. 75, pp. 289-297, 2009.
20. W. Yu, H.K. Lee, S. Hariharan, W. Bu, and S. Ahmed, "Evolving generalized Voronoi diagrams for accurate cellular image segmentation," Cytometry, vol. 77, pp. 379-386, 2010.
21. T. R. Jones, A. Carpenter, and P. Golland, "Voronoi-based segmentation of cell on image manifolds," Comput. Vis. Biomed. Image Appl., vol. 3765,pp. 535-543, 2005. (Pubitemid 43741559)
22. G. Li, T. Liu, A. Tarokh, J. Nie, L. Guo, A. Mara, S. Holley, and S. T. C. Wong, "3D cell nuclei segmentation based on gradient flow tracking," Bio. Med. Central Cell Biol., vol. 8, pp. 1-10, 2007.
23. Q.Wen, H.Chang, and B. Parvin, "A delaunay triangulation approach for segmenting clumps on nuclei," in Proc. IEEE Int. Symp. Biomed. Imag., 2009, pp. 9-12.
24. S. Kothari, Q. Chaudry, and W. D. Wang, "Automated cell counting and cluster segmentation using convavity detection and ellipse fitting techniques," in Proc. IEEE Int. Symp. Biomed. Imag., 2009, pp. 795-798.
25. G. Diaz, F. Gonzalez, and E. Romero, "Automatic clump splitting for cell quantification in microscopical images," Progr. Pattern Recognit., Image Anal. Appl., vol. 1, pp. 763-772, 2007.
26. L. Yang, O. Tuzel, P. Meer, and D. J. Foran, "Automatic image analysis of histopathology specimens using concave vertex graph," in Proc. Int. Conf. Med. Image Comput. Comput. Assist. Intervent., 2008, vol. 5241, pp. 833-841.
27. G. M. Faustino, M. Gattass, S. Rehen, and C. J. P. Lucena, "Automatic embryonic stem cells detection and counting method in fluorescence microscopy images," in Proc. IEEE Int. Symp. Biomed. Imag., 2009, pp. 799-802.
28. C. Chen, H.Li, X. Zhou, and S. T. C.Wong, "Constraint factor graph cutbased active contour method for automated cellular image segmentation in RNAi screening," J. Microsc., vol. 230, pp. 177-191, 2008. (Pubitemid 351594956)
29. S. Nasr-Isfahani, A. Mirasfian, and A. Masoudi-Nejad, "A new approach for touching cells segmentation," in Proc. Int. Conf. BioMed. Eng. Informat., 2008, vol. 1, pp. 816-820.
30. M. Elter, V. Daum, and T. Wittenberg, "Maximum-intensity-linking for segmentation of fluorescence-stained cells," in Proc.Microsc. Image Anal. Appl. Biol., 2006, pp. 46-50.
31. Y. Al-Kofahi,W. Lassoued,W. Lee, and B. Roysam, "Improved automatic detection and segmentation of cell nuclei in histopathology images," IEEE Trans. Biomed. Eng., vol. 57, no. 4, pp. 841-852, Apr. 2010.
32. R. Malladi, J. A. Sethian, and B. C. Vermuri, "Shape modeling with front propagation: A level set approach," IEEE Trans. Pattern Anal. MacH.Intell., vol. 17, no. 2, pp. 158-174, Feb. 1995.
33. H.K. Zhao, T. F. Chan, B. Merriman, and S. Osher, "A variational level set approach to multiphase motion," J. Comput. Phys., vol. 127, pp. 179-195, 1996.
34. S. Osher and J. A. Sethian, "Fronts propagating with curvature-dependent speed: Algorithms based on Hamilton-Jacobi formulations," J. Comput. Phys., vol. 79, pp. 12-49, 1998.
35. L. A. Vese and T. F. Chan, "A multiphase level set framework for image segmentation using the Mumford and shah model," Int. J. Comput. Vis., vol. 50, pp. 271-293, 2002. (Pubitemid 35377416)
36. B. Zhang, C. Zimmer, and J. C. Olivo-Marin, "Tracking fluorescent cells with coupled geometric active contours," in Proc. Int. Symp. Biomed. Imag., 2004, vol. 1, pp. 476-479. (Pubitemid 40513977)
37. A. Dufour, V. Shinin, S. Tajbakhsh, N. Guillen-Aghion, J. C. Olivo-Marin, and C. Zimmer, "Segmenting and tracking fluoresent cells in dynamic 3D microscopy with coupled active surfaces," IEEE Trans. Image Process., vol. 14, no. 9, pp. 1396-1410, Sep. 2005. (Pubitemid 41430901)
38. P. Yan, X. Zhou, M. Shah, and S. T. C. Wong, "Automatic segmentation of high-throughput RNAi fluorescent cellular images," IEEE Trans. Inf. Technol. Biomed., vol. 12, no. 1, pp. 109-117, Jan. 2008. (Pubitemid 351266649)
39. X. Qi, F. Xing, D. J. Foran, and L. Yang, "GPU enabled parallel touching cell segmentation using mean shift based seed detection and repulsive level set," in Proc. High Perform. Comput. (HP) Workshop Assoc. Proc. Int. Conf. Med. Image Comput. Comput. Assist. Intervent. (MICCAI), 2010.
40. W. Chen,M.Reiss, andD. J. Foran, "Aprototype for unsupervised analysis of tissue microarrays for cancer research and diagnostics," IEEE Trans. Inf. Technol. Biomed., vol. 8, no. 2, pp. 89-96, Jun. 2004.
41. D. J. Foran, L. Yang, O. Tuzel, W. Chen, J. Hu, T. Kurc, R. Ferreira, and J. Saltz, "A caGrid-enabled, learning based image segmentation method for histopathology specimens," in Proc. Int. Symp. Biomed. Imag., 2009, pp. 1306-1309.
42. B. Parvin, Q. Yang, J. Han, H.Chang, B. Rydberg, and M. H.Barcellos-Hoff, "Iterative voting for inference of structural saliency and characterization of subcellular events," IEEE Trans. Image Process., vol. 16, no. 3, pp. 615-623, Mar. 2007. (Pubitemid 46431961)
43. T. F. Chan and L. A. Vese, "Active contours without edges," IEEE Trans. Image Process., vol. 10, no. 2, pp. 266-277, Feb. 2001. (Pubitemid 32254596)
44. R. Baeza-Yates and B. Ribeiro-Neto, Modern Information Retrieval, 1st ed. Reading, MA: Addison-Wesley, 2005.
45. L. Grady and E. L. Schwartz, "Isoperimetric graph partitioning for image segmetentation," IEEE Trans. Pattern Anal. MacH.Intell., vol. 28, no. 1, pp. 469-475, Mar. 2006. (Pubitemid 43159642)