A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy

Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings

Volumn , Issue , 2007, Pages 5559-5562

  Niemistö, Antti ^a,b   Korpelainen, Tomi ^b   Saleem, Ramsey ^a   Yli Harja, Olli ^b   Aitchison, John ^a   Shmulevich, Ilya ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

Author keywords

Confocal microscope; Image analysis; Image stack; K means clustering; Mathematical morphology; Segmentation; Three dimensional; Thresholding; Yeast

Indexed keywords

CONFOCAL MICROSCOPY; IMAGE ANALYSIS; MATHEMATICAL MORPHOLOGY; YEAST;

IMAGE STACKS; K MEANS CLUSTERING;

IMAGE SEGMENTATION;

ALGORITHM; ANATOMY; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; COMPUTER ASSISTED DIAGNOSIS; CONFOCAL MICROSCOPY; CYTOLOGY; EVALUATION STUDY; IMAGE ENHANCEMENT; METHODOLOGY; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANATOMY, CROSS-SECTIONAL; ARTIFICIAL INTELLIGENCE; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SENSITIVITY AND SPECIFICITY;

EID: 57649205399     PISSN: 05891019     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IEMBS.2007.4353606     Document Type: Conference Paper

References (16)

1. Z. Bar-Joseph, S. Farkash, D. K. Gifford, I. Simon, and R. Rosenfeld, "Deconvolving cell, cycle expression data with complementary information," Bioinformatics, vol. 20, no. Supplement 1, pp. i23-i30, Aug. 2004.
2. S. Cookson, N. Ostroff, W. L. Pang, D. Volfson, and J. Hasty, "Monitoring dynamics of single-cell gene expression over multiple cell cycles," Mol. Syst. Biol., vol. 1, Nov. 2005.
3. A. Gordon, A. Colman-Lerner, T. E. Chin, K. R. Benjamin, R. C. Yu, and R. Brent, "Single-cell quantification of molecules and rates using open-source microscope-based cytometry," Nat. Methods, vol. 4, no. 2, pp. 175-181, Feb. 2007.
4. M. Kaksonen, C. P. Toret, and D. G. Drubin, "A modular design for the clathrin- and actin-mediated endocytosis machinery," Cell, vol. 123, no. 2, pp. 305-230, Oct. 2005.
5. R. Narayanaswamy, W. Niu, A. D. Scouras, G. T. Hart, J. Davies, A. D. Ellington, V. R. Iyer, and E. M. Marcotte, "Systematic profiling of cellular phenotypes with spotted cell microarrays reveals matingpheromone response genes," Genome Biol., vol. 7, no. 1, Jan. 2006.
6. D. G. O'Shea and P. K. Walsh, "The effect of culture conditions on the morphology of the dimorphic yeast Kluyveromyces marxianus var. marxianus NRRLy2415: a study incorporating image analysis," Appl. Microbiol Biotechnol., vol. 53, no. 3, pp. 316-322, Mar. 2000.
7. T. L. Saito, et al., "SCMD: Saccharomyces cerevisiae morphological database," Nucleic Acids Res., vol. 32, pp. D319-D322, January 2004.
8. M. Kaksonen, Y. Sun, and D. G. Drubin, "A pathway for association of receptors, adaptors, and actin during endocytic internalization," Cell, vol. 115, no. 4, pp. 475-487, Nov. 2003.
9. A. Niemistö, T. Aho, H. Thesleff, M. Tiainen, K. Marjanen, M.-L. Linne, and O. Yli-Harja, "Estimation of population effects in synchronized budding yeast experiments," in Image Processing: Algorithms and Systems II, ser. Proc. SPIE, vol. 5014, 2003, pp. 448-459.
10. A. Niemistö, J. Selinummi, R. Saleem, I. Shmulevich, J. Aitchison, and O. Yli-Harja, "Extraction of the number of peroxisomes in yeast cells by automated image analysis," in Proc. 28th Ann. Int'l Conf. IEEE Engineering in Medicine and Biology Society (EMBC'06), New York, USA, Aug. 30 - Sept. 3 2006, pp. 2353-2356.
11. M. Ohtani, A. Saka, F. Sano, Y. Ohya, and S. Morishita, "Development of image processing program, for yeast cell morphology," J. Bioinform. Comput. Biol., vol. 1, no. 4, pp. 695-709, January 2004.
12. A. Robinson, N. Sadr-kazemi, G. Dickason, and S. T. L. Harrison, "Morphological characterisation of yeast colony growth, on solid media using image processing," Biotechnol. Tech., vol. 12, no. 10, pp. 763767, Oct. 1998.
13. J. A. Hartigan and M. A. Wong, "A K-means clustering algorithm," Appl. Stat, vol. 28, no. 1, pp. 100-108, 1979.
14. N. Otsu, "A threshold selection memod from gray-level histograms," IEEE Trans. Syst., Man, Cybern., vol. 9, no. 1, pp. 62-66, Jan. 1979.
15. B. Tso and R. C. Olsen, "Combining spectral and spatial information into hidden Markov models for unsupervised image classification," Int. J. Remote Sensing, vol. 26, no. 10, pp. 2113-2133, May 2005.
16. R. A. D. Carano, A. L. Ross, J. Ross, S. P. Williams, H. Koeppen, R. H. Schwall, and N. van Bruggen, "Quantification of tumor tissue populations by multispectral analysis," Magn. Reson. Med., vol. 51, no. 3, pp. 542-551, Mar. 2004.