Automated segmentation and classification of high throughput yeast assay spots

IEEE Transactions on Medical Imaging

Volumn 26, Issue 10, 2007, Pages 1401-1411

  Jafari Khouzani, Kourosh ^a,b   Soltanian Zadeh, Hamid ^a   Fotouhi, Farshad ^b   Parrish, Jodi R ^c   Finley Jr , Russell L ^c  

^a HENRY FORD HOSPITAL   (United States)

^b Wayne State University   (United States)

^c WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Color image analysis; High throughput yeast assays; Neural networks; Texture classification; Wavelet transforms

Indexed keywords

BIOASSAY; COLOR IMAGE PROCESSING; NEURAL NETWORKS; WAVELET TRANSFORMS; YEAST;

COLOR IMAGE ANALYSIS; HIGH THROUGHPUT YEAST ASSAYS; TEXTURE CLASSIFICATION;

IMAGE SEGMENTATION;

FUNGAL PROTEIN;

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; COLORIMETRY; COMPUTER ASSISTED DIAGNOSIS; EVALUATION; IMAGE ENHANCEMENT; METABOLISM; METHODOLOGY; PHYSIOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; TWO HYBRID SYSTEM; YEAST;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COLORIMETRY; FUNGAL PROTEINS; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TWO-HYBRID SYSTEM TECHNIQUES; YEASTS;

EID: 34948899353     PISSN: 02780062     EISSN: None     Source Type: Journal    
DOI: 10.1109/TMI.2007.900694     Document Type: Article

References (26)

1. E. Phizicky, P. I. Bastiaens, H. Zhu, M. Snyder, and S. Fields, "Protein analysis on a proteomic scale," Nature, vol. 422, no. 6928, pp. 208-215, 2003.
2. S. Fields, Y. Kohara, and D. J. Lockhart, "Functional genomics," in Proc. Natl Acad. Sci. USA, 1999, vol. 96, no. 16, pp. 8825-8826.
3. T. R. Hughes, M. D. Robinson, N. Mitsakakis, and M. Johnston, "The promise of functional genomics: Completing the encyclopedia of a cell," Curr. Opin. Microbiol., vol. 7, no. 5, pp. 546-554, 2004.
4. R. Brent and R. L. Finley Jr., "Understanding gene and allele function with two-hybrid methods," Annu. Rev. Genet., vol. 31, pp. 663-704, 1997.
5. S. Fields and O. Song, "A novel genetic system to detect protein-protein interactions," Nature, vol. 340, no. 6230, pp. 245-246, 1989.
6. A. Weiss, J. Delproposto, and C. N. Giroux, "High-throughput phenotypic profiling of gene-environment interactions by quantitative growth curve analysis in Saccharomyces cerevisiae," Anal Biochem., vol. 327, no. 1, pp. 23-34, 2004.
7. T. R. Hughes, "Yeast and drug discovery," Funct. Integr. Genomics., vol. 2, no. 4-5, pp. 199-211, 2002.
8. R. A. Butcher and S. L. Schreiber, "Identification of Ald6p as the target of a class of small-molecule suppressors of FK506 and their use in network dissection," in Proc. Natl Acad. Sci. USA, 2004, vol. 101, no. 21, pp. 7868-7873.
9. C. A. Stanyon, G. Liu, B. A. Mangiola, N. Patel, L. Giot, B. Kuang, H. Zhang, J. Zhong, and R. L. Finley Jr., "A Drosophila protein-interaction map centered on cell-cycle regulators," Genome. Biol., vol. 5, no. 12, p. R96, 2004.
10. P. Uetz et a!., "A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae," Nature, vol. 403, no. 6770, pp. 623-627, 2000.
11. J. Estojak, R. Brent, and E. A. Golemis, "Correlation, of two-hybrid affinity data with in vitro measurements," Mol. Cell Biol., vol. 15, no. 10, pp. 5820-5829, 1995.
12. J. Zhong, H. Zhang, C. A. Stanyon, G. Tromp, and R. L. Finley Jr., "A strategy for constructing large protein interaction maps using the yeast two-hybrid system: Regulated expression arrays and two-phase mating," Genome. Res., vol. 13, no. 12, pp. 2691-2699, 2003.
13. R. Nagarajan and C. A. Peterson, "Identifying spots in microarray images," IEEE Trans. Nanobiosci., vol. 1, no. 2, pp. 78-84, Jun. 2002.
14. R. Nagarajan, "Intensity-based segmentation of microarray images," IEEE Trans. Med Imag., vol. 22, no. 7, pp. 882-889, Jul. 2003.
15. M. Katzer, F. Kummert, and G. Sagerer, "Methods for automatic microarray image segmentation," IEEE Trans. Nanobiosci., vol. 2, no. 4, pp. 202-214, Dec. 2003.
16. A. W.-C. Liew, H. Yan, and M. Yang, "Robust adaptive spot segmentation of DNA microarray images," Pattern Recognit., vol. 36, no. 5, pp. 1251-1254, May 2003.
17. R. Hirata Jr., J. Barrera, R. F. Hashimoto, D. O. Dantas, and G. H. Esteves, "Segmentation of microarray images by mathematical morphology," Real-Time Imag., vol. 8, no. 6, pp. 491-505, Dec. 2002.
18. A. P. G. Damiance Jr., L. Zhao, and A. C. P. L. F. Carvalho, "A dynamical model with adaptive pixel moving for microarray images segmentation," Real-Time Imag., vol. 10, no. 4, pp. 189-195, Aug. 2004.
19. S. Trattner, H. Greenspan, G. Tepper, and S. Abboud, "Automatic identification of bacterial types using statistical imaging methods," IEEE Trans. Med. Imag., vol. 23, no. 7, pp. 807-820, Jul. 2004.
20. K. Jafari-Khouzani and H. Soltanian-Zadeh, "Radon transform orientation estimation for rotation invariant texture analysis," IEEE Trans. Pattern Anal Mach. Intell., vol. 27, no. 6, pp. 1004-1008, Jun. 2005.
21. H. Soltanian-Zadeh, J. P. Windham., and D. J. Peck, "Optimal linear transformation, for MRI feature extraction," IEEE Trans. Med. Imag., vol. 15, no. 6, pp. 749-767, Dec. 1996.
22. I. Daubechies, Ten Lectures on Wavelets, Soc. Ind. Appl Math., Philadelphia, PA: SIAM, 1992.
23. A. Laine and J. Fan, "Texture classification by wavelet packet signatures," IEEE Trans. Pattern Anal Mach. Intell., vol. 15, no. 11, pp. 1186-1191, Nov. 1993.
24. K. Sam-Deuk and S. Udpa, "Texture classification using rotated wavelet filters," IEEE Trans. Syst., Man, Cybern., A, Syst., Humans, vol. 30, no. 6, pp. 847-852, Nov. 2000.
25. E. Gose, R. Johnsonbaugh, and S. Jost, Pattern Recognition and Image Analysis. Englewood Cliffs, NJ: Prentice-Hall, 1996.
26. C. M. Bishop, Neural Networks for Pattern Recognition. Oxford, U.K.: Oxford Univ. Press, 1995.