Image analysis and length estimation of biomolecules using AFM

IEEE Transactions on Information Technology in Biomedicine

Volumn 16, Issue 6, 2012, Pages 1200-1207

  Sundstrom, Andrew ^a   Cirrone, Silvio ^b   Paxia, Salvatore ^c   Hsueh, Carlin ^d   Kjolby, Rachel ^e   Gimzewski, James K ^d,e   Reed, Jason ^e   Mishra, Bud ^a  

^a NEW YORK UNIVERSITY   (United States)

^b ACCENTURE   (United States)

^c Blackstone Group   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e CALIFORNIA NANOSYSTEMS INSTITUTE   (United States)

Author keywords

Atomic force microscopy (AFM); Beaton Tukey; biased estimation; biomolecule; biweight; cDNA; digital contour; DNA; image processing; length estimation; linear regression; machine learning; RNA; single molecule; supervised learning

Indexed keywords

BEATON-TUKEY; BIASED ESTIMATION; BIWEIGHT; CDNA; DIGITAL CONTOUR; LENGTH ESTIMATION; SINGLE MOLECULE;

ATOMIC FORCE MICROSCOPY; BIOMOLECULES; DNA; ESTIMATION; IMAGE ANALYSIS; IMAGE PROCESSING; LEARNING SYSTEMS; LINEAR REGRESSION; MOLECULES; RNA; SUPERVISED LEARNING; TRANSCRIPTION;

PROBLEM SOLVING;

DNA;

ARTIFICIAL INTELLIGENCE; ATOMIC FORCE MICROSCOPY; AUTOMATED PATTERN RECOGNITION; CHEMISTRY; IMAGE PROCESSING; PROCEDURES; STATISTICAL MODEL; ARTICLE; METHODOLOGY;

ARTIFICIAL INTELLIGENCE; DNA; IMAGE PROCESSING, COMPUTER-ASSISTED; LINEAR MODELS; MICROSCOPY, ATOMIC FORCE; PATTERN RECOGNITION, AUTOMATED;

EID: 84870947621     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2012.2206819     Document Type: Article

References (34)

1. B. Atal and L. Rabiner, "A pattern recognition approach to voiced-unvoiced-silence classification with applications to speech recognition," IEEE Trans. Acoust., Speech Signal Process., vol. 24, no. 3, pp. 201-212, Jun. 1976.
2. Y. Saeys, I. Inza, and P. Larrañaga, "A review of feature selection techniques in bioinformatics," Bioinformatics, vol. 23, no. 19, pp. 2507-2517, 2007.
3. M. Kirby and L. Sirovich, "Application of the Karhunen-Loeve procedure for the characterization of human faces," IEEE Trans. Pattern Anal. Mach. Intell., vol. 12, no. 1, pp. 103-108, 1990.
4. D. Forsyth, J. Malik, M. Fleck, H. Greenspan, T. Leung, S. Belongie, C. Carson, and C. Bregler, "Finding pictures of objects in large collections of images," in Object Representation in Computer Vision II (Lecture Notes in Computer Science) Berlin, Germany: Springer, 1996, pp. 335-360.
5. P. Hanchuan, "Bioimage informatics: A new area of engineering biology," Bioinformatics, vol. 24, no. 17, pp. 1827-1836, 2008.
6. V. Jain, J. F. Murray, F. Roth, S. Turaga, V. Zhigulin, K. Briggman, M. Helmstaedter, W. Denk, and H. S. Seung, "Supervised learning of image restoration with convolutional networks," in Proc. IEEE 11th Int. Conf. Comput. Vision, 2007, pp. 1-8.
7. P. Marjoram, J. Molitor, V. Plagnol, and S. Traveré, "Markov chain monte carlo without likelihoods," Proc. Nat. Acad. Sci. USA, vol. 100, no. 26, pp. 15324-15328, 2003.
8. J. Reed, B. Mishra, B. Pittenger, S. Magonov, J. Troke, M. A. Teitell, and J. K. Gimzewski, "Single molecule transcription profiling with AFM," Nanotechnology, vol. 18, no. 4, pp. 1-15, 2007.
9. J. Marek, E. Demjénová, Z. Tomori, J. Janáč ek, I. Zolotová, F. Valle, M. Favre, and G. Dietler, "Interactive measurement and characterization of DNA molecules by analysis of AFM images," Cytometry, vol. 63A, no. 2, pp. 87-93, 2005.
10. T. S. Spisz, N. D'Costa, C. K. Seymour, J. H. Hoh, R. Reeves, and I. N. Bankman, "Length determination of DNA fragments in atomic force microscope images," in Proc. Intl. Conf. Image, 1997, pp. 154-157.
11. T. S. Spisz, Y. Fang, R. H. Reeves, C. K. Seymour, I. N. Bankman, and J. H. Hoh, "Automated sizing of DNA fragments in atomic force microscope images," Med. Biol. Eng. Comput., vol. 36, pp. 667-672, 1998.
12. Y. Fang, T. S. Spisz, T. Wiltshire, N. P. D'Costa, I. N. Bankman, R. H. Reeves, and J. H. Hoh, "Solid-state DNA sizing by atomic force microscopy," Anal. Chem., vol. 70, no. 10, pp. 2123-2129, 1998.
13. C. Rivetti and S. Codeluppi, "Accurate length determination of DNA molecules visualized by atomic force microscopy: Evidence for a partial b-to a-form transition on mica," Ultramicroscopy, vol. 87, pp. 55-66, 2001.
14. A. Sanchez-Sevilla, J. Thimonier, M. Marilley, J. Rocca-Serra, and J. Barbet, "Accuracy of AFM measurements of the contour length of DNA fragments adsorbed on mica in air and in aqueous buffer," Ultra-microscopy, vol. 92, pp. 151-158, 2002.
15. E. Ficarra, L. Benini, B. Ricco, and G. Zuccheri, "Automated DNA sizing in atomic force microscope images," IEEE Intl. Symp Biomed. Imaging, vol. 17, no. 10:30.0, pp. 453-456, 2002.
16. E. Ficarra, D. Masotti, L. Benini, M. Milano, and A. Bergia, "A robust algorithm for automated analysis of DNA molecules in AFM images," AI*IA Notizie, vol. 4, pp. 64-68, 2002.
17. E. Ficarra, E. Macii, L. Benini, and G. Zuccheri, "A robust algorithm for automated analysis of DNA molecules in AFM images," in Proc. Biomed. Eng., 2004, vol. 417, pp. 213-218.
18. E. Ficarra, L. Benini, E. Macii, and G. Zuccheri, "Automated DNA fragments recognition and sizing through AFM image processing," IEEE Trans. Info. Technol. Biomed., vol. 9, no. 4, pp. 508-517, Dec. 2005.
19. L. Lam, S.-W. Lee, and C. Y. Suen, "Thinning methodologies-A comprehensive survey," IEEE Trans. Patt. Anal. Mach. Intel., vol. 14, no. 9, pp. 869-885, Sep. 1992.
20. H. Freeman, "Techniques for the digital computer analysis of chain-encoded arbitrary plane curves," in Proc. Nat. Elec. Conf., 1961, vol. 17, pp. 421-432.
21. L. Dorst and A. W. M. Smeulders, "Length estimators for digitized contours," Comp. Vis. Graph. Image Proc., vol. 40, pp. 311-333, 1987.
22. L. Dorst and A. W. M. Smeulders, "Discrete straight line segments: Parameters, primitives and properties," in Vision Geometry, Series Contemporary Mathematics,Providence, RI: American Mathematical Society, 1991, pp. 45-62.
23. M. Worring and A. W. M. Smeuldrers, "Digitized circular arcs: Characterization and parameter estimation," IEEE Trans. Patt. Anal. Mach. Intel., vol. 17, no. 6, pp. 587-598, Jun. 1995.
24. R. Marcondes Cesar, Jr. and L. da Fontoura Costa, "Towards effective planar shape representation with multiscale digital curvature analysis based on signal processing techniques," Patt. Recog., vol. 29, pp. 1559-1569, 1996.
25. A. W. M. Smeulders, L. Dorst, and M. Worring, "Measurement and characterisation in vision geometry," in Proc. SPIE Series, 1997, vol. 3168, pp. 2-21.
26. R. Klette, V. Kovalevsky, and B. Yip, "On the length estimation of digital curves," Univ. Auckland, Auckland, New Zealand, Tech. Rep. CITR-TR-45, May 1999.
27. M. A. T. Figueiredo, J. M. N. Leitão, and A. K. Jain, "Unsupervised contour representation and estimation using B-splines and a minimum description length criterion," IEEE Trans. Image Proc., vol. 9, no. 6, pp. 1075-1087, Jun. 2000.
28. D. Coeurjolly and R. Klette, "A comparative evaluation of length estimators of digital curves," IEEE Trans. Patt. Anal. Mach. Intel., vol. 26, no. 2, pp. 252-258, Feb. 2004.
29. V. Kalmykov, "Structural analysis of contours as the sequences of the digital straight segments and of the digital curve arcs," Intl. J. Info. Th. Appl., vol. 14, no. 3, pp. 238-243, 2007.
30. G. Zuccheri, A. Scipioni, V. Cavaliere, G. Gargiulo, P. De Santis, and B. Samori, "Mapping the intrinsic curvature and flexibility along the DNA chain," Proc. Nat. Acad. Sci., USA, vol. 98, no. 6, pp. 3074-3079, 2001.
31. E. Ficarra, D. Masotti, E. Macii, L. Benini, and B. Samori, "Automatic intrinsic DNA curvature computation from AFM images," IEEE Trans. Biomed. Eng., vol. 52, no. 12, pp. 2074-2086, Dec. 2005.
32. A. E. Beaton and J. W. Tukey, "The fitting of power series, meaning polynomials, illustrated on band-spectroscopic data," Technometrics, vol. 16, no. 2, pp. 147-185, 1974.
33. W. James and C. Stein, "Estimation with quadratic loss," in Proc. Berkeley Symp. Math. Stat. Prob., 1961, pp. 316-379.
34. J. Reed, C. Hsueh, M.-L. Lam, R. Kjolby, A. Sundstrom, B. Mishra, and J. K. Gimzewski, "Identifying individual DNA species in a complex mixture by precisely measuring the spacing between nicking restriction enzymes with atomic force microscope," J. Royal Soc. Interface, Mar. 28, 2012, [Online]. doi: 10.1098/rsif.2012.0024.