Automated identification of filaments in cryoelectron microscopy images

Journal of Structural Biology

Volumn 135, Issue 3, 2001, Pages 302-312

  Zhu, Yuanxin ^a   Carragher, Bridget ^a   Kriegman, David J ^b   Milligan, Ronald A ^c   Potter, Clinton S ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b University of Illinois at Urbana Champaign   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Automation; Cryoelectron microscopy; Perceptual organization; Phase correlation; Three dimensional reconstruction of helical objects

Indexed keywords

ACCURACY; ARTICLE; AUTOANALYSIS; CONTROLLED STUDY; CRYOELECTRON MICROSCOPY; CRYOPRESERVATION; ELECTRON MICROSCOPE; EVALUATION; INFORMATION PROCESSING; INTERMEDIATE FILAMENT; NONHUMAN; PRIORITY JOURNAL; THREE DIMENSIONAL IMAGING; TOBACCO MOSAIC VIRUS;

NICOTIANA TABACUM; TOBACCO MOSAIC VIRUS;

EID: 0035783362     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2001.4415     Document Type: Article

References (52)

1. Al-Ali, L., and Frank, J. (1980) Resolution estimation in electron microscopy. Optik 56, 31-40.
2. Atiquzzaman, M., and Akhtar, M. W. (1994) Complete line segment description using the Hough transform. Image Vision Comput. 12, 267-273.
3. Bluemke, D. A., Carragher, B., and Josephs, R. (1988) The reconstruction of helical particles with variable pitch. Ultramicroscopy 26, 255-270.
4. Bremer, A., Henn, C., Goldie, K. N., Engel, A., Smith, P. R., and Aebi, U. (1994) Towards atomic interpretation of F-actin filament three-dimensional reconstruction. J. Mol. Biol. 242, 683-700.
5. Canny, J. (1986) A computation approach for edge detection. IEEE Trans. Patt. Anal. Machine Intell. 8, 679-698.
6. Carragher, B., Bluemke, D. A., Gabriel, B., Potel, M. J., and Josephs, R. (1988) Structural analysis of polymers of sickle cell hemoglobin. I. Sickle hemoglobin fibers. J. Mol. Biol. 199, 315-331.
7. Carragher, B., Whittaker, M., and Milligan, R. A. (1996) Helical processing using Phoelix. J. Struct. Biol. 116, 107-112.
8. Carragher, B., Kisseberth, N., Kriegman, D., Milligan, R. A., Potter, C. S., Pulokas, J., and Reilein, A. (2000) Leginon: An automated system for acquisition of images from vitreous ice specimens. J. Struct. Biol. 132, 33-45.
9. DeRosier, D. J., and Moore, P. B. (1970) Reconstruction of three-dimensional images from electron micrographs of structures with helical symmetry. J. Mol. Biol. 52, 355-369.
10. Duda, R. O., and Hart, P. (1972) Use of the Hough transformation to detect lines and curves in pictures. Commun. ACM 15, 11-15.
11. Egelman, E. H. (1986) An algorithm for straightening images of curved filamentous structures. Ultramicroscopy 19, 367-374.
12. Egelman, E. H. (2000) A robust algorithm for the reconstruction of helical filaments using single-particle methods. Ultramicroscopy 85, 225-234.
13. Frank, J. (1980) The role of correlation techniques in computer image processing. In Hawkes, P. W. (Ed.), Computer Processing of Electron Microscope Images, pp. 187-222, Springer Verlag, Berlin.
14. Frank, J., and Wagenknecht, T. (1984) Automatic selection of molecular images from electron micrographs. Ultramicroscopy 12, 169-176.
15. Fuller, S. D. (1987) The T-4 envelope of sindbis virus is organized by interactions with a complimentary T-3 capsid. Cell 48, 923.
16. Harauz, G., and Fong-Lochovsky, A. (1989) Automatic selection of macromolecules from electron micrographs by component labeling and symbolic processing. Ultramicroscopy 31, 333-344.
17. Heath, M. D., Sarkar, S., Sanocki, T., and Bowyer, K. W. (1997) A robust visual method for assessing the relative performance of edge-detection algorithms. IEEE Trans. Patt. Anal. Machine Intell. 19, 1338-1359.
18. Henderson, R. (1995) The potential and limitations of neutrons, electrons, and X-rays for atomic resolution microscopy of unstained biological macromolecules. Quart. Rev. Biophys. 28, 171-193.
19. Hough, P. V. S. (1962) Method and Means for Recognizing Complex Patterns. U.S. Patent 3,069,654.
20. Jeng, T.-W., Crowther, R. A., Stubbs, G., and Chiu, W. (1989) Visualization of alpha-helices in tobacco mosaic virus by cryo-electron microscopy. J. Mol. Biol. 205, 251-257.
21. Karmat-Sadekar, V., and Ganesan, S. (1998) Complete description of multiple line segments using the Hough transform. Image Vision Comput. 16, 597-613.
22. Koffka, K. (1935) Principles of Gestalt Psychology, Harcourt, Brace & World, New York.
23. Kohler, W. (1947) Gestalt Psychology, Liveright, New York.
24. Kuglin, C. D., and Hines, D. C. (1975) The phase correlation image alignment method. Proc. Int. Conf. Cybernetics Soc. 163-165.
25. Lata, K. R., Penczek, P., and Frank, J. (1995) Automatic particle picking from electron micrographs. Ultramicroscopy 58, 381-391.
26. Lowe, D. G. (1985) Perceptual Organization and Visual Recognition, Kluwer Academic, Boston.
27. Lowe, D. G. (1987) Three-dimensional object recognition from single two-dimensional images. Artificial Intelligence 31, 355-395.
28. Ludtke, S. J., Baldwin, P. R., and Chiu, W. (1999) EMAN: Semi-automated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82-97.
29. Martin, I. M. B., Marinescu, D. C., Lynch, R. E., and Baker, T. S. (1997) Identification of spherical virus particles in digitized images of entire electron micrographs. J. Struct. Biol. 120, 146-157.
30. McLaughlin, R. A., and Alder, M. D. (1997) Technical Report - The Hough Transform Versus the Upwrite, Technical Report TR97-02, CIIPS, Department of Electrical and Electronic Engineering, University of Western Australia.
31. Milligan, R. A., and Flicker, P. F. (1987) Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy. J. Cell Biol. 105, 29-39.
32. Mohan, R., and Nevatia, R. (1992) Perceptual organization for scene segmentation and description. IEEE Trans. Patt. Anal. Machine Intell. 14, 616-634.
33. Nogales, E., and Grigorieff, N. (2001) Molecular machines: Putting the pieces together. J. Cell Biol. 152, F1-F10.
34. Owen, C. H., Morgan, D. G., and DeRosier, D. J. (1996) Image analysis of helical objects: The Brandeis helical package. J. Struct. Biol. 116, 167-174.
35. Palmer, S. E. (1983) The psychology of perceptual organization: A transformational approach. In Beck, J., Hope, B., and Rosenfeld, A. (Eds.), Human and Machine Vision, pp. 269-339, Academic Press, New York.
36. Potter, C. S., Chu, H., Frey, B., Green, C., Kisseberth, N., Madden, T. J., Miller, K. L., Nahrstedt, K., Pulokas, J., Reilein, A., Tcheng, D., Weber, D., and Carragher, B. (1999) Leginon: A system for fully automated acquisition of 1000 micrographs a day. Ultramicroscopy 77, 153-161.
37. Sarkar, S., and Boyer, K. L. (1993) Integration, inference, and management of spatial information using bayesian networks: Perceptual organization. IEEE Trans. Patt. Anal. Machine Intell. 15, 256-273.
38. Sarkar, S., and Boyer, K. L. (1994) Computing Perceptual Organization in Computer Vision, World Scientific, Singapore.
39. Saxton, W. O. (1994) Accurate alignment of sets of images. J. Microsc. 174(Pt. 2), 61-68.
40. Schrag, J. D., Prasad, B. V. V., Rixon, F. J., and Chiu, W. (1989) Three-dimensional structure of the HSV1 nucleocapsid. Cell 56, 651.
41. Shi, J., and Malik, J. (2000) Normalized cuts and image segmentation. IEEE Trans. Patt. Anal. Machine Intell. 22, 888-905.
42. Stewart, M., Kessler, M. W., and Levine, R. J. C. (1981) Structure of Limulus telson muscle thick filaments. J. Mol. Biol. 153, 781-790.
43. Thuman-Commike, P. A., and Chiu, W. (1995) Automatic detection of spherical particles from spot-scan electron microscopy images. J. Micros. Soc. Am. 1, 191-201.
44. Trucco, E., and Verri, A. (1998) Introductory Techniques for 3-D Computer Vision. Prentice Hall International, Englewood Cliffs, NJ.
45. Unwin, P. N. T., and Klug, A. (1974) Electron microscopy of the stacked disk aggregate of tobacco mosaic virus protein. I. Three-dimensional image reconstruction. J. Mol. Biol. 87, 641-656.
46. van Heel, M. (1982) Detection of objects in quantum-noise-limited images. Ultramicroscopy 8, 331-342.
47. Wagenknecht, T., DeRosier, D. J., Shapiro, L., and Weissborn, A. (1981) Three-dimensional reconstruction of the flagellar hook from Caulobacter crescentus. J. Mol. Biol. 151, 439-465.
48. Whittaker, M., Carragher, B. O., and Milligan, R. A. (1995) PHOELEX: A package for semi-automated helical reconstruction. Ultramicroscopy 58, 245-259.
49. Williams, L. R., and Thornber, K. K. (1998) A comparison of measures for detecting natural shapes in cluttered backgrounds. In Burkhardt, H., and Neumann, B. (Eds.), Proceedings of the 5th European Conf. Computer Vision, Vol. 2, pp. 432-448, Springer, New York.
50. Yamato, J., Ishii, I., and Makino, H. (1990) Highly accurate segment detection using Hough transformation. Sys. Comp. Jpn. 21, 68-77.
51. Zhou, Z. H. (1995) High Resolution 3-Dimensional Electron Cryomicroscopy and Reconstructions of Herpes Simplex Virus Capsids. Ph.D. thesis, Baylor College of Medicine.
52. Zhou, Z. H., and Chiu, W. (1993) Prospects of using an IVEM with FEG to record images towards atomic resolution. Ultramicroscopy 49, 407-416.