Detecting circular and rectangular particles based on geometric feature detection in electron micrographs

Journal of Structural Biology

Volumn 145, Issue 1-2, 2004, Pages 168-180

  Yu, Zeyun ^a   Bajaj, Chandrajit ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANISOTROPY; ATOMIC PARTICLE; AUTOMATION; CONFERENCE PAPER; ELECTRON MICROSCOPY; GEOMETRY; IMAGING; MACROMOLECULE; PRIORITY JOURNAL;

EID: 0347355581     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jsb.2003.10.027     Document Type: Conference Paper

References (39)

1. Andrews D.W., Yu A.H.C., Ottensmerer F.P. Automatic selection of molecular images from dark field electron micrographs. Ultramicroscopy. 19:1986;1-14.
2. Bajaj, C., Wu, Q., Xu, G., 2003. Level-set based volumetric anisotropic diffusion for 3D image denoising. ICES Technical Report #301, University of Texas at Austin.
3. Baker T.S., Olson N.H., Fuller S.D. Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Microbiol. Mol. Biol. Rev. 63(4):1999;862-922.
4. Barash D. A fundamental relationship between bilateral filtering, adaptive smoothing and the nonlinear diffusion equation. IEEE Trans. Pattern Anal. Machine Intelligence. 24(6):2002;844-847.
5. Canny J. A computational approach to edge detection. IEEE Trans. Pattern Anal. Machine Intelligence. 8:1986;679-698.
6. Carragher B.et al. Leginon: an automated system for acquisition of images from vitreous ice specimens. J. Struct. Biol. 132:2000;33-45.
7. Durand, F., Dorsey, J., 2002. Fast bilateral filtering for the display of high-dynamic-range images. In: Proceedings of the ACM Conference on Computer Graphics (SIGGRAPH), pp. 257-266.
8. Elad M. On the bilateral filter and ways to improve it. IEEE Trans. Image Processing. 11(10):2002;1141-1151.
9. Frank J. Three-dimensional electron microscope of macromolecular assemblies. 1996;Academic Press, San Diego.
10. Frank J., Wagenknecht T. Automatic selection of molecular images from electron micrographs. Ultramicroscopy. 12:1984;169-176.
11. Gavrila, D.M., 1998. Multi-feature hierarchical template matching using distance transforms. In: Proceedings of the 1998 International Conference on Pattern Recognition, pp. 439-444.
12. Gonzalez R.C., Woods R.E. Digital Image Processing. 1992;Addison-Wesley.
13. Guan W., Ma S. A list-processing approach to compute Voronoi diagram and Euclidean distance transform. IEEE Trans. Pattern Anal. Machine Intelligence. 20(7):1998;757-761.
14. Hamza A.B.et al. Removing noise and preserving details with relaxed median filters. J. Math. Imaging and Vis. 11(2):1999;161-177.
15. Harauz G., Fong-Lochovsky A. Automatic selection of macromolecules from electron micrographs by component labeling and symbolic processing. Ultramicroscopy. 31(4):1989;333-344.
16. Heath, M.D., 1996. A robust visual method for assessing the relative performance of edge-detection algorithms (Master's Thesis). Department of Computer Sceince, University of South Florida, Tampa, Florida, p. 145.
17. Heel M.v. Detection of objects in quantum-noise-limited images. Ultramicroscopy. 7:1982;331-342.
18. Heel M.v.et al. Single-particle electron cryo-microscopy: to-wards atomic resolution. Q. Rev. Biophys. 33(4):2000;307-369.
19. Henderson R. The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological macromolecules. Quart. Rev. Biophys. 28:1995;171-193.
20. Huttenlocher D.P., Klanderman G.A., Rucklidge W.J. Comparing images using the Hausdorff distance. IEEE Trans. Pattern Anal. Machine Intelligence. 15(9):1993;850-863.
21. Kivioja T.et al. Local average intensity-based method for identifying spherical particles in electron micrographs. J. Struct. Biol. 131(2):2000;126-134.
22. Lata K.R., Renczek P., Frank J. Automatic particle picking from electronic micrographs. Ultramicroscopy. 58:1995;381-391.
23. Ludtke S.J., Baldwin P.R., Chiu W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128(1):1999;82-97.
24. Martin I.M.B.et al. Identification of spherical virus particles in digitized images of entire electron micrographs. J. Struct. Biol. 120(2):1997;146-157.
25. Nicholson W.V., Glaeser R.M. Review: automatic particle detection in electron microscopy. J. Struct. Biol. 133(2-3):2001;90-101.
26. Ogura T., Sato C. An automatic particle pickup method using a neural network applicable to low-contrast electron micrographs. J. Struct. Biol. 136:2001;227-238.
27. Perona P., Malik J. Scale-space and edge detection using anisotropic diffusion. IEEE Trans. Pattern Anal. Machine Intelligence. 12(7):1990;629-639.
28. Potter C.S.et al. Leginon: A system for fully automated acquisition of 1000 micrographs a day. Ultramicroscopy. 77:1999;153-161.
29. Roseman A.M. Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy. 94:2003;225-236.
30. Rucklidge, W.J., 1995. Locating objects using the Hausdorff distance. In: Proceedings of the 1995 IEEE Conference on Computer Vision, pp. 457-464.
31. Saad, A., Chiu, W., Thuman-Commike, P., 1998. Multiresolution approach to automatic detection of spherical particles from electron cryomicroscopy images. In: Proceedings of the IEEE International Conference on Image Processing, pp. 8-10.
32. Stoschek A., Hegerl R. Automated detection of macromolecules from electron micrographs using advanced filter techniques. J. Microsc. (Oxford). 185:1997;76-94.
33. Thuman-Commike P., Chiu W. Automatic detection of spherical particles from spot-scan electron cryomicroscopy images. J. Micros. Soc. Am. 1:1995;191-201.
34. Thuman-Commike P., Chiu W. PTOOL: a software package for the selection of particles from electron cryomicroscopy spot-scan images. J. Struct. Biol. 116(1):1996;41-47.
35. Tomasi, C., Manduchi, R., 1998. Bilateral filtering for gray and color images. In: Proceedings of the IEEE International Conference on Computer Vision, pp. 836-846.
36. Weickert, J., 1998. Anisotropic Diffusion In Image Processing. ECMI Series, Teubner, Stuttgart, ISBN 3-519-02606-6.
37. Xu Y.et al. Wavelet Transform Domain Filters: a spatially selective noise filtration technique. IEEE Trans. Image Processing. 3(6):1994;747-758.
38. Zhu Y.et al. Automated identification of filaments in cryo-electron microscopy images. J. Struct. Biol. 135(3):2001;302-312.
39. Zhu, Y., Carragher, B., Potter, C.S., 2002. Fast detection of generic biological particles in cryo-EM images through efficient Hough transforms. In: Proceedings of the 2002 IEEE International Symposium for Biomedical Imaging, pp. 205-208.