Edged watershed segmentation: A semi-interactive algorithm for segmentation of low-resolution maps from electron cryomicroscopy

Journal of Structural Biology

Volumn 176, Issue 1, 2011, Pages 127-132

  Baker, Lindsay A ^a,b   Rubinstein, John L ^a,b,c  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Electron cryomicroscopy; Low resolution; Map interpretation; Segmentation

Indexed keywords

PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ALGORITHM; ARTICLE; CRYOELECTRON MICROSCOPY; ENZYME STRUCTURE; ENZYME SUBUNIT; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; CRYOELECTRON MICROSCOPY; MODELS, MOLECULAR; MULTIPROTEIN COMPLEXES;

EID: 80052290628     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2011.06.012     Document Type: Article

References (25)

1. Abramoff M.D., Magelhaes P.J., Ram S.J. Image processing with ImageJ. Biophoton. Int. 2004, 11:36-42.
2. Beucher S., Meyer F. The morphological approach to segmentation: the watershed transformation. Mathematical Morphology in Image Processing 1993, 433-481. Marcel Dekker, New York. E.R. Dougherty (Ed.).
3. Canny J. A computational approach to edge detection. IEEE Trans. Pattern Anal. Mach. Intell. 1986, 8:679-698.
4. Crowther R.A., Henderson R., Smith J.M. MRC image processing programs. J. Struct. Biol. 1996, 116:9-16.
5. Frangakis A.S., Hegerl R. Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis. J. Struct. Biol. 2002, 138:105-113.
6. Frigo M., Johnson S.G. The Design and implementation of FFTW3. Proc. IEEE 2005, 93:216-231.
7. Gledhill J.R., Montgomery M.G., Leslie A.G., Walker J.E. How the regulatory protein, IF1, inhibits F1-ATPase from bovine mitochondria. Proc. Natl. Acad. Sci. USA 2007, 104:15671-15676.
8. Hagyard D., Razaz M., Atkin P. Analysis of watershed algorithms for greyscale images. Proc. IEEE Int. Conf. Image Process. 1996, 3:41-44.
9. Jiang W., Baker M.L., Jakana J., Weigele P.R., King J., et al. Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 2008, 451:1130-1134.
10. Lau W.C.Y., Rubinstein J.L. Structure of intact Thermus thermophilus V-ATPase by cryo-EM reveals organization of the membrane-bound V(O) motor. Proc. Natl. Acad. Sci. USA 2010, 107:1367-1372.
11. Lee S., Choi J.M., Tsai F.T. Visualizing the ATPase cycle in a protein disaggregating machine: structural basis for substrate binding by ClpB. Mol. Cell 2007, 25:261-271.
12. Liu H., Jin L., Koh S.B., Atanasov I., Schein S., et al. Atomic structure of human adenovirus by Cryo-EM reveals interactions among protein networks. Science 2010, 329:1038-1043.
13. Liu C., Young A.L., Starling-Windhof A., Bracher A., Saschenbrecker S., et al. Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Nature 2010, 463:197-202.
14. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
15. Pintilie G.D., Zhang J., Goddard T.D., Chiu W., Gossard D.C. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 2010, 170:427-438.
16. Pruggnaller S., Mayr M., Frangakis A.S. A visualization and segmentation toolbox for electron microscopy. J. Struct. Biol. 2008, 164:161-165.
17. Serra J. Image Analysis and Mathematical Morphology 1982, Academic Press, Toronto.
18. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., Ludtke S.J. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 2007, 157:38-46.
19. Vincent L., Soille P. Watersheds in digital space: an efficient algorithm based on immersion simulations. IEEE Trans. Pattern Anal. Mach. Intell. 1991, 13:583-598.
20. Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 2002, 138:123-129.
21. Wriggers W., Milligan R.A., Mccammon J.A. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J. Struct. Biol. 1999, 125:185-195.
22. Yu X., Jin L., Zhou Z.H. 3.88A structure of cytoplasmic polyhedrosis virus by cryo-electron microscopy. Nature 2008, 453:415-419.
23. Yu Z., Bajaj C. Automatic ultrastructure segmentation of reconstructed cryoEM maps of icosahedral viruses. IEEE Trans. Image Process. 2005, 14:1324-1337.
24. Zhang X., Settembre E., Xu C., Dormitzer P.R., Bellamy R., et al. Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc. Natl. Acad. Sci. USA 2008, 105:1867-1872.
25. Zhang X., Jin L., Fang Q., Hui W.H., Zhou Z.H. 3.3Å cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. Cell 2010, 141:472-482.