Methods for generating high-resolution structural models from electron microscope tomography data

Structure

Volumn 12, Issue 10, 2004, Pages 1763-1774

  Ress, David B ^a   Harlow, Mark L ^a   Marshall, Robert M ^a   McMahan, Uel J ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANIMAL TISSUE; ARTICLE; CELL STRUCTURE; CONTROLLED STUDY; ELECTRON MICROSCOPY; EXPERIMENTAL MODEL; FROG; HIGH RESOLUTION COMPUTER TOMOGRAPHY; MACROMOLECULE; METHODOLOGY; NEUROMUSCULAR SYNAPSE; NONHUMAN; PRIORITY JOURNAL; RELIABILITY; STRUCTURE ANALYSIS;

ANIMALIA; ANURA;

EID: 4644328746     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.07.022     Document Type: Note

References (45)

1. Bajaj C., Yu Z., Auer M. Volumetric feature extraction and visualization of tomographic molecular imaging. J. Struct. Biol. 144:2003;132-143
2. Bocker W., Rolf W., Bauch T., Muller W.U., Streffer C. Automated comet assay analysis. Cytometry. 35:1999;134-144
3. Cooper D.M., Turinsky A.L., Sensen C.W., Hallgrimsson B. Quantitative 3D analysis of the canal network in cortical bone by micro-computed tomography. Anat. Rec. 274B:2003;169-179
4. Frank J. Electron Tomography. Three-Dimensional Imaging with the Transmission Electron Microscope:1992;Plenum Press, New York
5. Frank J., Radermacher M., Penczek P., Zhu J., Li Y., Ladjadj M., Leith A. Spider and web. processing and visualization of images in 3D electron microscopy and related fields J. Struct. Biol. 116:1996;190-199
6. Grau V., Mewes A.U., Alcaniz M., Kikinis R., Warfield S.K. Improved watershed transform for medical image segmentation using prior information. IEEE Trans. Med. Imaging. 23:2004;447-458
7. Harlow M.L., Ress D., Stoschek A., Marshall R.M., McMahan U.J. The architecture of active zone material at the frog's neuromuscular junction. Nature. 409:2001;479-484
8. He W., Cowin P., Stokes D.L. Untangling desmosomal knots with electron tomography. Science. 302:2003;109-113
9. Hessler D., Young S.J., Carragher B.O., Martone M.E., Lamont S., Whittaker M., Milligan R.A., Masliah E., Hinshaw J.E., Ellisman M.H. Programs for visualization in three-dimensional microscopy. Neuroimage. 1:1992;55-67
10. Heuser J.E., Reese T.S. Handbook of Physiology. 1977;American Physiological Society, Bethseda, MD. pp. 261-294.
11. Heuser J.E., Reese T.S. Structural changes after transmitter release at the frog neuromuscular junction. J. Cell Biol. 88:1981;564-580
12. Heuser J.E., Reese T.S., Dennis M.J., Jan Y., Jan L., Evans L. Synaptic vesicle exocytosis captured by quick freezing and correlated with quantal transmitter release. J. Cell Biol. 81:1979;275-300
13. Horowitz R.A., Agard D.A., Sedat J.W., Woodcock C.L. The three-dimensional architecture of chromatin in situ. electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon J. Cell Biol. 125:1994;1-10
14. Hsieh C.E., Marko M., Frank J., Mannella C.A. Electron tomographic analysis of frozen-hydrated tissue sections. J. Struct. Biol. 138:2002;63-73
15. Katz S.B. The Release of Neural Transmitter Substances. 1969;CC Thomas, Springfield, IL
16. Klemencic A., Kovacic S., Pernus F. Automated segmentation of muscle fiber images using active contour models. Cytometry. 32:1998;317-326
17. Kozerke S., Botnar R., Oyre S., Scheidegger M.B., Pedersen E.M., Boesiger P. Automatic vessel segmentation using active contours in cine phase contrast flow measurements. J. Magn. Reson. Imaging. 10:1999;41-51
18. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:1996;71-76
19. Ladinsky M.S., Mastronarde D.N., McIntosh J.R., Howell K.E., Staehelin L.A. Golgi structure in three dimensions. functional insights from the normal rat kidney cell J. Cell Biol. 144:1999;1135-1149
20. Lenzi D., Runyeon J.W., Crum J., Ellisman M.H., Roberts W.M. Synaptic vesicle populations in saccular hair cells reconstructed by electron tomography. J. Neurosci. 19:1999;119-132
21. Li Y., Leith A., Frank J. Tinkerbell-a tool for interactive segmentation of 3D data. J. Struct. Biol. 120:1997;266-275
22. Lin G., Adiga U., Olson K., Guzowski J.F., Barnes C.A., Roysam B. A hybrid 3D watershed algorithm incorporating gradient cues and object models for automatic segmentation of nuclei in confocal image stacks. Cytometry. 56A:2003;23-36
23. Marko M., Leith A. Sterecon-three-dimensional reconstructions from stereoscopic contouring. J. Struct. Biol. 116:1996;93-98
24. Martone M.E., Jones Y.Z., Young S.J., Ellisman M.H., Zivin J.A., Hu B.R. Modification of postsynaptic densities after transient cerebral ischemia. a quantitative and three-dimensional ultrastructural study J. Neurosci. 19:1999;1988-1997
25. McEwen B.F., Radermacher M., Rieder C.L., Frank J. Tomographic three-dimensional reconstruction of cilia ultrastructure from thick sections. Proc. Natl. Acad. Sci. USA. 83:1986;9040-9044
26. McEwen B.F., Arena J.T., Frank J., Rieder C.L. Structure of the colcemid-treated PtK1 kinetochore outer plate as determined by high voltage electron microscopic tomography. J. Cell Biol. 120:1993;301-312
27. McMahan U.J., Slater C.R. The influence of basal lamina on the accumulation of acetylcholine receptors at synaptic sites in regenerating muscle. J. Cell Biol. 98:1984;1453-1473
28. Medalia O., Weber I., Frangakis A.S., Nicastro D., Gerisch G., Baumeister W. Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography. Science. 298:2002;1209-1213
29. Ofverstedt L.G., Zhang K., Isaksson L.A., Bricogne G., Skoglund U. Automated correlation and averaging of three-dimensional reconstructions obtained by electron tomography. J. Struct. Biol. 120:1997;329-342
30. Ortiz de Solorzano C., Garcia Rodriguez E., Jones A., Pinkel D., Gray J.W., Sudar D., Lockett S.J. Segmentation of confocal microscope images of cell nuclei in thick tissue sections. J. Microsc. 193:1999;212-226
31. Perkins G.A., Renken C.W., Song J.Y., Frey T.G., Young S.J., Lamont S., Martone M.E., Lindsey S., Ellisman M.H. Electron tomography of large, multicomponent biological structures. J. Struct. Biol. 120:1997;219-227
32. Ress, D., Harlow, M.L., Marshall, R.A., and McMahan, U.J. (2003). Optimization Method for Isodensity Surface Models Obtained with Electron Microscope Tomography Data. Paper presented at: Engineering in Medicine and Biology Society, 2003. Proceedings of the 25th Annual International Conference of the IEEE.
33. Robitaille R., Garcia M.L., Kaczorowski G.J., Charlton M.P. Functional colocalization of calcium and calcium-gated potassium channels in control of transmitter release. Neuron. 11:1993;645-655
34. Sedzik J., Ofverstedt L.G., Skoglund U. Three-dimensional reconstruction of bovine intradural spinal root myelin by electron microscope tomography. J. Neurosci. Res. 31:1992;387-393
35. Suri J.S., Liu K., Singh S., Laxminarayan S.N., Zeng X., Reden L. Shape recovery algorithms using level sets in 2-D/3-D medical imagery. a state-of-the-art review IEEE Trans. Inf. Technol. Biomed. 6:2002;8-28
36. Taylor K.A., Schmitz H., Reedy M.C., Goldman Y.E., Franzini-Armstrong C., Sasaki H., Tregear R.T., Poole K., Lucaveche C., Edwards R.J., et al. Tomographic 3D reconstruction of quick-frozen, Ca2+-activated contracting insect flight muscle. Cell. 99:1999;421-431
37. Teo P.C., Sapiro G., Wandell B.A. Creating connected representations of cortical gray matter for functional MRI visualization. IEEE Trans. Med. Imaging. 16:1997;852-863
38. Van Essen D.C., Drury H.A., Dickson J., Harwell J., Hanlon D., Anderson C.H. An integrated software suite for surface-based analyses of cerebral cortex. J. Am. Med. Inform. Assoc. 8:2001;443-459
39. van Vliet L.J., Young I.T., Mayall B.H. The Athena semi-automated karyotyping system. Cytometry. 11:1990;51-58
40. Volkmann N. A novel three-dimensional variant of the watershed transform for segmentation of electron density maps. J. Struct. Biol. 138:2002;123-129
41. Woodcock C.L., McEwen B.F., Frank J. Ultrastructure of chromatin. II. Three-dimensional reconstruction of isolated fibers. J. Cell Sci. 99:1991;107-114
42. Wriggers W., Chacon P. Modeling tricks and fitting techniques for multiresolution structures. Structure. 9:2001;779-788
43. Wu Q.J., Bourland J.D. Three-dimensional skeletonization for computer-assisted treatment planning in radiosurgery. Comput. Med. Imaging Graph. 24:2000;243-251
44. Yezzi A. Jr., Kichenassamy S., Kumar A., Olver P., Tannenbaum A. A geometric snake model for segmentation of medical imagery. IEEE Trans. Med. Imaging. 16:1997;199-209
45. Zavaljevski A., Dhawan A.P., Gaskil M., Ball W., Johnson J.D. Multi-level adaptive segmentation of multi-parameter MR brain images. Comput. Med. Imaging Graph. 24:2000;87-98