TxBR montage reconstruction for large field electron tomography

Journal of Structural Biology

Volumn 180, Issue 1, 2012, Pages 154-164

  Phan, Sébastien ^a   Lawrence, Albert ^a   Molina, Tomas ^a   Lanman, Jason ^a   Berlanga, Monica ^a   Terada, Masako ^a   Kulungowski, Alexander ^a   Obayashi, James ^a   Ellisman, Mark ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

3D reconstruction; Electron tomography; Montaging; Section flattening; TxBR; Whole cell tomography

Indexed keywords

ANIMAL TISSUE; ARTICLE; COMPUTER PROGRAM; ELECTRON MICROSCOPY; ELECTRON TOMOGRAPHY; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE RECONSTRUCTION; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; ROTATION; VOLUMETRY;

ALGORITHMS; ANIMALS; BRAIN; DROSOPHILA; ELECTRON MICROSCOPE TOMOGRAPHY; IMAGING, THREE-DIMENSIONAL; INSECT VIRUSES; MICE; NEURONS; SOFTWARE;

EID: 84866984821     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2012.06.006     Document Type: Article

References (48)

1. Amat F., Moussavi F., Comolli L.R., Elidan G., Downing K.H., et al. Markov random field based automatic image alignment for electron tomography. Journal of Structural Biology 2008, 131:260-275.
2. Berlanga, M.L., Phan, S., Bushong, E.A., Wu, S., Kwon, O., et al., 2011. Three-dimensional reconstruction of serial mouse brain sections: Solution for flattening high-resolution large-scale mosaics. Frontiers in Neuroanatomy 5.
3. Bouwer, J., Lawrence, A.F., 2009. Electron tomography tutorial Part I: Instrumentation. In: Advances in Electron Microscope Instrumentation and Exploration of Biological Structures, Boston.
4. Braumann U.D., Scherf N., Einenkel J., Horn L.C., Wentzensen N., et al. Large histological serial sections for computational tissue volume reconstruction. Methods of Information Medicine 2007, 46:614-622.
5. Cantele F., Paccagnini E., Pigino G., Lupetti P., Lanzavecchia S. Simultaneous alignment of dual-axis tilt series. Journal of Structural Biology 2010, 169:192-199.
6. Capek M., Brůza P., Janácek J., Karen P., Kubínová L., et al. Volume reconstruction of large tissue specimens from serial physical sections using confocal microscopy and correction of cutting deformations by elastic registration. Microscopy Research and Technique 2009, 72:110-119.
7. Cardone G., Grünewald K., Steven A.C. A resolution criterion for electron tomography based on cross-validation. Journal of Structural Biology 2005, 151:117-129.
8. Chen, H., Clyborne, W.K., Sedat, J.W., Agard, D.A., 1992. Priism: an integrated system for display and analysis of 3-d microscope images, SPIE, pp. 784-790.
9. Chow S.K., Hakozaki H., Price D.L., MacLean N.A.B., Deerinck T.J., et al. Automated microscopy system for mosaic acquisition and processing. Journal of Microscopy 2006, 222:76-84.
10. Denk W., Horstmann H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biology 2004, 2:e329.
11. van den Essen, A.R.P., 2000. Polynomial automorphisms and the Jacobian conjecture, volume 190 of Progress in mathematics. Birkhäuser Verlag, Basel.
12. Frank, J., 2006. Electron Tomography, second ed., Plenum Publishing Corporation, New York.
13. Gelfand, I.M., Kapranov, M.M., Zelevinsky, A.V., 1994. Discriminants, resultants, and multidimensional determinants. Mathematics: Theory and Applications, Birkhäuser, Boston.
14. Gracias N., Mahoor M.H., Negahdaripour S., Gleason A. Fast image blending using watersheds and graph cuts. Image and Vision Computing 2009, 27:597-607.
15. Heymann J.B., Cardone G., Winkler D.C., Steven A.C. Computational resources for cryo-electron tomography in bsoft. Journal of Structural Biology 2008, 161:232-242.
16. Höög, J.L., Antony, C., 2007. Whole cell investigation of microtubule cytoskeleton architecture by electron tomography. In: McIntosh, J.R. (Ed.), Cellular Electron Microscopy, volume 79 of Methods in Cell Biology, Academic Press, pp. 145-167.
17. Ju T., Warren J., Carson J., Bello M., Kakadiaris I., et al. 3D volume reconstruction of a mouse brain from histological sections using warp filtering. Journal of Neuroscience Methods 2006, 156:84-100.
18. Korinek A., Beck F., Baumeister W., Nickell S., Plitzko J.M. Computer controlled cryo-electron microscopy - tom2 a software package for high-throughput applications. Journal of Structural Biology 2011, 175:394-405.
19. Kremer J.R., Mastronarde D.N., McIntosh J.R. Computer visualization of three-dimensional image data using imod. Journal of Structural Biology 1996, 116:71-76.
20. Kukulski W., Schorb M., Welsch S., Picco A., Kaksonen M., Briggs J.A. Correlated fluorescence and 3d electron microscopy with high sensitivity and spatial precision. Journal of Cell Biology 2011, 192:111-119.
21. Lanman J., Crum J., Deerinck T.J., Gaietta G.M., Schneemann A., et al. Visualizing flock house virus infection in drosophila cells with correlated fluorescence and electron microscopy. Journal of Structural Biology 2008, 161:439-446.
22. Lawrence A.F., Bouwer J.C., Perkins G., Ellisman M.H. Transform-based backprojection for volume reconstruction of large format electron microscope tilt series. Journal of Structural Biology 2006, 154:144-167.
23. Lee S.C., Bajcsy P. Trajectory fusion for three-dimensional volume reconstruction. Computer Vision and Image Understanding 2008, 110:19-31.
24. Lučić, V., Förster, F., Baumeister, W., 2005. Structural studies by electron tomography: From cells to molecules. Annual Review of Biochemistry.
25. Luysberg, M., Tillmann, K., Weirich, T., Genoud, C., Mancuso, J., et al., 2008. Automatic acquisition of large amounts of 3D data at the ultrastructural level, using serial block face scanning electron microscopy. Springer, Berlin, Heidelberg, pp. 547-548.
26. Marsh B.J. Lessons from tomographic studies of the mammalian golgi. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2005, 1744:273-292.
27. Marsh, B.J., McIntosh, J.R., 2007. Reconstructing Mammalian Membrane Architecture by Large Area Cellular Tomography, vol. 79. Academic Press, pp. 193-220.
28. Mastronarde D.N. Dual-axis tomography: an approach with alignment methods that preserve resolution. Journal of Structural Biology 1997, 120:343-352.
29. Mastronarde D.N. Automated electron microscope tomography using robust prediction of specimen movements. Journal of Structural Biology 2005, 152:36-51.
30. Mastronarde D.N. Fiducial marker and hybrid alignment methods for single- and double-axis tomography. Electron Tomography 2006, 163-185.
31. Mastronarde D.N. Tomographic reconstruction with the imod software package. Microscopy and Microanalysis 2006, 12:178-179.
32. Mastronarde D.N., van der Heide P.A., Morgan G.P., Marsh B.J. Supermontaging: reconstructing large cellular volumes by stitching together laterally adjacent tomograms. Microscopy and Microanalysis 2008, 14:106-107.
33. Messaoudi C., Boudier T., Sorzano C., Marco S. Tomoj: tomography software for three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics 2007, 8:288.
34. Messaoudi C., de Loubresse N.G., Boudier T., Dupuis-Williams P., Marco S. Multiple-axis tomography: applications to basal bodies from paramecium tetraurelia. Biology of the Cell 2006, 98:415-425.
35. Noske A.B., Costin A.J., Morgan G.P., Marsh B.J. Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets. Journal of Structural Biology 2008, 161:298-313.
36. Peltier S.T., Bouwer J.C., Jin L., Khodjasaryan K., Geist S., et al. Design of a new 8k×8k lens coupled detector for wide-field, high-resolution transmission electron microscopy. Microscopy and Microanalysis 2005, 11:610-611.
37. Phan, S., Bouwer, J., Lanman, J., Terada, M., Lawrence, A.F., 2009a. Non-linear bundle adjustment for electron tomography. In: Proceedings of the 2009 WRI World Congress on Computer Science and Information Engineering - Volume 01, IEEE Computer Society, Washington, DC, USA, pp. 604-612.
38. Phan, S., Lawrence, A.F., 2008. Tomography of large format electron microscope tilt series: image alignment and volume reconstruction. Congress on Image and Signal Processing (CISP '08), vol. 2, pp. 176-182.
39. Phan, S., Terada, M., Lawrence, A.F., 2009b. Serial reconstruction and montaging from large-field electron microscope tomograms. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE, pp. 5772-5776.
40. Sanchez Sorzano, C.O., Messaoudi, C., Eibauer, M., Bilbao-Castro, J., Hegerl, R., Nickell, S., Marco, S., Carazo, J., 2009. Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10, 124.
41. Sorzano C.O.S., Marabini R., Velázquez-Muriel J., Bilbao-Castro J.R., Scheres S.H.W., Carazo J.M., Pascual-Montano A. Xmipp: a new generation of an open-source image processing package for electron microscopy. Journal of Structural Biology 2004, 148:194-204.
42. Soto G.E., Young S.J., Martone M.E., Deerinck T.J., Lamont S., Carragher B.O., Hama K., Ellisman M.H. Serial section electron tomography: a method for three-dimensional reconstruction of large structures. NeuroImage 1994, 1:230-243.
43. Sturmfels, B., 2002. Solving Systems of Polynomial Equations, volume no. 97 of Conference Board of the Mathematical Sciences Regional Conference Series in Mathematics. Published for the Conference Board of the Mathematical Sciences by the American Mathematical Society, Providence, R.I.
44. Suloway C., Shi J., Cheng A., Pulokas J., Carragher B., Potter C.S., Zheng S.Q., Agard D.A., Jensen G.J. Fully automated, sequential tilt-series acquisition with leginon. Journal of Structural Biology 2009, 167:11-18.
45. TxBR, 2012. http://confluence.crbs.ucsd.edu/display/ncmir/TxBR.
46. Wan X., Zhang F., Chu Q., Zhang K., Sun F., Yuan B., Liu Z. Three-dimensional reconstruction using an adaptive simultaneous algebraic reconstruction technique in electron tomography. Journal of Structural Biology 2011, 175:277-287.
47. Zampighi G.A., Zampighi L., Fain N., Wright E.M., Cantele F., Lanzavecchia S. Conical tomography ii: a method for the study of cellular organelles in thin sections. Journal of Structural Biology 2005, 151:263-274.
48. Zheng S.Q., Kollman J.M., Braunfeld M.B., Sedat J.W., Agard D.A. Automated acquisition of electron microscopic random conical tilt sets. Journal of Structural Biology 2007, 157:148-155.