Visualizing Escherichia coli sub-cellular structure using sparse deconvolution spatial light interference tomography

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Mir, Mustafa ^a,b   Babacan, S Derin ^b   Bednarz, Michael ^a   Do, Minh N ^a,b   Golding, Ido ^a,c   Popescu, Gabriel ^a,b  

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

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

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MINCE PROTEIN; MREB PROTEIN; UNCLASSIFIED DRUG;

ALGORITHM; ARTICLE; BACTERIAL CELL; CELL STRUCTURE; ESCHERICHIA COLI; FOURIER TRANSFORMATION; IMAGE ANALYSIS; IMAGE QUALITY; IMAGING; INTERMETHOD COMPARISON; MICROSCOPY; NONHUMAN; SPATIAL LIGHT INTERFERENCE TOMOGRAPHY; SPATIAL LIGHT MICROSCOPY; STRUCTURE ANALYSIS;

ESCHERICHIA COLI; FLUORESCENT DYES; LIGHT; SUBCELLULAR FRACTIONS; TOMOGRAPHY;

ESCHERICHIA COLI;

EID: 84863001314     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0039816     Document Type: Article

References (57)

1. Abbe E, (1873) Beitrage zur Theorie des Mikroscps und der mikrskopischen Wahrnehmung. Arch Mikrosk Anat 9.
2. Popescu G, (2011) Quantitative phase imaging of cells and tissues. New York: McGraw-Hill. 362 p.
3. Stephens DJ, Allan VJ, (2003) Light microscopy techniques for live cell imaging. Science 300: 82-86.
4. Tsien RY, (1998) The green fluorescent protein. Annual Review of Biochemistry 67: 509-544.
5. Hell SW, Wichmann J, (1994) Breaking the Diffraction Resolution Limit by Stimulated-Emission - Stimulated-Emission-Depletion Fluorescence Microscopy. Optics Letters 19: 780-782.
6. Rust MJ, Bates M, Zhuang XW, (2006) Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods 3: 793-795.
7. Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, et al. (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313: 1642-1645.
8. Hess ST, Girirajan TPK, Mason MD, (2007) Nanoscale visualization of fluorescent protein distributions in cells by fluorescence photoactivation localization microscopy (FPALM). Biophysical Journal pp. 419a-419a.
9. Gustafsson MGL, (2005) Nonlinear structured-illumination microscopy: Wide-field fluorescence imaging with theoretically unlimited resolution. Proceedings of the National Academy of Sciences of the United States of America 102: 13081-13086.
10. Hell SW, (2009) Microscopy and its focal switch. Nat Methods 6: 24-32.
11. Zernike F, (1955) How I Discovered Phase Contrast. Science 121: 345-349.
12. Wright SJ, Wright DJ, (2002) Introduction to confocal microscopy. Cell Biological Applications of Confocal Microscopy, Second Edition 70: 1-+.
13. Hell S, Stelzer EHK, (1992) Fundamental Improvement of Resolution with a 4pi-Confocal Fluorescence Microscope Using 2-Photon Excitation. Optics Communications 93: 277-282.
14. Huang B, Wang WQ, Bates M, Zhuang XW, (2008) Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319: 810-813.
15. Ikeda T, Popescu G, Dasari RR, Feld MS, (2005) Hilbert phase microscopy for investigating fast dynamics in transparent systems. Opt Lett 30: 1165-1167.
16. Popescu G, Ikeda T, Dasari RR, Feld MS, (2006) Diffraction phase microscopy for quantifying cell structure and dynamics. Opt Lett 31: 775-777.
17. Popescu G, Deflores LP, Vaughan JC, Badizadegan K, Iwai H, et al. (2004) Fourier phase microscopy for investigation of biological structures and dynamics. Optics Letters 29: 2503-2505.
18. Joo C, Akkin T, Cense B, Park BH, de Boer JE, (2005) Spectral-domain optical coherence phase microscopy for quantitative phase-contrast imaging. Optics Letters 30: 2131-2133.
19. Rockward WS, Thomas AL, Zhao B, DiMarzio CA, (2008) Quantitative phase measurements using optical quadrature microscopy. Applied Optics 47: 1684-1696.
20. Chen BQ, Stamnes JJ, (1998) Validity of diffraction tomography based on the first Born and the first Rytov approximations. Applied Optics 37: 2996-3006.
21. Gbur G, Wolf E, (2001) Relation between computed tomography and diffraction tomography. J Opt Soc Am A Opt Image Sci Vis 18: 2132-2137.
22. Zysk AM, Reynolds JJ, Marks DL, Carney PS, Boppart SA, (2003) Projected index computed tomography. Opt Lett 28: 701-703.
23. Choi W, Fang-Yen C, Badizadegan K, Oh S, Lue N, et al. (2007) Tomographic phase microscopy. Nat Methods 4: 717-719.
24. Charriere F, Marian A, Montfort F, Kuehn J, Colomb T, et al. (2006) Cell refractive index tomography by digital holographic microscopy. Opt Lett 31: 178-180.
25. Charriere F, Pavillon N, Colomb T, Depeursinge C, Heger TJ, et al. (2006) Living specimen tomography by digital holographic microscopy: morphometry of testate amoeba. Opt Express 14: 7005-7013.
26. Fiolka R, Wicker K, Heintzmann R, Stemmer A, (2009) Simplified approach to diffraction tomography in optical microscopy. Opt Express 17: 12407-12417.
27. Debailleul M, Georges V, Simon B, Morin R, Haeberle O, (2009) High-resolution three-dimensional tomographic diffractive microscopy of transparent inorganic and biological samples. Optics Letters 34: 79-81.
28. Maire G, Drsek F, Girard J, Giovannini H, Talneau A, et al. (2009) Experimental Demonstration of Quantitative Imaging beyond Abbe's Limit with Optical Diffraction Tomography. Physical Review Letters 102.
29. Wang Z, Millet L, Mir M, Ding H, Unarunotai S, et al. (2011) Spatial light interference microscopy (SLIM). Opt Express 19: 1016-1026.
30. Mir M, Wang Z, Shen Z, Bednarz M, Bashir R, et al. (2011) Optical measurement of cycle-dependent cell growth. Proc Natl Acad Sci U S A 108: 13124-13129.
31. Wang Z, Chun IS, Li XL, Ong ZY, Pop E, et al. (2010) Topography and refractometry of nanostructures using spatial light interference microscopy. Optics Letters 35: 208-210.
32. Wang Z, Marks DL, Carney PS, Millet LJ, Gillette MU, et al. (2011) Spatial light interference tomography (SLIT). Optics Express 19: 19907-19918.
33. Van Aert S, Van Dyck D, den Dekker AJ, (2006) Resolution of coherent and incoherent imaging systems reconsidered - Classical criteria and a statistical alternative. Optics Express 14: 3830-3839.
34. Sarder P, Nehorai A, (2006) Deconvolution methods for 3-D fluorescence microscopy images. Ieee Signal Processing Magazine 23: 32-45.
35. Wallace W, Schaefer LH, Swedlow JR, (2001) A workingperson's guide to deconvolution in light microscopy. Biotechniques 31: 1076-1078, 1080, 1082 passim.
36. Cotte Y, Toy MF, Pavillon N, Depeursinge C, (2010) Microscopy image resolution improvement by deconvolution of complex fields. Optics Express 18: 19462-19478.
37. Haldar JP, Wang Z, Popescu G, Liang ZP, (2011) Deconvolved Spatial Light Interference Microscopy for Live Cell Imaging. Ieee Transactions on Biomedical Engineering 58: 2489-2497.
38. Babacan SD, Wang Z, Do M, Popescu G, (2011) Cell imaging beyond the diffraction limit using sparse deconvolution spatial light interference microscopy. Biomed Opt Express 2: 1815-1827.
39. Donachie WD, (1993) The Cell-Cycle of Escherichia-Coli. Annual Review of Microbiology 47: 199-230.
40. Shih YL, Le T, Rothfield L, (2003) Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles. Proceedings of the National Academy of Sciences of the United States of America 100: 7865-7870.
41. Donachie WD, (2001) Co-ordinate regulation of the Escherichia coli cell cycle or The cloud of unknowing. Molecular Microbiology 40: 779-785.
42. Raskin DM, de Boer PAJ, (1999) Rapid pole-to-pole oscillation of a protein required for directing division to the middle of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 96: 4971-4976.
43. Sun Q, Margolin W, (1998) FtsZ dynamics during the division cycle of live Escherichia coli cells. Journal of Bacteriology 180: 2050-2056.
44. Ghosh AS, Young KD, (2005) Helical disposition of proteins and lipopolysaccharide in the outer membrane of Escherichia coli. Journal of Bacteriology 187: 1913-1922.
45. Wang Z, Popescu G, (2010) Quantitative phase imaging with broadband fields. Applied Physics Letters 96:-.
46. Wang Z, Millet L, Chan V, Ding HF, Gillette MU, et al. (2011) Label-free intracellular transport measured by spatial light interference microscopy. Journal of Biomedical Optics 16.
47. Wang R, Wang Z, Millet L, Gillette MU, Levine AJ, et al. (2011) Dispersion-relation phase spectroscopy of intracellular transport. Optics Express 19: 20571-20579.
48. Mir M, Tangella K, Popescu G, (2011) Blood testing at the single cel level using quantitative phase and amplitude microscopy. Biomed Opt Exp 2: 3259-3266.
49. Wang Z, Balla A, Tangella K, Popescu G, (2011) Tissue refractive index as marker of disease. J Biomed Opt 16: 116017-116011-116015.
50. Sridharan S, Mir M, Popescu G, (2011) Simultaneous optical measurement of cell motility and growth. Biomed Opt Exp 2: 2815-2820.
51. Donoho D, (2004) For most large underdetermined systems of linear equations the minimal L1-norm near solution approximates the sparsest solution. Technical Report.
52. Szameit A, Shechtman Y, Osherovich E, Bullkich E, Sidorenko P, et al. (2012) Sparsity-based single-shot subwavelength coherent diffractive imaging. Nat Mater.
53. Shechtman Y, Eldar YC, Szameit A, Segev M, (2011) Sparsity based sub-wavelength imaging with partially incoherent light via quadratic compressed sensing. Opt Express 19: 14807-14822.
54. Babacan SD, Molina R, Katsaggelos AK, (2010) Sparse Bayesian Image Restoration. IEEE International Conference on Image Processing (ICP 2010). Hong Kong.
55. Nikolova M, Ng MK, (2005) Analysis of half-quadratic minimization methods for signal and image recovery. Siam Journal on Scientific Computing 27: 937-966.
56. Allain M, Idier J, Goussard Y, (2006) On global and local convergence of half-quadratic algorithms. Ieee Transactions on Image Processing 15: 1130-1142.
57. Ding H, Wang Z, Nguyen F, Boppart SA, Popescu G, (2008) Fourier Transform Light Scattering of Inhomogeneous and Dynamic Structures. PRL 101.