Problems and Solutions in 3-D Analysis of Phase Biological Objects by Optical Diffraction Tomography

REFERENCES

• Cuche , E. ; Bevilacqua , F. ; Depeursinge , C. Digital holography for quantitative phase-contrast imaging . Opt. Lett. 1999 , 24 , 291 – 293 .
   PubMed Web of Science ®Google Scholar
• Lue , N. ; Choi, W.; Popescu, G.; Ikeda, T.; Dasari, R.; Badizadegan, K.; Feld, M. Quantitative phase imaging of live cells using fast Fourier phase microscopy . Appl. Opt. 2007 , 46 , 1836 – 1842 .
   PubMed Web of Science ®Google Scholar
• Dubois , F. ; Yourassowsky, C.; Monnom, O.; Legros, J.C.; Debeir, O.; Van Ham, P.; Kiss, R.; Decaestecker, C. Digital holographic microscopy for the three-dimensional dynamic analysis of in vitro cancer cell migration . J. Biomed. Opt. 2006 , 11 , 054032 .
   Web of Science ®Google Scholar
• Kemper , B. ; Carl, D.; Schnekenburger, J.; Bredebusch, I.; Schäfer, M.; Domschke, W.; von Bally, G. Investigation of living pancreas tumor cells by digital holographic microscopy . J. Biomed. Opt. 2006 , 11 , 034005 .
   PubMed Web of Science ®Google Scholar
• Marquet , P. ; Rappaz, B.; Magistretti, P.J.; Cuche, E.; Emery, Y.; Colomb, T.; Depeursinge, C. Digital holographic microscopy: A noninvasive contrast imaging technique allowing quantitative visualization of living cells with subwavelength axial accuracy . Opt. Lett. 2005 , 30 , 468 – 470 .
   PubMed Web of Science ®Google Scholar
• Charrière , F. ; Marian, A.; Montfort, F.; Kuehn, J.; Colomb, T.; Cuche, E.; Marquet, P.; Depeursinge, C . Cell refractive index tomography by digital holographic microscopy . Opt. Lett. 2006 , 31 , 178 – 180 .
   PubMed Web of Science ®Google Scholar
• Debailleul , M. ; Georges, V.; Simon, B.; Morin, R.; Haeberlé, O. High-resolution three-dimensional tomographic diffractive microscopy of transparent inorganic and biological samples . Opt. Lett. 2009 , 34 , 79 – 81 .
   PubMedGoogle Scholar
• Sung , Y. ; Choi, W.; Fang-Yen, C.; Badizadegan, K.; Dasari, R.R.; Feld, M.S. Optical diffraction tomography for high resolution live cell imaging . Opt. Express 2009 , 17 , 266 – 277 .
   PubMed Web of Science ®Google Scholar
• Kozacki , T. ; Kujawińska , M. ; Kniażewski , P. Investigation of limitations of optical diffraction tomography . Opto-Electron. Rev. 2007 , 15 , 102 – 109 .
   Web of Science ®Google Scholar
• Kak , A.C. ; Slaney , M. Principles of Computerized Tomographic Imaging . Society for Industrial and Applied Mathematics , Philadelphia , 2001 .
   Google Scholar
• Devaney , A.J. A filtered backpropagation algorithm for diffraction tomography. Ultrasonic Imaging 1982 , 4 , 336 – 350 .
   PubMed Web of Science ®Google Scholar
• Charrière , F. ; Pavillon, N.; Colomb, T.; Depeursinge, C.; Heger, T.J.; Mitchell, E.A.; Marquet, P.; Rappaz, B. Living specimen tomography by digital holographic microscopy: morphometry of testate amoeba . Opt. Express 2006 , 14 , 7005 – 13 .
   PubMed Web of Science ®Google Scholar
• Fauver , M. ; Seibel, E.; Rahn, J.R.; Meyer, M.; Patten, F.; Neumann, T.; Nelson, A. Three-dimensional imaging of single isolated cell nuclei using optical projection tomography. Opt. Express 2005, 13, 4210–23.
   PubMed Web of Science ®Google Scholar
• Kus , A. ; Dudek, M.; Kemper, B.; Kujawińska, M.; Vollmer, A. Tomographic phase microscopy of living 3D cell cultures . J. Biomed. Opt. 2014 , 19 , 46009 .
   Web of Science ®Google Scholar
• La Porta , A. ; Wang , M. Optical torque wrench: Angular trapping, rotation, and torque detection of quartz microparticles . Phys. Rev. Lett. 2004 , 92 , 9 – 12 .
   Web of Science ®Google Scholar
• Kreysing , M.K. ; Kiessling, T.; Fritsch, A.; Dietrich, C.; Guck, J.R.; Käs, J.A. The optical cell rotator . Opt. Express 2008 , 16 , 912 – 914 .
   Web of Science ®Google Scholar
• Carmon , G. ; Feingold , M. Controlled alignment of bacterial cells with oscillating optical tweezers . J. Nanophotonics 2011 , 5 , 051803 .
   Web of Science ®Google Scholar
• Bingelyte , V. ; Leach , J. ; Courtial , J. ; Padgett , M.J. Optically controlled three-dimensional rotation of microscopic objects . Appl. Phys. Lett. 2003 , 82 , 829 .
   Web of Science ®Google Scholar
• Hörner , F. ; Woerdemann, M.; Müller, S.; Maier, B.; Denz, C. Full 3D translational and rotational optical control of multiple rod-shaped bacteria . J. Biophotonics 2010 , 3 , 468 – 475 .
   PubMed Web of Science ®Google Scholar
• Kus , A. ; Krauze , W. ; Kujawińska , M. Limited-angle hybrid diffraction tomography for biological samples . Proc. SPIE 2014 , 9132 , 9132 – 24 .
   Google Scholar
• Kim , K. ; Yoon, H.; Diez-Silva, M.; Dao, M.; Dasari, R.R.; Park, Y. High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography . J. Biomed. Opt. 2014 , 19 , 011005 .
   Web of Science ®Google Scholar
• Lauer , V. New approach to optical diffraction tomography yielding a vector equation of diffraction tomography and a novel tomographic microscope . J. Microsc. 2002 , 205 , 165 – 176 .
   PubMed Web of Science ®Google Scholar
• Debailleul , M. ; Simon, B.; Georges, V.; Haeberlé, O.; Lauer, V. Holographic microscopy and diffractive microtomography of transparent samples . Meas. Sci. Technol. 2008 , 19 , 074009 .
   Web of Science ®Google Scholar
• Fang-Yen , C. ; Choi, W.; Sung, Y.; Holbrow, C.J.; Dasari, R.R.; Feld, MS. Video-rate tomographic phase microscopy . J. Biomed. Opt. 2011 , 16 , 011005 .
   Web of Science ®Google Scholar
• Cotte , Y. ; Toy, F.; Jourdain, P.; Pavillon, N.; Boss, D.; Magistretti, P.; Marquet, P.; Depeursinge, C. Marker-free phase nanoscopy . Nat. Photonics 2013 , 7 , 113 – 117 .
   Web of Science ®Google Scholar
• Su , T.-W. ; Isikman, S.O.; Bishara, W.; Tseng, D.; Erlinger, A.; Ozcan, A. Multi-angle lensless digital holography for depth resolved imaging on a chip . Opt. Express 2010 , 18 , 9690 – 711 .
   PubMed Web of Science ®Google Scholar
• Isikman , S.O. ; Bishara, W.; Mavandadi, S.; Yu, F.W.; Feng, S.; Lau, R.; Ozcan, A. Lens-free optical tomographic microscope with a large imaging volume on a chip . Proc. Natl. Acad. Sci. U. S. A. 2011 , 108 , 7296 – 7301 .
   PubMed Web of Science ®Google Scholar
• Wedberg , T.C. ; Stamnes , J.J. ; Singer , W. Comparison of the filtered backpropagation and the filtered backprojection algorithms for quantitative tomography . Appl. Opt. 1995 , 34 , 6575 – 6581 .
   PubMedGoogle Scholar
• Kostencka , J. ; Kozacki , T. Optical diffraction tomography: accuracy of an off-axis reconstruction . Proc. SPIE 2014 , 9132 , 9132 – 22 .
   Google Scholar
• Brenner , K.-H. ; Singer , W. Light propagation through microlenses: A new simulation method . Appl. Opt. 1993 , 32 , 4984 – 4988 .
   PubMedGoogle Scholar
• Taflove , A. ; Hagness , S. Computational Electrodynamics . Artech House : Norwood , 2000 .
   Google Scholar
• Kozacki , T. ; Falaggis , K. ; Kujawińska , M. Computation of diffracted fields for the case of high numerical aperture using the angular spectrum method . Appl. Opt. 2012 , 51 , 7080 – 8 .
   PubMed Web of Science ®Google Scholar
• Fang-Yen , C. ; Choi, W.; Sung, Y.; Holbrow, C.J.; Dasari, R.R.; Feld, MS. Video-rate tomographic phase microscopy . J. Biomed. Opt. 2011 , 16 , 011005
   Web of Science ®Google Scholar
• Natterer , F. The Mathematics of Computerized Tomography . Wiley : New York , 1986 .
   Google Scholar
• Vertu , S. ; Yamada, I.; Delaunay, J-J.; Haeberlé, O.; Flüge, J. Diffraction microtomography with sample rotation: primary result on the influence of a missing apple core in the recorded frequency space. Proc. SPIE 2009, 7390, 7390-1D.
   Google Scholar
• Likhachov , A. Projection data replenishment algorithm for limited angle tomography . Optoelec. Instr. Data Proc. 2009 , 45 , 55 – 61 .
   Google Scholar
• Andersen , A. Simultaneous algebraic reconstruction technique (SART): A superior implementation of the ART algorithm . Ultrasonic Imaging 1984 , 6 , 81 – 94 .
   PubMed Web of Science ®Google Scholar
• Verhoeven , D. Limited-data computed tomography algorithms for the physical sciences . Appl. Opt. 1993 , 32 , 3736 – 3754 .
   PubMed Web of Science ®Google Scholar
• Krauze , W. ; Kujawińska , M. Limited-angle tomography applied to biological objects . Phot. Lett. Poland 2013 , 5 , 149 – 151 .
   Google Scholar
• Sidky , E. ; Kao , C. ; Pan , X. Accurate image reconstruction from few-views and limited-angle data in divergent-beam CT . J. X-Ray Sci. Technol. 2006 , 14 , 119 – 139 .
   Web of Science ®Google Scholar
• Takeda , M. ; Ina , H. ; Kobayashi , S. Fourier-transform method of fringe-pattern analysis for computer-based topography; and interferometry . J. Opt. Soc. Am. 1982 . 72 , 156 .
   Web of Science ®Google Scholar
• Kemper , B. ; Vollmer, A.; Rommel, C.E.; Schnekenburger, J.; von Bally, G. Simplified approach for quantitative digital holographic phase contrast imaging of living cells . J. Biomed. Opt. 2011 , 16 , 026014 .
   Web of Science ®Google Scholar
• Ziółkowska , K. ; Stelmachowska, A.; Kwapiszewski, R.; Chudy, M.; Dybko, A.; Brzózka, Z. Long-term three-dimensional cell culture and anticancer drug activity evaluation in a microfluidic chip . Biosens. Bioelectron. 2013 , 40 , 68 – 74 .
   PubMed Web of Science ®Google Scholar
• Kostencka , J. ; Kozacki, T.; Kuś, A.; Dudek, M.; Kujawińska, M.; Kemper, B. Holographic method for capillary induced aberration compensation for 3D tomographic measurements of living cells . Proc. SPIE 2013 , 8792 , 8792-04 .
   Google Scholar
• Garcia , D. Robust smoothing of gridded data in one and higher dimensions with missing values . Comput. Statist. Data Anal. 2010 , 54 , 1167 – 1178 .
   PubMed Web of Science ®Google Scholar
• Wang , G. ; Garcia, D.; Liu, Y.; de Jeu, R.; Dolman, J. A three- dimensional gap filling method for large geophysical datasets: Application to global satellite soil moisture observations . Environ. Modell. Softw. 2012 , 30 , 139 – 142 .
   Web of Science ®Google Scholar
• Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/uopt.
   Google Scholar