Motion analysis of live objects by super-resolution fluorescence microscopy

Computational and Mathematical Methods in Medicine

Volumn 2012, Issue , 2012, Pages

  Yao, Chunyan ^a,b   Zhang, Jianwei ^b   Wu, Guang ^c,d   Zhang, Houxiang ^e  

^a ZHEJIANG UNIVERSITY OF TECHNOLOGY   (China)

^b UNIVERSITY OF HAMBURG   (Germany)

^c NATIONAL ENGINEERING RESEARCH CENTER FOR NON FOOD BIOREFINERY   (China)

^d DreamSciTech Consulting   (China)

^e NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS; FLUORESCENCE; FLUORESCENCE MICROSCOPY; MEDICAL APPLICATIONS; OBJECT DETECTION; OBJECT TRACKING; VIRUSES;

BIOLOGICAL ENGINEERING; BIOMEDICAL APPLICATIONS; DETECTION AND TRACKING; MOTION BEHAVIOR; MOTION STATISTICS; RESEARCH TOPICS; STATE OF THE ART; SUPER RESOLUTION;

MOTION TRACKING;

ALGORITHM; CELL ACTIVITY; CELL COUNT; CELL NUCLEUS; CELL TRANSPORT; CELLULAR DISTRIBUTION; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE ANALYSIS; MOTION ANALYSIS SYSTEM; NONHUMAN; PROTEIN FUNCTION; REVIEW; SINGLE CELL ANALYSIS; VIRION; BACTERIAL PHENOMENA AND FUNCTIONS; METHODOLOGY; MOTION; PHYSIOLOGY; THREE DIMENSIONAL IMAGING; TRANSPORT AT THE CELLULAR LEVEL; VIRAL PHENOMENA AND FUNCTIONS;

ALGORITHMS; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOLOGICAL TRANSPORT; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, FLUORESCENCE; MOTION; VIRUS PHYSIOLOGICAL PHENOMENA;

EID: 84855604913     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2012/859398     Document Type: Review

References (68)

1. Veigel C., Schmidt C. F., Moving into the cell: single-molecule studies of molecular motors in complex environments Nature Reviews Molecular Cell Biology 2011 12 3 163 176
2. Huang B., Wang W., Bates M., Zhuang X., Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy Science 2008 319 5864 810 813 (Pubitemid 351225870)
3. Huang B., Bates M., Zhuang X., Super-resolution fluorescence microscopy Annual Review of Biochemistry 2009 78 993 1016
4. Bates M., Huang B., Dempsey G. T., Zhuang X., Multicolor super-resolution imaging with photo-switchable fluorescent probes Science 2007 317 5845 1749 1753 (Pubitemid 47461839)
5. Kajstura J., Rota M., Hall S. R., Hosoda T., D'Amario D., Sanada F., Zheng H., Ogrek B., Rondon-Clavo C., Ferreira-Martins J., Matsuda A., Arranto C., Goichberg P., Giordano G., Haley K. J., Bardelli S., Rayatzadeh H., Liu X., Quaini F., Liao R., Leri A., Perrella M. A., Loscalzo J., Anversa P., Evidence for human lung stem cells New England Journal of Medicine 2011 364 19 1795 1806
6. Smal I., Meijering E., Draegestein K., Galjart N., Grigoriev I., Akhmanova A., van Royen M. E., Houtsmuller A. B., Niessen W., Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering Medical Image Analysis 2008 12 6 764 777
7. Dange T., Joseph A., Grnwald D., A perspective of the dynamic structure of the nucleus explored at the single-molecule level Chromosome Research 2011 19 1 117 129
8. Michelotti N., de Silva C., Johnson-Buck A. E., Manzo A. J., Walter N. G., A bird's eye view. Tracking slow nanometer-scale movements of single molecular nano-assemblies Methods in Enzymology 2010 475 C 121 148
9. Wieser S., Schtz G. J., Tracking single molecules in the live cell plasma membrane-Do's and Don't's Methods 2008 46 2 131 140
10. Villa C. E., Caccia M., Sironi L., D'Alfonso L., Collini M., Rivolta I., Miserocchi G., Gorletta T., Zanoni I., Granucci F., Chirico G., Accumulative difference image protocol for particle tracking in fluorescence microscopy tested in mouse lymphonodes PLoS ONE 2010 5 8
11. Saunter C. D., Quantifying subpixel accuracy: an experimental method for measuring accuracy in image-correlation-based, single-particle tracking Biophysical Journal 2010 98 8 1566 1570
12. Joo C., Balci H., Ishitsuka Y., Buranachai C., Ha T., Advances in single-molecule fluorescence methods for molecular biology Annual Review of Biochemistry 2008 77 51 76
13. MacHin M., Santomaso A., Mazzucato M., Cozzi M. R., Battiston M., De Marco L., Canu P., Single particle tracking across sequences of microscopical images: application to platelet adhesion under flow Annals of Biomedical Engineering 2006 34 5 833 846 (Pubitemid 43824032)
14. Chen S. Y., Tong H., Wang Z., Liu S., Li M., Zhang B., Improved generalized belief propagation for vision processing Mathematical Problems in Engineering 2011 2011 12
15. Chen S. Y., Tong H., Cattani, C., Markov models for image labeling Mathematical Problems in Engineering 2012 2012 18
16. Fredricks D. N., Fiedler T. L., Marrazzo J. M., Molecular identification of bacteria associated with bacterial vaginosis New England Journal of Medicine 2005 353 18 1899 1911 (Pubitemid 41565955)
17. Fischer S. A., Graham M. B., Kuehnert M. J., Kotton C. N., Srinivasan A., Marty F. M., Comer J. A., Guarner J., Paddock C. D., DeMeo D. L., Shieh W. J., Erickson B. R., Bandy U., DeMaria A., Davis J. P., Delmonico F. L., Pavlin B., Likos A., Vincent M. J., Sealy T. K., Goldsmith C. S., Jernigan D. B., Rollin P. E., Packard M. M., Patel M., Rowland C., Helfand R. F., Nichol S. T., Fishman J. A., Ksiazek T., Zaki S. R., Transmission of lymphocytic choriomeningitis virus by organ transplantation New England Journal of Medicine 2006 354 21 2235 2249 (Pubitemid 43788138)
18. Kukura P., Ewers H., Mller C., Renn A., Helenius A., Sandoghdar V., High-speed nanoscopic tracking of the position and orientation of a single virus Nature Methods 2009 6 12 923 927
19. Helmuth J. A., Burckhardt C. J., Greber U. F., Sbalzarini I. F., Shape reconstruction of subcellular structures from live cell fluorescence microscopy images Journal of Structural Biology 2009 167 1 1 10
20. Wu X. P., Li J. Y., Xu Y. K., Xu K. D., Zheng X. X., Three-dimensional tracking of GLUT4 vesicles in TIRF microscopy Journal of Zhejiang University: Science A 2008 9 2 232 240
21. Schelhaas M., Ewers H., Rajamki M. L., Day P. M., Schiller J. T., Helenius A., Human papillomavirus type 16 entry: retrograde cell surface transport along actin-rich protrusions PLoS Pathogens 2008 4 9
22. Chen S. Y., Li Y. F., Determination of stripe edge blurring for depth sensing IEEE Sensors Journal 2011 11 2 389 390
23. Godinez W. J., Lampe M., Wrz S., Mller B., Eils R., Rohr K., Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences Medical Image Analysis 2009 13 2 325 342
24. Pécot T., Kervrann C., Bouthemy P., Network tomography-based tracking for intracellular traffic analysis in fluorescence microscopy imaging 1 Proceedings of the 1st International Conference on Bio-inspired Systems and Signal Processing (Biosignals '08) January 2008 154 161
25. Ruusuvuori P., ij T., Chowdhury S., Garmendia-Torres C., Selinummi J., Birbaumer M., Dudley A. M., Pelkmans L., Yli-Harja O., Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images BMC Bioinformatics 2010 11, article 248
26. Soppina V., Rai A. K., Mallik R., Simple non-fluorescent polarity labeling of microtubules for molecular motor assays BioTechniques 2009 46 7 543 549
27. Pécot T., Kervrann C., Bardin S., Goud B., Salamero J., Patch-based Markov models for event detection in fluorescence bioimaging Proceedings of the International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI '08) 2008 11 2 95 103
28. Nitzsche B., Bormuth V., Bruer C., Howard J., Ionov L., Kerssemakers J., Korten T., Leduc C., Ruhnow F., Diez S., Studying kinesin motors by optical 3D-nanometry in gliding motility assays Methods in Cell Biology 2010 95 C 247 271
29. Mach R., Hof M., Lipid diffusion in planar membranes investigated by fluorescence correlation spectroscopy Biochimica et Biophysica ActaBiomembranes 2010 1798 7 1377 1391
30. Boulanger J., Kervrann C., Bouthemy P., A simulation and estimation framework for intracellular dynamics and trafficking in video-microscopy and fluorescence imagery Medical Image Analysis 2009 13 1 132 142
31. Levi V., Gratton E., Chromatin dynamics during interphase explored by single-particle tracking Chromosome Research 2008 16 3 439 449 (Pubitemid 351644871)
32. Payne C. K., Imaging gene delivery with fluorescence microscopy Nanomedicine 2007 2 6 847 860
33. Tang J., Akerboom J., Vaziri A., Looger L. L., Shank C. V., Near-isotropic 3D optical nanoscopy with photon-limited chromophores Proceedings of the National Academy of Sciences of the United States of America 2010 107 22 10068 10073
34. Aguet F., Geissbuhler S., Marki I., Lasser T., Unser M., Super-resolution orientation estimation and localization of fluorescent dipoles using 3-D steerable filters Optics Express 2009 17 8 6829 6848
35. Wang C., Fu G., Wang J., Wang G., Cheng Y., Xu Z. Z., Direct visualization of the dynamics of membrane-anchor proteins in living cells Journal of Microscopy 2008 229 1 67 77 (Pubitemid 350292335)
36. Claytor K., Khatua S., Guerrero J. M., Tcherniak A., Tour J. M., Link S., Accurately determining single molecule trajectories of molecular motion on surfaces Journal of Chemical Physics 2009 130 16
37. Zhao Y., Gaidarov I., Keen J. H., Phosphoinositide 3-kinase C2 links clathrin to microtubule-dependent movement Journal of Biological Chemistry 2007 282 2 1249 1256 (Pubitemid 47076586)
38. Ueno H., Nishikawa S., Iino R., Tabata K. V., Sakakihara S., Yanagida T., Noji H., Simple dark-field microscopy with nanometer spatial precision and microsecond temporal resolution Biophysical Journal 2010 98 9 2014 2023
39. Morrison I. E. G., Karakikes I., Barber R. E., Fernndez N., Cherry R. J., Detecting and Quantifying Colocalization of Cell Surface Molecules by Single Particle Fluorescence Imaging Biophysical Journal 2003 85 6 4110 4121 (Pubitemid 37490318)
40. Koyama-Honda I., Ritchie K., Fujiwara T., Iino R., Murakoshi H., Kasai R. S., Kusumi A., Fluorescence imaging for monitoring the colocalization of two single molecules in living cells Biophysical Journal 2005 88 3 2126 2136 (Pubitemid 40976221)
41. Feng L., Xu Y., Yang Y., Zheng X., Multiple dense particle tracking in fluorescence microscopy images based on multidimensional assignment Journal of Structural Biology 2011 137 2 219 228
42. Genovesio A., Liedl T., Emiliani V., Parak W. J., Coppey-Moisan M., Olivo-Marin J. C., Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots IEEE Transactions on Image Processing 2006 15 5 1062 1070
43. Pécot T., Kervrann C., Bouthemy P., Minimal paths and probabilistic models for origin-destination traffic estimation in live cell imaging Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI '08) May 2008 843 846
44. Olivo-Marin J. C., An overview of image analysis in multidimensional biological microscopy Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP '06) May 2006 V1173 V1176
45. Chen S. Y., Li Y. F., Zhang J., Vision processing for realtime 3-D data acquisition based on coded structured light IEEE Transactions on Image Processing 2008 17 2 167 176 (Pubitemid 351279245)
46. Chen S. Y., Li Y. F., Vision sensor planning for 3-D model acquisition IEEE Transactions on Systems, Man and Cybernetics, Part B 2005 35 5 894 904 (Pubitemid 41444575)
47. Yu J., Wu C., Sahu S. P., Fernando L. P., Szymanski C., McNeill J., Nanoscale 3D tracking with conjugated polymer nanoparticles Journal of the American Chemical Society 2009 131 51 18410 18414
48. Braeckmans K., Buyens K., Naeye B., Vercauteren D., Deschout H., Raemdonck K., Remaut K., Sanders N. N., Demeester J., De Smedt S. C., Advanced fluorescence microscopy methods illuminate the transfection pathway of nucleic acid nanoparticles Journal of Controlled Release 2010 148 1 69 74
49. van de Linde S., Wolter S., Sauer M., Single-molecule photoswitching and localization Australian Journal of Chemistry 2011 64 5 503 511
50. Flier B. M.I., Baier M., Huber J., Mllen K., Mecking S., Zumbusch A., Wll D., Single molecule fluorescence microscopy investigations on heterogeneity of translational diffusion in thin polymer films Physical Chemistry Chemical Physics 2011 13 5 1770 1775
51. Bates M., Huang B., Rust M. J., Dempsey G. T., Wang W., Zhuang X., Sub-diffraction-limit imaging with stochastic optical reconstruction microscopy Springer Series in Chemical Physics 2010 96 400 415
52. Hohlbein J., Gryte K., Heilemann M., Kapanidis A. N., Surfing on a new wave of Single-molecule fluorescence methods Physical Biology 2010 7 3
53. Konopka M. C., Weisshaar J. C., Heterogeneous motion of secretory vesicles in the actin cortex of live cells: 3D tracking to 5-nm accuracy Journal of Physical Chemistry A 2004 108 45 9814 9826
54. Walter N. G., Huang C. Y., Manzo A. J., Sobhy M. A., Do-it-yourself guide: how to use the modern single-molecule toolkit Nature Methods 2008 5 6 475 489 (Pubitemid 351761755)
55. Smal I., Loog M., Niessen W., Meijering E., Quantitative comparison of spot detection methods in fluorescence microscopy IEEE Transactions on Medical Imaging 2010 29 2 282 301
56. Jung C., Kirstein J., Platschek B., Bein T., Budde M., Frank I., Mllen K., Michaelis J., Bruchle C., Diffusion of oriented single molecules with switchable mobility in networks of long unidimensional nanochannels Journal of the American Chemical Society 2008 130 5 1638 1648 (Pubitemid 351214082)
57. L Z. J., Lu J. Z., Wu Y. Q., Chen L. Y., Introduction to theories of several super-resolution fluorescence microscopy methods and recent advance in the field Progress in Biochemistry and Biophysics 2009 36 12 1626 1634
58. Moerner W. E., Single-molecule mountains yield nanoscale cell images Nature Methods 2006 3 10 781 782 (Pubitemid 44445822)
59. Smal I., Draegestein K., Galjart N., Niessen W., Meijering E., Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: application to microtubule growth analysis IEEE Transactions on Medical Imaging 2008 27 6 789 804 (Pubitemid 351760851)
60. Sbalzarini I. F., Koumoutsakos P., Feature point tracking and trajectory analysis for video imaging in cell biology Journal of Structural Biology 2005 151 2 182 195 (Pubitemid 41074826)
61. Ji W. Y., Bruckbauer A., Fitzgerald W. J., Klenerman D., Bayesian inference for improved single molecule fluorescence tracking Biophysical Journal 2008 94 12 4932 4947
62. Toprak E., Selvin P. R., New fluorescent tools for watching nanometer-scale conformational changes of single molecules Annual Review of Biophysics and Biomolecular Structure 2007 36 349 369 (Pubitemid 46998123)
63. Petrou M., Jaward M., Chen S., Briers M., Super-resolution in practice: the complete pipeline from image capture to super-resolved subimage creation using a novel frame selection method. Machine Vision and Applications. In press
64. Lin D., Ma W., Liu X., Sun Y., Wu Y., Three-dimensional imaging and tracking for constrained Brownian motion of single nano-scaled particles in solution 4 Proceedings of the 1st International Congress on Image and Signal Processing (CISP '08) May 2008 244 248
65. Jung S., Dickson R. M., Hidden Markov analysis of short single molecule intensity trajectories Journal of Physical Chemistry B 2009 113 42 13886 13890
66. Rogers S. S., Waigh T. A., Zhao X., Lu J. R., Precise particle tracking against a complicated background: polynomial fitting with Gaussian weight Physical Biology 2007 4 3 220 227 (Pubitemid 47568918)
67. Chen S., Wang Y., Cattani C., Key issues in modeling of complex 3D structures from video sequences Mathematical Problems in Engineering 2012 2012 12
68. Dorn J. F., Danuser G., Yang G., Computational processing and analysis of dynamic fluorescence image data Methods in Cell Biology 2008 85 497 538