Live cell imaging: A computational perspective

Journal of Real-Time Image Processing

Volumn 1, Issue 3, 2007, Pages 195-212

  Bhaskar, Harish ^a   Singh, Sameer ^a  

^a LOUGHBOROUGH UNIVERSITY   (United Kingdom)

Author keywords

Image segmentation; Live cell imaging; Microscopy; Particle tracking; Visualization

Indexed keywords

CELLS; COMPUTER VISION; IMAGE SEGMENTATION; LIVING SYSTEMS STUDIES; VISUALIZATION;

CELL BIOLOGY; DYNAMIC PROCESSES; LIVE CELL IMAGING; MOLECULAR FUNCTIONAL; PARTICLE TRACKING;

IMAGING TECHNIQUES;

EID: 34248401978     PISSN: 18618200     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11554-007-0022-4     Document Type: Conference Paper

References (98)

1. Adie, E.J., et al.: A pH-sensitive fluor, CypHer 5, used to monitor agonist-induced G protein-coupled receptor internalization in live cells. Biotechniques 33, 1152-1154 (2002)
2. Al-Awadhi, F., Jennison, C., Hurnz, M.: Statistical image analysis for a confocal microscopy 2D section of cartilage growth (2003)
3. Anderson C.M., Georgiou G.G., Morrison I.E.G., Stevenson, G.V.W., Cherry, R.J.: Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charge-coupled device camera: low-density lipoprotein and influenza virus receptor mobility at 4°C. J. Cell Sci. 101, 415-425 (1992)
4. Apgar J., Tseng Y., Federov E., Herwig M.B., Almo S.C., Wirtz, D.: Multiple-particle tracking measurements of the heterogeneities of solutions of actin filaments and actin bundles. Biophys. J. 79, 1095-1106 (2000)
5. Babcock, H.P., Chen, C., Zhuang, X.: Using single-particle tracking to study nuclear traficking of viral Genes. Biophys. J. 87, 2749-2758 (2004)
6. Bar-Shalom Y., Fortmann T.E., Scheffe M.: Joint probabilistic data association for multiple targets in clutter. In: Proceedings of the Conference on Information Sciences and Systems (1980)
7. Beaudouin J., et al.: Nuclear envelope breakdown proceeds by microtubule-induced tearing of the lamina. Cell 108, 83-96 (2002)
8. Berg, H.C.: Motile behavior of bacteria. Phys. Today 53(1), 24-29 (2000)
9. Berglund A.J., Mabuchi, H.: Feedback controller design for tracking a single fluorescent molecule. Appl. Phys. B 78, 653-659 (2004)
10. Betz, W.J., Angleson, J.K.: The synaptic vesicle cycle. Annu. Rev. Physiol. 60, 347-363 (1998)
11. Bookstein, F.L.: Principal warps: thin-plate splines and the decomposition of deformations. IEEE Trans. Pattern Anal. Mach. Intell. 11, 567-585 (1989)
12. Bornfleth, H., Sätzler, K., Eils, R., Cremer C.: High precision distance measurements and volume-conserving segmentation of objects near and below the resolution limit in three-dimensional confocal fluorescence microscopy. J. Microscopy. 189, 118-136 (1998)
13. Borst, H. Abmayr, W., Gais, P.: A thresholding method for automatic cell image segmentation 27(1), 180-187 (1979)
14. Bray, D.: Cell movements: from molecules to motility. Garland Science Publishing, New York (2002)
15. Blümich, B., Kühn, W.: Magnetic resonance microscopy: methods and applications in materials science, agriculture and biomedicine (1992)
16. Calapez A., et al.: The intranuclear mobility of messenger RNA binding proteins is ATP dependent and temperature sensitive. J. Cell Biol. 15, 795-805 (2002)
17. Cheezum M.K., Walker W.F., Guilford W.H.: Quantitative comparison of algorithms for tracking single fluorescent particles. Biophys. J. 81, 2378-2388 (2001)
18. Chalfie, M., et al.: Green fluorescent protein as a marker for gene expression. Science 263, 802-805 (1994)
19. Comaniciu, D., Meer, P.: Cell image segmentation for diagnostic pathology, advanced algorithmic approaches to medical image segmentation: state-of-the-art applications in cardiology, neurology, mammography and pathology. In: Suri, J., Singh, S., Setarehdan, K. (eds.) Springer, Heidelberg (2001)
20. da F. Costa, L., Cesar, Jr., R.M.: Shape analysis and classification, theory and practice, CRC Press, Boca Raton (2001)
21. Cox, I.J., Leonard, J.J.: Modeling a dynamic environment using a Bayesian multiple hypothesis approach. Artif. Intell. 66(2), 311-344 (1994)
22. Cline H.E., et al.: Two algorithms for the three-dimensional reconstruction of tomograms. Med. Phys. 15, 320-327 (1988)
23. deBrabrander M., Nuydens R., Ishihara A., Holifield B., Jacobson K., Geerts H.: Lateral diffusion and retrograde movements of individual cell surface components on single motile cells observed with Nanovid microscopy. Cell Biol. 112, 1143-1150 (1991)
24. Deshpande, A.V., Narote, S.P., Udupi, V.R., Inamdar, H.P.: A region growing segmentation for detection of microcalcificationin digitized mammograms. In: Proceedings of the International Conference on Cognition and Recognition (2005)
25. Dierksen, K., Typke, D., Hegerl, R., Koster, A.J., Baumeister, W.: Towards automatic electron tomography. Ultramicroscopy 40, 71-87 (1992)
26. Doucet, A., Gordon, N.J., Krishnamurthy, V.: Particle filters for state estimation of jump Markov linear systems. IEEE Trans. Signal Process. 49(3), 613-624 (2001)
27. Edidin M (1993) Patches and fences: probing for plasma membrane domains. J. Cell Sci. Suppl. 17, 165-169
28. Eils, R., Athale, C.: Computational imaging in cell biology. J. Cell Biol. 161(3), 477-481 (2003)
29. Elis, R., et al.: Quantitative imaging of pre-mRNA splicing factors in living cells. Mol. Biol. Cell. 11, 413-418 (2000)
30. Ehrhardt, D.: GFP technology for live cell imaging. Curr. Opin. Plant Biol. 6(6), 622-628(7) (2003)
31. Fletcher, L.M., Welsh, G.I., Oatey, P.B., Tavare, J.M.: Role for the microtubule cytoskeleton in the regulation of insulin-stimulated glucose uptake and GLUT4 trafficking. Biochem. J. 352, 267-276 (2000)
32. Fletcher, L.M., Tavare, J.M.: Divergent signalling mechanisms involved in insulin-stimulated GLUT4 vesicle trafficking to the plasma membrane. Biochem. Soc. Trans. 27, 677-683 (1999)
33. Gebhard, M. et al.: Segmentation of 3D objects using NURBS surfaces for quantification of surface and volume dynamics. In: Conference on Diagnostic Imaging and Analysis (ICDIA), Shanghai, China, pp. 125-130 (2002)
34. Gelles, J., Schnapp, B.J., Sheetz, M.P.: Tracking kinesin-driven movements with nanometre-scale precision. Nature 331, 450-453 (1988)
35. Gerlich, D., et al.: Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 112, 751-764 (2003)
36. Ghosh, R.N., Webb, W.W.: Automated detection and tracking of individual and clustered cell surface low density lipoprotein receptor molecules. Biophys. J. 66, 1301-1318 (1994)
37. Gross, D.J., Webb, W.W.: Cell surface clustering and mobility of the liganded LDL receptor measured by digital video fluorescence microscopy. In: Spectroscopic Membrane Probes II, pp. 19-45 (1988)
38. Guilak, F., et al.: Compression-induced changes in the shape and volume of the chondrocyte nucleus. J. Biomech. 28, 1529-1541 (1995)
39. Han, J., Kamber, M.: Data mining: concepts and techniques, Academic Press, New York (2001)
40. Herman, B.: Fluorescence microscopy, 2nd edn. Springer, New York, 170 pp. (1998)
41. Hicks, B.W., Angelides, K.J.: Tracking movements of lipids and Thy1 molecules in the plasmalemma of living fibroblasts by fluorescence video microscopy with nanometer scale precision. Membr. Biol. 144, 231-244 (1995)
42. Jacobs, R.E., Fraser, S.E.: Magnetic resonance microscopy of embryonic cell lineages and movements. Science 263(5147), 681-684 (1994)
43. Khan, Z., Balch, T., Dellaert, F.: An MCMC-based particle filter for tracking multiple interacting targets. Technical report number GIT-GVU-03-35 (2003)
44. Kitano, H.: Computational systems biology. Nature 420, 206-210 (2002)
45. Koster, A.J., Klumperman, J.: Electron microscopy in cell biology: an integrated view on structure and function. Suppl. Nat. Rev. Mol. Cell Biol. (2003)
46. Koster A.J., Grimm R., Typke D., Hegerl R., Stoschek A., Walz J., Baumeister,W.: Perspectives of molecular and cellular electron tomography. J. Struct. Biol. 120(3), 276-308 (1997)
47. Kneen, M., Farinas, J., Verkman, A.S.: Green fluorescent protein as a noninvasive intracellular pH indicator. Biophys. J. 74, 1591-1599 (1998)
48. Kusumi, A., Sako, Y., Yamamoto, M.: Confined lateral diffusion of membrane receptors as studied by single particle tracking (Nanovidmicroscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J. 65, 2021-2040 (1993)
49. Latecki, L.J., Lakamper, R., Eckhardt, U.: Shape descriptors for non-rigid shapes with a single closed contour. In: IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 424-429 (2000)
50. Lavallee, S., Szeliski, R.: Recovering the position and orientation of free-form objects from image contours using 3d distance maps. IEEE Trans. PAMI 17, 195-201 (1995)
51. Lee, G.M., Ishihara, A., Jacobson, K.: Direct observation of Brownian motion of lipids in membranes. Proc. Natl. Acad. Sci. USA 88, 6274-7278 (1991)
52. Loew, L.M.: Voltage-sensitive dyes: measurement of membrane potentials induced by DC and AC electric fields. Bioelectromagnetics. supplement 1, 179-189 (1992)
53. Maddox, P.: An introduction to live cell fluorescence imaging (2000)
54. Maintz, J.B.A., Viergever, M.A.: A survey of medical image registration. Medical image analysis. 2, 1-36 (1998)
55. May, M.: Advances in cellular image processing. The Scientist, 18(5), 40-43 (2004)
56. Marshall, W.F., et al.: Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7, 930-939 (1997)
57. Mitiche, A., et al.: Computation and analysis of image motion: a synopsis of current problems and methods. Int. J. Comp. Vis. 19, 29-55 (1996)
58. O'Toole, E.T., Winey, M.J., McIntosh, J.R., Mastronarde, D.N.: Electron tomography of yeast cells. Meth. Enzymol 351, 81-95 (2002)
59. Palmer, A., Cha, B., Wirtz, D.: Structure and dynamics of actin filament solutions in the presence of latrunculin A. J. Polym. Sci. Phys. Educ. 36, 3007-3015 (1998)
60. Palmer, A., Xu, J., Kuo, S.C., Wirtz, D.: Diffusing wave spectroscopy microrheology of actin filament networks. Biophys. J. 76, 1063-1071 (1999)
61. Pedley, T.J., Kessler, J.O.: Hydrodynamic phenomena in suspensions of swimming microorganisms. Annu. Rev. Fluid Mech. 24, 313-358 (1992)
62. Perkins, G.A., Renken, C.W., van der Klei, I.J., Ellisman, M.H., Neupert, W., Frey, T.G.: Electron tomography of mitochondria after the arrest of protein import associated with Tom19 depletion. Eur. J. Cell Biol. 80(2), 139-150 (2001)
63. Periasamy, A.: Methods in Cellular Imaging. Oxford University Press, New York, 434 pp. (2001)
64. Phair, R.D., Misteli, T.: Kinetic modelling approaches to in vivo imaging. Nat. Rev. Mol. Cell Biol. 2, 898-907 (2001)
65. Piston, D.W., Patterson, G.H., Knobel, S.M.: Quantitative imaging of the green fluorescent protein (GFP). Methods Cell Biol. 58, 31-48 (1999)
66. Qian, H., Sheetz, M.P., Elson, E.L.: Single particle tracking: analysis of diffusion and flow in two-dimensional systems. Biophys. J. 60, 910-921 (1991)
67. Qian, H.: Single-particle tracking: Brownian dynamics of visco-elastic materials. Biophys. J. 79, 137-143 (2000)
68. Rohr, K., Stiehl, H.S.: Characterization and Localization of Anatomical Landmarks in Medical Images. In: Hütter, B.O., Gilsbach, J.M. (eds), Proc. First Aachen Conf. on Neuropsychology in Neurosurgery, Psychiatry, and Neurology, Aachen, Germany, 9-12 (1997)
69. Sako, Y., Kusumi, A.: Barriers for lateral diffusion of transferring receptor in the plasma membrane as characterized by receptor dragging by laser tweezers: fence versus tether. J. Cell Biol. 129, 1559-1574 (1995)
70. Saxton, M.J.: Anomalous diffusion due to obstacles: a Monte Carlo study. Biophys. J. 66, 394-401 (1994)
71. Saxton, M.J., Jacobson, K.: Single particle tracking: applications to membrane dynamics. Annu. Rev. Biophys. J. 26, 373-399 (1997)
72. Sheng, J., Meng, H. (1998) A genetic algorithm particle pairing technique for 3D velocity field extraction in holographic particle image velocimetry. Exp. Fluids 25, 461-473
73. Schultz, G.J., Schindler, H., Schmidt, T.: Single-molecule microscopy on model membranes reveals anomalous diffusion. Biophys. J. 73, 1073-1080 (1997)
74. Sekar, R.B., Periasamy, A.: Fluorescence resonance microscopy imaging of live cell protein localizations. J. Cell Biol. 160(5), 629-633 (2003)
75. Sheetz, M.P., Turney, S., Qian, H., Elson, E.L.: Nanometer-level analysis demonstrates that lipid flow does not drive membrane glycoprotein movement. Nature 340, 284-288 (1989)
76. Singh, S., et al.: Multiple particle tracking for live cell imaging with green fluorescent protein (GFP) tagged videos. In: 3rd International Conference on Advances in Pattern Recognition (ICAPR'2005). Lecture Notes in Computer Science (LNCS). Springer, Bath (2005)
77. Simson, R., Sheets, E.D., Jacobson, K. (1995) Detection of temporary lateral confinement of membrane proteins using single particle tracking. Biophys. J. 69, 989-993
78. Smith, C.B., Betz, W.J.: Simultaneous independent measurement of endo- and exocytosis. Nature 380, 531-534 (1996)
79. Smolle, J., Helige, C., Tritthart, H.A.: An image analysis and statistical evaluation program for the assessment of tumour cell invasion in vitro. 4(1), 49-57 (1992)
80. Soni, G.V., Ali, B.M.J., Hatwalney, Y., Shivashankar, G.V.: Single particle tracking of correlated bacterial dynamics. Biophys. J. 84, 2634-2637 (2003)
81. Stephens, D.J., Allan, V.J.: Light microscopy techniques for live cell imaging. Science 300(5616), 82-86 (2003)
82. Tavare, J.M., Fletcher, L.M., Welsh, G.I.: Using green fluorescent protein to study intracellular signaling. J. Endocrinol 170, 297-306
83. Terzopoulos, D., Metaxas, D.: Dynamic 3D models with local and global deformations: deformable superquadrics. IEEE Transactions on Pattern Analysis and Machine Intelligence. 13(7), 703-714 (1991)
84. Terzopoulos, D., McInerney, T.: Deformable models in medical images analysis: a survey. Medical Image Analysis. 1(2), 91-108 (1996)
85. Tseng, Y., Kole, T.P., Wirtz, D.: Micromechanical mapping of live cells by multiple-particle-tracking microrheology. Biophys. J. 83, 3162-3176 (2002)
86. Tseng, Y., Wirtz, D.: Mechanics and multiple-particle tracking micro-heterogeneity of a-actinin-cross-linked actin filament networks. Biophys. J. 81, 1643-1656 (2001)
87. Tseng, Y., Kole, T.P., Lee, S.H.J., Wirtz, D.: Local dynamics and viscoelastic properties of cell biological systems. Curr. Opin. Colloid Interface Sci. 7, 210-217 (2002)
88. Tseng, Y., Wirtz, D.: Mechanics and multiple-particle tracking microhetrogeneity of alpha-actinin-cross-linked actin filament networks. Biophys. J. 81, 1643-1656 (2001)
89. Tsien, R.Y.: The green fluorescent protein. Annu Rev Biochem 67, 509-544 (1998)
90. Valentine, M.T., Kaplan, P.D., Thota, D., Crocker, J.C., Gisler, T., Prudhomme, R.K., Beck, M., Weitz, D.A.; Investigating the microenvironments of inhomogeneous soft materials with multiple particle tracking. Phys. Rev. E 64(6), (2001)
91. Vrljic, M., Nishinura, S.Y., Brasselet, S., Moerner, W.E., McConnell, H.M.: Translational diffusion of individual class II MHC membrane proteins in cells. Biophys. J. 83, 2681-2692 (2002)
92. Wang, Y., Silverman, J.D., Cao, L.: Single particles tracking of surface receptor movement during cell division. Cell Biol. 127, 963-971 (1994)
93. Waterman-Storer, M.C.: Fluorescent Speckle Microscopy (FSM) of microtubules and actin in living cells. Curr. Protoc. Cell Biol. (2002)
94. Waterman-Storer, M.C., Desai, A., Bulinski, C., Salmon, E.D.: Fluorescent speckle microscopy, a method to visualize the dynamics of protein assemblies in living cells. Curr. Biol. 61, 155-173 (1998)
95. White, N.S.: Visualization systems for multidimensional CLSM images. In: Handbook of Biological Confocal Microscopy. Plenum Press, New York (1995)
96. Wilson, K.M., Morrison, I.E.G., Smith, P.R., Fernandez, N, Cherry, R.J.; Single particle tracking of cell-surface HLA-DR molecules using R-phycoerythrin labeled monoclonal antibodies and fluorescence digital imaging. J. Cell Sci. 109, 2101-2109 (1996)
97. Xu, J., Viasnoff, V., Wirtz, D.: Compliance of actin filament networks measured by particle-tracking microrheology and diffusing wave spectroscopy. Rheologica Acta 37, 387-398 (1998)
98. Zia Khan, Tucker, R., Balch, Manuela M. Veloso: Automatically tracking and analyzing the behavior of live insect colonies. Agents, 521-528 (2001)