Tracking in cell and developmental biology

Seminars in Cell and Developmental Biology

Volumn 20, Issue 8, 2009, Pages 894-902

  Meijering, Erik ^a   Dzyubachyk, Oleh ^a   Smal, Ihor ^a   van Cappellen, Wiggert A ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

Cell tracking; Image analysis; Live cell microscopy; Particle tracking; Pattern recognition

Indexed keywords

BEHAVIOR; COMPUTER ANALYSIS; DEVELOPMENTAL BIOLOGY; EMBRYO DEVELOPMENT; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE ANALYSIS; IMAGING SYSTEM; LIVE CELL MICROSCOPY; MICROSCOPY; NONHUMAN; PATTERN RECOGNITION; REVIEW;

ANIMALS; CYTOLOGICAL TECHNIQUES; DEVELOPMENTAL BIOLOGY; HUMANS; MICROSCOPY; MOLECULAR IMAGING;

EID: 70449084866     PISSN: 10849521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.semcdb.2009.07.004     Document Type: Review

References (100)

1. Moser M., Frühwirth M., and Kenner T. The symphony of life: importance, interaction, and visualization of biological rhythms. IEEE Engineering in Medicine and Biology Magazine 27 (2008) 29-37
2. Tsien R.Y. Imagining imaging's future. Nature Cell Biology 5 (2003) S16-S21
3. Lippincott-Schwartz J., and Patterson G.H. Development and use of fluorescent protein markers in living cells. Science 300 (2003) 87-91
4. Giepmans B.N.G., Adams S.R., Ellisman M.H., and Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 312 (2006) 217-224
5. Stephens D.J., and Allan V.J. Light microscopy techniques for live cell imaging. Science 300 (2003) 82-86
6. Pawley J.B. Handbook of biological confocal microscopy. 3rd ed. (2006), Springer, New York
7. Hell S.W. Microscopy and its focal switch. Nature Methods 6 (2009) 24-32
8. Garini Y., Vermolen B.J., and Young I.T. From micro to nano: recent advances in high-resolution microscopy. Current Opinion in Biotechnology 16 (2005) 3-12
9. Vonesch C., Aguet F., Vonesch J.L., and Unser M. The colored revolution of bioimaging. IEEE Signal Processing Magazine 23 (2006) 20-31
10. Swedlow J.R., Goldberg I., Brauner E., and Sorger P.K. Informatics and quantitative analysis in biological imaging. Science 300 (2003) 100-102
11. Eils R., and Athale C. Computational imaging in cell biology. Journal of Cell Biology 161 (2003) 477-481
12. Murphy R.F., Meijering E., and Danuser G. Special issue on molecular and cellular bioimaging. IEEE Transactions on Image Processing 14 (2005) 1233-1236
13. Swedlow J.R., Lewis S.E., and Goldberg I.G. Modelling data across labs, genomes, space and time. Nature Cell Biology 8 (2006) 1190-1194
14. Zhou X., and Wong S.T.C. Informatics challenges of high-throughput microscopy. IEEE Signal Processing Magazine 23 (2006) 63-72
15. Pepperkok R., and Ellenberg J. High-throughput fluorescence microscopy for systems biology. Nature Reviews Molecular Cell Biology 7 (2006) 690-696
16. Ahmed W.M., Leavesley S.J., Rajwa B., Ayyaz M.N., Ghafoor A., and Robinson J.P. State of the art in information extraction and quantitative analysis for multimodality biomolecular imaging. Proceedings of the IEEE 96 (2008) 512-531
17. Dorn J.F., Danuser G., and Yang G. Computational processing and analysis of dynamic fluorescence image data. Methods in Cell Biology 85 (2008) 497-538
18. Peng H. Bioimage informatics: a new area of engineering biology. Bioinformatics 24 (2008) 1827-1836
19. Duncan J.S., and Ayache N. Medical image analysis: progress over two decades and the challenges ahead. IEEE Transactions on Pattern Analysis and Machine Intelligence 22 (2000) 85-106
20. Suri J.S., Wilson D., and Laximinarayan S. Handbook of biomedical image analysis (2005), Kluwer Academic/Plenum Publishers, New York, NY
21. Bankman I.N. Handbook of medical image processing and analysis. 2nd ed. (2008), Academic Press, Burlington, MA
22. Wu Q., Merchant F.A., and Castleman K.R. Microscope image processing (2008), Elsevier Academic Press, Burlington, MA
23. Rittscher J., Machiraju R., and Wong S.T.C. Microscopic image analysis for life science applications (2008), Artech House, Norwood, MA
24. Meijering E., Smal I., and Danuser G. Tracking in molecular bioimaging. IEEE Signal Processing Magazine 23 (2006) 46-53
25. Zimmer C., Zhang B., Dufour A., Thébaud A., Berlemont S., Meas-Yedid V., et al. On the digital trail of mobile cells. IEEE Signal Processing Magazine 23 (2006) 54-62
26. Gerlich D., Mattes J., and Eils R. Quantitative motion analysis and visualization of cellular structures. Methods 29 (2003) 3-13
27. Kalaidzidis Y. Multiple objects tracking in fluorescence microscopy. Journal of Mathematical Biology 58 (2009) 57-80
28. Dormann D., and Weijer C.J. Imaging of cell migration. EMBO Journal 25 (2006) 3480-3493
29. Hand A.J., Sun T., Barber D.C., Hose D.R., and MacNeil S. Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration. Journal of Microscopy 234 (2009) 62-79
30. Meijering E., Smal I., Dzyubachyk O., and Olivo-Marin J.C. Time-lapse imaging. In: Wu Q., Merchant F.A., and Castleman K.R. (Eds). Microscope image processing (2008), Elsevier Academic Press, Burlington, MA 401-440
31. Kachouie N.N., Fieguth P., Ramunas J., and Jervis E. Probabilistic model-based cell tracking. International Journal of Biomedical Imaging (2006) 1-10
32. Wählby C., Sintorn I.M., Erlandsson F., Borgefors G., and Bengtsson E. Combining intensity, edge and shape information for 2D and 3D segmentation of cell nuclei in tissue sections. Journal of Microscopy 215 (2004) 67-76
33. Yang X., Li H., and Zhou X. Nuclei segmentation using marker-controlled watershed, tracking using mean-shift, and Kalman filter in time-lapse microscopy. IEEE Transactions on Circuits and Systems I: Regular Papers 53 (2006) 2405-2414
34. Lin G., Chawla M.K., Olson K., Barnes C.A., Guzowski J.F., Bjornsson C., et al. A multi-model approach to simultaneous segmentation and classification of heterogeneous populations of cell nuclei in 3D confocal microscope images. Cytometry Part A 71 (2007) 724-736
35. Zhou X., Li F., Yan J., and Wong S.T.C. A novel cell segmentation method and cell phase identification using Markov model. IEEE Transactions on Information Technology in Biomedicine 13 (2009) 152-157
36. Zimmer C., Labruyère E., Meas-Yedid V., Guillén N., and Olivo-Marin J.C. Segmentation and tracking of migrating cells in videomicroscopy with parametric active contours: a tool for cell-based drug testing. IEEE Transactions on Medical Imaging 21 (2002) 1212-1221
37. Dormann D., Libotte T., Weijer C.J., and Bretschneider T. Simultaneous quantification of cell motility and protein-membrane-association using active contours. Cell Motility and the Cytoskeleton 52 (2002) 221-230
38. Ray N., Acton S.T., and Ley K. Tracking leukocytes in vivo with shape and size constrained active contours. IEEE Transactions on Medical Imaging 21 (2002) 1222-1235
39. Debeir O., Camby I., Kiss R., Ham P.V., and Decaestecker C. A model-based approach for automated in vitro cell tracking and chemotaxis analyses. Cytometry Part A 60A (2004) 29-40
40. Mukherjee D.P., Ray N., and Acton S.T. Level set analysis for leukocyte detection and tracking. IEEE Transactions on Medical Imaging 13 (2004) 562-572
41. Dufour A., Shinin V., Tajbakhsh S., Guillen-Aghion N., Olivo-Marin J.C., and Zimmer C. Segmenting and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Transactions on Image Processing 14 (2005) 1396-1410
42. Shen H., Nelson G., Kennedy S., Nelson D., Johnson J., Spiller D., et al. Automatic tracking of biological cells and compartments using particle filters and active contours. Chemometrics and Intelligent Laboratory Systems 82 (2006) 276-282
43. Chang H., Yang Q., and Parvin B. Segmentation of heterogeneous blob objects through voting and level set formulation. Pattern Recognition Letters 28 (2007) 1781-1787
44. Li K., Miller E.D., Chen M., Kanade T., Weiss L.E., and Campbell P.G. Cell population tracking and lineage construction with spatiotemporal context. Medical Image Analysis 12 (2008) 546-566
45. Degerman J., Thorlin T., Faijerson J., Althoff K., Eriksson P.S., Put R.V.D., et al. An automatic system for in vitro cell migration studies. Journal of Microscopy 233 (2009) 178-191
46. Padfield D., Rittscher J., Thomas N., and Roysam B. Spatio-temporal cell cycle phase analysis using level sets and fast marching methods. Medical Image Analysis 13 (2009) 143-155
47. Debeir O., Ham P.V., Kiss R., and Decaestecker C. Tracking of migrating cells under phase-contrast video microscopy with combined mean-shift processes. IEEE Transactions on Medical Imaging 24 (2005) 697-711
48. Chen Y., Ladi E., Herzmark P., Robey E., and Roysam B. Automated 5-D analysis of cell migration and interaction in the thymic cortex from time-lapse sequences of 3-D multi-channel multi-photon images. Journal of Immunological Methods 340 (2009) 65-80
49. Wilson C.A., and Theriot J.A. A correlation-based approach to calculate rotation and translation of moving cells. IEEE Transactions on Image Processing 15 (2006) 1939-1951
50. Matula P., Matula P., Kozubek M., and Dvořák V. Fast point-based 3-D alignment of live cells. IEEE Transactions on Image Processing 15 (2006) 2388-2396
51. Yang S., Kohler D., Teller K., Cremer T., Baccon P.L., Heard E., et al. Nonrigid registration of 3-D multichannel microscopy images of cell nuclei. IEEE Transactions on Image Processing 17 (2008) 493-499
52. Ray N., and Acton S.T. Motion gradient vector flow: an external force for tracking rolling leukocytes with shape and size constrained active contours. IEEE Transactions on Medical Imaging 23 (2004) 1466-1478
53. Xie J., Khan S., and Shah M. Automatic tracking of Escherichia coli in phase-contrast microscopy video. IEEE Transactions on Biomedical Engineering 56 (2009) 390-399
54. Cui J., Acton S.T., and Lin Z. A Monte Carlo approach to rolling leukocyte tracking in vivo. Medical Image Analysis 10 (2006) 598-610
55. Pincus Z., and Theriot J.A. Comparison of quantitative methods for cell-shape analysis. Journal of Microscopy 227 (2007) 140-156
56. Bahnson A., Athanassiou C., Koebler D., Qian L., Shun T., Shields D., et al. Automated measurement of cell motility and proliferation. BMC Cell Biology 6 (2005) 19
57. Demou Z.N., and McIntire L.V. Fully automated three-dimensional tracking of cancer cells in collagen gels: determination of motility phenotypes at the cellular level. Cancer Research 62 (2002) 5301-5307
58. Lippincott-Schwartz J., Altan-Bonnet N., and Patterson G.H. Photobleaching and photoactivation: following protein dynamics in living cells. Nature Cell Biology 5 (2003) S7-S13
59. Saxton M.J. Single-particle tracking: connecting the dots. Nature Methods 5 (2008) 671-672
60. Ram S., Ward E.S., and Ober R.J. Beyond Rayleigh's criterion: a resolution measure with application to single-molecule microscopy. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 4457-4462
61. Carter B.C., Shubeita G.T., and Gross S.P. Tracking single particles: a user-friendly quantitative evaluation. Physical Biology 2 (2005) 60-72
62. Zhang B., Zerubia J., and Olivo-Marin J.C. Gaussian approximations of fluorescence microscope point-spread function models. Applied Optics 46 (2007) 1819-1829
63. Cheezum M.K., Walker W.F., and Guilford W.H. Quantitative comparison of algorithms for tracking single fluorescent particles. Biophysical Journal 81 (2001) 2378-2388
64. Yildiz A., and Selvin P.R. Fluorescence imaging with one nanometer accuracy: application to molecular motors. Accounts of Chemical Research 38 (2005) 574-582
65. Thomann D., Rines D.R., Sorger P.K., and Danuser G. Automatic fluorescent tag detection in 3D with super-resolution: application to the analysis of chromosome movement. Journal of Microscopy 208 (2002) 49-64
66. Smal I, Loog M, Niessen W, Meijering E. Quantitative comparison of spot detection methods in fluorescence microscopy. IEEE Transactions on Medical Imaging, in press.
67. Genovesio A., Liedl T., Emiliani V., Parak W.J., Coppey-Moisan M., and 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 15 (2006) 1062-1070
68. Sage D., Neumann F.R., Hediger F., Gasser S.M., and Unser M. Automatic tracking of individual fluorescence particles: application to the study of chromosome dynamics. IEEE Transactions on Image Processing 14 (2005) 1372-1383
69. Smal I., Meijering E., Draegestein K., Galjart N., Grigoriev I., Akhmanova A., et al. Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering. Medical Image Analysis 12 (2008) 764-777
70. Jiang S., Zhou X., Kirchhausen T., and Wong S.T.C. Detection of molecular particles in live cells via machine learning. Cytometry Part A 71 (2007) 563-575
71. Schiffmann D.A., Dikovskaya D., Appleton P.L., Newton I.P., Creager D.A., Allan C., et al. Open Microscopy Environment and FindSpots: integrating image informatics with quantitative multidimensional image analysis. BioTechniques 41 (2006) 199-208
72. Bonneau S., Dahan M., and Cohen L.D. Single quantum dot tracking based on perceptual grouping using minimal paths in a spatiotemporal volume. IEEE Transactions on Image Processing 14 (2005) 1384-1395
73. Racine V., Sachse M., Salamero J., Fraisier V., Trubuil A., and Sibarita J.B. Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells. Journal of Microscopy 225 (2007) 214-228
74. Vallotton P., Ponti A., Waterman-Storer C.M., Salmon E.D., and Danuser G. Recovery, visualization, and analysis of actin and tubulin polymer flow in live cells: a fluorescent speckle microscopy study. Biophysical Journal 85 (2003) 1289-1306
75. Sbalzarini I.F., and Koumoutsakos P. Feature point tracking and trajectory analysis for video imaging in cell biology. Journal of Structural Biology 151 (2005) 182-195
76. Jaqaman K., Loerke D., Mettlen M., Kuwata H., Grinstein S., Schmid S.L., et al. Robust single-particle tracking in live-cell time-lapse sequences. Nature Methods 5 (2008) 695-702
77. Smal I., Draegestein K., Galjart N., Niessen W., and Meijering E. Particle filtering for multiple object tracking in dynamic fluorescence microscopy images: application to microtubule growth analysis. IEEE Transactions on Medical Imaging 27 (2008) 789-804
78. Yoon J.W., Bruckbauer A., Fitzgerald W.J., and Klenerman D. Bayesian inference for improved single molecule fluorescence tracking. Biophysical Journal 94 (2008) 4932-4947
79. Godinez W.J., Lampe M., Wörz S., Müller B., Eils R., and Rohr K. Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences. Medical Image Analysis 13 (2009) 325-342
80. Suh J., Dawson M., and Hanes J. Real-time multiple-particle tracking: application to drug and gene delivery. Advanced Drug Delivery Reviews 57 (2005) 63-78
81. Martin D.S., Forstner M.B., and Käs J.A. Apparent subdiffusion inherent to single particle tracking. Biophysical Journal 83 (2002) 2109-2117
82. Ponti A., Machacek M., Gupton S.L., Waterman-Storer C.M., and Danuser G. Two distinct actin networks drive the protrusion of migrating cells. Science 305 (2004) 1782-1786
83. Ewers H., Smith A.E., Sbalzarini I.F., Lilie H., Koumoutsakos P., and Helenius A. Single-particle tracking of murine polyoma virus-like particles on live cells and artificial membranes. Proceedings of the National Academy of Sciences of the United States of America 102 (2005) 15110-15115
84. Arhel N., Genovesio A., Kim K.A., Miko S., Perret E., Olivo-Marin J.C., et al. Quantitative four-dimensional tracking of cytoplasmic and nuclear HIV-1 complexes. Nature Methods 3 (2006) 817-824
85. Bacher C.P., Reichenzeller M., Athale C., Herrmann H., and Eils R. 4-D single particle tracking of synthetic and proteinaceous microspheres reveals preferential movement of nuclear particles along chromatin-poor tracks. BMC Cell Biology 5 (2004) 1-14
86. Hamahashi S., Onami S., and Kitano H. Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinformatics 6 (2005) 125
87. Murray J.I., Bao Z., Boyle T.J., Boeck M.E., Mericle B.L., Nicholas T.J., et al. Automated analysis of embryonic gene expression with cellular resolution in C. elegans. Nature Methods 5 (2008) 703-709
88. Keller P.J., Schmidt A.D., Wittbrodt J., and Stelzer E.H.K. Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322 (2008) 1065-1069
89. Vermot J., Fraser S.E., and Liebling M. Fast fluorescence microscopy for imaging the dynamics of embryonic development. HFSP Journal 2 (2008) 143-155
90. Heid P.J., Voss E., and Soll D.R. 3D-DIASemb: a computer-assisted system for reconstructing and motion analyzing in 4D every cell and nucleus in a developing embryo. Developmental Biology 245 (2002) 329-347
91. Tassy O., Daian F., Hudson C., Bertrand V., and Lemaire P. A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis. Current Biology 16 (2006) 345-358
92. Bao Z., Murray J.I., Boyle T., Ooi S.L., Sandel M.J., and Waterston R.H. Automated cell lineage tracing in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America 103 (2006) 2707-2712
93. Murray J.I., Bao Z., Boyle T.J., and Waterston R.H. The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nature Protocols 1 (2006) 1468-1476
94. Al-Kofahi O., Radke R.J., Goderie S.K., Shen Q., Temple S., and Roysam B. Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells. Cell Cycle 5 (2006) 327-335
95. Roussel N., Morton C.A., Finger F.P., and Roysam B. A computational model for C. elegans locomotory behavior: application to multiworm tracking. IEEE Transactions on Biomedical Engineering 54 (2007) 1786-1797
96. Geng W., Cosman P., Berry C.C., Feng Z., and Schafer W.R. Automatic tracking, feature extraction and classification of C. elegans phenotypes. IEEE Transactions on Biomedical Engineering 51 (2004) 1811-1820
97. Cronin C.J., Mendel J.E., Mukhtar S., Kim Y.M., Stirbl R.C., Bruck J., et al. An automated system for measuring parameters of nematode sinusoidal movement. BMC Genetics 6 (2005) 5
98. Hoshi K., and Shingai R. Computer-driven automatic identification of locomotion states in Caenorhabditis elegans. Journal of Neuroscience Methods 157 (2006) 355-363
99. Braun V., Azevedo R.B.R., Gumbel M., Agapow P.M., Leroi A.M., and Meinzer H.P. ALES: cell lineage analysis and mapping of developmental events. Bioinformatics 19 (2003) 851-858
100. Boyle T., Bao Z., Murray J.I., Araya C.L., and Waterston R.H. AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis. BMC Bioinformatics 7 (2006) 275