Quantification and its applications in fluorescent microscopy imaging

Traffic

Volumn 10, Issue 8, 2009, Pages 951-961

  Hamilton, Nicholas ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Confocal microscopy; Image analysis; Image quantification; Subcellular imaging; Visualization

Indexed keywords

AUTOMATION; CELL SCREENING; CELL STRUCTURE; CYTOLOGY; DATA ANALYSIS SOFTWARE; FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPY; HIGH THROUGHPUT SCREENING; HUMAN; IMAGE ANALYSIS; IMAGE PROCESSING; IMAGE RETRIEVAL; INFORMATION PROCESSING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; REVIEW;

CELLS; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; PROTEINS; SOFTWARE; TIME FACTORS;

EID: 67649891333     PISSN: 13989219     EISSN: 16000854     Source Type: Journal    
DOI: 10.1111/j.1600-0854.2009.00938.x     Document Type: Review

References (53)

1. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK. Global analysis of protein localization in budding yeast. Nature 2003; 425: 686-691.
2. Auer M, Peng H, Singh A. Development of multiscale biological image data analysis: Review of 2006 International Workshop on Multiscale Biological Imaging, Data Mining and Informatics, Santa Barbara, USA (BII06). BMC Cell Biol 2007; 8 (Suppl. 1): S1.
3. Haralick RM. Statistical and structural approaches to texture. Proc IEEE 1979; 67: 768-804.
4. Broser PJ, Schulte R, Lang S, Roth A, Helmchen F, Waters J, Sakmann B, Wittum G. Nonlinear anisotropic diffusion filtering of three-dimensional image data from image data from two-photon microscopy. J Biomed Opt 2004; 9: 1253-1264.
5. Ronneberger O, Baddeley D, Scheipl F, Verveer PJ, Burkhardt H, Cremer C, Fahrmeir L, Cremer T, Joffe B. Spatial quantitative analysis of fluorescently labeled nuclear structures: Problems, methods, pitfalls. Chromosome Res 2008; 16: 523-562.
6. Carpenter A, Jones T, Lamprecht M, Clarke C, Kang I, Friman O, Guertin D, Chang J, Lindquist R, Moffat J, Golland P, Sabatini D. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006; 7: R100.
7. Gudla PR, Nandy K, Collins J, Meaburn KJ, Misteli T, Lockett SJ. A high-throughput system for segmenting nuclei using multiscale techniques. Cytometry A 2008; 73: 451-466.
8. Stacey DW, Hitomi M. Cell cycle studies based upon quantitative image analysis. Cytometry A 2008; 73: 270-278.
9. Long FH, Peng HC, Sudar D, Lelievre SA, Knowles DW. Phenotype clustering of breast epithelial cells in confocal images based on nuclear protein distribution analysis. BMC Cell Biol 2007; 8 (Suppl. 1): S3.
10. Pham TD, Crane DI, Tran TH, Nguyen TH. Extraction of fluorescent cell puncta by adaptive fuzzy segmentation. Bioinformatics 2004; 20: 2189-2196.
11. Niemisto A, Selinummi J, Saleem R, Shmulevich I, Aitchison J, Yli-Harja O. Extraction of the number of peroxisomes in yeast cells by automated image. Conf Proc IEEE Eng Med Biol Soc 2006; 1: 2353-2356.
12. Schiffmann DA, Dikovskaya D, Appleton PL, Newton IP, Creager DA, Allan C, Nathke IS, Goldberg IG. Open microscopy environment and findspots: integrating image informatics with quantitative multidimensional image analysis. Biotechniques 2006; 41: 199-208.
13. Abdul-Karim MA, Roysam B, Dowell-Mesfin NM, Jeromin A, Yuksel M, Kalyanaraman S. Automatic selection of parameters for vessel/neurite segmentation algorithms. IEEE Trans Image Process 2005; 14: 1338-1350.
14. Kalaidzidis Y. Multiple objects tracking in fluorescence microscopy. J Math Biol 2009; 58: 57-80.
15. Li G, Liu T, Tarokh A, Nie J, Guo L, Mara A, Holley S, Wong S. 3D cell nuclei segmentation based on gradient flow tracking. BMC Cell Biol 2007; 8: 40.
16. Dufour A, Shinin V, Tajbakhsh S, Guillen-Aghion N, Olivo-Marin JC, Zimmer C. Segmentation and tracking fluorescent cells in dynamic 3-D microscopy with coupled active surfaces. IEEE Trans Image Process 2005; 14: 1396-1410.
17. Gniadek TJ, Warren G. WatershedCounting3D: A new method for segmenting and counting punctate structures from confocal image data. Traffic 2007; 8: 339-346.
18. Feng D, Marshburn D, Jen D, Weinberg RJ, Taylor RM II, Burette A. Stepping into the third dimension. J Neurosci 2007; 27: 12757-12760.
19. Wollman R, Stuurman N. High throughput microscopy: From raw images to discoveries. J Cell Sci 2007; 120: 3715-3722.
20. Conrad C, Erfle H, Warnat P, Daigle N, Lorch T, Ellenberg J, Pepperkok R, Eils R. Automatic identification of subcellular phenotypes on human cell arrays. Genome Res 2004; 14: 1130-1136.
21. Bishop CM. Neural Networks for Pattern Recognition Oxford Oxford University Press 1995.
22. Cortes C, Vapnik V. Support vector networks. Mach Learn 1995; 20: 273-297.
23. Boland MV, Markey MK, Murphy RF. Automated recognition of patterns characteristic of subcellular structures in fluorescence microscopy images. Cytometry 1998; 33: 366-375.
24. Hamilton N, Pantelic R, Hanson K, Karunaratne S, Teasdale RD. Fast automated cell phenotype image classification. BMC Bioinformatics 2007; 8: 113.
25. Huang K, Murphy RF. From quantitative microscopy to automated image understanding. J Biomed Opt 2004; 9: 893-912.
26. Chen S-C, Zhao T, Gordon GJ, Murphy RF. Automated image analysis of protein localization in budding yeast. Bioinformatics 2007; 23: I66-i71.
27. Wang M, Zhou X, Li F, Huckins J, King RW, Wong ST. Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy. Bioinformatics 2008; 24: 94-101.
28. Harder N, Eils R, Rohr K, Kevin FS. Automated classification of mitotic phenotypes of human cells using fluorescent proteins. Methods in Cell Biology Academic Press, New York 2008; pp. 539-554.
29. Yi Q, Coppolino MG. Automated classification and quantification of F-actin-containing ruffles in confocal micrographs. Biotechniques 2006; 40: 745-746 8, 50 passim.
30. Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A 2009; 2: 2.
31. Hamilton N, Wang J, Kerr MC, Teasdale RD. Statistical and visual differentiation of high throughput subcellular imaging. BMC Bioinformatics 2009; 10: 94.
32. Hamilton N, Teasdale RD. Visualizing and clustering high throughput sub-cellular localization imaging. BMC Bioinformatics 2008; 9: 81.
33. Newberg J, Murphy R. A framework for the automated analysis of subcellular patterns in human protein atlas images. J Proteome Res 2008; 7: 2300-2308.
34. García Osuna E, Hua J, Bateman N, Zhao T, Berget P, Murphy R. Large-scale automated analysis of location patterns in randomly tagged 3T3 cells. Ann Biomed Eng 2007; 35: 1081-1087.
35. Fink JL, Karunaratne S, Mittel A, Gardiner D, Hamilton N, Teasdale RD. Towards defining the nuclear proteome. Genome Biol 2008; 9: R15.
36. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, Milo R
37. Cohen-Saidon C, Liron Y, Kam Z, Cohen L, Danon T, Perzov N, Alon U. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008; 322: 1511-1516.
38. Lang P, Yeow K, Nichols A, Scheer A. Cellular imaging in drug discovery. Nat Rev Drug Discov 2006; 5: 343-356.
39. Zhao T, Soto S, Murphy R, editors. Improved comparison of protein subcellular location patterns 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro. Arlington, Virginia IEEE 2006.
40. Bonneau S, Dahan M, Cohen LD. Single quantum dot tracking based on perceptual Grouping using minimal paths in a spatiotemporal volume. IEEE Trans Image Process 2005; 14: 1384-1395.
41. Altinok A, Kiris E, Peck AJ, Feinstein SC, Wilson L, Manjunath BS, Rose K. Model based dynamics analysis in live cell microtubule images. BMC Cell Biol 2007; 8 (Suppl. 1): S4.
42. Sage D, Neumann FR, Hediger F, Gasser SM, Unser M. Automatic tracking of individual fluorescence particles: Application to the study of chromosome dynamics. IEEE Trans Image Process 2005; 14: 1372-1383.
43. Bao Z, Murray JI, Boyle T, Ooi SL, Sandel MJ, Waterston RH. Automated cell lineage tracing in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2006; 103: 2707-2712.
44. Chen Y-CM, Kappel C, Beaudouin J, Eils R, Spector DL. Live cell dynamics of promyelocytic leukemia nuclear bodies upon entry into and exit from mitosis. Mol Biol Cell 2008; 19: 3147-3162.
45. Kerr MC, Wang JTH, Hamilton N, Jeanes A, Yap AS, Meunier FA, Brown N, Stow JL, Teasdale RD. 3-Phosphoinostides have sequential and discrete roles during Macropinocytosis. 2008; (In press).
46. Tufte ER. 2nd edn. The Visual Display of Quantitative Information Cheshire, CT Graphics Press 2001.
47. Racine V, Sachse M, Salamero J, Fraisier V, Trubuil A, Sibarita JB. Visualization and quantification of vesicle trafficking on a three-dimensional cytoskeleton network in living cells. J Microsc 2007; 225: 214-228.
48. Kerr MC, Lindsay MR, Luetterforst R, Hamilton N, Simpson F, Parton RG, Gleeson PA, Teasdale RD. Visualisation of macropinosome maturation by the recruitment of sorting nexins. J Cell Sci 2006; 119 (19): 3967-3980.
49. Gordon A, Colman-Lerner A, Chin TE, Benjamin KR, Yu RC, Brent R. Single-cell quantification of molecules and rates using open-source microscope-based cytometry. Nat Methods 2007; 4: 175-181.
50. Mullassery D, Horton CA, Wood CD. Single live-cell imaging for systems biology 9. Essays Biochem 2008; 45: 121-134.
51. Nelson DE, Ihekwaba AE, Elliott M, Johnson JR, Gibney CA, Foreman BE, Nelson G, See V, Horton CA, Spiller DG, Edwards SW, McDowell HP, Unitt JF, Sullivan E, Grimley R, Benson N, Broomhead D, Kell DB, White MR. Oscillations in NF-kappaB signaling control the dynamics of gene expression. Science 2004; 306: 704-708.
52. Zhao T, Murphy RF. Automated learning of generative models for subcellular location: Building blocks for systems biology. Cytometry Part A 2007; 71A: 978-990.
53. Hamilton N, Kerr MC, Burrage K, Teasdale RD. Analysing real-time video microscopy: The dynamics and geometry of vesicles and tubules in endocytosis In: Morgan K, editor. Current Protocols in Cell Biology Wiley Interscience, New York 2007.