Application of information-theoretic measures to quantitative analysis of immunofluorescent microscope imaging

Computer Methods and Programs in Biomedicine

Volumn 97, Issue 2, 2010, Pages 114-129

  Shutin, Dmitriy ^a   Zlobinskaya, Olga ^b  

^a GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

Confocal microscopy; Fluorescence quantification; Hellinger distance; Immunolabeling; Kullback Leibler divergence

Indexed keywords

BIOLOGICAL EXPERIMENTS; CLOSED-FORM EXPRESSION; DISTANCE MEASURE; DNA LESIONS; FLUORESCENCE INTENSITIES; FLUORESCENCE QUANTIFICATION; GAUSSIANS; HELLINGER DISTANCE; HIGH-CONTENT SCREENING; IMMUNOLABELING; IN-VITRO; IN-VIVO; KERNEL DENSITY; KULLBACK LEIBLER DIVERGENCE; MODEL PARAMETERS; MODEL-BASED; NUMERICAL SIMULATION; PROTEOMICS; QUANTITATIVE ANALYSIS; REPAIR RATE;

COMPUTER SIMULATION; CONFOCAL MICROSCOPY; FEATURE EXTRACTION; INFORMATION THEORY; MOLECULAR BIOLOGY;

FLUORESCENCE;

PROTEIN P8;

ARTICLE; CLINICAL EFFECTIVENESS; CONCEPTUAL FRAMEWORK; CONFOCAL MICROSCOPY; DNA DAMAGE; FUNCTIONAL ASSESSMENT; FUNCTIONAL PROTEOMICS; GENETIC DISORDER; HIGH THROUGHPUT SCREENING; IMAGE ACQUISITION; IMAGE ANALYSIS; IMAGE PROCESSING; IMMUNOFLUORESCENCE MICROSCOPY; IN VIVO STUDY; INFORMATION SYSTEM; KERNEL METHOD; LASER; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; QUANTITATIVE ANALYSIS; TRICHOTHIODYSTROPHY GROUP A; ULTRAVIOLET RADIATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; INFORMATION THEORY; MICROSCOPY, FLUORESCENCE; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 74649085855     PISSN: 01692607     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cmpb.2009.05.009     Document Type: Article

References (36)

1. Kumar V. Immunofluorescence and enzyme immunomicroscopy methods. J Immunoassay 21 (2000) 235-253
2. Pound J.D. Immunochemical Protocols (Methods in Molecular Biology) (2003), Humana Press
3. Qian H., and Elson E. On the analysis of high order moments of fluorescence fluctuations. Biophys J. 57 2 (1990) 375-380
4. Papoulis A. Probability, Random Variables, and Stochastic Processes (1991), McGraw-Hill Inc.
5. Zhou X., and Wong S.T. Informatics challenges of high-throughput microscopy. IEEE Signal Process. Mag. (2006) 63-72
6. Elson E.L., and Magde D. Fluorescence correlation spectroscopy. I. Conceptual basis and theory. Biopolymers 13 1 (1974) 1-27
7. Kask P., Palo K., Ullmann D., and Gall K. Fluorescence-intensity distribution analysis and its application in biomolecular detection technology. Proc. Natl. Acad. Sci. U.S.A. 96 24 (1999) 13756-13761
8. Pluim J.P., Maintz J.A., and Viergever M. f-Information measures in medical image registration. IEEE Trans. Med. Imag. 23 12 (2004) 1508-1516
9. Vajda I. Theory of Statistical Inference and Information (1989), Kluwer-Academic, Dodrecht, The Netherlands
10. Kullback S. Information Theory and Statistics (1959), Wiley, New York
11. MacKay D.J. Information Theory, Inference, and Learning Algorithms (2003), Cambridge University Press
12. Johnson D., and Orsak G. Relation of signal set choice to the performance of optimal non-Gaussian detectors. IEEE Trans. Commun. 41 9 (1993) 1319-1328
13. Bhattacharyya A. On a measure of divergence between two statistical populations defined by probability distributions. Bull. Calcutta Math. Soc. 35 (1943) 99-109
14. Jeffrey H. An invariant form of the prior probability in estimation problems. Proc. R. Stat. Soc. (Lond.) A186 (1946) 453-461
15. Moon T.K., and Stirling W.C. Mathematical Methods and Algorithms for Signal Processing (2000), Prentice-Hall
16. Kreyszig E. Advanced Engineering Mathematics (1999), John Wiley and Sons, Inc.
17. Abramowitz M., and Stegun I.A. Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables (1972), Dover
18. Lipan O., Navenot J.-M., Wang Z., Huang L., and Peiper S.C. Heat shock response in CHO mammalian cells is controlled by a nonlinear stochastic process. PLoS Comput. Biol. 3 10 (2007) e187
19. Duda R.O., Hart P.E., and Stork D.G. Pattern Classification. 2nd edition (2000), John Wiley & Sons, Inc.
20. Atkinson K.A. An Introduction to Numerical Analysis (1989), John Wiley & Sons
21. Hut H.M.J., Lemstra W., Blaauw E.H., Cappellen G.W.A.V., Kampinga H.H., and Sibon O.C.M. Centrosomes split in the presence of impaired DNA integrity during mitosis. Mol. Biol. Cell 14 5 (2003) 1993-2004. http://dx.doi.org/10.1091/mbc.E02-08-0510 http://dx.doi.org/10.1091/mbc.E02-08-0510
22. Bcker W., and Iliakis G. Computational Methods for analysis of foci: validation for radiation-induced gamma-H2AX foci in human cells. Radiat. Res. 165 1 (2006) 113-124
23. Pepperkok R., and Ellenberg J. High-throughput fluorescence microscopy for systems biology. Nat. Rev. Mol. Cell Biol. 7 9 (2006) 690-696
24. Yan P., Zhou X., Shah M., and Wong S.T.C. Automatic segmentation of high-throughput RNAi fluorescent cellular images. IEEE Trans. Inform. Technol. Biomed. 12 1 (2008) 109-117
25. Malpica N., de Solorzano C.O., Vaquero J.J., Santos A., Vallcorba I., Garcia-Sagredo J.M., and del Pozo F. Applying watershed algorithms to the segmentation of clustered nuclei. Cytometry 28 4 (1997) 289-297
26. Hoeijmakers J.H. Genome maintenance mechanisms for preventing cancer. Nature 411 6835 (2001) 366-374
27. Giglia-Mari G., Coin F., Ranish J., Hoogstraten D., Theil A., Wijgers N., Jaspers N., Raams A., Argentini M., van der Spek P., Botta E., Stefanini M., Egly J., Aebersold R., Hoeijmakers J., and Vermeulen W. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat. Genet. 36 7 (2004) 677-678
28. Hoogstraten D., Nigg A., Heath H., Mullenders L., van Driel R., Hoeijmakers J., Vermeulen W., and Houtsmuller A. Rapid switching of TFIIH between RNA polymerase I and II transcription and DNA repair in vivo. Mol. Cell 10 5 (2002) 1163-1174
29. von Wettstein D. From analysis of mutants to genetic engineering. Annu. Rev. Plant Biol. 58 1 (2007) 1-19 pMID: 17067283
30. Vitorino M., Coin F., Zlobinskaya O., Atkinson R., Moras D., Egly J., Poterszman A., and Kieffer B. Solution structure and self-association properties of the p8 TFIIH subunit responsible for trichothiodystrophy. J. Mol. Biol. 368 2 (2007) 473-480
31. Mould R. Introductory Medical Statistics (1998), Taylor & Francis
32. Molho-Pessach V., and Lotem M. Ultraviolet radiation and cutaneous carcinogenesis. Curr. Prob. Dermatol. 35 (2007) 14-27
33. de Laat W., Jaspers N., and Hoeijmakers J. Molecular mechanismof nucleotide excision repair. Genes Dev. 13 7 (1999) 768-785
34. Mori T., Nakane M., Hattori T., Matsunaga T., Ihara M., and Nikaido O. Simultaneous establishment of monoclonal antibodies specific for either cyclobutane pyrimidine dimer or 6-4 photoproducts from the same mouse immunized with ultraviolet-irradiated DNA. Photochem. Photobiol. 54 54 (1991) 225-232
35. Riou L., Eveno E., van Hoffen A., van Zeeland A., Sarasin A., and Mullenders L. Differential repair of the two major UV-induced photolesions in trichothiodystrophy fibroblasts. Cancer Res. 64 3 (2004) 889-894
36. Gentile M., Latonen L., and Laiho M. Cell cycle arrest and apoptosis provoked by UV radiation-induced DNA damage are transcriptionally highly divergent responses. Nucl. Acids Res. 31 16 (2003) 4779-4790