Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila

Bioinformatics

Volumn 25, Issue 3, 2009, Pages 346-352

  Myasnikova, Ekaterina ^a   Surkova, Svetlana ^a   Panok, Lena ^b   Samsonova, Maria ^b   Reinitz, John ^b  

^a PETER THE GREAT ST PETERSBURG POLYTECHNIC UNIVERSITY   (Russian Federation)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; BLASTODERM; CONFOCAL MICROSCOPY; CONTROLLED STUDY; DROSOPHILA; GENE EXPRESSION REGULATION; IMAGE ANALYSIS; NOISE REDUCTION; NONHUMAN; PHOTON; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SIGNAL NOISE RATIO; SYSTEMS BIOLOGY;

ANIMALS; BLASTODERM; DROSOPHILA; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENES, INSECT; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, CONFOCAL; REGRESSION ANALYSIS;

EID: 59549101336     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn620     Document Type: Article

References (21)

1. Dey,N. et al. (2006) Richardson-lucy algorithm with total variation regularization for 3d confocal microscope deconvolution. Microsc. Res. Tech., 69, 260-266.
2. Ekstrom,C. et al. (2004) Spot shape modelling and data transformations for microarrays. Bioinformatics, 20, 2270-2278.
3. Foe,V. and Alberts,B. (1983) Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis. J. Cell Sci., 61, 31-70.
4. Glasbey,C. et al. (2007) Estimation of expression levels in spotted microarrays with saturated pixels. Stat. Appl. Genet. Mol. Biol., 6, 34.
5. Gonzalez,R. and Woods,R. (2002) Digital Image Processing, 2nd edn. Prentice Hall, Upper Saddle River.
6. Greene,W.H. (2000) Econometric Analysis, 4th edn. Prentice Hall International, London.
7. Ingham,P.W. (1988) The molecular genetics of embryonic pattern formation in Drosophila. Nature, 335, 25-34.
8. Janssens,H. et al. (2005) A high-throughput method for quantifying gene expression data from early Drosophila embryo. Dev. Genes Evol. 225, 374-381.
9. Kosman,D. et al. (1997) Automated assay of gene expression at cellular resolution. In Altman,R. et al. (eds), Proceedings of the 1998 Pacific Symposium on Biocomputing. World Scientific Press, Singapore, pp. 6-17.
10. Kosman,D. et al. (1998) Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins. Dev. Genes Evol., 208, 290-294.
11. Pawley,J. (1995) Fundamental limits in confocal microscopy. In Handbook of Biological Confocal Microscopy, 2nd edn. Springer, New York, pp. 18-39.
12. Pawley,J. (2006) Points, pixels, and gray levels: Digitizing image data. In Handbook of Biological Confocal Microscopy, 3rd edn. Springer, New York, pp. 20-41, 59-79.
13. Poustelnikova,E. et al. (2004) A database for management of gene expression data in situ. Bioinformatics, 20, 2212-2221.
14. Press,W.H. et al. (1988) Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge.
15. Shepp,L. and Vardi,Y. (1982) Maximum likelihood. reconstruction for emission tomography. IEEE Trans. Med. Imaging, MI-1, 113-122.
16. van Kempen,G. and van Vliet,L. (2000) Background estimation in non linear image restoration. J. Opt. Soc. Am., A17, 425-433.
17. Wilkie,G. et al. (1999) Transcribed genes are localized according to chromosomal position within polarized Drosophila embryonic nuclei. Curr. Biol., 9, 1263-1266.
18. Wit,E. and McClure,J. (2003) Statistical adjustment of signal censoring in gene expression experiments. Bioinformatics, 19, 1055-1060.
19. Wu,S.-J. (2002) Estimation of the parameters of the Weibull distribution with progressively censored data. J. Japan Stat. Soc., 32, 155-163.
20. Zucker,R. and Price,O. (2001a) Evaluation of confocal microscopy system performance. Cytometry, 44, 273-294.
21. Zucker,R. and Price,O. (2001b) Statistical evaluation of confocal microscopy images. Cytometry, 44, 295-308.