Robust DNA microarray image analysis

Machine Vision and Applications

Volumn 15, Issue 1, 2003, Pages 11-28

  Brändle, Norbert ^a   Bischof, Horst ^b   Lapp, Hilmar ^c  

^a VIENNA UNIVERSITY OF TECHNOLOGY   (Austria)

^b GRAZ UNIVERSITY OF TECHNOLOGY   (Austria)

^c GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

Genomics; Gridding; Microarrays; Parametric fitting; Robust statistics

Indexed keywords

ARRAYS; CONFORMAL MAPPING; DNA; FLUORESCENCE; GENES; IMAGE SEGMENTATION; MATHEMATICAL MODELS; NUCLEIC ACIDS; RNA; ROBUSTNESS (CONTROL SYSTEMS); STATISTICAL METHODS;

GENOMICS; GRIDDING; MICROARRAYS; PARAMETRIC FITTING; ROBUST STATISTICS;

IMAGE ANALYSIS;

EID: 11144277252     PISSN: 09328092     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00138-002-0114-x     Document Type: Article

References (40)

1. Adams R, Bischof L (1994) Seeded region growing. IEEE transactions on pattern analysis and machine intelligence 16(6):641-647
2. Axon Instruments (1999) GenePix 400A User's Guide. Foster City, CA
3. Bergemann T, Quiaoit F, Delrow J. Zhao LP (2001) Statistical issues in signal extraction from microarrays. In: Microarrays: optical technologies and informatics, vol 4266. Proceedings of SPIE: progress in biomedial optics and imaging, San Jose, CA, 21-22 January 2001, pp 24-34
4. Bertsekas DP (1999) Nonlinear programming. Athena Scientific, Belmont, MA
5. Bettens E, Scheunders P, Sijbers J, Van Dyck J, Moens L (1996) Automatic segmentation and modelling of two-dimensional electrophoresis gels. In: Proceedings of IEEE international conference on image processing, vol II. Lausanne Switzerland, September 1996, pp 665-668
6. Beucher S, Meyer F (1993) The morphological approach to segmentation: the watershed transformation. In: Optical engineering, vol 34, ch 12: Mathematical morphology in image processing, Marcel Dekker, New York, pp 433-481
7. Bishop CM (1995) Neural networks for pattern recognition. Clarendon Press, Oxford
8. Brandie N, Lapp H, Bischof H (1999) Automatic Grid fitting for genetic spot array images containing guide spots. In: Solina F, Leonardis A (eds) Computer analysis of images and patterns, CAIP99, vol 1689 of LNCS, Springer, Berlin Heidelberg New York, pp 357-366
9. Brändie N, Lapp H, Bischof H (2000) Fully automatic grid fitting for genetic spot array images containing guide spots. Technical report PRIP-TR-058, PRIP, TU Wien
10. Buhler J, Ideker T, Haynor D (2000) Dapple: improved techniques for finding spots on DNA microarrays. Technical report UWTR 200-08-05, University of Washington
11. Chen Y, Dougherty ER, Bittner ML (1997) Ratio-based decicions and the quantitative analysis of cDNA microarray images. J Biomed Opt 2(4):364-374
12. Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G (1999) Making and reading microarrays. Nat Genet Suppl 21:15-19
13. Dougherty ER (1990) Probability and statistics for the engineering, computing, and physical sciences. Prentice-Hall, Englewood Cliffs, NJ
14. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM (1999) Expression profiling using cDNA microarrays. Nat Genet Suppl 21:10-14
15. Eisen MB (1999) ScanAnalyze documentation. http://rana.Standford.edu/ software.
16. Groch K, Kuklin A, Petrov A, Shams S (2001) Image segmentation and quality control measures in microarray image analysis. J Assoc Lab Automation 6(3):73-76
17. Hartelius K (1996) Analysis of irregularly distributed points. PhD thesis, Institute of Mathematical Modelling, Technical University of Denmark
18. Hartung J (1989) Multivariate Statistik. R. Oldenburg Verlag, München Wien
19. Herzel H, Beule D, Kielbasa S, Korbel J, Sers C, Malik A, Eickhoff H, Lehrach H, Schuchhardt J (2001) Extracting information from cDNA arrays. CHAOS: an interdisciplinary journal of nonlinear science 11(1):98-107
20. Huber PJ (1981) Robust statistics. Wiley, New York
21. Jain AK (1986) Fundamentals of digital image processing. Prentice-Hall, Englewood Cliffs, NJ
22. Jolion JM, Rosenfeld A (1994) A pyramid framework for early vision. Kluwer, Dordrecht
23. Jureckova J (1984) Robust statistical procedures, vol 4. Handbook of statistics, ch M-, L- and R-estimators, pp 463-485 Elsevier, 1984.
24. Kaifei T, Schiekel C, Kämpke T (2000) Spotting approaches for biochip arrays. In: 15th international conference on pattern recognition, vol 4, IAPR, IEEE Computer Society, Barcelona, pp 356-361
25. Kuklin A, Shams S, Shah S (2000) Automation in microarray image analysis with AutoGene™. J Assoc Lab Automation 5(5):67-70
26. Lewin B (1997) Genes VI. Oxford University Press, Oxford
27. Lockhart DJ, Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405(6788):827-836
28. GSI Lumonics (1999) QuantArray analysis software, Operator's manual
29. Maronna RA (1976) Robust M-estimators of multivariate location and scatter. Ann Stat 4(1):51-67
30. Meier-Ewert S, Lange J, Gerst H, Herwig R, Schmitt A, Freund J et al (1998) Comparative gene expression profiling by oligonucleotide fingerprinting. Nucleic Acids Res26(9):2216-2223
31. Meier-Ewert S, Maier E, Ahmadi AR, Curtis J, Lehrach H (1993) An automated approach to generating expressed sequence catalogues. Nature 361:375-376
32. Nayar SK, Poggio T (eds) (1996) Early visual learning. Oxford University Press, Oxford
33. Noordmans HJ, Smeulders AWM (1998) Detection and characterization of isolated and overlapping spots. Comput Vision Image Understand 70(1):23-35
34. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1992) Numerical recipes in C. Cambridge University Press
35. Rousseeuw PJ, Leroy AM (1987) Robust regression & outlier detection. Wiley, New York
36. Shoemaker DD, Schadt EE, Armour CD (2001) Experimental annotation of the human genome using microarray technology. Nature 409(6822):922-927
37. Steinfath M, Wruck W, Seidel H, Lehrach H, Radelof U, O'Brien J (2001) Automated image analysis for array hybridization experiments. Bioinformatics 17(7):634-641
38. Yang YH, Buctdey MJ, Dudoit S, Speed TP (2000) Comparison of methods for image analysis on cDNA microarray data. Technical report 584, Department of Statistics, University of California at Berkeley
39. Zhang Z (1995) Parameter estimation techniques: a tutorial with application to conic fitting. Technical report 2676, Institut de recherche en informatique et en automatique
40. Zhou ZZ, Stein JA, Ji QZ (2001) GLEAMS: a novel approach to high throughput genetic micro-array image capture and analysis. In: Microarrays: optical technologies and informatics, vol 4266, Proceedings of SPIE: progress in biomedial optics and imaging, San Jose, CA, 21-22 January 2001, pp 13-23