Methods for automatic microarray image segmentation

Katzer M, Kummert F, Sagerer G (2003)
IEEE Transactions on Nanobioscience 2(4): 202-214.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Abstract / Bemerkung
This paper describes image processing methods for automatic spotted microarray image analysis. Automatic gridding is important to achieve constant data quality and is, therefore, especially interesting for large-scale experiments as well as for integration of microarray expression data from different sources. We propose a Markov random field (MRF) based approach to high-level grid segmentation, which is robust to common problems encountered with array images and does not require calibration. We also propose an active contour method for single-spot segmentation. Active contour models describe objects in images by properties of their boundaries. Both MRFs and active contour models have been used in various other computer vision applications. The traditional active contour model must be generalized for successful application to microarray spot segmentation. Our active contour model is employed for spot detection in the MRF score functions as well as for spot signal segmentation in quantitative array image analysis. An evaluation using several image series from different sources shows the robustness of our methods.
Stichworte
microarrays; active contour models; Markov random fields
Erscheinungsjahr
2003
Zeitschriftentitel
IEEE Transactions on Nanobioscience
Band
2
Ausgabe
4
Seite(n)
202-214
ISSN
1536-1241
Page URI
https://pub.uni-bielefeld.de/record/1608553

Zitieren

Katzer M, Kummert F, Sagerer G. Methods for automatic microarray image segmentation. IEEE Transactions on Nanobioscience. 2003;2(4):202-214.
Katzer, M., Kummert, F., & Sagerer, G. (2003). Methods for automatic microarray image segmentation. IEEE Transactions on Nanobioscience, 2(4), 202-214. https://doi.org/10.1109/TNB.2003.817023
Katzer, Mathias, Kummert, Franz, and Sagerer, Gerhard. 2003. “Methods for automatic microarray image segmentation”. IEEE Transactions on Nanobioscience 2 (4): 202-214.
Katzer, M., Kummert, F., and Sagerer, G. (2003). Methods for automatic microarray image segmentation. IEEE Transactions on Nanobioscience 2, 202-214.
Katzer, M., Kummert, F., & Sagerer, G., 2003. Methods for automatic microarray image segmentation. IEEE Transactions on Nanobioscience, 2(4), p 202-214.
M. Katzer, F. Kummert, and G. Sagerer, “Methods for automatic microarray image segmentation”, IEEE Transactions on Nanobioscience, vol. 2, 2003, pp. 202-214.
Katzer, M., Kummert, F., Sagerer, G.: Methods for automatic microarray image segmentation. IEEE Transactions on Nanobioscience. 2, 202-214 (2003).
Katzer, Mathias, Kummert, Franz, and Sagerer, Gerhard. “Methods for automatic microarray image segmentation”. IEEE Transactions on Nanobioscience 2.4 (2003): 202-214.

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Grow-cut based automatic cDNA microarray image segmentation.
Katsigiannis S, Zacharia E, Maroulis D., IEEE Trans Nanobioscience 14(1), 2015
PMID: 25438323
Unsupervised image segmentation for microarray spots with irregular contours and inner holes.
Belean B, Borda M, Ackermann J, Koch I, Balacescu O., BMC Bioinformatics 16(), 2015
PMID: 26698293
A novel neural network approach to cDNA microarray image segmentation.
Wang Z, Zineddin B, Liang J, Zeng N, Li Y, Du M, Cao J, Liu X., Comput Methods Programs Biomed 111(1), 2013
PMID: 23669179
A glance at DNA microarray technology and applications.
Saei AA, Omidi Y., Bioimpacts 1(2), 2011
PMID: 23678411
Automatic Spot Identification for High Throughput Microarray Analysis.
Wu E, Su YA, Billings E, Brooks BR, Wu X., J Bioeng Biomed Sci Suppl 5(), 2011
PMID: 24298393
M3G: maximum margin microarray gridding.
Bariamis D, Iakovidis DK, Maroulis D., BMC Bioinformatics 11(), 2010
PMID: 20100338
3-D spot modeling for automatic segmentation of cDNA microarray images.
Zacharia E, Maroulis D., IEEE Trans Nanobioscience 9(3), 2010
PMID: 20519160
The COP9 signalosome mediates transcriptional and metabolic response to hormones, oxidative stress protection and cell wall rearrangement during fungal development.
Nahlik K, Dumkow M, Bayram O, Helmstaedt K, Busch S, Valerius O, Gerke J, Hoppert M, Schwier E, Opitz L, Westermann M, Grond S, Feussner K, Goebel C, Kaever A, Meinicke P, Feussner I, Braus GH., Mol Microbiol 78(4), 2010
PMID: 21062371
A Comparison of Fuzzy Clustering Approaches for Quantification of Microarray Gene Expression.
Wang YP, Gunampally M, Chen J, Bittel D, Butler MG, Cai WW., J Signal Process Syst 50(3), 2008
PMID: 28163819
Automatic microarray spot segmentation using a Snake-Fisher model.
Ho J, Hwang WL., IEEE Trans Med Imaging 27(6), 2008
PMID: 18541491
DNA microarray technology in toxicogenomics of aquatic models: methods and applications.
Ju Z, Wells MC, Walter RB., Comp Biochem Physiol C Toxicol Pharmacol 145(1), 2007
PMID: 16828578
Vector edge operators for cDNA microarray spot localization.
Lukac R, Plataniotis KN., Comput Med Imaging Graph 31(7), 2007
PMID: 17707611
WaveRead: automatic measurement of relative gene expression levels from microarrays using wavelet analysis.
Bidaut G, Manion FJ, Garcia C, Ochs MF., J Biomed Inform 39(4), 2006
PMID: 16298556
Probe classification of on-off type DNA microarray images with a nonlinear matching measure.
Ryu M, Kim JD, Min BG, Kim J, Kim YY., J Biomed Opt 11(1), 2006
PMID: 16526904
Segmentation of cDNA microarray spots using markov random field modeling.
Demirkaya O, Asyali MH, Shoukri MM., Bioinformatics 21(13), 2005
PMID: 15840703
Impact of microarray technology in nutrition and food research.
Spielbauer B, Stahl F., Mol Nutr Food Res 49(10), 2005
PMID: 16189797
Storage and transmission of microarray images.
Luo Y, Lonardi S., Drug Discov Today 10(23-24), 2005
PMID: 16376830
Copasetic analysis: a framework for the blind analysis of microarray imagery.
Fraser K, O'Neill P, Wang Z, Liu X., Syst Biol (Stevenage) 1(1), 2004
PMID: 17052129
A multichannel order-statistic technique for cDNA microarray image processing.
Lukac R, Plataniotis KN, Smolka B, Venetsanopoulos AN., IEEE Trans Nanobioscience 3(4), 2004
PMID: 15631139

33 References

Daten bereitgestellt von Europe PubMed Central.

The Stanford Microarray Database.
Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry JM., Nucleic Acids Res. 29(1), 2001
PMID: 11125075
Gene discovery using the maize genome database ZmDB.
Gai X, Lal S, Xing L, Brendel V, Walbot V., Nucleic Acids Res. 28(1), 2000
PMID: 10592191

chang, LIBSVM A library for support vector machines (), 2001

AUTHOR UNKNOWN, 0
Automated image analysis for array hybridization experiments.
Steinfath M, Wruck W, Seidel H, Lehrach H, Radelof U, O'Brien J., Bioinformatics 17(7), 2001
PMID: 11448881

AUTHOR UNKNOWN, 0
Automatic analysis of DNA microarray images using mathematical morphology.
Angulo J, Serra J., Bioinformatics 19(5), 2003
PMID: 12651712

li, Markov Random Field Modeling in Image Analysis (), 2001

kindermann, Markov Random Fields and Their Applications (), 1980

jähne, Digital Image Processing (), 1997

press, Numerical Recipes in C (), 1992

stoyan, Stochastic Geometry and its Applications (), 1995

ballard, Computer Vision (), 1982
Sequencing-by-hybridization revisited: the analog-spectrum proposal.
Preparata FP., IEEE/ACM Trans Comput Biol Bioinform 1(1), 2004
PMID: 17048407

AUTHOR UNKNOWN, 0
calibration-free methods in segmentation of cdna microarray images
vesanen, Proc IS& T/SPIE 12th Symp Electronic Imaging Science and Technology (), 2002

AUTHOR UNKNOWN, 0
robust automatic microarray image analysis
katzer, Proc Int Conf Bioinformatics North-South Networking (), 2002

AUTHOR UNKNOWN, 0

schürmann, Pattern Classification (), 1996

AUTHOR UNKNOWN, 0
Microarray fabrication with covalent attachment of DNA using bubble jet technology.
Okamoto T, Suzuki T, Yamamoto N., Nat. Biotechnol. 18(4), 2000
PMID: 10748527
the chipping forecast ii
AUTHOR UNKNOWN, Nature Genetics Suppl 32(), 2002

yang, Comparison of methods for image analysis on cDNA microarray data (), 2001
Fully automatic quantification of microarray image data.
Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D., Genome Res. 12(2), 2002
PMID: 11827952
DNA arrays for analysis of gene expression.
Eisen MB, Brown PO., Meth. Enzymol. 303(), 1999
PMID: 10349646

pevzner, Computational Molecular Biology An Algorithmic Approach (), 2000
probabilistic network inference for cooperative high and low level vision
chou, Markov Random Fields Theory and Applications (), 1993

AUTHOR UNKNOWN, 0
Ratio-based decisions and the quantitative analysis of cDNA microarray images.
Chen Y, Dougherty ER, Bittner ML., J Biomed Opt 2(4), 1997
PMID: 23014960

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 15376910
PubMed | Europe PMC

Suchen in

Google Scholar