A noise-resistant algorithm for grid finding in microarray image analysis

被引：5

作者：

Novikov, Eugene ^{[1
]}

Barillot, Emmanuel ^{[1
]}

机构：

[1] Inst Curie, Serv Bioinformat, F-75248 Paris 05, France

来源：

MACHINE VISION AND APPLICATIONS | 2006年 / 17卷 / 05期

关键词：

microarray image analysis; automatic spot localization; grid finding; spot addressing;

D O I：

10.1007/s00138-006-0040-4

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

We present an algorithm for automatic spot localization for microarray images with rectangular spot and block packing. As an input, the algorithm requires only the common array design parameters: number of block rows and columns and number of spot rows and columns within each block. It proved to be robust with respect to different types of contamination and can tolerate a high percentage of the missing spots. The validity of the developed algorithm has been tested and confirmed using a large set of images of various designs from different microarray platforms. Comparison with academic and commercial packages has shown that for uncontaminated images our algorithm performs similarly, whereas for certain problematic images it outperforms the other packages.

引用

页码：337 / 345

页数：9

共 14 条

[1] Automatic analysis of DNA microarray images using mathematical morphology [J].

Angulo, J ;

Serra, J .

BIOINFORMATICS, 2003, 19 (05) :553-562

[2]

*AX INSTR INC, 2003, GENEPIX PRO 5 0

[3]

BUHLER J, 2000, 20000805 UW CSE UWTP

[4] Automatic registration of microarray images. I. Rectangular grid [J].

Galinsky, VL .

BIOINFORMATICS, 2003, 19 (14) :1824-1831

[5] A concise guide to cDNA microarray analysis [J].

Hegde, P ;

Qi, R ;

Abernathy, K ;

Gay, C ;

Dharap, S ;

Gaspard, R ;

Hughes, JE ;

Snesrud, E ;

Lee, N ;

Quackenbush, J .

BIOTECHNIQUES, 2000, 29 (03) :548-+

[6] Extracting information from cDNA arrays [J].

Herzel, H ;

Beule, D ;

Kielbasa, S ;

Korbel, J ;

Sers, C ;

Malik, A ;

Eickhoff, H ;

Lehrach, H ;

Schuchhardt, J .

CHAOS, 2001, 11 (01) :98-107

[7] A tiling resolution DNA microarray with complete coverage of the human genome [J].

Ishkanian, AS ;

Malloff, CA ;

Watson, SK ;

deLeeuw, RJ ;

Chi, B ;

Coe, BP ;

Snijders, A ;

Albertson, DG ;

Pinkel, D ;

Marra, MA ;

Ling, V ;

MacAulay, C ;

Lam, WL .

NATURE GENETICS, 2004, 36 (03) :299-303

[8] Fully automatic quantification of microarray image data [J].

Jain, AN ;

Tokuyasu, TA ;

Snijders, AM ;

Segraves, R ;

Albertson, DG ;

Pinkel, D .

GENOME RESEARCH, 2002, 12 (02) :325-332

[9] An automatic block and spot indexing with k-nearest neighbors graph for microarray image analysis [J].

Jung, HY ;

Cho, HG .

BIOINFORMATICS, 2002, 18 :S141-S151

[10]

*KOAD TECHN, 2004, KOAD V2 3 16

← 1 2 →