Abstract
Carefully studied in-situ hybridization Gene expression patterns (GEP) can provide a first glance at possible relationships among genes. Automatic comparative analysis tools are an indispensable requirement to manage the constantly growing amount of such GEP images. We present here an automated processing pipeline for Segmenting, Classification, and Clustering large-scale sets of Drosophila melanogaster GEP images that facilitates automatic GEP analysis.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Gawantka V, Pollet N, Delius H, et al. Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech Dev. 1998;77:95–141.
Neidhardt L, Gasca S, Wertz K, et al. Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev. 2000;98:77–93.
Kudoh T, Tsang M, Hukriede NA, et al. A gene expression screen in zebrafish embryogenesis. Genome Res. 2001;11:1979–1987.
Tomancak P, Beaton A, Weiszmann R, et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 2002;3:0088.
Schubert W, Bonnekoh B, Pommer AJ, et al. Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nat Biotechnol. 2006;24:1270–1278.
BDGP: Berkeley Drosophila Genome Project. http://www.fruitfly.org/.
Tomancak P, Berman BP, Beaton A, et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biology. 2007;8:R145.
Montalta-He H, Reichert H. Impressive expressions: Developing a systematic database of gene-expression patterns in Drosophila embryogenesis. Genome Biology. 2003; p. 205–205.
FlyBase: A Database of Drosophila Genes and Genomes. http://flybase.bio.indiana.edu/.
Van Emden B, Ramos H, Panchanathan S, et al. FlyExpress: An image-matching web-tool for finding genes with overlapping patterns of expression in Drosophila embryos; 2006. www.flyexpress.net.
Kumar S, Jayaraman K, Panchanathan S, et al. BEST: A novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics. 2002;162:2037–2047.
Peng H, Myers EW. Comparing in situ mRNA expression patterns of Drosophila embryos. In: Proc Int Conf Res Comput Mol Biol; 2004. p. 157–166.
Peng H, Long F, Zhou J, et al. Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biology. 2007;8(Suppl 1):S7.
Heffel A, Stadler PF, Prohaska SJ, et al. Process flow for classification and clustering of fruit fly gene expression patterns. Proc IEEE ICIP. 2008; p. 721. http://www-video.eecs.berkeley.edu/Proceedings/ICIP2008/ICIP2008.html.
Pernkopf F, Bouchaffra D. Genetic-based EM algorithm for learning Gaussian mixture models. IEEE Trans Pattern Anal Mach Intell. 2005;27:1344–1348.
Moon TK. The expectation-maximization algorithm. IEEE Signal Processing Magazine. 1996;(6):47–60.
Xu C, Prince JL. Snakes, shapes, and gradient vector flow. IEEE Trans Image Process. 1998;7:359–369.
Kass M, Witkin A, Terzopoulos D. Snakes: Active contour models. Int J Computer Vis. 2004;1:321–331.
Gottesfeld Brown L. A survey of image registration techniques. ACM Computing Surveys. 1992;24:325–376.
Braumann UD, Kuska JP. A new equation for nonlinear image registration with control over the vortex structure in the displacement field. Proc IEEE Int Conf Image Process. 2006; p. 329–332.
Braumann UD, Kuska JP. Influence of the boundary conditions on the result of non-linear image registration. Proc IEEE Int Conf Image Process. 2005; p. I–1129–I–1132.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Heffel, A., Prohaska, S.J., Stadler, P.F., Kauer, G., Kuska, JP. (2009). Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns. In: Meinzer, HP., Deserno, T.M., Handels, H., Tolxdorff, T. (eds) Bildverarbeitung für die Medizin 2009. Informatik aktuell. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-93860-6_84
Download citation
DOI: https://doi.org/10.1007/978-3-540-93860-6_84
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-93859-0
Online ISBN: 978-3-540-93860-6
eBook Packages: Computer Science and Engineering (German Language)