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An Automatic Quantification and Registration Strategy to Create a Gene Expression Atlas of Zebrafish Embryogenesis

Carlos Castro Gonzalez, Miguel Angel Luengo-Oroz, Sophie Desnoulez, Louise Duloquin, Laura Fernández-de-Manuel, Sara Montagna, Maria J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyrieras, Andres Santos
In order to properly understand and model the gene regulatory networks in animals development, it is crucial to obtain detailed measurements, both in time and space, about their gene expression domains. In this paper, we propose a complete computational framework to fulfill this task and create a 3D Atlas of the early zebrafish embryogenesis annotated with both the cellular localizations and the level of expression of different genes at different developmental stages. The strategy to construct such an Atlas is described here with the expression pattern of 5 different genes at 6 hours of development post fertilization.
Keywords: 3D Gene Expression Atlas, zebrafish embryogenesis, Developmental Biology
31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2009), pages 1469-1472, 2-6 September 2009, IEEE EMBS, Minneapolis, MN, USA
@inproceedings{genesimageprocessing-embc09,
	Address = {Minneapolis, MN, USA},
	Author = {Castro Gonzalez, Carlos and Luengo-Oroz, Miguel Angel and Desnoulez, Sophie and Duloquin, Louise and Fern{\'a}ndez-de-Manuel, Laura and Montagna, Sara and Ledesma-Carbayo, Maria J. and Bourgine, Paul and Peyrieras, Nadine and Santos, Andres},
	Booktitle = {31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2009)},
	Isbn = {978-1-4244-3296-7},
	Keywords = {3D Gene Expression Atlas, zebrafish embryogenesis, Developmental Biology},
	Month = {2-6~} # sep,
	Pages = {1469--1472},
	Publisher = {IEEE EMBS},
	PubMedId = {11585/85925},
	ScopusId = {2-s2.0-84903872300},
	Title = {An Automatic Quantification and Registration Strategy to Create a Gene Expression Atlas of Zebrafish Embryogenesis},
	Url = {http://www.embc09.org/},
	Year = 2009}