Molecular genetics of axis formation in zebrafish, Annu Rev Genet, vol.39, pp.561-613, 2005. ,
Quantitative approaches in developmental biology, Nature Reviews Genetics, vol.10, pp.517-530, 2009. ,
Imaging in systems biology, Cell, vol.130, pp.784-795, 2007. ,
Microscopic marvels: Seeing the system, Nature, vol.459, p.630, 2009. ,
Advances in multiphoton microscopy for imaging embryos, Current Opinion in Genetics & Development, pp.538-548, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00803777
Fluorescent proteins and their applications in imaging living cells and tissues, Physiological Reviews, vol.90, pp.1103-1163, 2010. ,
Programmable in situ amplification for multiplexed imaging of mRNA expression, Nature Biotechnology, vol.28, pp.1208-1212, 2010. ,
Image analysis for understanding embryo development: a bridge from microscopy to biological insights, Current Opinion in Genetics & Development, vol.21, issue.5, pp.630-637, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00636953
Assembling models of embryo development: Image analysis and the construction of digital atlases, Birth Defects Research Part C: Embryo Today: Reviews, vol.96, pp.109-120, 2012. ,
Image registration methods: a survey, Image and vision computing, vol.21, pp.977-1000, 2003. ,
A 3D digital atlas of C. elegans and its application to single-cell analyses, Nature Methods, vol.6, pp.667-672, 2009. ,
Cell lineage reconstruction of early zebrafish embryos using label-free nonlinear microscopy, Science, vol.329, pp.967-971, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00519834
Genome-wide atlas of gene expression in the adult mouse brain, Nature, vol.445, pp.168-176, 2007. ,
A quantitative spatiotemporal atlas of gene expression in the drosophila blastoderm, Cell, vol.133, pp.364-374, 2008. ,
BrainAligner: 3D registration atlases of Drosophila brains, Nature Methods, vol.8, pp.493-498, 2011. ,
Whole-body gene expression pattern registration in Platynereis larvae, EvoDevo, vol.3, pp.1-13, 2012. ,
Cancer genetics and drug discovery in the zebrafish, Nature Reviews Cancer, vol.3, pp.533-539, 2003. ,
Developmental gene regulatory networks in the zebrafish embryo, Biochimica et Biophysica Acta (BBA), vol.1789, pp.279-298, 2009. ,
Efficient reverse-engineering of a developmental gene regulatory network, PLoS Computational Biology, vol.8, p.1002589, 2012. ,
A conserved developmental patterning network produces quantitatively different output in multiple species of drosophila, PLoS Genetics, vol.7, p.1002346, 2011. ,
ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains, Nature Methods, vol.9, pp.735-742, 2012. ,
Predictive computation of genomic logic processing functions in embryonic development, Proceedings of the National Academy of Sciences, vol.109, pp.16434-16442, 2012. ,
Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium, Cell, vol.142, pp.800-809, 2010. ,
reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology, PLoS Computational Biology, vol.8, p.1002837, 2012. ,
An automatic quantification and registration strategy to create a gene expression atlas of zebrafish embryogenesis, Int Conf IEEE Eng Med Biol Soc, pp.1469-1472, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00444514
Integrating data clustering and visualization for the analysis of 3D gene expression data, IEEE/ ACM Transactions on Computational Biology and Bioinformatics, vol.7, pp.64-79, 2010. ,
Icy: an open bioimage informatics platform for extended reproducible research, Nature Methods, vol.9, pp.690-696, 2012. ,
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets, Nature Biotechnology, vol.28, pp.348-353, 2010. ,
CellProfiler Analyst: data exploration and analysis software for complex image-based screens, BMC Bioinformatics, vol.9, p.482, 2008. ,
Axis-inducing activities and cell fates of the zebrafish organizer, Development, vol.127, pp.3407-3417, 2000. ,
A gene expression screen in zebrafish embryogenesis, Genome Research, vol.11, pp.1979-1987, 2001. ,
Integrating technologies for comparing 3D gene expression domains in the developing chick limb, Developmental Biology, vol.317, pp.13-23, 2008. ,
Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape, Molecular Systems Biology, vol.6, p.345, 2010. ,
EMAGE-Edinburgh Mouse Atlas of Gene Expression: 2008 update, Nucleic Acids Research, vol.36, pp.860-865, 2008. ,
Defining diversity, specialization, and gene specificity in transcriptomes through information theory, Proceedings of the National Academy of Sciences, vol.105, pp.9709-9714, 2008. ,
More than a decade of developmental gene expression atlases: where are we now?, Nucleic Acids Research, vol.37, pp.7349-7359, 2009. ,
Stages of embryonic development of the zebrafish, American Journal of Anatomy, vol.203, pp.253-310, 1995. ,
Zebrafish whole mount high-resolution double uorescent in situ hybridization, Journal of Visualized Experiments, p.1229, 2009. ,
Image analysis and mathematical morphology, 1982. ,
A survey of medical image registration, Medical Image Analysis, vol.2, pp.1-36, 1998. ,
Synexpression groups in eukaryotes, Nature, vol.402, pp.483-487, 1999. ,
A comparison of branching diagrams derived by various phenetic and cladistic methods, Systematic Botany, pp.264-293, 1980. ,
The comparison of dendrograms by objective methods, Taxon, vol.11, pp.33-40, 1962. ,
Comparison of hierarchical cluster analysis methods by cophenetic correlation, Journal of Inequalities and Applications, vol.2013, pp.1-8, 2013. ,