A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis.

ABSTRACT: A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of z

SUBMITTER: Castro-Gonzalez C 

PROVIDER: S-EPMC4063669 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature