title: Towards a digital model of zebrafish embryogenesis. Integration of cell tracking and gene expression quantification.
abstract: We elaborate on a general framework composed of a set of computational tools to accurately quantificate cellular position and gene expression levels throughout early zebrafish embryogenesis captured over a time-lapse series of in vivo 3D images. Our modeling strategy involves nuclei detection, cell geometries extraction, automatic gene levels quantification and cell tracking to reconstruct cell trajectories and lineage tree which describe the animal development. Each cell in the embryo is then precisely described at each given time t by a vector composed of the cell 3D spatial coordinates (x; y; z) along with its gene expression level g. This comprehensive description of the embryo development is used to assess the general connection between genetic expression and cell movement. We also investigate genetic expression propagation between a cell and its progeny in the lineage tree. More to the point, this paper focuses on the evolution of the expression pattern of transcriptional factor goosecoid (gsc) through the gastrulation process between 6 and 9 hours post fertilization (hpf).
authors.affiliation: Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, 28040, Spain. ccastro@die.upm.es
authors.forename: Carlos
authors.initials: C
authors.lastname: Castro-Gonzalez
authors.forename: Miguel Angel
authors.initials: MA
authors.lastname: Luengo-Oroz
authors.forename: Louise
authors.initials: L
authors.lastname: Douloquin
authors.forename: Thierry
authors.initials: T
authors.lastname: Savy
authors.forename: Camilo
authors.initials: C
authors.lastname: Melani
authors.forename: Sophie
authors.initials: S
authors.lastname: Desnoulez
authors.forename: Maria Jesus
authors.initials: MJ
authors.lastname: Ledesma-Carbayo
authors.forename: Paul
authors.initials: P
authors.lastname: Bourginey
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyrieras
authors.forename: Andres
authors.initials: A
authors.lastname: Santos
mesh_terms: D000818:Animals; D019070:Cell Lineage; D002467:Cell Nucleus / Q000378:metabolism; D058948:Cell Tracking / Q000379:methods*; D004625:Embryo, Nonmammalian / Q000166:cytology* / Q000378:metabolism; D047108:Embryonic Development / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D051956:Goosecoid Protein / Q000235:genetics / Q000378:metabolism; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008954:Models, Biological; D015203:Reproducibility of Results; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*
chemical_list: D051956:Goosecoid Protein