title: Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy.
abstract: Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Luengo-Oroz
authors.forename: Jose L
authors.initials: JL
authors.lastname: Rubio-Guivernau
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Faure
authors.forename: Thierry
authors.initials: T
authors.lastname: Savy
authors.forename: Louise
authors.initials: L
authors.lastname: Duloquin
authors.forename: Nicolas
authors.initials: N
authors.lastname: Olivier
authors.forename: David
authors.initials: D
authors.lastname: Pastor
authors.forename: Maria
authors.initials: M
authors.lastname: Ledesma-Carbayo
authors.forename: Delphine
authors.initials: D
authors.lastname: Débarre
authors.forename: Paul
authors.initials: P
authors.lastname: Bourgine
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Beaurepaire
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
authors.forename: Andres
authors.initials: A
authors.lastname: Santos
mesh_terms: D000465:Algorithms; D000818:Animals; D058948:Cell Tracking / Q000379:methods*; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D015027:Zebrafish / Q000033:anatomy & histology* / Q000196:embryology*