title: Cells segmentation from 3-D confocal images of early zebrafish embryogenesis.
abstract: We designed a strategy for extracting the shapes of cell membranes and nuclei from time lapse confocal images taken throughout early zebrafish embryogenesis using a partial-differential-equation-based segmentation. This segmentation step is a prerequisite for an accurate quantitative analysis of cell morphodynamics during embryogenesis and it is the basis for an integrated understanding of biological processes. The segmentation of embryonic cells requires live zebrafish embryos fluorescently labeled to highlight sub-cellular structures and designing specific algorithms by adapting classical methods to image features. Our strategy includes the following steps: the signal-to-noise ratio is first improved by an edge-preserving filtering, then the cell shape is reconstructed applying a fully automated algorithm based on a generalized version of the Subjective Surfaces technique. Finally we present a procedure for the algorithm validation either from the accuracy and the robustness perspective.
authors: DEIS, Bologna University, 40136 Bologna, Italy. cecilia.zanella2@unibo.it
authors: Cecilia
authors: C
authors: Zanella
authors: Matteo
authors: M
authors: Campana
authors: Barbara
authors: B
authors: Rizzi
authors: Camilo
authors: C
authors: Melani
authors: Gonzalo
authors: G
authors: Sanguinetti
authors: Paul
authors: P
authors: Bourgine
authors: Karol
authors: K
authors: Mikula
authors: Nadine
authors: N
authors: Peyrieras
authors: Alessandro
authors: A
authors: Sarti
mesh_terms: D000465:Algorithms; D000818:Animals; D002455:Cell Division; D002462:Cell Membrane; D002467:Cell Nucleus; D048430:Cell Shape; D004625:Embryo, Nonmammalian / Q000166:cytology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D015203:Reproducibility of Results; D015027:Zebrafish / Q000196:embryology*