Cells Segmentation from 3-D Confocal Images of Early Zebrafish Embryogenesis.

Cecilia Zanella (1) , Matteo Campana (1) , Barbara Rizzi (1) , Camilo Melani (2) , Gonzalo Sanguinetti (3) , Paul Bourgine (2) , Karol Mikula , Nadine Peyriéras (4, 5) , Alessandro Sarti

1 DEIS - Department of Electronics, Computer Science and Systems [Bologne]
2 CREA - Centre de recherche en épistémologie appliquée
3 CASA - Centre for Analysis, Scientific computing and Applications
4 INAF - Institut de Neurobiologie Alfred Fessard
5 DEPSN - Développement, évolution et plasticité du système nerveux

We designed a strategy for extracting the shapes of cell membranes andnuclei from time lapse confocal images taken throughout early zebrafish embryogenesisusing a partial-differential-equationbased segmentation. This segmentationstep 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.

Domaines: Neurosciences [q-bio.NC]

Cecilia Zanella, Matteo Campana, Barbara Rizzi, Camilo Melani, Gonzalo Sanguinetti, et al.. Cells Segmentation from 3-D Confocal Images of Early Zebrafish Embryogenesis.. IEEE Transactions on Image Processing, 2009, 19 (3), pp.770-781. ⟨10.1109/TIP.2009.2033629⟩. ⟨hal-00444516⟩