title: Segmentation of cells from 3-D confocal images of live zebrafish embryo.
abstract: In this paper, we use partial-differential-equation-based segmentation to accurately extract the shapes of membranes and nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. This strategy is a prerequisite for an accurate quantitative analysis of cell shape and morphodynamics during organogenesis and is the basis for an integrated understanding of biological processes. This data will also serve for the measurement of the variability between individuals in a population. The segmentation of cellular structures is achieved by first using an edge-preserving image filtering method for noise reduction and then applying an algorithm for cell shape reconstruction based on the Subjective Surfaces technique.
authors.affiliation: Dipartimento di Elettronica, Informatica e Sistemistica (DEIS), Bologna University, Italy. cecilia.zanella2@unibo.it
authors.forename: Cecilia
authors.initials: C
authors.lastname: Zanella
authors.forename: Barbara
authors.initials: B
authors.lastname: Rizzi
authors.forename: Camilo
authors.initials: C
authors.lastname: Melani
authors.forename: Matteo
authors.initials: M
authors.lastname: Campana
authors.forename: Paul
authors.initials: P
authors.lastname: Bourgine
authors.forename: Karol
authors.initials: K
authors.lastname: Mikula
authors.forename: Nadine
authors.initials: N
authors.lastname: Peyriéras
authors.forename: Alessandro
authors.initials: A
authors.lastname: Sarti
mesh_terms: D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D004625:Embryo, Nonmammalian / Q000166:cytology*; D006801:Humans; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D015027:Zebrafish / Q000033:anatomy & histology* / Q000196:embryology*