SpheresDT/Mpacts-PiCS: Cell Tracking and Shape Retrieval in Membrane-labeled Embryos.

ABSTRACT: Uncovering the cellular and mechanical processes that drive embryo formation requires an accurate read out of cell geometries over time. However, automated extraction of 3D cell shapes from time lapse microscopy remains challenging, especially when only membranes are labeled. We present an image analysis framework for automated tracking and three-dimensional cell segmentation in confocal time lapses. A sphere clustering approach allows for local thresholding and application of logical rules to facilitate tracking and unseeded segmentation of variable cell shapes. Next, the segmentation is refined by a discrete element method simulation where cell shapes are constrained by a biomechanical cell shape model. We apply the framework on C. elegans embryos in various stages of early development a

SUBMITTER: Thiels W 

PROVIDER: S-EPMC8665764 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature