Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells.

ABSTRACT: Three-dimensional (3D) segmentation of cells in microscopy images is crucial to accurately capture signals that extend across optical sections. Using brightfield images for segmentation has the advantage of being minimally phototoxic and leaving all other channels available for signals of interest. However, brightfield images only readily provide information for two-dimensional (2D) segmentation. In radially symmetric cells, such as fission yeast and many bacteria, this 2D segmentation can be computationally extruded into the third dimension. However, current methods typically make the simplifying assumption that cells are straight rods. Here, we report Pomegranate, a pipeline that performs the extrusion into 3D using spheres placed along the topological skeletons of the 2D-segmented regio

SUBMITTER: Baybay EK 

PROVIDER: S-EPMC7538417 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature