3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images.

ABSTRACT:

Summary

Segmentation of single cells in microscopy images is one of the major challenges in computational biology. It is the first step of most bioimage analysis tasks, and essential to create training sets for more advanced deep learning approaches. Here, we propose 3D-Cell-Annotator to solve this task using 3D active surfaces together with shape descriptors as prior information in a semi-automated fashion. The software uses the convenient 3D interface of the widely used Medical Imaging Interaction Toolkit (MITK). Results on 3D biological structures (e.g. spheroids, organoids and embryos) show that the precision of the segmentation reaches the level of a human expert.

Availability and implementation

3D-Cell-Annotator is implemented in CUDA/C++ as a patch for the segmentatio

SUBMITTER: Tasnadi EA 

PROVIDER: S-EPMC7203751 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature