3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 176 - 13
• Main Authors: Cao, Jianfeng, Wong, Ming-Kin, Zhao, Zhongying, Yan, Hong
• Format: Journal Article
• Language: English
• Published: England BioMed Central 08.04.2019; BMC
• Subjects: 3D morphological segmentation; Algorithms; Animals; Bioinformatics; C. elegans; Caenorhabditis elegans - embryology; Cell Division; Cell Nucleus; Cell size; Communication; Developmental stages; Embryo, Nonmammalian; Embryonic Development; Embryos; Experts; Image processing; Image reconstruction; Image segmentation; Imaging, Three-Dimensional; International conferences; Methodology; Microscopy; Models, Theoretical; Morphology; Nematodes; Nuclei (cytology); Proteins; Quantitative analysis; Shape features; Statistical analysis; Three dimensional analysis; Watershed segmentation; Watersheds; Shape features; C. elegans; 3D morphological segmentation; Watershed segmentation
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2720-x

Understanding the cellular architecture is a fundamental problem in various biological studies. C. elegans is widely used as a model organism in these studies because of its unique fate determinations. In recent years, researchers have worked extensively on C. elegans to excavate the regulations of genes and proteins on cell mobility and communication. Although various algorithms have been proposed to analyze nucleus, cell shape features are not yet well recorded. This paper proposes a method to systematically analyze three-dimensional morphological cellular features. Three-dimensional Membrane Morphological Segmentation (3DMMS) makes use of several novel techniques, such as statistical intensity normalization, and region filters, to pre-process the cell images. We then segment membrane stacks based on watershed algorithms. 3DMMS achieves high robustness and precision over different time points (development stages). It is compared with two state-of-the-art algorithms, RACE and BCOMS. Quantitative analysis shows 3DMMS performs best with the average Dice ratio of 97.7% at six time points. In addition, 3DMMS also provides time series of internal and external shape features of C. elegans. We have developed the 3DMMS based technique for embryonic shape reconstruction at the single-cell level. With cells accurately segmented, 3DMMS makes it possible to study cellular shapes and bridge morphological features and biological expression in embryo research.