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Background  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.    Results  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 .    Conclusion  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.    Electronic supplementary material  The online version of this article (10.1186/s12859-019-2720-x) contains supplementary material, which is available to authorized users.

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