TY - JOUR
T1 - Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation
AU - Cao, Jianfeng
AU - Guan, Guoye
AU - Ho, Vincy Wing Sze
AU - Wong, Ming Kin
AU - Chan, Lu Yan
AU - Tang, Chao
AU - Zhao, Zhongying
AU - Yan, Hong
N1 - The C. elegans strains were provided by the C. elegans Genetic Center (CGC), which is funded by the National Institutes of Health, Office of Research Infrastructure Programs, Grant P40 OD010440. This work was supported by the Hong Kong Research Grants Council (HKBU12100118, HKBU12100917, HKBU12123716, N_HKBU201/18, C1007-15G), the HKBU Interdisciplinary Research Cluster Fund, the Ministry of Science and Technology of China (2015CB910300), the National Natural Science Foundation of China (91430217), the Hong Kong Innovation and Technology Commission (ITC), and the Hong Kong Institute for Data Science.
PY - 2020/12
Y1 - 2020/12
N2 - The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, cell migration and cell fate differentiation, cell morphology during development has not yet been systematically characterized in any metazoan, including C. elegans. This knowledge gap substantially hampers many studies in both developmental and cell biology. Here we report an automatic pipeline, CShaper, which combines automated segmentation of fluorescently labeled membranes with automated cell lineage tracing. We apply this pipeline to quantify morphological parameters of densely packed cells in 17 developing C. elegans embryos. Consequently, we generate a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with resolved cell identities. We anticipate that CShaper and the morphological atlas will stimulate and enhance further studies in the fields of developmental biology, cell biology and biomechanics.
AB - The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, cell migration and cell fate differentiation, cell morphology during development has not yet been systematically characterized in any metazoan, including C. elegans. This knowledge gap substantially hampers many studies in both developmental and cell biology. Here we report an automatic pipeline, CShaper, which combines automated segmentation of fluorescently labeled membranes with automated cell lineage tracing. We apply this pipeline to quantify morphological parameters of densely packed cells in 17 developing C. elegans embryos. Consequently, we generate a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with resolved cell identities. We anticipate that CShaper and the morphological atlas will stimulate and enhance further studies in the fields of developmental biology, cell biology and biomechanics.
UR - http://www.scopus.com/inward/record.url?scp=85097304658&partnerID=8YFLogxK
U2 - 10.1038/s41467-020-19863-x
DO - 10.1038/s41467-020-19863-x
M3 - Journal article
C2 - 33288755
AN - SCOPUS:85097304658
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 6254
ER -