In multicellular organisms, groups of cells cooperatively behave and change morphology, resulting in dynamic tissue deformation.In vertebrate gastrula, for example, coordinated migration of mesodermal cells occurs, including convergent extension, to establish complex structures inside the embryo to complete gastrulation (Keller & Danilchik, 1988). For understanding tissue deformation, it is necessary to describe the overall cell arrangement. Several methods for describing cell arrangement have been reported (Blanchard et al., 2009;Guirao et al., 2015;Merkel & Manning, 2017) that use strategies such as the relative position of the cell center (Guirao et al., 2015), the vertical cell shape by fitting of an ellipse (Blanchard et al., 2009), or direct tracing of the cell shape, including the apical cell area. These cell shape data are crucial for understanding cell movements, morphology, cell-cell interactions, and competitions during differentiation and migration (Lecuit & Le Goff, 2007;Oates et al., 2009). These cell shape data are usually obtained by labeling the cell membrane with either membrane-bound GFP in living cells or phalloidin staining in fixed cells. Then the fluorescent image is transformed into a line drawing for subsequent analyses. The critical points for segmentation methods are accuracy and time. The