CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues
Fig 5
Application of CellMet to different tissues.
A. (Left) Schematic of the Drosophila embryo from a dorsal view, with anterior up. The red dashed region corresponds to the images to the right. (Centre) Heart cells in a stage 16 Drosophila embryo, just as the heart lumen forms with segmentation from CellPose. (Right) Connectivity of the heart cells, demonstrating the cell alignment. Numbers correspond to cell labels ID. B. (Left) schematic of the zebrafish embryo, highlighting the myotome region with red box. (Centre) Myotome in 48hpf zebrafish embryo, with segmentation from CellPose. Green dashed line shows the chevron form of the myotome. Bottom shows cross-sectional view. (Right) 3D visualisation of muscle fibres showing the different cell morphologies. For the twisted cell, we can trace the rotation along the cell long axis. Vertex colours are the same as edges showed in 3D. C. (Left) Schematic of organoid culture constrained to triangular domain. (Centre) Organoid culture at 48 hours, with CellPose segmentation. Views shown in x-y and x-z axes. (Right) Comparison of cell sphericity with cell connectivity. Scale bar: A: ; B and C:
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