Fig. 1 S1

Multiscale analysis from individual cilia to 3D modeling of the Kupffer’s vesicle (KV).

(A) 3D-CiliaMap workflow pipeline: 3D live imaging with cilia analysis, followed by 2D visualization of cilia maps, 3D flow calculation based on live datasets, and flow visualization. (B) List of the KV and cilia features extracted using 3D-CiliaMap. (C–E) Successive steps forming the 3D-CiliaMap workflow from 3D live imaging to cilia vectorization (see also Video 1): (C) 3D live imaging of the total volume of the KV, using Tg (actb2:Mmu.Arl13b-GFP) (Borovina et al., 2010) embryos soaked for 60 min in Bodipy TR (Molecular Probe) - dashed white lines underline the KV. (D) Using Imaris (Bitplane Inc.), the KV surface is manually segmented to reveal only the cilia belonging to the surface of the KV cells. (E) Slow acquisition speed with standard laser scanning microscopy allows detecting the cilia orientation in the KV using the Tg (actb2:Mmu.Arl13b-GFP) line: dashed white lines underline the KV (upper panel); dorsal view of the whole vesicle showing the vectors obtained from the GFP signal (middle panel); high magnification of a cilium with a vector corresponding to its rotational axis orientation (bottom panel).