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Fig. 1
Definition of coordinate systems of the Kupffer’s vesicle (KV).
(A) Side view of a zebrafish embryo at 5-somite stage (left panel) and its schematic drawing (middle panel), highlighting the KV localization (grey box). The zoom-up box (right panel) shows the schematic transverse section of the KV, depicting the cilia (in green), their rotational orientation (black curved arrows) and the directional flow (thick black arrows). (B) em, en, ef are the local basis on the ellipsoid, which are used to define cilia orientation. The vector em is aligned along a meridian (blue) from the ventral to the dorsal pole; ef follows a parallel (red) in the direction of the typical directional flow within the vesicle; en is the vector normal to the KV surface and pointing towards the center of the vesicle (green). (C) Cilia 3D orientation is quantified by two angles: θ (tilt angle from the surface normal en) and φ (angle between the surface projection of the cilia vector and the meridional direction). (D) 2D flat map representation of the KV surface with coordinates α and β. The origin is set in the anterior pole. The embryonic body plan directions are marked as A (anterior), P (posterior), L (left), R (right), D (dorsal) and V (ventral). The body plan reference frame is defined as vectors eD, eL, eA.