Fig. 2

Acquisition and processing protocols used to extract the 3D trajectory of root growth for each plant. The first step of system calibration is performed only once and consists of a standard single camera calibration for lens distortion using a chessboard pattern followed by stereo cameras calibration for extrinsic parameters extraction (to enable stereo vision 3D reconstruction). The system calibration includes the calibration for the distortion introduced by water. Water distortion calibration is performed using the chessboard pattern to model (linear modelling) the distortion introduced in the depth component. The time-lapse acquisition step consists of a simultaneous acquisition of pictures by the two cameras every 3 min. The obtained time-lapse video is processed in the video processing step using a semi-automatic tracking software [38]. The 2D trajectories obtained by each camera are then triangulated using the calibration parameters to extract the 3D trajectory of the root growth