Automatic tracking of Arabidopsis thaliana root meristem in confocal microscopy

The Arabidopsis thaliana is a well defined and a suited system to study plant development at the cellular level. To follow in vivo the root meristem activity under a confocal microscope the image acquisition process was automated through a coherent observation of a fixed point of the root tip. This position information allows the microscope stage control to track the root tip. Root tip estimation is performed following two approaches: computing the root central line intersection with the contour or the maximum filtered contour curvature point. The first method fits the root border with lines, using the Radon transform and a classification procedure. The central line is defined as the line that bisects the angle between these lines. The intersection of the central line with the root contour provides an estimate for the root tip position. The second method is based on contour traversing, followed by convolution of the contour coordinates with a Gaussian kernel. Curvature is computed for this filtered contour. The maximum curvature point provides another root tip estimate. A third method, based on a Kalman estimator is used to select between the previous two outputs. The system allowed the tracking of the root meristem for more than 20 hours in several experiments.