3D spatial drift correction using Kalman filtering for fluorescence based imaging

In this paper we present a framework for correcting the spatial drift that can occur in 3D optical fluorescence microscopy images. These shifts happen during long time acquisition and can corrupt further analysis. This artifact has to be taken into account especially if the application requires an high spatial detection accuracy. Our correction method is based on the use of a microsphere located within the biological assay. As the bead does not provide the same correction quality for each Z-slice, we propose here, to include a level of confidence depending on the depth in a Kalman filtering process. This framework allows then to extend the motion compensation along the complete 3D images. This method is validated on real data and provides an easy and accurate way to correct 3D images corrupted along Z by a XY motion.