A method of estimating relative change of the 3D position of an object (e.g., sample drift in a microscopy system) having fiduciary markers that have an asymmetric joint point spread function distribution includes generating a plurality of calibration curves for each of the markers during a calibration phase including first calibration curves for a PSF width and second calibration curves for lateral bias. The method further includes capturing a first image of the markers during a data acquisition phase, generating a first joint 3D position for the markers using the first image, the first calibration curves and the second calibration curves, capturing a second image of the markers during the data acquisition phase, generating a second joint 3D position for the markers using the second image and the first and second calibration curves, and estimating the sample drift using the first joint 3D position and the second joint 3D position.