A computer-implemented method for analyzing at least one object under a first microscope and a second microscope the method comprising: receiving a first set of position coordinates of the at least one object under the first microscope as a set of features taken from 3D topographic data of a surface of the at least one object are successively displayed within a field of view thereof, the first microscope having a first coordinate system; receiving a second set of position coordinates of the at least one object under the second microscope as a set of features taken from 3D topographic data of the surface of the at least one object are successively displayed within a field of view thereof, the second microscope having a second coordinate system; computing (110, 306, 610) a transformation to link (112, 308, 612) the first coordinate system and the second coordinate system using the first set of position coordinates and the second set of position coordinates and irrespectively of an initial positioning of the at least one object under a respective one of the first microscope and the second microscope; generating guidance data when one of the first microscope and the second microscope is displaced, the guidance data corresponding to a set of operations to be applied to the other of the first microscope and the second microscope to follow movement of the one of the first microscope and the second microscope for bringing the set of features displayed within the field of view of the first microscope to match the set of features displayed within the field of view of the second microscope; and wherein the first microscope is a physical microscope and the second microscope is a virtual microscope, and wherein receiving a second set of position coordinates of the at least one object under the second microscope comprises receiving a set of coordinates for a set of features in an image of the at least one object on the virtual microscope. receiving a first set of position coordinates of the at least one object under the first microscope as a set of features taken from 3D topographic data of a surface of the at least one object are successively displayed within a field of view thereof, the first microscope having a first coordinate system; receiving a second set of position coordinates of the at least one object under the second microscope as a set of features taken from 3D topographic data of the surface of the at least one object are successively displayed within a field of view thereof, the second microscope having a second coordinate system; computing (110, 306, 610) a transformation to link (112, 308, 612) the first coordinate system and the second coordinate system using the first set of position coordinates and the second set of position coordinates and irrespectively of an initial positioning of the at least one object under a respective one of the first microscope and the second microscope; generating guidance data when one of the first microscope and the second microscope is displaced, the guidance data corresponding to a set of operations to be applied to the other of the first microscope and the second microscope to follow movement of the one of the first microscope and the second microscope for bringing the set of features displayed within the field of view of the first microscope to match the set of features displayed within the field of view of the second microscope; and wherein the first microscope is a physical microscope and the second microscope is a virtual microscope, and wherein receiving a second set of position coordinates of the at least one object under the second microscope comprises receiving a set of coordinates for a set of features in an image of the at least one object on the virtual microscope.