A method for the microscopy of samples using optical microscopy and particle beam microscopy provides that the samples are divided into a partial quantity and a residual quantity and the samples of the partial quantity are prepared to contain registration marks. The samples of the partial quantity are imaged using optical microscopy and particle beam microscopy, with the result that a pair of optical microscopy images and particle beam microscopy images is obtained for each sample of the partial quantity. The pairs are position-registered relative to each other using the registration marks. The images of the position-registered pairs are modified by removing the registration marks. A registration algorithm is trained which evaluates the image contents and issues a quality measure for a position registration of each pair. The objects of the residual quantity are imaged. These pairs are position-registered by the trained registration algorithm to maximize the quality measure.