The invention relates to a method of preparing and imaging a sample using a particle-optical apparatus, equipped with an electron column and an ion beam column, a camera system, a manipulator. The method comprises the steps of deriving a first ptychographic image of the sample from a first electron image, thinning the sample, and forming a second ptychographic image of the sample. In an embodiment of the invention the seed image used for the second image is the first ptychographic image. In another embodiment the second ptychographic image is the image of the layer removed during the thinning. In another embodiment the inner potential of the sample is determined and dopant concentrations are determined.