1. A method of preparing and imaging a sample using a particle-optical apparatus, the particle-optical apparatus comprising: an electron column mounted on an evacuable sample chamber, the electron column equipped to produce a beam of electrons, the beam of electrons for irradiating the sample, a camera system for forming an electron image of the diffraction pattern caused by electrons transmitted through the sample, and a manipulator for positioning the sample in the sample chamber with respect to the beam of electrons, the method comprising the steps of: preparing the sample, positioning the sample in the sample chamber with respect to the beam of electrons, forming an electron image on the camera system using the electron column, and deriving a first ptychographic image of the sample from said first electron image, the ptychographic image the result of an iterative converging process in which estimates of the sample are formed, wherein: the particle-optical apparatus comprises a focused ion beam column mounted on the sample chamber for producing a focused ion beam, the focused ion beam for machining the sample, preparing the sample involves positioning the sample with respect to the ion beam and thinning the sample using the focused ion beam, after forming the first image, a layer of the sample is removed using the ion beam, after which a second electron image is formed using the electron column, and a second ptychographic image of the sample is derived using the second electron image, and the sample is kept under vacuum at least from the moment that the sample is prepared by thinning the sample with the focused ion beam until the moment that the second electron image is taken.