A method is provided for performing electron diffraction pattern analysis upon a sample in a vacuum chamber of a microscope. Firstly a sample is isolated from part of a specimen using a focused particle beam. A manipulator end effector is then attached to the sample so as to effect a predetermined orientation between the end effector and the sample. With the sample detached, the manipulator end effector is rotated about a rotation axis to bring the sample into a predetermined geometry with respect to an electron beam and diffraction pattern imaging apparatus so as to enable an electron diffraction pattern to be obtained from the sample while the sample is still fixed to the manipulator end effector. An electron beam is caused to impinge upon the sample attached to the manipulator end effector so as to obtain an electron diffraction pattern.