Abstract: The invention relates to Transmission Charged Particle Beam (TCPB) apparatus comprising a sample holder, for holding a sample, a source for producing a beam of charged particles and an illuminator for directing said beam so as to irradiate the sample; The TCPB apparatus comprises an imaging system, for receiving a flux of charged particles transmitted through the sample and directing it onto a sensing device. Further, a controller is provided for controlling at least some operational aspects of the TCPB apparatus. As defined herein, the controller is arranged for receiving calibration data of said TCPB apparatus and using said calibration data for optically aligning said TCPB apparatus. Said calibration data may be obtained in a calibration session, wherein different settings for eucentric focus can be used as a measure of eucentric height, so that the TCPB apparatus can be optically aligned in absence of a sample on the sample holder.