The disclosed technology relates to an apparatus for tomographic analysis of a specimen based on STEM images of the specimen, as well as for tomographic analysis of the chemical composition of the specimen based on X-ray detection by EDS detectors. In one aspect, the apparatus comprises an elongated specimen holder that is rotatable about a longitudinal axis and is configured to hold a pillar-shaped specimen at the end of the holder. The longitudinal axis is positioned in a sample plane which is perpendicular to the beam direction of an electron beam produced by an electron gun. The apparatus also comprises at least two EDS detectors, each EDS detector having a detecting surface oriented perpendicularly to the sample plane and intersecting with the sample plane, wherein the two EDS detectors are positioned on opposite lateral sides of the specimen.