An electron microscope is offered which can analyze the three-dimensional structure of a specimen without sectioning it by making use of computerized tomography. The microscope has solved the problems intrinsic to the microscope and permits application of computerized tomography to general cases. A series of transmission images is obtained by tilting the specimen by plural angles. Two-dimensional correlation processing is performed between each of the series of images and a reference image. The same field of view is selected and extracted. Thus, positional deviation of the specimen is corrected.