One of the main problems of 3D imaging in optical microscopy is unisotropic optical resolution of acquired 3D data. For instance in confocal laser scanning microscopy, axial resolution is 2-3 times worse than the lateral one. A sophisticated solution of this problem is so-called micro axial tomography that provides a good means for microscopic image acquisition of cells or sub- cellular components like cell nuclei with an improved resolution achieved by object tilting and acquisition of a series of mutually tilted 3D image data. Since the very early developments of micro axial tomography a considerable drawback of this method was a complicated image acquisition and processing procedure that requires much operator time. In order to solve this problem advanced microscopy and automated computer image acquisition and analysis were brought together. Special software that drives all hardware components required for automated micro axial tomography was developed. It performs multi-view 3D image acquisition as well as related image processing.