A system includes a multi-beam particle microscope for imaging a 3D sample layer by layer, and a computer system with a multi-tier architecture is disclosed. The multi-tier architecture can allow for an optimized image processing by gradually reducing the amount of parallel processing speed when data exchange between different processing systems and/or of data originating from different detection channels takes place. A method images a 3D sample layer by layer. A computer program product includes a program code for carrying out the method.