For tomogram reconstruction, we use the IMOD software (13). Tomograms are reconstructed by weighted back projection (WBP) or by simultaneous iterative reconstruction technique (SIRT) with 25 iterations using the standard settings of the IMOD software package version 4.1.2. For segmentation and data display, we use the AMIRA or the IMOD software.

The presented tomography method by tilting a semi thin section in the electron beam and reconstructing the data to a three-dimensional tomogram is currently challenged by block face methods. These methods work on the principle of classical SEM, imaging the trimmed blockface of a stained and resin embedded sample, and then gradually remove some resin before taking the next picture. Resin is removed either by focused ion beam (21) or by ultra thin sectioning using an ultra microtome in the SEM (22). These methods have the advantage that the process can be iterated many times and, therefore, much larger volumes can be analyzed than with STEM tomography, where section thickness is limited to about 1 μm, as explained above. The ultrastructural resolution of STEM tomography is, however, still considerably better, especially in X and Y direction.