Experience Report on the 3D-EM Course "TOM Software Toolbox: Acquisition and Analysis for Electron Tomography"

27.03.-31.03.2006, Max-Planck-Institute of Biochemistry, Martinsried, Germany,

Course leaders: Dr. Juergen M. Plitzko and Dr. Stephan Nickell

Cryo-electron tomography of beam-sensitive biological samples showing only weak contrast is probably the most challenging technique in structural biology. Recording a tomogram requires tilting the specimen incrementally around an axis perpendicular to the electron beam, while a projection image is taken at each tilt angle. To compensate for the mechanical imperfection of the goniometer, tracking routines have to be implemented. Furthermore, imaging, tracking and corrections for focus and astigmatism at each tilt angle have to be combined with low-dose imaging routines in order to minimize the total dose applied to the area of interest.

The TOM Toolbox developed at the MPI for Biochemistry in Martinsried provides a unified, powerful software platform, which covers all aspects of electron tomography under cryo-low dose conditions (Nickell et al. (2005) J. Struct. Biol. 149, 227-234). It combines an elaborate user interface for automated data acquisition, tools for alignment of tilt series, filtering and 3D reconstruction. At the same time, based on Matlab, it is highly flexible and can be easily adapted to the users need.

The good organization, competent lecturers and well-balanced practical and theoretical parts, respectively, made the TOM training course within the 3D-EM Network of Excellence, held in Martinsried in March 2006, an ideal introduction into the complex matter. Although participants came from different fields such as material science and biology, the lecturers were responsive to the particular specific problems. The course was rounded by comfortable lodging (including long Bavarian evenings). We are looking forward to implement the TOM toolbox on our Tecnai G2 Polara system, which requires adaptation for our TVIPS 4k CCD camera. So far, we setup the TOM Toolbox to use the alignment and reconstruction programs.


    Dr. Thorsten Mielke
    - UltraStrukturNetzwerk -
    Max Planck Institute for Molecular Genetics
    Ihnestr. 63-73
    D-14195 Berlin


More pictures of this course you will find here.