Experimental Physics/Electron- and Ion-Nanooptics

Software Developments of the Working Group

Methodological developments in electron microscopy also require powerful software. The following software packages are maintained in the working group:


PyTEM is a Python-based TEM simulation and processing tool. It includes the following features:

  • Multislice calculations
  • Bloch threshold calculation
  • Howie-Whelan-Basinski calculations
  • Geometry-based sample properties (e.g., stresses using finite element calculations)
  • Fit of simulation parameters to experimental recordings
  • Many import&export filters, e.g. DM3, HDF5, TDF, EMD (partially), EMS, JEMS (partially), VTK (partially)
  • Parallel processing on symmetric multiprocessor systems (SMP)

For further details please contact Dr. Tore Niermann.


HoloAverage is a Python program for reconstructing and averaging series of electron holograms taken in the transmission electron microscope. The averaging is iterative so that instabilities of the microscope, such as sample and biprism drift, can be measured and corrected between successive images.

For details on averaging, see the accompanying publication:

T. Niermann, M. Lehmann
Averaging scheme for atomic resolution off-axis electron holograms
Micron 63 (2014) 28 - 34
DOI: 10.1016/j.micron.2014.01.008

HD5 Plugin for DigitalMicrograph

This is a plugin for reading and writing HDF5 files under DigitalMicrograph (Gatan Inc.). The plugin provides functions that can be called by the DigitalMicrograph scripting language.


The TEMscript module provides a Python wrapper for scripting FEI microscopes (Tecnai & Titan). Additionally, it provides an HTTP-based interface for remote scripting.


Organization name Institute of Optics and Atomic Physics
Building ER
Room ER 295