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PyTEM is a Python based TEM simulation and processing toolkit.


  • Multislice calculations
  • Blochwave calculations
  • Howie-Whelan-Basinski calculations
  • Geometry based sample properties (e.g. strain from FEM calculations)
  • Fitting of simulation parameters to experimental images
  • Many import/export filters: e.g. DM3, HDF5, TDF, EMD (partially), EMS, JEMS (partially), VTK (partially)
  • Parallel execution on SMP system

For details please contact: Tore Niermann [1]


Holoaverage is a Python program for the reconstruction and averaging of series of off-axis electron holograms recorded in a transmission electron microscope. The averaging is performed iteratively, such that instabilities of the microscope, like specimen and biprism drifts, can be tracked and corrected between consecutive exposures.

  • Online-Documentation: https://holoaverage.readthedocs.io [2]
  • Sources: https://github.com/niermann/holoaverage [3]
  • Project page in PyPI (Python Package Index) [4]

Details of the averaging procedure can be found in the accompanying paper:

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 [5]

HDF5 Plugin for DigitalMicrograph

This is a plugin allowing to read and write HDF5 files under DigitalMicrograph by Gatan Inc. The plugin provides functions to be called from the DigitalMicrograph scripting language.

  • Releases: https://github.com/niermann/gms_plugin_hdf5/releases [6]
  • Sources: https://github.com/niermann/gms_plugin_hdf5 [7]


The temscript module provides a Python wrapper for the scripting of FEI microscopes (Tecnai & Titan). Additionally it provides a HTTP-based interface for remote scripting.

  • Sources: https://github.com/niermann/temscript [8]
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