Software Developments of 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.

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

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

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.

• Releases: https://github.com/niermann/gms_plugin_hdf5/releases
• Sources: https://github.com/niermann/gms_plugin_hdf5

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

• Sources: https://github.com/niermann/temscript