Data Processing and Analysis Software

The majority of the data acquired at the SuperSTEM are currently in theGatan Microscopy Suite® (GMS) software .dm3 and .dm4 file format. A free of charge configuration of Gatan Microscopy Suite® (GMS) software and information on the commercial versions and plugins can be found here.

For those users who have access to the DM™ software, a variety of useful freeware scripts can be found in the Digital Micrograph™Script Database, hosted by FELMI at the Graz University of Technology.

Great tools for DM™, as well as examples and tutorials for scripting can be found at Dave Mitchell's Digital Micrograph™ Scripting Website.

If you have access to DM™ but not the Gatan Spectrum Imaging package look out especially for Dave Mitchell's SITools (very handy!!).

Nion Swift is an open source scientific image processing software platform integrating hardware control, data acquisition, visualization, processing, and analysis using Python. Nion Swift is easily extended using Python. It runs on Windows, Linux, and macOS.

While being developed for the operation of Nion electron microscope instruments, it is also useful as an offline tool to visualize, process, and analyze data. It is being developed with the intention of supporting additional instrumentation and fields.

Another very good freeware alternative is the Java-based ImageJ image processing software, available for all major OS platforms. Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

Advanced Data Processing and Simulations

HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image).

HyperSpy aims at making it easy and natural to apply analytical procedures that operate on an individual signal to multi-dimensional arrays, as well as providing easy access to analytical tools that exploit the multi-dimensionality of the dataset.

Its modular structure makes it easy to add features to analyze different kinds of signals.

HREM Research provides a selection of commercial and free ware tools for DM™.

We are proud to serve as an Associated Demonstration Site for several HREM research tools; including MSA, SmartAlign and DeConvHAADF.

QSTEM by Christoph Koch is a freeware package for quantitative simulations of TEM STEM images, and CBED calculations, using the multislice algorithm.

On the QSTEM page you'll find a comprehensive tutorial and several useful examples.

The Dr. Probe software is a free tool package for multi-slice image simulations in high-resolution scanning and imaging transmission electron microscopy. It comprises a graphical user interface version for direct visualization of STEM image calculations, as well as a bundle of command-line modules for more comprehensive calculation tasks.

This software package has been developed by Juri Barthel and Lothar Houben at the Forschungszentrum Juelich GmbH and the RWTH Aachen University.

Learn how to tune aberrations on ronchigrams with Dr. Probe Light

Prismatic is a CUDA/C++/Python software package for fast image simulation in scanning transmission electron microscopy (STEM), developed by Colin Ophus and AJ Pryor.

It includes parallel, data-streaming implementations of both the plane-wave reciprocal-space interpolated scattering matrix (PRISM) and multislice algorithms using multicore CPUs and CUDA-enabled GPU(s), in some cases achieving accelerations as high as 1000x or more relative to traditional methods. Prismatic is fast, free, open-sourced, and contains a graphical user interface.

EELSMODEL is software for the quantification of quantify Electron Energy Loss (EELS) spectra by using model fitting. This provides a more accurate and reliable way of extracting quantitative information from EELS spectra compared to the conventional quantification technique.

The aim of this program is to give as many people in the EELS community access to an improved method for quantifying spectra with a more or less user friendly program.

CTM4XAS is a freeware for the simulation of transition metal core level spectra, including XAS, EELS, XES and XPS.

Other microscopy resources

Electron microscopy basics

The Australian Microscopy and Microanalysis Research Facility's website features comprehensive learning guides and interactive resources to progress your training in advanced instrumentation and techniques.

EELS database

The EELS Data Base is a compilation of valence and core-loss spectra from Electron Energy Loss Spectroscopy experiments and X-Ray spectra. With 274 spectra covering 43 elements of the periodic table, it is the largest open access EELS database. Find out more