It is a mission of ESTEEM3 to provide a web-based platform where TEM users can access the latest software, protocols, results and methods. All ESTEEM3 deliverables will be made freely available on the project website.

On this page you can find the latest software developed by the ESTEEM consortium.

Absolute integrator: MatLab code forautomated HAADF STEM image quantification to determine absolute scattering cross-sections of atomic-columns

DM Script for PCA Analysis of EELS data: Principal Component Analysis script for EELS data as a DM plugin. It operates on 1D or 2D spectrum images and allows the user to select a specific energy region and the number of PCA components that need to be retained. See literature for a warning on the statistical consequences of its use

Dr. Probe: High-resolution STEM and CTEM image simulation software

Dr. Probe Light: STEM probe and ronchigram simulation software

EELSModel: Standalone software to perform model based quantification of EELS spectra

GEMPA: General purpose electron micrograph processing and analysis software

Jitterbug: MatLab code to correct image drift and localised scan-distortion in HAADF STEM data for the improvement of resolution and signal-noise ratio

MULTEM: Open source user friendly software code to perform accurate and fast electron diffraction and image simulations using CPU/GPU

Oxygen Octahedra Picker: a software tool to extract quantitative information from STEM (HAADF-ABF) images. It was written in Digital Micrograph (DM, Gatan Inc) scripting language as a DM plugin. Center-of-mass and 2D Gaussian fitting methods were implemented to locate positions of individual atom columns. It enables mapping of atomic column positions from HAADF and ABF images and quantification of both crystal lattice and BO6 octahedral distortions

StatSTEM: Open source user friendly software code to quantify scanning transmission electron microscopy (STEM) images by using model based fitting. This provides an accurate and precise way of extracting quantitative information from STEM images

Turboslice: GPU based Multislice image simulation software

Graptor 0.1

To be dowloaded on Zenodo:

The Graz Application for Tomographic Reconstruction (Graptor) is a software tool developed to allow for efficient, high quality tomographic reconstruction from Radon-transform data. It originates from a project concerning Scanning Transmission Electron Tomography of the Institute of Mathematics and Scientific Computing at the University of Graz together with the Institute for Electron Microscopy and Nanoanalysis and the Centre for Electron Microscopy at Graz University of Technology, though it is not limited to such applications. A special feature of this toolbox is the coupling in multi-channel tomography (originally developed for joint HAADF-EDX reconstruction), yielding superior reconstruction quality for data sets with complementing information. The reconstruction algorithm bases on an iterative procedure that minimizes the Tikhonov functional associated with the tomographic reconstruction problem and multi-channel total generalized variation regularization. The code features a powerful OpenCL/GPU implementation, resulting in high reconstruction speed, and a Graphical User Interface allowing for easy use.


  • High quality tomography reconstructions.
  • Easy to use graphical user interface.
  • Fast reconstruction due to custom OpenCL/GPU-implementation.
  • Preprocessing options to ensure data fits the framework.