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.

Graptor 0.1The Graz Application for Tomographic Reconstruction (Graptor) is a software tool developed to allow for efficient, high quality tomographic reconstruction from Radon-transform data. 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.

HyperSpy: a scientific Python library used to analyse a large variety of multidimensional data, with a focus on transmission electron microscopy. HyperSpy development now drives towards the creation of hyperspyextension packages for specific applications such as pyxem and lumispy currently being developed by ESTEEM3 partners (see below). 

pyxem: crystallographic diffraction microscopy: Pyxem is a hyperspy-extension library written in python and developed for multi-dimensional diffraction microscopy using, for example, 4D-STEM data. The package defines objects and functions for the analysis of numerous diffraction patterns. It has been primarily developed as a platform for hybrid diffraction-microscopy based on 4D scanning diffraction microscopy data in which a 2D diffraction pattern is recorded at every position in a 2D scan of a specimen. 

LumiSpy: analysis of luminescence data: LumiSpy is an extension Python package for multi-dimensional data analysis provided by the HyperSpy library. It is aimed at helping with the analysis of luminescence spectroscopy data (cathodoluminescence, photoluminescence, electroluminescence, Raman, SNOM).

LiberTEM: LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets using a simplified MapReduce programming model. The current focus is pixelated scanning transmission electron microscopy (STEM) and scanning electron beam diffraction data.

LiberTEM-live: LiberTEM-Live is an extension module for LiberTEM [CWR+21] that allows live data processing.

Ptychography 4.0: The Ptychography 4.0 project develops algorithms, applications, and software for ptychography. That includes an implementation for live, interactive single side band ptychography using LiberTEM. The unique
capability of live imaging through processing high-speed detector data streams using non-trivial user-defined algorithms is developed by ESTEEM3 partners.

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