LiberTEM

About LiberTEM

LiberTEM is an open source platform for high-throughput distributed processing of electron microscopy datasets. Written primarily in Python, it is capable of processing live data streams, processing offline data interactively, and providing a computation engine for other libraries. The library allows a user to explore the vast, diverse landscape of interesting features which are revealed in electron microscope imagery.

Advanced analyses like ptychography, strain mapping or phase and orientation mapping require the acquisition and processing of large amounts of data. In the past this would take hours, but high-speed imaging detectors for electrons that became available from 2014 onwards created the potential to perform such analyses interactively in real time, as is already the case in conventional microscopy.

However, the software available at the time was fundamentally not capable of processing data at the rate these new detectors produced it. That’s why we started the LiberTEM project: to leverage the full potential of high-speed imaging detectors in electron microscopy and other fields, and make it possible to apply advanced computational imaging techniques in real time. This opens the possibility to control microscopes with closed-loop feedback, and of course to process huge datasets that modern detectors can acquire, offline.

LiberTEM is split into several sub-projects: the processing engine, an interactive web interface that is currently packaged with the processing engine, live data processing infrastructure, several application-specific packages, and spin-off packages with more general application such as sparseconverter.

LiberTEM projects

LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets and live data streams using a modified MapReduce programming model.
is an extension module for LiberTEM that allows live data processing.
is a package for correlation-based peak finding and strain mapping.
Off-axis electron holography (WIP)
Format detection, identifiers and converter matrix for a range of numerical array formats, focusing on sparse arrays.
Tools to calibrate a microscope

Other projects that use LiberTEM

Implementations for ptychography that result from the work of the Ptychography 4.0 project. Most notably, this includes an implementation for Single Side Band ptychography that can process live data streams.

Applications

Try it out

Download a sample dataset
Install LiberTEM and run the web GUI
Download examples for Python API usage
Install LiberTEM-live for live data processing and see example usage

Citing

To help us spread the word, please credit and cite LiberTEM in publications where it has been significant. Resources for citing LiberTEM are linked through the links or DOI badges below.

LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy
LiberTEM
LiberTEM-live
LiberTEM-blobfinder

Publications

Other media

One million frames per second

Acknowledgements

See Acknowledgements!

Funding

LiberTEM kindly acknowledges funding and support from the following sources:

ERC Proof-of-Concept grant VIDEO

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement No 780487.

CritCat

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 686053.

ESTEEM3

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 823717.

ERC Synergy grant 3D MAGiC

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme ( grant agreement No 856538).

moreSTEM

Helmholtz Gemeinschaft Deutscher Forschungszentren

We gratefully acknowledge funding from the Initiative and Networking Fund of the Helmholtz Association within the Helmholtz Young Investigator Group moreSTEM under Contract No. VH-NG-1317 at Forschungszentrum Jülich in Germany.

Ptychography 4.0

We gratefully acknowledge funding from the Information & Data Science Pilot Project "Ptychography 4.0" of the Helmholtz Association.

Google Summer of Code

We kindly acknowledge funding from Google Summer of Code 2019 and 2020 under the umbrella of the Python software foundation.

AIDAS

LiberTEM development is supported by AIDAS

Joint Lab MDMC

LiberTEM development is part of the Joint Lab MDMC.

Forschungszentrum Jülich, Ernst-Ruska Centrum

Forschungszentrum Jülich is supporting LiberTEM with funding for personnel, access to its infrastructure and administrative support.

Industry partners

Gatan Inc.

STEMx equipment and software for 4D STEM data acquisition with K2 IS camera courtesy of Gatan Inc.

Quantum Detectors

We thank Quantum Detectors for their help in implementing support for their cameras and file formats.

DECTRIS

We thank DECTRIS for their help in implementing support for their cameras and file formats, outreach, and for providing access to prototypes.

Amsterdam Scientific Instruments

We thank Amsterdam Scientific Instruments for their help in implementing support for their cameras and file formats, co-developing practical 4D STEM support with event-based detectors, outreach, and for providing access to prototypes.

CEOS

We thank CEOS for cooperation regarding instrument control and live data processing.

TVIPS

We thank TVIPS for cooperation regarding instrument control and support for their file formats.

Direct Electron

We thank Direct Electron for their help in implementing support for their cameras and file formats.

X-Spectrum

We thank X-Spectrum for their help in implementing support for their cameras and file formats.

Contact

Gitter chat
Dieter Weber d.weber@fz-juelich.de
Alexander Clausen a.clausen@fz-juelich.de
Matthew Bryan matthew.bryan@cea.fr
GitHub issue trackers, see repo links above!

We thank all of our authors and contributors!