LiberTEM - Open Pixelated STEM platform
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. The current focus is pixelated scanning transmission electron microscopy (STEM) [MNR+16, Oph19] and scanning electron beam diffraction data.
MapReduce-like processing allows to specify an algorithm through two functions: One function that is mapped on portions of the input data, and another function that merges (reduces) a partial result from this mapping step into the complete result. A wide range of TEM and 4D STEM processing tasks can be expressed in this fashion, see Applications.
The UDF interface of LiberTEM offers a standardized, versatile API to decouple the mathematical core of an algorithm from details of data source, parallelism, and use of results. Mapping and merging can be performed in any order and with different subdivisions of the input data, including running parts of the calculation concurrently. That means the same implementation can be used in a wide range of modalities, including massive scaling on clusters. Since each merge step produces an intermediate result, this style of processing is suitable for displaying live results from a running calculation in a GUI application and for processing live data streams. A closed-loop feedback between processing and instrument control can be realized as well. See User-defined functions for more details on the LiberTEM UDF interface.
The LiberTEM back-end offers high throughput and scalability on PCs, single server nodes, clusters and cloud services. On clusters it can use fast distributed local storage on high-performance SSDs. That way it achieves very high aggregate IO performance on a compact and cost-efficient system built from stock components. All CPU cores and CUDA devices in a system can be used in parallel.
LiberTEM is supported on Linux, Mac OS X and Windows. Other platforms that allow installation of Python 3.6+ and the required packages will likely work as well. The GUI is running in a web browser.
The short version:
$ virtualenv -p python3 ~/libertem-venv/ $ source ~/libertem-venv/bin/activate (libertem-venv) $ python -m pip install "libertem[torch]" # optional for GPU support # See also https://docs.cupy.dev/en/stable/install.html (libertem-venv) $ python -m pip install cupy
Please see our documentation for details!
Alternatively, to run the LiberTEM Docker image:
$ docker run -p localhost:9000:9000 --mount type=bind,source=/path/to/your/data/,dst=/data/,ro libertem/libertem
$ singularity exec docker://libertem/libertem /venv/bin/libertem-server
Deployment for offline data processing on a single-node system for a local user is thoroughly tested and can be considered stable. Deployment on a cluster is experimental and still requires some additional work, see Issue #105. Back-end support for live data processing is still experimental as well, see https://github.com/LiberTEM/LiberTEM-live.
Since LiberTEM is programmable through user-defined functions (UDFs), it can be used for a wide range of processing tasks on array-like data and data streams. The following applications have been implemented already:
Virtual detectors (virtual bright field, virtual HAADF, center of mass [KMM+16], custom shapes via masks)
The Python API and user-defined functions (UDFs) can be used for complex operations such as arbitrary linear operations and other features like data export. Example Jupyter notebooks are available in the examples directory. If you are having trouble running the examples, please let us know by filing an issue or by joining our Gitter chat.
LiberTEM is suitable as a high-performance processing backend for other applications, including live data streams. Contact us if you are interested!
LiberTEM is evolving rapidly and prioritizes features following user demand and contributions. Currently we are working on live data processing, integration with Dask arrays and HyperSpy, support for sparse data, and implementing analysis methods for various applications of pixelated STEM and other large-scale detector data. If you like to influence the direction this project is taking, or if you’d like to contribute, please join our gitter chat and our general mailing list.
Raw binary files
Thermo Fisher EMPAD detector [TPC+16] files
Nanomegas .blo block files
Direct Electron DE5 files (HDF5-based) and Norpix SEQ files for DE-Series detectors
Gatan K2 IS raw format
Stacks of Gatan DM3 and DM4 files (via openNCEM)
FRMS6 from PNDetector pnCCD cameras [SRB+15] (currently alpha, gain correction still needs UI changes)
FEI SER files (via openNCEM)
MRC (via openNCEM)
HDF5-based formats such as HyperSpy files, NeXus and EMD
TVIPS binary files
Please contact us if you are interested in support for an additional format!
Currently the Quantum Detectors Merlin camera is supported for live processing. Support for the Gatan K2 IS camera is in a prototype state. Please contact us if you are interested in this feature! See https://github.com/LiberTEM/LiberTEM-live for more details on live processing.
LiberTEM is licensed under GPLv3. The I/O parts are also available under the MIT license, please see LICENSE files in the subdirectories for details.
- GUI usage
- Loading data
- Sample Datasets
- Python API
- User-defined functions (UDFs)
- Dask integration
- Python API reference
- Tips and tricks
- Using SSH forwarding
- Activating ipywidgets in Jupyter
- Running in a top-level script
- Gatan Digital Micrograph and other embedded interpreters
- Show deprecation warnings
- Profiling long-running tests
- Platform-dependent code and remote executor
- Benchmark Numba compilation time
- Simulating slow systems with control groups
- Package overview
- Why Python?
- Setting up a development environment
- How does I/O work in LiberTEM?
- LiberTEM executors
- GSoC 2020 ideas
- Authorship policy
Indices and tables
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Giulio Guzzinati, Wannes Ghielens, Christoph Mahr, Armand Béché, Andreas Rosenauer, Toon Calders, and Jo Verbeeck. Electron Bessel beam diffraction patterns, line scan of Si/SiGe multilayer. February 2019. URL: https://doi.org/10.5281/zenodo.2566137, doi:10.5281/zenodo.2566137.
Matus Krajnak, Damien McGrouther, Dzmitry Maneuski, Val O\textquotesingle Shea, and Stephen McVitie. Pixelated detectors and improved efficiency for magnetic imaging in STEM differential phase contrast. Ultramicroscopy, 165:42–50, jun 2016. doi:10.1016/j.ultramic.2016.03.006.
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Colin Ophus. Four-dimensional scanning transmission electron microscopy (4d-STEM): from scanning nanodiffraction to ptychography and beyond. Microscopy and Microanalysis, 25(3):563–582, may 2019. doi:10.1017/s1431927619000497.
Colin Ophus and Benjamin Savitzky. Simulated calibration dataset for 4D scanning transmission electron microscopy. December 2019. URL: https://doi.org/10.5281/zenodo.3592520, doi:10.5281/zenodo.3592520.
Ouliana Panova, Colin Ophus, Christopher J. Takacs, Karen C. Bustillo, Luke Balhorn, Alberto Salleo, Nitash Balsara, and Andrew M. Minor. Diffraction imaging of nanocrystalline structures in organic semiconductor molecular thin films. Nature Materials, jun 2019. doi:10.1038/s41563-019-0387-3.
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Achim Strauch, Alexander Clausen, Dieter Weber, and Knut Müller-Caspary. High-resolution 4D STEM dataset of SrTiO3 along the [1 0 0] axis at high magnification. July 2021. Achim Strauch and Knut Müller-Caspary were supported by funding from the Initiative and Network Fund of the Helmholtz Association (Germany) under contract VH-NG-1317 (moreSTEM project). Knut Müller-Caspary acknowledges support from Helmholtz within the project "Ptychography 4.0" under contract ZT-I-0025. URL: https://doi.org/10.5281/zenodo.5113449, doi:10.5281/zenodo.5113449.
Achim Strauch, Dieter Weber, Alexander Clausen, and Knut Müller-Caspary. Synthetic 4D STEM dataset based on a SrTiO3 supercell with two additional artificial spatial frequencies. July 2021. Achim Strauch and Knut Müller-Caspary were supported by funding from the Initiative and Network Fund of the Helmholtz Association (Germany) under contract VH-NG-1317 (moreSTEM project). Knut Müller-Caspary acknowledges support from Helmholtz within the project "Ptychography 4.0" under contract ZT-I-0025. URL: https://doi.org/10.5281/zenodo.5113235, doi:10.5281/zenodo.5113235.
Mark W. Tate, Prafull Purohit, Darol Chamberlain, Kayla X. Nguyen, Robert Hovden, Celesta S. Chang, Pratiti Deb, Emrah Turgut, John T. Heron, Darrell G. Schlom, Daniel C. Ralph, Gregory D. Fuchs, Katherine S. Shanks, Hugh T. Philipp, David A. Muller, and Sol M. Gruner. High dynamic range pixel array detector for scanning transmission electron microscopy. Microscopy and Microanalysis, 22(01):237–249, jan 2016. doi:10.1017/s1431927615015664.
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