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000888560 1001_ $$0P:(DE-Juel1)174151$$aClausen, Alexander$$b0$$eCorresponding author
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000888560 520__ $$a<div class='document'> <strong>Homepage: <a href='https://libertem.github.io/LiberTEM/'>https://libertem.github.io/LiberTEM/</a><br></strong><strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM/'>https://github.com/LiberTEM/LiberTEM/</a><br></strong><strong>PyPI: <a href='https://pypi.org/project/libertem/'>https://pypi.org/project/libertem/</a><br></strong><p>LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets using a simplified <a class='reference external' href='https://en.wikipedia.org/wiki/MapReduce'>MapReduce programming model</a>. The current focus is <a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy#Universal_detectors_(4D_STEM)'>pixelated</a> scanning transmission electron microscopy (<a class='reference external' href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy'>STEM</a>) and scanning electron beam diffraction data.</p> <p>It is <a class='reference external' href='https://libertem.github.io/LiberTEM/architecture.html'>designed for high throughput and scalability</a> 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 <a class='reference external' href='https://libertem.github.io/LiberTEM/performance.html'>very high aggregate IO performance</a> on a compact and cost-efficient system built from stock components.</p> <p>LiberTEM is supported on Linux, Mac OS X and Windows. Other platforms that allow installation of Python 3 and the required packages will likely work as well. The GUI is running in a web browser.</p> <div class='section'> <p><strong>Installation</strong></p><p>The short version:</p> <pre class='code shell literal-block'>$ virtualenv -p python3.6 ~/libertem-venv/ $ <span class='name builtin'>source</span> ~/libertem-venv/bin/activate <span class='operator'>(</span>libertem<span class='operator'>)</span> $ pip install libertem<span class='operator'>[</span>torch<span class='operator'>]</span> </pre> <p>Please see <a class='reference external' href='https://libertem.github.io/LiberTEM/install.html'>our documentation</a> for details!</p> <p>Deployment as 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 <a class='reference external' href='https://github.com/LiberTEM/LiberTEM/issues/105'>Issue #105</a>.</p> </div> <div class='section'> <p><strong>Applications</strong></p><ul class='simple'> <li>Virtual detectors (virtual bright field, virtual HAADF, center of mass , custom shapes via masks)</li> <li><a class='reference external' href='https://libertem.github.io/LiberTEM/app/amorphous.html'>Analysis of amorphous materials</a></li> <li><a class='reference external' href='https://libertem.github.io/LiberTEM-blobfinder/'>Strain mapping</a></li> <li><a class='reference external' href='https://libertem.github.io/LiberTEM/udf.html'>Custom analysis functions (user-defined functions)</a></li> <li><a class='reference external' href='https://libertem.github.io/LiberTEM/app/holography.html'>Off-axis electron holography reconstruction</a></li> </ul> <p>Please see <a class='reference external' href='https://libertem.github.io/LiberTEM/applications.html'>the applications section</a> of our documentation for details!</p> <p>The Python API and user-defined functions (UDFs) can be used for more complex operations with arbitrary masks and other features like data export. There are example Jupyter notebooks available in the <a class='reference external' href='https://github.com/LiberTEM/LiberTEM/tree/master/examples'>examples directory</a>. If you are having trouble running the examples, please let us know, either by filing an issue or by <a class='reference external' href='https://gitter.im/LiberTEM/Lobby'>joining our Gitter chat</a>.</p> <p>LiberTEM is suitable as a high-performance processing backend for other applications, including live data streams. <a class='reference external' href='https://gitter.im/LiberTEM/Lobby'>Contact us</a> if you are interested!</p> <p>LiberTEM is evolving rapidly and prioritizes features following user demand and contributions. In the future we'd like to implement live acquisition, and more analysis methods for all 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 <a class='reference external' href='https://libertem.github.io/LiberTEM/contributing.html'>contribute</a>, please join our <a class='reference external' href='https://gitter.im/LiberTEM/Lobby'>gitter chat</a> and our <a class='reference external' href='https://groups.google.com/forum/#!forum/libertem'>general mailing list</a>.</p> </div> <div class='section'> <p><strong>File formats</strong></p><p>LiberTEM currently opens most file formats used for pixelated STEM. See <a class='reference external' href='https://libertem.github.io/LiberTEM/formats.html'>our general information on loading data</a> and <a class='reference external' href='https://libertem.github.io/LiberTEM/reference/dataset.html#formats'>format-specific documentation</a> for more information!</p> <ul class='simple'> <li>Raw binary files</li> <li>Thermo Fisher EMPAD detector files</li> <li><a class='reference external' href='http://quantumdetectors.com/wp-content/uploads/2017/01/1532-Merlin-for-EM-Technical-Datasheet-v2.pdf'>Quantum Detectors MIB format</a></li> <li>Nanomegas .blo block files</li> <li><a class='reference external' href='https://web.archive.org/web/20180809021832/http://www.gatan.com/products/tem-imaging-spectroscopy/k2-camera'>Gatan K2 IS</a> raw format</li> <li>Stacks of Gatan DM3 and DM4 files (via <a class='reference external' href='https://github.com/ercius/openNCEM'>openNCEM</a>)</li> <li>FRMS6 from PNDetector pnCCD cameras (currently alpha, gain correction still needs UI changes)</li> <li>FEI SER files (via <a class='reference external' href='https://github.com/ercius/openNCEM'>openNCEM</a>)</li> <li>HDF5-based formats such as Hyperspy files, NeXus and EMD</li> <li>Please contact us if you are interested in support for an additional format!</li> </ul> </div> <div class='section'> <p><strong>License</strong></p><p>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.</p> </div> </div>
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