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000888562 1001_ $$0P:(DE-Juel1)174151$$aClausen, Alexander$$b0$$eCorresponding author
000888562 245__ $$aLiberTEM/LiberTEM: 0.5.1
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000888562 520__ $$a<p><strong>Homepage: <a href='https://libertem.github.io/LiberTEM/'>https://libertem.github.io/LiberTEM/</a></strong><br> <strong>GitHub repository: <a href='https://github.com/LiberTEM/LiberTEM/'>https://github.com/LiberTEM/LiberTEM/</a></strong><br> <strong>PyPI: <a href='https://pypi.org/project/libertem/'>https://pypi.org/project/libertem/</a></strong></p> <p>LiberTEM is an open source platform for high-throughput distributed processing of large-scale binary data sets using a simplified <a href='https://en.wikipedia.org/wiki/MapReduce'>MapReduce programming model</a>. The current focus is <a href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy#Universal_detectors_(4D_STEM)'>pixelated</a> scanning transmission electron microscopy (<a href='https://en.wikipedia.org/wiki/Scanning_transmission_electron_microscopy'>STEM</a>) and scanning electron beam diffraction data.</p> <p>It is <a 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 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> <p><strong>Installation</strong></p> <p>The short version:</p> <pre>$ virtualenv -p python3 ~/libertem-venv/ $ source ~/libertem-venv/bin/activate (libertem) $ pip install "libertem[torch]" </pre> <p>Please see <a 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 href='https://github.com/LiberTEM/LiberTEM/issues/105'>Issue #105</a>.</p> <p><strong>Applications</strong></p> <ul> <li>Virtual detectors (virtual bright field, virtual HAADF, center of mass , custom shapes via masks)</li> <li><a href='https://libertem.github.io/LiberTEM/app/amorphous.html'>Analysis of amorphous materials</a></li> <li><a href='https://libertem.github.io/LiberTEM-blobfinder/'>Strain mapping</a></li> <li><a href='https://libertem.github.io/LiberTEM/udf.html'>Custom analysis functions (user-defined functions)</a></li> <li><a href='https://libertem.github.io/LiberTEM/app/holography.html'>Off-axis electron holography reconstruction</a></li> </ul> <p>Please see <a 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 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 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 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&#39;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&#39;d like to <a href='https://libertem.github.io/LiberTEM/contributing.html'>contribute</a>, please join our <a href='https://gitter.im/LiberTEM/Lobby'>gitter chat</a> and our <a href='https://groups.google.com/forum/#!forum/libertem'>general mailing list</a>.</p> <p><strong>File formats</strong></p> <p>LiberTEM currently opens most file formats used for pixelated STEM. See <a href='https://libertem.github.io/LiberTEM/formats.html'>our general information on loading data</a> and <a href='https://libertem.github.io/LiberTEM/reference/dataset.html#formats'>format-specific documentation</a> for more information!</p> <ul> <li>Raw binary files</li> <li>Thermo Fisher EMPAD detector files</li> <li><a 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>Direct Electron DE5 files (HDF5-based) for <a href='http://www.directelectron.com/de-series/'>DE-Series</a> detectors</li> <li><a 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 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 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> <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>
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