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@MISC{Clausen:888561,
author = {Clausen, Alexander and Weber, Dieter and Ruzaeva, Karina
and Migunov, Vadim and Baburajan, Anand and Bahuleyan,
Abijith and Caron, Jan and Chandra, Rahul and Dey,
Shankhadeep and Halder, Sayandip and Levin, Barnaby D. A.
and Nord, Magnus and Ophus, Colin and Peter, Simon and
Schyndel van, Jay and Shin, Jaeweon and Sunku, Sai and
Müller-Caspary, Knut and Dunin-Borkowski, Rafal E.},
title = {{L}iber{TEM}/{L}iber{TEM}: 0.5.0},
reportid = {FZJ-2020-05025},
series = {LiberTEM: 0.5.0},
year = {2020},
abstract = {<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\'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
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>},
cin = {ER-C-1 / ER-C-2},
cid = {I:(DE-Juel1)ER-C-1-20170209 / I:(DE-Juel1)ER-C-2-20170209},
pnm = {143 - Controlling Configuration-Based Phenomena (POF3-143)
/ ESTEEM3 - Enabling Science and Technology through European
Electron Microscopy (823717)},
pid = {G:(DE-HGF)POF3-143 / G:(EU-Grant)823717},
typ = {PUB:(DE-HGF)33 / PUB:(DE-HGF)3},
doi = {10.5281/ZENODO.3763313},
url = {https://juser.fz-juelich.de/record/888561},
}
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