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@MISC{Clausen:888559,
author = {Clausen, Alexander and Weber, Dieter and Ruzaeva, Karina
and Migunov, Vadim and Bahuleyan, Abijith and Caron, Jan and
Chandra, Rahul and Nord, Magnus and Ophus, Colin and Peter,
Simon and Schyndel van, Jay and Shin, Jaeweon and
Müller-Caspary, Knut and Dunin-Borkowski, Rafal E.},
title = {{L}iber{TEM}/{L}iber{TEM}: 0.4.0},
reportid = {FZJ-2020-05023},
series = {LiberTEM: 0.4.0},
year = {2020},
abstract = {<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>},
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.3666686},
url = {https://juser.fz-juelich.de/record/888559},
}
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