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@MISC{ClausenAlexander:894131,
author = {ClausenAlexander and WeberDieter and RuzaevaKarina and
MigunovVadim and BaburajanAnand and BahuleyanAbijith and
CaronJan and ChandraRahul and DeyShankhadeep and
HalderSayandip and , KatzDaniel S. and , LevinBarnaby D. A.
and NordMagnus and OphusColin and PeterSimon and vanJay,
Schyndel and ShinJaeweon and SunkuSai and
Müller-CasparyKnut and , Dunin-BorkowskiRafal E.},
title = {{L}iber{TEM}/{L}iber{TEM}: 0.6.0},
reportid = {FZJ-2021-03058},
year = {2021},
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. All CPU
cores and CUDA devices in a system can be used in
parallel.</p> <p>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.</p>
<p><strong>Installation</strong></p> <p>The short
version:</p> <pre>$ virtualenv -p python3 ~/libertem-venv/ $
source ~/libertem-venv/bin/activate (libertem) $ python -m
pip install "libertem[torch]" # optional for GPU support
(libertem) $ python -m pip install cupy </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) and
Norpix SEQ files 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>MRC (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>},
keywords = {STEM (Other) / TEM (Other) / pixelated STEM (Other) / 4D
STEM (Other) / high-throughput (Other) / electron microscopy
(Other)},
cin = {ER-C-1},
cid = {I:(DE-Juel1)ER-C-1-20170209},
pnm = {5351 - Platform for Correlative, In Situ and Operando
Characterization (POF4-535) / Ptychography 4.0 - Proposal
for a pilot project "Information $\&$ Data Science"
(ZT-I-0025) / ESTEEM3 - Enabling Science and Technology
through European Electron Microscopy (823717) / 3D MAGiC -
Three-dimensional magnetization textures: Discovery and
control on the nanoscale (856538) / CritCat - Towards
Replacement of Critical Catalyst Materials by Improved
Nanoparticle Control and Rational Design (686053) / VIDEO -
Versatile and Innovative Detector for Electron Optics
(780487)},
pid = {G:(DE-HGF)POF4-5351 / G:(DE-HGF)ZT-I-0025 /
G:(EU-Grant)823717 / G:(EU-Grant)856538 / G:(EU-Grant)686053
/ G:(EU-Grant)780487},
typ = {PUB:(DE-HGF)33},
doi = {10.5281/ZENODO.4543704},
url = {https://juser.fz-juelich.de/record/894131},
}
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