docs/source/references-libertem.bib
% Encoding: UTF-8
@Misc{Weber2018,
author = {Weber, Dieter},
title = {Development of {IT} system and {TEM} camera performance},
year = {2018},
doi = {10.5281/zenodo.2450624},
keywords = {throughput, system design, performance, big data, data science},
language = {en},
publisher = {Zenodo},
}
@Article{Bon2012,
author = {Pierre Bon and Serge Monneret and Benoit Wattellier},
title = {Noniterative boundary-artifact-free wavefront reconstruction from its derivatives},
journal = {Applied Optics},
year = {2012},
volume = {51},
number = {23},
pages = {5698},
month = {aug},
doi = {10.1364/ao.51.005698},
file = {:Bon12_Phasereconstruction_from_derivatives.pdf:PDF},
publisher = {The Optical Society},
}
@Misc{K2IS2018,
author = {{{Gatan Inc.}}},
title = {{K2} {IS} camera},
howpublished = {Online},
year = {2018},
url = {https://web.archive.org/web/20180809021832/http://www.gatan.com/products/tem-imaging-spectroscopy/k2-camera},
}
@Misc{Clausen2018,
author = {Clausen, Alexander and Weber, Dieter and {Probonopd} and Caron, Jan and Nord, Magnus and Müller-Caspary, Knut and Ophus, Colin and Dunin-Borkowski, Rafal},
title = {Libertem/Libertem: 0.1.0},
year = {2018},
doi = {10.5281/zenodo.1477847},
keywords = {STEM, TEM, pixelated STEM, 4D STEM, high-throughput, electron microscopy},
publisher = {Zenodo},
}
@Article{Sauter2013,
author = {Nicholas K. Sauter and Johan Hattne and Ralf W. Grosse-Kunstleve and Nathaniel Echols},
title = {New Python-based methods for data processing},
journal = {Acta Crystallographica Section D Biological Crystallography},
year = {2013},
volume = {69},
number = {7},
pages = {1274--1282},
month = {jun},
doi = {10.1107/s0907444913000863},
publisher = {International Union of Crystallography ({IUCr})},
}
@Article{Koennecke2015,
author = {Mark Könnecke and Frederick A. Akeroyd and Herbert J. Bernstein and Aaron S. Brewster and Stuart I. Campbell and Björn Clausen and Stephen Cottrell and Jens Uwe Hoffmann and Pete R. Jemian and David Männicke and Raymond Osborn and Peter F. Peterson and Tobias Richter and Jiro Suzuki and Benjamin Watts and Eugen Wintersberger and Joachim Wuttke},
title = {The {NeXus} data format},
journal = {Journal of Applied Crystallography},
year = {2015},
volume = {48},
number = {1},
pages = {301--305},
month = {jan},
doi = {10.1107/s1600576714027575},
publisher = {International Union of Crystallography ({IUCr})},
}
@Article{Fangohr2018,
author = {Fangohr, Hans and Aplin, Steve and Barty, Anton and Beg, Marijan and Bondar, Valerii and Boukhelef, Djelloul and Brockhauser, Sandor and Danilevski, Cyril and Ehsan, Wajid and Esenov, Sergey and Flucke, Gero and Giovanetti, Gabriele and Goeries, Dennis and Hauf, Steffen and Heisen, Burkhard and Hickin, David and Khakhulin, Dmitry and Klimovskaia, Anna and Kluyver, Thomas and Kuhn, Manuela and Kuster, Markus and Lang, Philipp-Michael and Maia, Luis and Mariani, Valerio and Mekinda, Leonce and Michelat, Thomas and Parenti, Andrea and Previtali, Gianpietro and Santos, Hugo and Silenzi, Alessandro and Sztuk-Dambietz, Jolanta and Szuba, Janusz and Teichmann, Martin and Weger, Kerstin and Wiggins, John and Wrona, Krzysztof and Xu, Chen},
title = {Data Analysis Support in Karabo at European XFEL},
journal = {Proceedings of the 16th Int. Conf. on Accelerator and Large Experimental Control Systems, ICALEPCS2017, Barcelona, Spain},
year = {2018},
doi = {10.18429/jacow-icalepcs2017-tucpa01},
keywords = {Accelerator Physics, Data Analytics},
language = {en-us},
publisher = {JACoW, Geneva, Switzerland},
}
@Article{Jesse2016,
author = {S. Jesse and M. Chi and A. Belianinov and C. Beekman and S. V. Kalinin and A. Y. Borisevich and A. R. Lupini},
title = {Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography},
journal = {Scientific Reports},
year = {2016},
volume = {6},
number = {1},
month = {may},
doi = {10.1038/srep26348},
publisher = {Springer Nature},
}
@Article{Belianinov2015,
author = {Alex Belianinov and Rama Vasudevan and Evgheni Strelcov and Chad Steed and Sang Mo Yang and Alexander Tselev and Stephen Jesse and Michael Biegalski and Galen Shipman and Christopher Symons and Albina Borisevich and Rick Archibald and Sergei Kalinin},
title = {Big data and deep data in scanning and electron microscopies: deriving functionality from multidimensional data sets},
journal = {Advanced Structural and Chemical Imaging},
year = {2015},
volume = {1},
number = {1},
month = {may},
doi = {10.1186/s40679-015-0006-6},
publisher = {Springer Nature},
}
@Article{Krajnak2016,
author = {Matus Krajnak and Damien McGrouther and Dzmitry Maneuski and Val O{\textquotesingle} Shea and Stephen McVitie},
title = {Pixelated detectors and improved efficiency for magnetic imaging in {STEM} differential phase contrast},
journal = {Ultramicroscopy},
year = {2016},
volume = {165},
pages = {42--50},
month = {jun},
doi = {10.1016/j.ultramic.2016.03.006},
publisher = {Elsevier {BV}},
}
@Article{Yang2015,
author = {H Yang and L Jones and H Ryll and M Simson and H Soltau and Y Kondo and R Sagawa and H Banba and I MacLaren and P D Nellist},
title = {4D {STEM}: High efficiency phase contrast imaging using a fast pixelated detector},
journal = {Journal of Physics: Conference Series},
year = {2015},
volume = {644},
pages = {012032},
month = {oct},
doi = {10.1088/1742-6596/644/1/012032},
publisher = {{IOP} Publishing},
}
@Article{Sagawa2017,
author = {Ryusuke Sagawa and Hao Yang and Lewys Jones and Martin Simson and Martin Huth and Heike Soltau and Peter D. Nellist and Yukihito Kondo},
title = {Development of Fast Pixelated {STEM} Detector and its Applications using 4-Dimensional Dataset},
journal = {Microscopy and Microanalysis},
year = {2017},
volume = {23},
number = {S1},
pages = {52--53},
month = {jul},
doi = {10.1017/s1431927617000940},
publisher = {Cambridge University Press ({CUP})},
}
@InBook{doi:10.1002/9783527808465.EMC2016.6284,
pages = {663-664},
title = {Pixelated STEM detectors: opportunities and challenges},
publisher = {American Cancer Society},
year = {2016},
author = {MacLaren, Ian and Nord, Magnus and Ross, Andrew and Krajnak, Matus and Hart, Martin and Doye, Alastair and McGrouther, Damien and Bali, Rantej and Banerjee, Archan and Hadfield, Robert},
isbn = {9783527808465},
abstract = {Conventionally, imaging in Scanning Transmission Electron Microscopy (STEM) has been performed using annular detectors that integrate up large fractions of the scattered electrons into a single value for each position in a scan, leading to a loss of information. Recently, advances in counting detection have enabled the development of fast 2-D pixelated detectors, such as the Medipix-3 detector used in this work. These can be used to collect a large fraction of the scattered electrons in the back focal plane yielding a STEM diffraction pattern (Fig. 1a) for every scan position. The end result is a 4-D dataset, with two spatial sample positions and two reciprocal detector positions. This diffraction pattern contains a wealth of information, and being able acquire them at Ångström spatial resolutions enables many exciting applications, however there are many challenges in how to use and analyse these large datasets. In this presentation we focus on recent progress at University of Glasgow on pixelated STEM imaging, and how analysing different aspects of the diffraction images can yield information about the material properties. In standard STEM imaging, one usually gets information about the spatial dimensions orthogonal to the electron beam. By using a pixelated STEM detector, the lattice parameter parallel to the electron beam can also be extracted. This is achieved by looking using the higher order Laue zone rings (arrow in Fig. 1a). When this is combined with conventional atomic resolution STEM images, information of 3-D crystallography can be determined from just one projection. Examples will be given on how the 3-D structure of perovskite oxides has been determined. The magnetic induction of a sample can be imaged in Lorentz mode, where the objective lens is usually turned off. In STEM mode, magnetic induction in the sample causes the electron beam to deflect through a typically small angle, 1-100μrads, which can be seen as a shift in the bright field disc. This has conventionally been mapped using the Differential Phase Contrast Technique with a split detector (e.g. into quadrants), but this suffers from additional contrast due to diffraction effects which affect intensity distribution within the bright field disc. Pixelated detection allows an improved methodology accurate disc-shift measurements using edge-detection of the disc, which separates these disc shifts from diffraction contrast more robustly. The resulting imaged magnetic induction in a patterned FeAl film is shown in Fig. 1b, which visualizes ferromagnetic domains in a nanostructure created using focused ion beam nanopatterning. Since the 4-D datasets contain the full diffraction patterns, it is possible to create virtual apertures in post-processing. This allows the construction of arbitrary shaped “detectors”. Making it possible to get HAADF, MAADF, LAADF, ABF and BF from the same dataset. Such a virtual ADF-aperture is shown in Fig. 1c, for gold deposited on a carbon film. We will also describe how this detector can be used to determine ordering in amorphous materials using a fluctuation electron microscopy based method, and Figure 1d shows one diffraction pattern from a series of ∼ 2000 diffraction patterns taken on a thin ∼5 nm film of amorphous MoSix for use in a superconducting nanowire single-photon detector (SNSPD). The use of the Medipix detector has significant advantages over earlier CCD detectors, due to the absence of electronic detection noise, meaning that the statistics are much cleaner and more interpretable at lower beam doses, and thus higher acquisition rates. The resulting variance plots and conclusions about short- and medium-range ordering in the material will be briefly summarised. In conclusion, we will demonstrate a range of new and interesting applications for pixelated detectors in STEM, which allow new or improved imaging modes and the improved extraction of information relevant to the understanding of the nanoscale or atomic scale structure of materials, nanostructures and devices.},
booktitle = {European Microscopy Congress 2016: Proceedings},
doi = {10.1002/9783527808465.EMC2016.6284},
keywords = {STEM, direct electron detectors, medipix, laue zone, lorentz microscopy, magnetic domains, virtual detectors, fluctuation microscopy, amorphous materials},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527808465.EMC2016.6284},
}
@Article{Nguyen2016,
author = {Kayla X. Nguyen and Prafull Purohit and Robert Hovden and Emrah Turgut and Mark W. Tate and Lena F. Kourkoutis and Gregory D. Fuchs and Sol M. Gruner and David A. Muller},
title = {4D-{STEM} for Quantitative Imaging of Magnetic Materials with Enhanced Contrast and Resolution},
journal = {Microscopy and Microanalysis},
year = {2016},
volume = {22},
number = {S3},
pages = {1718--1719},
month = {jul},
doi = {10.1017/s1431927616009430},
publisher = {Cambridge University Press ({CUP})},
}
@Article{Cowley1979,
author = {J.M. Cowley},
title = {Coherent interference in convergent-beam electron diffraction and shadow imaging},
journal = {Ultramicroscopy},
year = {1979},
volume = {4},
number = {4},
pages = {435--449},
month = {jan},
doi = {10.1016/s0304-3991(79)80021-2},
publisher = {Elsevier {BV}},
}
@Article{Hoppe1969,
author = {W. Hoppe},
title = {Beugung im inhomogenen Primärstrahlwellenfeld. I. Prinzip einer Phasenmessung von Elektronenbeungungsinterferenzen},
journal = {Acta Crystallographica Section A},
year = {1969},
volume = {25},
number = {4},
pages = {495--501},
month = {jul},
doi = {10.1107/s0567739469001045},
publisher = {International Union of Crystallography ({IUCr})},
}
@Article{Hegerl1970,
author = {R. Hegerl and W. Hoppe},
title = {Dynamische Theorie der Kristallstrukturanalyse durch Elektronenbeugung im inhomogenen Primärstrahlwellenfeld},
journal = {Berichte der Bunsengesellschaft für physikalische Chemie},
year = {1970},
volume = {74},
number = {11},
pages = {1148--1154},
month = {nov},
doi = {10.1002/bbpc.19700741112},
publisher = {Wiley},
}
@Article{Nellist1995,
author = {P. D. Nellist and B. C. McCallum and J. M. Rodenburg},
title = {Resolution beyond the {\textquotesingle}information limit{\textquotesingle} in transmission electron microscopy},
journal = {Nature},
year = {1995},
volume = {374},
number = {6523},
pages = {630--632},
month = {apr},
doi = {10.1038/374630a0},
publisher = {Springer Nature},
}
@Article{McCallum1993,
author = {B. C. McCallum and J. M. Rodenburg},
title = {Simultaneous reconstruction of object and aperture functions from multiple far-field intensity measurements},
journal = {Journal of the Optical Society of America A},
year = {1993},
volume = {10},
number = {2},
pages = {231},
month = {feb},
doi = {10.1364/josaa.10.000231},
publisher = {The Optical Society},
}
@Article{Friedman1992,
author = {S L Friedman and J M Rodenburg},
title = {Optical demonstration of a new principle of far-field microscopy},
journal = {Journal of Physics D: Applied Physics},
year = {1992},
volume = {25},
number = {2},
pages = {147--154},
month = {feb},
doi = {10.1088/0022-3727/25/2/003},
publisher = {{IOP} Publishing},
}
@Article{Humphreys1988,
author = {C.J. Humphreys and D.J. Eaglesham and D.M. Maher and H.L. Fraser},
title = {{CBED} and {CBIM} from semiconductors and superconductors},
journal = {Ultramicroscopy},
year = {1988},
volume = {26},
number = {1-2},
pages = {13--23},
month = {jan},
doi = {10.1016/0304-3991(88)90371-3},
publisher = {Elsevier {BV}},
}
@InCollection{Steeds1979,
author = {J. W. Steeds},
title = {Convergent Beam Electron Diffraction},
booktitle = {Introduction to Analytical Electron Microscopy},
publisher = {Springer {US}},
year = {1979},
pages = {387--422},
doi = {10.1007/978-1-4757-5581-7_15},
}
@Article{Tate2016,
author = {Mark W. Tate and Prafull Purohit and Darol Chamberlain and Kayla X. Nguyen and Robert Hovden and Celesta S. Chang and Pratiti Deb and Emrah Turgut and John T. Heron and Darrell G. Schlom and Daniel C. Ralph and Gregory D. Fuchs and Katherine S. Shanks and Hugh T. Philipp and David A. Muller and Sol M. Gruner},
title = {High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy},
journal = {Microscopy and Microanalysis},
year = {2016},
volume = {22},
number = {01},
pages = {237--249},
month = {jan},
doi = {10.1017/s1431927615015664},
publisher = {Cambridge University Press ({CUP})},
}
@Article{Jiang2018,
author = {Yi Jiang and Zhen Chen and Yimo Han and Pratiti Deb and Hui Gao and Saien Xie and Prafull Purohit and Mark W. Tate and Jiwoong Park and Sol M. Gruner and Veit Elser and David A. Muller},
title = {Electron ptychography of 2D materials to deep sub-{\aa}ngström resolution},
journal = {Nature},
year = {2018},
volume = {559},
number = {7714},
pages = {343--349},
month = {jul},
doi = {10.1038/s41586-018-0298-5},
publisher = {Springer Nature},
}
@Article{Ophus2014,
author = {Colin Ophus and Peter Ercius and Michael Sarahan and Cory Czarnik and Jim Ciston},
title = {Recording and Using 4D-{STEM} Datasets in Materials Science},
journal = {Microscopy and Microanalysis},
year = {2014},
volume = {20},
number = {S3},
pages = {62--63},
month = {aug},
doi = {10.1017/s1431927614002037},
publisher = {Cambridge University Press ({CUP})},
}
@Article{Simson2015,
author = {M. Simson and H. Ryll and H. Banba and R. Hartmann and M. Huth and S. Ihle and L. Jones and Y. Kondo and K. Muller and P.D. Nellist and R. Sagawa and J. Schmidt and H. Soltau and L. Striider and H. Yang},
title = {4D-{STEM} Imaging With the {pnCCD} (S){TEM}-Camera},
journal = {Microscopy and Microanalysis},
year = {2015},
volume = {21},
number = {S3},
pages = {2211--2212},
month = {aug},
doi = {10.1017/s1431927615011836},
publisher = {Cambridge University Press ({CUP})},
}
@Article{Pennycook2015,
author = {Timothy J. Pennycook and Andrew R. Lupini and Hao Yang and Matthew F. Murfitt and Lewys Jones and Peter D. Nellist},
title = {Efficient phase contrast imaging in {STEM} using a pixelated detector. Part 1: Experimental demonstration at atomic resolution},
journal = {Ultramicroscopy},
year = {2015},
volume = {151},
pages = {160--167},
month = {apr},
doi = {10.1016/j.ultramic.2014.09.013},
publisher = {Elsevier {BV}},
}
@Article{Yang2015a,
author = {Hao Yang and Timothy J. Pennycook and Peter D. Nellist},
title = {Efficient phase contrast imaging in {STEM} using a pixelated detector. Part {II}: Optimisation of imaging conditions},
journal = {Ultramicroscopy},
year = {2015},
volume = {151},
pages = {232--239},
month = {apr},
doi = {10.1016/j.ultramic.2014.10.013},
publisher = {Elsevier {BV}},
}
@Misc{QuantumMerlin2017,
author = {{Quantum Detectors}},
title = {Merlin for {EM} technical datasheet},
year = {2017},
url = {https://quantumdetectors.com/products/merlinem/},
}
@Article{Lawrence2017,
author = {Ethan L. Lawrence and Shery L. Y. Chang and Peter A. Crozier},
title = {In situ {TEM} observations of Oxygen Surface Dynamics in {CeO}2 Cubes},
journal = {Microscopy and Microanalysis},
year = {2017},
volume = {23},
number = {S1},
pages = {1994--1995},
month = {jul},
doi = {10.1017/s1431927617010637},
publisher = {Cambridge University Press ({CUP})},
}
@Article{Li2013,
author = {Xueming Li and Paul Mooney and Shawn Zheng and Christopher R Booth and Michael B Braunfeld and Sander Gubbens and David A Agard and Yifan Cheng},
title = {Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-{EM}},
journal = {Nature Methods},
year = {2013},
volume = {10},
number = {6},
pages = {584--590},
month = {may},
doi = {10.1038/nmeth.2472},
publisher = {Springer Nature},
}
@Misc{XSpectrum-LambdaM2,
author = {X-Spectrum},
title = {{Lambda2M} large area {Medipix3} based detector array},
url = {http://www.x-spectrum.de/index_htm_files/X-Spectrum_datasheet_2M.pdf},
}
@Article{Li:2018ngp,
author = {Li, Xin and Dyck, Ondrej and Kalinin, Sergei V. and Jesse, Stephen},
title = {Compressed Sensing of Scanning Transmission Electron Microscopy {(STEM)} on Non-Rectangular Scans},
journal = {ArXiv},
year = {2018},
archiveprefix = {arXiv},
eprint = {1805.04957},
primaryclass = {physics.ins-det},
slaccitation = {%%CITATION = ARXIV:1805.04957;%%},
url = {https://arxiv.org/abs/1805.04957},
}
@Book{Nielsen1994,
title = {Usability Engineering},
publisher = {Elsevier Science},
year = {1994},
author = {Nielsen, Jakob},
note = {{p. 135}},
date = {1994-11-11},
ean = {9780080520292},
pagetotal = {362},
url = {https://www.ebook.de/de/product/21119819/jakob_nielsen_usability_engineering.html},
}
@Article{Lee2011,
author = {Craig A. Lee and Samuel D. Gasster and Antonio Plaza and Chein-I Chang and Bormin Huang},
title = {Recent Developments in High Performance Computing for Remote Sensing: A Review},
journal = {{IEEE} Journal of Selected Topics in Applied Earth Observations and Remote Sensing},
year = {2011},
volume = {4},
number = {3},
pages = {508--527},
month = {sep},
doi = {10.1109/jstars.2011.2162643},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@Article{Tezduyar1996,
author = {T. Tezduyar and S. Aliabadi and M. Behr and A. Johnson and V. Kalro and M. Litke},
title = {Flow simulation and high performance computing},
journal = {Computational Mechanics},
year = {1996},
volume = {18},
number = {6},
pages = {397--412},
month = {dec},
doi = {10.1007/bf00350249},
publisher = {Springer Nature America, Inc},
}
@Article{Allcock2002,
author = {Bill Allcock and Joe Bester and John Bresnahan and Ann L. Chervenak and Ian Foster and Carl Kesselman and Sam Meder and Veronika Nefedova and Darcy Quesnel and Steven Tuecke},
title = {Data management and transfer in high-performance computational grid environments},
journal = {Parallel Computing},
year = {2002},
volume = {28},
number = {5},
pages = {749--771},
month = {may},
doi = {10.1016/s0167-8191(02)00094-7},
publisher = {Elsevier {BV}},
}
@InCollection{Pan2016,
author = {Ming Pan and Cory Czarnik},
title = {Image Detectors for Environmental Transmission Electron Microscopy ({ETEM})},
booktitle = {Controlled Atmosphere Transmission Electron Microscopy},
publisher = {Springer International Publishing},
year = {2016},
pages = {143--164},
doi = {10.1007/978-3-319-22988-1_5},
}
@Article{Knuth1974,
author = {Donald E. Knuth},
title = {Structured Programming with go to Statements},
journal = {{ACM} Computing Surveys},
year = {1974},
volume = {6},
number = {4},
pages = {261--301},
month = {dec},
doi = {10.1145/356635.356640},
publisher = {Association for Computing Machinery ({ACM})},
}
@Misc{Busch2016,
author = {Busch, Kat},
title = {The Rules of Optimization: Why So Many Performance Efforts Fail},
howpublished = {Online},
year = {2016},
url = {https://hackernoon.com/the-rules-of-optimization-why-so-many-performance-efforts-fail-cf06aad89099},
}
@Misc{Delvecchio2011,
author = {Delvecchio, Paul},
title = {De-Mystifying Software Performance Optimization},
howpublished = {Online},
year = {2011},
url = {https://software.intel.com/en-us/articles/de-mystifying-software-performance-optimization},
}
@Article{Mavridis2017,
author = {Ilias Mavridis and Helen Karatza},
title = {Performance evaluation of cloud-based log file analysis with Apache Hadoop and Apache Spark},
journal = {Journal of Systems and Software},
year = {2017},
volume = {125},
pages = {133--151},
month = {mar},
doi = {10.1016/j.jss.2016.11.037},
publisher = {Elsevier {BV}},
}
@Article{Dean2008,
author = {Jeffrey Dean and Sanjay Ghemawat},
title = {{MapReduce}},
journal = {Communications of the {ACM}},
year = {2008},
volume = {51},
number = {1},
pages = {107},
month = {jan},
doi = {10.1145/1327452.1327492},
publisher = {Association for Computing Machinery ({ACM})},
}
@Article{Stegmaier2017,
author = {Stegmaier, Johannes},
title = {New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty},
year = {2017},
doi = {10.5445/ksp/1000060221},
keywords = {3D Bildanalyse, Entwicklungsbiologie, Algorithmen, Data Mining, Software, 3D Image Analysis, Developmental Biology, Algorithms, Data Mining, Software},
language = {en},
publisher = {KIT Scientific Publishing},
}
@Article{Goscinski2014,
author = {Wojtek J. Goscinski and Paul McIntosh and Ulrich Felzmann and Anton Maksimenko and Christopher J. Hall and Timur Gureyev and Darren Thompson and Andrew Janke and Graham Galloway and Neil E. B. Killeen and Parnesh Raniga and Owen Kaluza and Amanda Ng and Govinda Poudel and David G. Barnes and Toan Nguyen and Paul Bonnington and Gary F. Egan},
title = {The multi-modal Australian {ScienceS} Imaging and Visualization Environment ({MASSIVE}) high performance computing infrastructure: applications in neuroscience and neuroinformatics research},
journal = {Frontiers in Neuroinformatics},
year = {2014},
volume = {8},
month = {mar},
doi = {10.3389/fninf.2014.00030},
publisher = {Frontiers Media {SA}},
}
@InProceedings{Foust2015,
author = {Gabriel Foust and Jaakko Järvi and Sean Parent},
title = {Generating reactive programs for graphical user interfaces from multi-way dataflow constraint systems},
booktitle = {Proceedings of the 2015 {ACM} {SIGPLAN} International Conference on Generative Programming: Concepts and Experiences - {GPCE} 2015},
year = {2015},
publisher = {{ACM} Press},
doi = {10.1145/2814204.2814207},
}
@Book{Shneiderman2009,
title = {Designing the User Interface: Strategies for Effective Human-Computer Interaction (5th Edition)},
publisher = {Pearson},
year = {2009},
author = {Ben Shneiderman and Catherine Plaisant and Maxine Cohen and Steven Jacobs},
isbn = {978-0321537355},
note = {Ch. 9},
url = {https://www.amazon.com/Designing-User-Interface-Human-Computer-Interaction/dp/0321537351?SubscriptionId=AKIAIOBINVZYXZQZ2U3A&tag=chimbori05-20&linkCode=xm2&camp=2025&creative=165953&creativeASIN=0321537351},
}
@Article{Tsukamoto2014,
author = {Takafumi Tsukamoto and Takuo Yasunaga},
title = {Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and {PIONE} with Eos},
journal = {Microscopy},
year = {2014},
volume = {63},
number = {suppl 1},
pages = {i32.3--i33},
month = {oct},
doi = {10.1093/jmicro/dfu070},
publisher = {Oxford University Press ({OUP})},
}
@Misc{Rogic,
author = {Ivan Rogic},
title = {{React}, {Redux} and {Immutable.js}: Ingredients for Efficient Web Applications},
howpublished = {Online},
url = {https://www.toptal.com/react/react-redux-and-immutablejs},
}
@Misc{Lachlan,
author = {Lachlan Miller},
title = {Redux-driven {UI} design},
howpublished = {Online},
year = {2017},
url = {https://medium.com/@lachlanmiller_52885/redux-driven-ui-design-8586a84d808f},
}
@Article{Taylor1996,
author = {R.N. Taylor and N. Medvidovic and K.M. Anderson and E.J. Whitehead and J.E. Robbins and K.A. Nies and P. Oreizy and D.L. Dubrow},
title = {A component- and message-based architectural style for {GUI} software},
journal = {{IEEE} Transactions on Software Engineering},
year = {1996},
volume = {22},
number = {6},
pages = {390--406},
month = {jun},
doi = {10.1109/32.508313},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@Misc{pyFAI,
author = {{Data analysis unit, European Synchrotron Radiation Facility, Grenoble}},
title = {General introduction to {PyFAI}},
howpublished = {Online},
year = {2018},
url = {https://pyfai.readthedocs.io/en/latest/pyFAI.html},
}
@Article{Alted2010,
author = {Francesc Alted},
title = {Why Modern {CPUs} Are Starving and What Can Be Done about It},
journal = {Computing in Science {\&} Engineering},
year = {2010},
volume = {12},
number = {2},
pages = {68--71},
month = {mar},
doi = {10.1109/mcse.2010.51},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@Misc{Clausen2018a,
author = {Clausen, Alexander and Weber, Dieter and {Probonopd} and Caron, Jan and Nord, Magnus and Müller-Caspary, Knut and Ophus, Colin and Dunin-Borkowski, Rafal},
title = {Libertem/Libertem: 0.1.0},
year = {2018},
doi = {10.5281/zenodo.1478763},
keywords = {STEM, TEM, pixelated STEM, 4D STEM, high-throughput, electron microscopy},
publisher = {Zenodo},
}
@Misc{IntelLustre,
author = {{Intel High Performance Data Division}},
title = {Architecting a High Performance Storage System},
year = {2014},
url = {https://www.intel.com/content/dam/www/public/us/en/documents/white-papers/architecting-lustre-storage-white-paper.pdf},
}
@InProceedings{Patel2012,
author = {Aditya B. Patel and Manashvi Birla and Ushma Nair},
title = {Addressing big data problem using {Hadoop} and {Map Reduce}},
booktitle = {2012 Nirma University International Conference on Engineering ({NUiCONE})},
year = {2012},
month = {dec},
publisher = {{IEEE}},
doi = {10.1109/nuicone.2012.6493198},
}
@Article{Larsen2000,
author = {Samuel Larsen and Saman Amarasinghe},
title = {Exploiting superword level parallelism with multimedia instruction sets},
journal = {{ACM} {SIGPLAN} Notices},
year = {2000},
volume = {35},
number = {5},
pages = {145--156},
month = {may},
doi = {10.1145/358438.349320},
publisher = {Association for Computing Machinery ({ACM})},
}
@Article{Walt2011,
author = {St{\'{e}}fan van der Walt and S Chris Colbert and Gaël Varoquaux},
title = {The {NumPy} Array: A Structure for Efficient Numerical Computation},
journal = {Computing in Science {\&} Engineering},
year = {2011},
volume = {13},
number = {2},
pages = {22--30},
month = {mar},
doi = {10.1109/mcse.2011.37},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@InProceedings{Thadani19951AE,
author = {Moti Thadani and Yousef Y. A. Khalidi},
title = {An Efficient Zero-Copy {I / O} Framework for {UNIX} ®},
year = {1995},
}
@Misc{Stancevic2003,
author = {Dragan Stancevic},
title = {Zero Copy I: User-Mode Perspective},
howpublished = {Online},
year = {2003},
url = {https://www.linuxjournal.com/article/6345?page=0,0},
}
@Misc{Kelly2003,
author = {Paul H J Kelly},
title = {Advanced Computer Architecture: Caches and Memory Systems},
year = {2003},
url = {https://www.doc.ic.ac.uk/~phjk/AdvancedCompArchitecture/2003-04/Lectures/Ch03/ACA-CH03-CurrentVersion.pdf},
}
@InProceedings{Shvachko2010,
author = {Konstantin Shvachko and Hairong Kuang and Sanjay Radia and Robert Chansler},
title = {The Hadoop Distributed File System},
booktitle = {2010 {IEEE} 26th Symposium on Mass Storage Systems and Technologies ({MSST})},
year = {2010},
month = {may},
publisher = {{IEEE}},
doi = {10.1109/msst.2010.5496972},
}
@Misc{HDFS-Short,
author = {{Apache Software Foundation}},
title = {{HDFS} Short-Circuit Local Reads},
howpublished = {Online},
year = {2018},
url = {https://hadoop.apache.org/docs/current/hadoop-project-dist/hadoop-hdfs/ShortCircuitLocalReads.html},
}
@Article{Cooley1965,
author = {James W. Cooley and John W. Tukey},
title = {An algorithm for the machine calculation of complex Fourier series},
journal = {Mathematics of Computation},
year = {1965},
volume = {19},
number = {90},
pages = {297--297},
month = {may},
doi = {10.1090/s0025-5718-1965-0178586-1},
publisher = {American Mathematical Society ({AMS})},
}
@Article{Zaharia2016,
author = {Matei Zaharia and Michael J. Franklin and Ali Ghodsi and Joseph Gonzalez and Scott Shenker and Ion Stoica and Reynold S. Xin and Patrick Wendell and Tathagata Das and Michael Armbrust and Ankur Dave and Xiangrui Meng and Josh Rosen and Shivaram Venkataraman},
title = {Apache Spark},
journal = {Communications of the {ACM}},
year = {2016},
volume = {59},
number = {11},
pages = {56--65},
month = {oct},
doi = {10.1145/2934664},
publisher = {Association for Computing Machinery ({ACM})},
}
@InProceedings{Rocklin2015,
author = {Matthew Rocklin},
title = {Dask: Parallel Computation with Blocked algorithms and Task Scheduling},
booktitle = {Proceedings of the 14th Python in Science Conference},
year = {2015},
publisher = {{SciPy}},
doi = {10.25080/majora-7b98e3ed-013},
}
@Manual{BLAS,
title = {{BLAS} ({Basic Linear Algebra Subprograms})},
edition = {3.8.0},
year = {2017},
url = {http://www.netlib.org/blas/},
}
@Misc{PyTorch,
title = {PyTorch},
howpublished = {Online},
year = {2018},
url = {https://pytorch.org/},
}
@Misc{MKL,
author = {Intel},
title = {Intel® Math Kernel Library},
howpublished = {Online},
year = {2018},
url = {https://software.intel.com/en-us/mkl},
}
@Misc{Godbolt,
author = {Matt Godbolt},
title = {Compiler Explorer},
howpublished = {Online},
url = {https://godbolt.org/},
}
@Misc{Numba,
title = {Numba: A high-performance {Python} compiler},
howpublished = {Online},
year = {2018},
url = {http://numba.pydata.org/},
}
@Misc{ReactJS,
author = {{Facebook Inc.}},
title = {React: A {JavaScript} library for building user interfaces},
howpublished = {Online},
year = {2018},
url = {https://reactjs.org/},
}
@Misc{ReduxJS,
author = {Dan Abramov},
title = {Redux: A predictable state container for {JavaScript} apps.},
howpublished = {Online},
year = {2018},
url = {https://redux.js.org/},
}
@Article{MerkelDocker,
author = {Dirk Merkel},
title = {Docker: Lightweight Linux Containers for Consistent Development and Deployment},
journal = {Linux Journal},
year = {2014},
url = {https://www.linuxjournal.com/content/docker-lightweight-linux-containers-consistent-development-and-deployment},
}
@Article{Bernstein2014,
author = {David Bernstein},
title = {Containers and Cloud: From {LXC} to Docker to Kubernetes},
journal = {{IEEE} Cloud Computing},
year = {2014},
volume = {1},
number = {3},
pages = {81--84},
month = {sep},
doi = {10.1109/mcc.2014.51},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@Article{Shaw1990,
author = {Mary Shaw},
title = {Prospects for an engineering discipline of software},
journal = {{IEEE} Software},
year = {1990},
volume = {7},
number = {6},
pages = {15--24},
month = nov,
doi = {10.1109/52.60586},
publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
@Article{Schindelin2012,
author = {Johannes Schindelin and Ignacio Arganda-Carreras and Erwin Frise and Verena Kaynig and Mark Longair and Tobias Pietzsch and Stephan Preibisch and Curtis Rueden and Stephan Saalfeld and Benjamin Schmid and Jean-Yves Tinevez and Daniel James White and Volker Hartenstein and Kevin Eliceiri and Pavel Tomancak and Albert Cardona},
title = {Fiji: an open-source platform for biological-image analysis},
journal = {Nature Methods},
year = {2012},
volume = {9},
number = {7},
pages = {676--682},
month = jul,
doi = {10.1038/nmeth.2019},
publisher = {Springer Nature},
}
@Article{Willinsky2005,
author = {John Willinsky},
title = {The unacknowledged convergence of open source, open access, and open science},
journal = {First Monday},
year = {2005},
volume = {10},
number = {8},
month = aug,
doi = {10.5210/fm.v10i8.1265},
publisher = {University of Illinois Libraries},
}
@Article{Zuiderwijk2012,
author = {Anneke Zuiderwijk and Keith Jeffery and Marijn Janssen},
title = {The Potential of Metadata for Linked Open Data and its Value for Users and Publishers},
journal = {{JeDEM} - {eJournal} of {eDemocracy} and Open Government},
year = {2012},
volume = {4},
number = {2},
pages = {222--244},
month = {dec},
doi = {10.29379/jedem.v4i2.138},
publisher = {{JEDEM} Journal of e-Democracy and Open Government},
}
@Manual{HDF5,
title = {High Level Introduction to {HDF5}},
organization = {The HDF Group},
year = {2016},
url = {https://support.hdfgroup.org/HDF5/Tutor/HDF5Intro.pdf},
}
@Article{Okoli2015,
author = {Chitu Okoli and Johannes Nguyen},
title = {Business Models for Free and Open Source Software},
journal = {{SSRN} Electronic Journal},
year = {2015},
doi = {10.2139/ssrn.2568185},
publisher = {Elsevier {BV}},
}
@Misc{ApacheFoundation,
author = {{{The APACHE Software Foundation}}},
title = {The {APACHE} Software Foundation},
howpublished = {Online},
year = {2018},
url = {https://www.apache.org/},
}
@Misc{Linuxfoundation,
author = {{The Linux Foundation}},
title = {The Linux Foundation},
year = {2018},
url = {https://www.linuxfoundation.org/},
}
@InCollection{Williams1996,
author = {David B. Williams and C. Barry Carter},
title = {The Transmission Electron Microscope},
booktitle = {Transmission Electron Microscopy},
publisher = {Springer {US}},
year = {1996},
pages = {3--17},
doi = {10.1007/978-1-4757-2519-3_1},
}
@Article{Goto2008,
author = {Kazushige Goto and Robert A. van de Geijn},
title = {Anatomy of high-performance matrix multiplication},
journal = {{ACM} Transactions on Mathematical Software},
year = {2008},
volume = {34},
number = {3},
pages = {1--25},
month = {may},
doi = {10.1145/1356052.1356053},
publisher = {Association for Computing Machinery ({ACM})},
}
@Misc{DaskSpark,
author = {{Anaconda Inc.}},
title = {Comparison to Spark},
howpublished = {Online},
year = {2018},
url = {http://docs.dask.org/en/latest/spark.html},
}
@Article{Lemire2012,
author = {Daniel Lemire and Leonid Boytsov},
title = {Decoding billions of integers per second through vectorization},
abstract = {In many important applications -- such as search engines and relational database systems -- data is stored in the form of arrays of integers. Encoding and, most importantly, decoding of these arrays consumes considerable CPU time. Therefore, substantial effort has been made to reduce costs associated with compression and decompression. In particular, researchers have exploited the superscalar nature of modern processors and SIMD instructions. Nevertheless, we introduce a novel vectorized scheme called SIMD-BP128 that improves over previously proposed vectorized approaches. It is nearly twice as fast as the previously fastest schemes on desktop processors (varint-G8IU and PFOR). At the same time, SIMD-BP128 saves up to 2 bits per integer. For even better compression, we propose another new vectorized scheme (SIMD-FastPFOR) that has a compression ratio within 10% of a state-of-the-art scheme (Simple-8b) while being two times faster during decoding.},
date = {2012-09-10},
doi = {10.1002/spe.2203},
eprint = {http://arxiv.org/abs/1209.2137v6},
eprintclass = {cs.IR},
eprinttype = {arXiv},
file = {:http\://arxiv.org/pdf/1209.2137v6:PDF},
journaltitle = {Software: Practice \& Experience 45 (1), 2015},
keywords = {cs.IR, cs.DB},
}
@InProceedings{grosser2011polly,
author = {Grosser, Tobias and Zheng, Hongbin and Aloor, Raghesh and Simb{\"u}rger, Andreas and Gr{\"o}{\ss}linger, Armin and Pouchet, Louis-No{\"e}l},
title = {Polly-Polyhedral optimization in {LLVM}},
url = {http://perso.ens-lyon.fr/christophe.alias/impact2011/impact-07.pdf},
}
@Article{Song2018,
author = {Dongsheng Song and Zi-An Li and Jan Caron and Andr{\'{a}}s Kov{\'{a}}cs and Huanfang Tian and Chiming Jin and Haifeng Du and Mingliang Tian and Jianqi Li and Jing Zhu and Rafal E. Dunin-Borkowski},
title = {Quantification of Magnetic Surface and Edge States in an {FeGe} Nanostripe by Off-Axis Electron Holography},
journal = {Physical Review Letters},
year = {2018},
volume = {120},
number = {16},
month = {apr},
doi = {10.1103/physrevlett.120.167204},
publisher = {American Physical Society ({APS})},
}
@Article{Mehta2016,
author = {Parmita Mehta and Sven Dorkenwald and Dongfang Zhao and Tomer Kaftan and Alvin Cheung and Magdalena Balazinska and Ariel Rokem and Andrew Connolly and Jacob Vanderplas and Yusra AlSayyad},
title = {Comparative Evaluation of Big-Data Systems on Scientific Image Analytics Workloads},
abstract = {Scientific discoveries are increasingly driven by analyzing large volumes of image data. Many new libraries and specialized database management systems (DBMSs) have emerged to support such tasks. It is unclear, however, how well these systems support real-world image analysis use cases, and how performant are the image analytics tasks implemented on top of such systems. In this paper, we present the first comprehensive evaluation of large-scale image analysis systems using two real-world scientific image data processing use cases. We evaluate five representative systems (SciDB, Myria, Spark, Dask, and TensorFlow) and find that each of them has shortcomings that complicate implementation or hurt performance. Such shortcomings lead to new research opportunities in making large-scale image analysis both efficient and easy to use.},
date = {2016-12-07},
eprint = {http://arxiv.org/abs/1612.02485v1},
eprintclass = {cs.DB},
eprinttype = {arXiv},
file = {:http\://arxiv.org/pdf/1612.02485v1:PDF},
keywords = {cs.DB},
}
@Article{Goy2018,
author = {Alexandre Goy and Kwabena Arthur and Shuai Li and George Barbastathis},
title = {Low Photon Count Phase Retrieval Using Deep Learning},
journal = {Physical Review Letters},
year = {2018},
volume = {121},
number = {24},
month = {dec},
doi = {10.1103/physrevlett.121.243902},
file = {:Goy2018 - Low Photon Count Phase Retrieval Using Deep Learning.pdf:PDF},
keywords = {Neural network},
publisher = {American Physical Society ({APS})},
}
@Misc{DistributedJourney,
author = {{{Anaconda, Inc}}},
title = {Journey of a Task},
howpublished = {Online},
year = {2018},
url = {https://distributed.dask.org/en/latest/journey.html},
}
@Misc{AbramovFlux,
author = {Dan Abramov},
title = {The Case for Flux},
year = {2015},
url = {https://medium.com/swlh/the-case-for-flux-379b7d1982c6},
}
@Misc{ReduxCore,
author = {Dan Abramov},
title = {Redux: Core Concepts},
howpublished = {Online},
year = {2018},
url = {https://redux.js.org/introduction/core-concepts},
}
@Misc{ReduxReact,
author = {Dan Abramov},
title = {{Redux}: Usage with {React}},
howpublished = {Online},
year = {2018},
url = {https://redux.js.org/basics/usage-with-react},
}
@Misc{FIO,
author = {Jens Axboe},
title = {Flexible I/O Tester},
howpublished = {Online},
url = {https://github.com/axboe/fio},
}
@Book{Caron2018,
author = {Caron, Jan},
publisher = {Forschungszentrum, Zentralbibliothek},
title = {Model-based reconstruction of magnetisation distributions in nanostructures from electron optical phase images [E-Book]},
year = {2018},
address = {Jülich},
series = {Schriften des Forschungszentrums Jülich. Reihe Schlüsseltechnologien / key technologies ;},
volume = {177},
groups = {weber:6},
keywords = {transmission electron microscopy},
pages = {1 Online-Ressource (XXI, 183 Seiten)},
url = {http://hdl.handle.net/2128/19740},
}
@Article{Guzzinati2019,
author = {Giulio Guzzinati and Wannes Ghielens and Christoph Mahr and Armand Béché and Andreas Rosenauer and Toon Calders and Jo Verbeeck},
journal = {Applied Physics Letters},
title = {Electron Bessel beam diffraction for precise and accurate nanoscale strain mapping},
year = {2019},
abstract = {Strain has a strong effect on the properties of materials and the performance of electronic devices. Their ever shrinking size translates into a constant demand for accurate and precise measurement methods with very high spatial resolution. In this regard, transmission electron microscopes are key instruments thanks to their ability to map strain with sub-nanometer resolution. Here we present a novel method to measure strain at the nanometer scale based on the diffraction of electron Bessel beams. We demonstrate that our method offers a strain sensitivity better than $2.5 \cdot 10^{-4}$ and an accuracy of $1.5 \cdot 10^{-3}$, competing with, or outperforming, the best existing methods with a simple and easy to use experimental setup.},
date = {2019-02-19},
doi = {10.1063/1.5096245},
eprint = {1902.06979v3},
eprintclass = {cond-mat.mtrl-sci},
eprinttype = {arXiv},
file = {:http\://arxiv.org/pdf/1902.06979v3:PDF},
journaltitle = {Appl. Phys. Lett. 114, 243501 (2019)},
keywords = {cond-mat.mtrl-sci, physics.optics},
}
@Article{Panova2019,
author = {Ouliana Panova and Colin Ophus and Christopher J. Takacs and Karen C. Bustillo and Luke Balhorn and Alberto Salleo and Nitash Balsara and Andrew M. Minor},
title = {Diffraction imaging of nanocrystalline structures in organic semiconductor molecular thin films},
journal = {Nature Materials},
year = {2019},
month = {jun},
doi = {10.1038/s41563-019-0387-3},
publisher = {Springer Science and Business Media {LLC}},
}
@Article{Gibson1997,
author = {J. M. Gibson and M. M. J. Treacy},
title = {Diminished Medium-Range Order Observed in Annealed Amorphous Germanium},
journal = {Physical Review Letters},
year = {1997},
volume = {78},
number = {6},
pages = {1074--1077},
month = {feb},
doi = {10.1103/physrevlett.78.1074},
publisher = {American Physical Society ({APS})},
}
@Article{Ophus_2019,
author = {Colin Ophus},
title = {Four-Dimensional Scanning Transmission Electron Microscopy (4D-{STEM}): From Scanning Nanodiffraction to Ptychography and Beyond},
journal = {Microscopy and Microanalysis},
year = {2019},
volume = {25},
number = {3},
pages = {563--582},
month = {may},
doi = {10.1017/s1431927619000497},
publisher = {Cambridge University Press ({CUP})},
}
@InProceedings{6980942,
author = {S. C. F. {Lin} and C. Y. {Wong} and G. {Jiang} and M. A. {Rahman} and N. M. {Kwok}},
title = {Radial fourier analysis ({{RFA}}) image descriptor},
booktitle = {2014 11th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD)},
year = {2014},
pages = {814-819},
month = {Aug},
doi = {10.1109/FSKD.2014.6980942},
issn = {null},
keywords = {data compression;Fourier analysis;Fourier transforms;frequency-domain analysis;image coding;image representation;spectral analysis;spectrum-based local image descriptor;radial Fourier analysis image descriptor;RFA image descriptor;Fourier transform;image gradient;spatial domain;frequency domain;transformed gradient frequency;low frequency Fourier coefficients;keypoint representation;image blurring;JPG compression;image description;local image patch spectral analysis;Lighting;Fourier transforms;Frequency-domain analysis;Performance evaluation;Image coding;Histograms;Spectral analysis},
}
@article{Lichte2008,
title = {Electron holography–basics and applications},
volume = {71},
doi = {10.1088/0034-4885/71/1/016102},
journal = {Rep. Prog. Phys.},
author = {Lichte, H. and Lehmann, M.},
year = {2008},
pages = {016102},
file = {Electron holography—basics and applications - IOPscience:/Users/migunov/Zotero/storage/7C3UUE82/meta\;jsessionid=3F5DA019F9A86C312BFD8889CFC17030.c2.iopscience.cld.iop.html:text/html;Lichte_H,Lehmann_M-E-holog-basics&app(2008).pdf:/Users/migunov/Zotero/storage/WRB52ACC/Lichte_H,Lehmann_M-E-holog-basics&app(2008).pdf:application/pdf}
}
@InProceedings{Schubert2018,
author = {Erich Schubert and Michael Gertz},
title = {Numerically stable parallel computation of (co-)variance},
booktitle = {Proceedings of the 30th International Conference on Scientific and Statistical Database Management - {SSDBM} 18},
year = {2018},
publisher = {{ACM} Press},
doi = {10.1145/3221269.3223036},
}
@misc{ophus_colin_2019_3592520,
author = {Ophus, Colin and
Savitzky, Benjamin},
title = {{Simulated calibration dataset for 4D scanning
transmission electron microscopy}},
month = dec,
year = 2019,
publisher = {Zenodo},
doi = {10.5281/zenodo.3592520},
url = {https://doi.org/10.5281/zenodo.3592520}
}
@misc{giulio_guzzinati_2019_2566137,
author = {Giulio Guzzinati and
Wannes Ghielens and
Christoph Mahr and
Armand Béché and
Andreas Rosenauer and
Toon Calders and
Jo Verbeeck},
title = {{Electron Bessel beam diffraction patterns, line
scan of Si/SiGe multilayer}},
month = feb,
year = 2019,
publisher = {Zenodo},
version = {v1},
doi = {10.5281/zenodo.2566137},
url = {https://doi.org/10.5281/zenodo.2566137}
}
@InCollection{Weber2020,
author = {Dieter Weber and Alexander Clausen and Rafal E. Dunin-Borkowski},
booktitle = {Handbook on Big Data and Machine Learning in the Physical Sciences},
publisher = {World Scientific},
title = {Next-Generation Information Technology Systems for Fast Detectors in Electron Microscopy},
year = {2020},
month = {mar},
pages = {83--120},
doi = {10.1142/9789811204579_0005},
eprint = {2003.11332v1},
url = {https://arxiv.org/abs/2003.11332},
}
@Article{Zeltmann2019,
author = {Steven E Zeltmann and Alexander Müller and Karen C Bustillo and Benjamin Savitzky and Lauren Hughes and Andrew M Minor and Colin Ophus},
title = {Patterned Probes for High Precision {4D-STEM} Bragg Measurements},
abstract = {Nanoscale strain mapping by four-dimensional scanning transmission electron microscopy (4D-STEM) relies on determining the precise locations of Bragg-scattered electrons in a sequence of diffraction patterns, a task which is complicated by dynamical scattering, inelastic scattering, and shot noise. These features hinder accurate automated computational detection and position measurement of the diffracted disks, limiting the precision of measurements of local deformation. Here, we investigate the use of patterned probes to improve the precision of strain mapping. We imprint a "bullseye" pattern onto the probe, by using a binary mask in the probe-forming aperture, to improve the robustness of the peak finding algorithm to intensity modulations inside the diffracted disks. We show that this imprinting leads to substantially improved strain-mapping precision at the expense of a slight decrease in spatial resolution. In experiments on an unstrained silicon reference sample, we observe an improvement in strain measurement precision from 2.7% of the reciprocal lattice vectors with standard probes to 0.3% using bullseye probes for a thin sample, and an improvement from 4.7% to 0.8% for a thick sample. We also use multislice simulations to explore how sample thickness and electron dose limit the attainable accuracy and precision for 4D-STEM strain measurements.},
date = {2019-07-11},
year = {2019},
doi = {10.1016/j.ultramic.2019.112890},
journal = {Ultramicroscopy},
eprint = {1907.05504v2},
eprintclass = {physics.app-ph},
eprinttype = {arXiv},
file = {:http\://arxiv.org/pdf/1907.05504v2:PDF},
keywords = {physics.app-ph, cond-mat.mtrl-sci},
}
@misc{strauch_achim_2021_5113449,
author = {Strauch, Achim and
Clausen, Alexander and
Weber, Dieter and
Müller-Caspary, Knut},
title = {{High-resolution {{4D STEM}} dataset of {{SrTiO3}} along
the [1 0 0] axis at high magnification}},
month = jul,
year = 2021,
note = {{Achim Strauch and Knut Müller-Caspary were
supported by funding from the Initiative and
Network Fund of the Helmholtz Association
(Germany) under contract VH-NG-1317 (moreSTEM
project). Knut Müller-Caspary acknowledges
support from Helmholtz within the project
"Ptychography 4.0" under contract ZT-I-0025.}},
publisher = {Zenodo},
doi = {10.5281/zenodo.5113449},
url = {https://doi.org/10.5281/zenodo.5113449}
}
@misc{strauch_achim_2021_5113235,
author = {Strauch, Achim and
Weber, Dieter and
Clausen, Alexander and
Müller-Caspary, Knut},
title = {{Synthetic 4D STEM dataset based on a SrTiO3
supercell with two additional artificial spatial
frequencies}},
month = jul,
year = 2021,
note = {{Achim Strauch and Knut Müller-Caspary were
supported by funding from the Initiative and
Network Fund of the Helmholtz Association
(Germany) under contract VH-NG-1317 (moreSTEM
project). Knut Müller-Caspary acknowledges
support from Helmholtz within the project
"Ptychography 4.0" under contract ZT-I-0025.}},
publisher = {Zenodo},
doi = {10.5281/zenodo.5113235},
url = {https://doi.org/10.5281/zenodo.5113235}
}
@misc{t_pennycook_2021_4476506,
author = {T. Pennycook},
title = {Graphene simulated dataset},
month = jan,
year = 2021,
publisher = {Zenodo},
doi = {10.5281/zenodo.4476506},
url = {https://doi.org/10.5281/zenodo.4476506}
}
@article{ROSE1976251,
title = {Nonstandard imaging methods in electron microscopy},
journal = {Ultramicroscopy},
volume = {2},
pages = {251-267},
year = {1976},
issn = {0304-3991},
doi = {https://doi.org/10.1016/S0304-3991(76)91538-2},
url = {https://www.sciencedirect.com/science/article/pii/S0304399176915382},
author = {H. Rose},
abstract = {A rigorous treatment of image formation, taking into account inelastic scattering and partially coherent illumination, is given for the CTEM. The results also hold for a STEM if the momentum vectors of the incident and outgoing waves are interchanged and the flight direction of the electrons is reversed. A generalized optical theorem is found which connects the anti-Friedel part of the elastic scattering amplitude with the squares of the elastic and inelastic scattering amplitudes. This theorem has important consequences for all approximation methods. For example, it shows that inelastic scattering influences the elastic scattering amplitude. It is further shown that the observed wings in optical diffractograms, obtained from micrographs of amorphous material taken using tilted beam illumination, can only be explained if double scattering (elastic and inelastic) is assumed. Hollow-cone illumination strongly suppresses the structural noise in the phase contrast image. The corresponding phase contrast transfer function (PCTF) is calculated for two different cone angles, assuming that no beam-limiting aperture is present. In addition, the PCTFs of a corrected microscope are calculated for two different illumination modes, one yielding negative and the other positive phase contrast. Finally, the contrast transfer has been investigated for a STEM operating with a split detector.}
}
@Comment{jabref-meta: databaseType:bibtex;}
@Comment{jabref-meta: grouping:
0 AllEntriesGroup:;
1 StaticGroup:Markings\;2\;1\;\;\;\;;
2 StaticGroup:weber:6\;2\;1\;\;\;\;;
}