Skip to main content Accessibility help

Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization

  • Gary W. Paterson (a1), Robert W. H. Webster (a1), Andrew Ross (a1), Kirsty A. Paton (a1), Thomas A. Macgregor (a1), Damien McGrouther (a1), Ian MacLaren (a1) and Magnus Nord (a1) (a2)...


Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post-acquisition processing and visualization of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualization of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilizing data from a 256 × 256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterization of the structural properties of materials. These include the techniques of virtual detector imaging; higher-order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate a nanoscale lattice parameter mapping with a fractional precision ≤6 × 10−4 (0.06%).

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the or variations. ‘’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization
      Available formats

      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization
      Available formats

      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization
      Available formats


This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (, which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

Corresponding author

*Authors for correspondence: Gary W. Paterson, E-mail:; Magnus Nord, E-mail:


Hide All

Current address: Institute of Physics, Johannes Gutenberg Universität Mainz, Staudingerweg 7, 55128 Mainz, Germany.

Current address: Department of Physics, Norwegian University of Science and Technology, Trondheim 7491, Norway.



Hide All
Aso, R, Kan, D, Shimakawa, Y & Kurata, H (2013). Atomic level observation of octahedral distortions at the perovskite oxide heterointerface. Sci Rep 3, 2214. doi:10.1038/srep02214.
Azough, F, Cernik, RJ, Schaffer, B, Kepaptsoglou, D, Ramasse, QM, Bigatti, M, Ali, A, MacLaren, I, Barthel, J, Molinari, M, Baran, JD, Parker, SC & Freer, R (2016). Tungsten bronze barium neodymium titanate (Ba6−3nNd8+2nTi18O54): An intrinsic nanostructured material and its defect distribution. Inorg Chem 55, 33383350. doi:10.1021/acs.inorgchem.5b02594.
Ballabriga, R, Alozy, J, Blaj, G, Campbell, M, Fiederle, M, Frojdh, E, Heijne, EHM, Llopart, X, Pichotka, M, Procz, S, Tlustos, L & Wong, W (2013). The Medipix3RX: A high resolution, zero dead-time pixel detector readout chip allowing spectroscopic imaging. J Instrum 8, C02016C02016. doi:10.1088/1748-0221/8/02/c02016.
Bashir, A, Millar, RW, Gallacher, K, Paul, DJ, Darbal, AD, Stroud, R, Ballabio, A, Frigerio, J, Isella, G & MacLaren, I (2019). Strain analysis of a Ge micro disk using precession electron diffraction. J Appl Phys 126, 235701. doi:10.1063/1.5113761.
Béché, A, Rouvière, J, Barnes, J & Cooper, D (2011). Dark field electron holography for strain measurement. Ultramicroscopy 111, 227238. doi:10.1016/j.ultramic.2010.11.030.
Béché, A, Rouvière, JL, Barnes, JP & Cooper, D (2013). Strain measurement at the nanoscale: Comparison between convergent beam electron diffraction, nano-beam electron diffraction, high resolution imaging and dark field electron holography. Ultramicroscopy 131, 1023. doi:10.1016/j.ultramic.2013.03.014.
Béché, A, Rouvière, JL, Clément, L & Hartmann, JM (2009). Improved precision in strain measurement using nanobeam electron diffraction. Appl Phys Lett 95, 123114. doi:10.1063/1.3224886.
Borisevich, AY, Ovchinnikov, OS, Chang, HJ, Oxley, MP, Yu, P, Seidel, J, Eliseev, EA, Morozovska, AN, Ramesh, R, Pennycook, SJ & Kalinin, SV (2010). Mapping octahedral tilts and polarization across a domain wall in BiFeO3 from Z-contrast scanning transmission electron microscopy image atomic column shape analysis. ACS Nano 4, 60716079. doi:10.1021/nn1011539.
Bücker, R, Hogan-Lamarre, P, Mehrabi, P, Schulz, EC, Bultema, LA, Gevorkov, Y, Brehm, W, Yefanov, O, Oberthür, D, Kassier, GH & Dwayne Miller, RJ (2020). Serial protein crystallography in an electron microscope. Nat Commun 11, 996. doi:10.1038/s41467-020-14793-0.
Clabbers, MTB, van Genderen, E, Wan, W, Wiegers, EL, Gruene, T & Abrahams, JP (2017). Protein structure determination by electron diffraction using a single three-dimensional nanocrystal. Acta Crystallogr D 73, 738748. doi:10.1107/S2059798317010348.
Clausen, A, Weber, D, @probonopd, Caron, J, Nord, M, Müller-Caspary, K, Ophus, C, Dunin-Borkowski, R, Ruzaeva, K, Chandra, R, Shin, J & van Schyndel, J (2019). Libertem/libertem: 0.2.2. Available at 10.5281/zenodo.3489385.
Collette, A (2013). Python and HDF5. Sebastopol USA: O'reilly Media, Inc.
Cooper, D, Barnes, J, Hartmann, J, Béché, A & Rouvière, J (2009). Dark field electron holography for quantitative strain measurements with nanometer-scale spatial resolution. Appl Phys Lett 95, 053501. doi:10.1063/1.3196549.
Cooper, D, Denneulin, T, Bernier, N, Béché, A & Rouvière, J-L (2016). Strain mapping of semiconductor specimens with nm-scale resolution in a transmission electron microscope. Micron 80, 145165. doi:10.1016/j.micron.2015.09.001.
Dask Development Team (2016). Dask: Library for dynamic task scheduling. Available at
de la Peña, F, Ostasevicius, T, Fauske, VT, Burdet, P, Prestat, E, Jokubauskas, P, Nord, M, Sarahan, M, MacArthur, KE, Johnstone, DN, Taillon, J, Caron, J, Migunov, V, Furnival, T, Eljarrat, A, Mazzucco, S, Aarholt, T, Walls, M, Slater, T, Winkler, F, Martineau, B, Donval, G, McLeod, R, Hoglund, ER, Alxneit, I, Hjorth, I, Henninen, T, Zagonel, LF, Garmannslund, A, & 5ht2 (2018) hyperspy/hyperspy: HyperSpy 1.3.1. Available at 10.5281/zenodo.1221347.
Donoho, DL & Johnstone, IM (1994). Ideal spatial adaptation by wavelet shrinkage. Biometrika 81, 425455. doi:10.1093/biomet/81.3.425.
Egerton, RF (2011). Electron Energy-Loss Spectroscopy in the Electron Microscope, 3rd ed. New York: Springer.
EMD authors (2019). Electron Microscopy Datasets: An HDF5-based interchange file format for electron microscopy data and metadata. Available at (retrieved June 3, 2018).
Emslie, AG (1934). Scattering of electrons by stibnite and galena. Phys Rev 45, 4346. doi:10.1103/PhysRev.45.43.
Findlay, SD, Shibata, N, Sawada, H, Okunishi, E, Kondo, Y & Ikuhara, Y (2010). Dynamics of annular bright field imaging in scanning transmission electron microscopy. Ultramicroscopy 110, 903923. doi:10.1016/j.ultramic.2010.04.004.
fpd demos devs (2018). Notebook examples for the fpd package. Available at (retrieved June 3, 2018).
fpd devs (2015). FPD: Fast pixelated detector data storage, analysis and visualisation. Available at (retrieved February 6, 2018).
Friedel, G (1913). Sur les symétries cristallines que peut révéler la diffraction des rayons röntgen. C R Acad Sci 157, 15331536.
Gammer, C, Ozdol, VB, Liebscher, CH & Minor, AM (2015). Diffraction contrast imaging using virtual apertures. Ultramicroscopy 155, 110. doi:10.1016/j.ultramic.2015.03.015.
Glazer, AM (1972). The classification of tilted octahedra in perovskites. Acta Crystallogr B 28, 33843392. doi:10.1107/S0567740872007976.
Gouillart, E, Nunez-Iglesias, J & van der Walt, S (2016). Analyzing microtomography data with Python and the scikit-image library. Adv Struct Chem Imaging 2, 18. doi:10.1186/s40679-016-0031-0.
Guzzinati, G, Ghielens, W, Mahr, C, Béché, A, Rosenauer, A, Calders, T & Verbeeck, J (2019). Electron Bessel beam diffraction for precise and accurate nanoscale strain mapping. Appl. Phys. Lett. 114, 243501 doi:
Hallsteinsen, I, Moreau, M, Grutter, A, Nord, M, Vullum, P-E, Gilbert, DA, Bolstad, T, Grepstad, JK, Holmestad, R, Selbach, SM, N'Diaye, AT, Kirby, BJ, Arenholz, E & Tybell, T (2016). Concurrent magnetic and structural reconstructions at the interface of (111)-oriented La0.7Sr0.3MnO3/LaFeO3. Phys Rev B 94, 201115. doi:10.1103/PhysRevB.94.201115.
Hammel, M & Rose, H (1995). Optimum rotationally symmetric detector configurations for phase-contrast imaging in scanning transmission electron microscopy. Ultramicroscopy 58, 403415. doi:10.1016/0304-3991(95)00007-N.
Hart, MJ, Bassiri, R, Borisenko, KB, Véron, M, Rauch, EF, Martin, IW, Rowan, S, Fejer, MM & MacLaren, I (2016). Medium range structural order in amorphous tantala spatially resolved with changes to atomic structure by thermal annealing. J Non-Cryst Solids 438, 1017. doi:10.1016/j.jnoncrysol.2016.02.005.
Hartel, P, Rose, H & Dinges, C (1996). Conditions and reasons for incoherent imaging in STEM. Ultramicroscopy 63, 93114. doi:10.1016/0304-3991(96)00020-4.
Huang, F-T, Gloter, A, Chu, M-W, Chou, FC, Shu, GJ, Liu, L-K, Chen, CH & Colliex, C (2010). Scanning transmission electron microscopy using selective high-order Laue zones: Three-dimensional atomic ordering in sodium cobaltate. Phys Rev Lett 105, 125502. doi:10.1103/PhysRevLett.105.125502.
Hunter, JD (2007). Matplotlib: A 2D graphics environment. Comput Sci Eng 9, 9095. doi:10.1109/MCSE.2007.55.
Hÿtch, M, Houdellier, F, Hüe, F & Snoeck, E (2008). Nanoscale holographic interferometry for strain measurements in electronic devices. Nature 453, 10861089. doi:10.1038/nature07049.
Hÿtch, MJ, Snoeck, E & Kilaas, R (1998). Quantitative measurement of displacement and strain fields from HREM micrographs. Ultramicroscopy 74, 131146. doi:10.1016/S0304-3991(98)00035-7.
Jin, Z, Nori, S, Lee, Y-F, Kumar, D, Wu, F, Prater, JT, Kim, KW & Narayan, J (2015). Strain induced room temperature ferromagnetism in epitaxial magnesium oxide thin films. J Appl Phys 118, 165309. doi:10.1063/1.4934498.
Johnstone, DN, Crout, P, Høgås, S, Martineau, B, Smeets, S, Laulainen, J, Collins, S, Morzy, J, Prestat, E, Ånes, H, phillipcrout, Doherty, T, Ostasevicius, T & Bergh, T (2019). pyxem/pyxem: pyxem 0.9.2. Available at
Jones, E, Oliphant, T, Peterson, P (2001). SciPy: Open source scientific tools for Python. Available at (retrieved October 30, 2018).
Jones, L, Varambhia, A, Sawada, H & Nellist, PD (2018). An optical configuration for fastidious STEM detector calibration and the effect of the objective-lens pre-field. J Microsc 270, 176187. doi:10.1111/jmi.12672.
Jones, PM, Rackham, GM & Steeds, JW (1977). Higher-order Laue zone effects in electron-diffraction and their use in lattice-parameter determination. Proc R Soc Lond A 354, 197. doi:10.1098/rspa.1977.0064.
Kim, Y-M, Pennycook, SJ & Borisevich, AY (2017). Quantitative comparison of bright field and annular bright field imaging modes for characterization of oxygen octahedral tilts. Ultramicroscopy 181, 17. doi:10.1016/j.ultramic.2017.04.020.
Klinger, M (2017). More features, more tools, more CrysTBox. J Appl Crystallogr 50, 12261234. doi:10.1107/S1600576717006793.
Kluyver, T, Ragan-Kelley, B, Pérez, F, Granger, B, Bussonnier, M, Frederic, J, Kelley, K, Hamrick, J, Grout, J, Corlay, S, Ivanov, P, Avila, D, Abdalla, S & Willing, C (2016). Jupyter notebooks: A publishing format for reproducible computational workflows. In Positioning and Power in Academic Publishing: Players, Agents and Agendas, Loizides, F & Schmidt, B (Eds.), pp. 8790. IOS Press.
Kolb, U, Gorelik, T, Kübel, C, Otten, M & Hubert, D (2007). Towards automated diffraction tomography: Part I–Data acquisition. Ultramicroscopy 107, 507513. doi:10.1016/j.ultramic.2006.10.007.
Krajnak, M, McGrouther, D, Maneuski, D, O'Shea, V & McVitie, S (2016). Pixelated detectors and improved efficiency for magnetic imaging in STEM differential phase contrast. Ultramicroscopy 165, 4250. doi:10.1016/j.ultramic.2016.03.006.
Krakow, W & Howland, LA (1976). A method for producing hollow cone illumination electronically in the conventional transmission microscope. Ultramicroscopy 2, 5367. doi:10.1016/S0304-3991(76)90416-2.
LeBeau, JM, D'Alfonso, AJ, Findlay, SD, Stemmer, S & Allen, LJ (2009). Quantitative comparisons of contrast in experimental and simulated bright-field scanning transmission electron microscopy images. Phys Rev B 80, 174106. doi:10.1103/PhysRevB.80.174106.
Lewis, LH, Marrows, CH & Langridge, S (2016). Coupled magnetic, structural, and electronic phase transitions in FeRh. J Phys D Appl Phys 49, 323002. doi:10.1088/0022-3727/49/32/323002.
MacLaren, I, Frutos-Myro, E, McGrouther, D, McFadzean, S, Weiss, JK, Cosart, D, Portillo, J, Robins, A, Nicolopoulos, S, del Busto, EN & Skogeby, R (2020). A comparison of a direct electron detector and a high speed video camera for scanning precession electron diffraction phase and orientation mapping. Microsc Microanal. doi:10.1017/S1431927620024411.
MacLaren, I & Richter, G (2009). Structure and possible origins of stacking faults in gamma-yttrium disilicate. Philos Mag 89, 169181. doi:10.1080/14786430802562132.
MacLaren, I, Wang, L, Morris, O, Craven, AJ, Stamps, RL, Schaffer, B, Ramasse, QM, Miao, S, Kalantari, K, Sterianou, I & Reaney, IM (2013). Local stabilisation of polar order at charged antiphase boundaries in antiferroelectric (Bi0.85Nd0.15)(Ti0.1Fe0.9)O3. APL Mater 1, 021102. doi:10.1063/1.4818002.
Mahr, C, Müller-Caspary, K, Ritz, R, Simson, M, Grieb, T, Schowalter, M, Krause, FF, Lackmann, A, Soltau, H, Wittstock, A & Rosenauer, A (2019). Influence of distortions of recorded diffraction patterns on strain analysis by nano-beam electron diffraction. Ultramicroscopy 196, 7482. doi:10.1016/j.ultramic.2018.09.010.
Martineau, BH, Johnstone, DN, van Helvoort, ATJ, Midgley, PA & Eggeman, AS (2019). Unsupervised machine learning applied to scanning precession electron diffraction data. Adv Struct Chem Imaging 5, 3. doi:10.1186/s40679-019-0063-3.
Mawson, T, Nakamura, A, Petersen, TC, Shibata, N, Sasakif, H, Paganin, DM, Morgan, MJ & Findlay, S (2020). Suppressing dynamical diffraction artefacts in differential phase contrast scanning transmission electron microscopy of long-range electromagnetic fields via precession. arXiv:2002.01595.
McMullan, G, Cattermole, D, Chen, S, Henderson, R, Llopart, X, Summerfield, C, Tlustos, L & Faruqi, A (2007). Electron imaging with Medipix2 hybrid pixel detector. Ultramicroscopy 107, 401413. doi:10.1016/j.ultramic.2006.10.005.
McVitie, S, McGrouther, D, McFadzean, S, MacLaren, DA, O'Shea, KJ & Benitez, MJ (2015). Aberration corrected Lorentz scanning transmission electron microscopy. Ultramicroscopy 152, 5762. doi:10.1016/j.ultramic.2015.01.003.
Midgley, PA & Eggeman, AS (2015). Precession electron diffraction: A topical review. IUCrJ 2, 126136. doi:10.1107/S2052252514022283.
Mir, JA, Clough, R, MacInnes, R, Gough, C, Plackett, R, Shipsey, I, Sawada, H, MacLaren, I, Ballabriga, R, Maneuski, D, O'Shea, V, McGrouther, D & Kirkland, AI (2017). Characterisation of the Medipix3 detector for 60 and 80 keV electrons. Ultramicroscopy 182, 4453. doi:10.1016/j.ultramic.2017.06.010.
Mugnaioli, E, Gorelik, T & Kolb, U (2009). “Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. Ultramicroscopy 109, 758765. doi:10.1016/j.ultramic.2009.01.011.
Naden, AB, O'Shea, KJ & MacLaren, DA (2018). Evaluation of crystallographic strain, rotation and defects in functional oxides by the moiré effect in scanning transmission electron microscopy. Nanotechnology 29, 165704. doi:10.1088/1361-6528/aaae50.
Nord, M, Ross, A, McGrouther, D, Barthel, J, Moreau, M, Hallsteinsen, I, Tybell, T & MacLaren, I (2019). Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films. Phys Rev Mater 3, 063605. doi:10.1103/PhysRevMaterials.3.063605.
Nord, M, Vullum, PE, MacLaren, I, Tybell, T & Holmestad, R (2017). Atomap: A new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting. Adv Struct Chem Imaging 3, 9. doi:10.1186/s40679-017-0042-5.
Nord, M, Webster, RWH, Paton, KA, McVitie, S, McGrouther, D, MacLaren, I & Paterson, GW (2020). Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage. Microsc. Microanal. 26(4), 653666. doi: 10.1017/S1431927620001713.
Oliphant, TE (2006). A guide to NumPy. USA: Trelgol Publishing.
Oliphant, TE (2007). Python for scientific computing. Comput Sci Eng 9, 1020. doi:10.1109/MCSE.2007.58.
Ophus, C (2019). Four-dimensional scanning transmission electron microscopy (4D-STEM): From scanning nanodiffraction to ptychography and beyond. Microsc Microanal 25, 563582. doi:10.1017/S1431927619000497.
Parkin, SSP, Kaiser, C, Panchula, A, Rice, PM, Hughes, B, Samant, M & Yang, S-H (2004). Giant tunnelling magnetoresistance at room temperature with MgO (100) tunnel barriers. Nat Mater 3, 862867. doi:10.1038/nmat1256.
Paterson, GW, Macauley, GM, Li, Y, Macêdo, R, Ferguson, C, Morley, SA, Rosamond, MC, Linfield, EH, Marrows, CH, Stamps, RL & McVitie, S (2019). Heisenberg pseudo-exchange and emergent anisotropies in field-driven pinwheel artificial spin ice. Phys Rev B 100, 174410. doi:10.1103/PhysRevB.100.174410.
Paterson, GW, Webster, RWH, Ross, A, Paton, KA, Macgregor, TA, McGrouther, D, MacLaren, I & Nord, M (2020) Dataset. 10.5281/zenodo.3903517
Pekin, TC, Gammer, C, Ciston, J, Minor, AM & Ophus, C (2017). Optimizing disk registration algorithms for nanobeam electron diffraction strain mapping. Ultramicroscopy 176, 170176. doi:10.1016/j.ultramic.2016.12.021.
Peng, L-M & Gjønnes, JK (1989). Bloch-wave channeling and HOLZ effects in high-energy electron diffraction. Acta Crystallogr A 45, 699703. doi:10.1107/S0108767389005982.
Pennycook, S & Jesson, D (1991). High-resolution Z-contrast imaging of crystals. Ultramicroscopy 37, 1438. doi:10.1016/0304-3991(91)90004-P.
pixStem devs (2015). pixStem: Analysis of pixelated STEM data. Available at (retrieved October 3, 2018).
Plackett, R, Horswell, I, Gimenez, EN, Marchal, J, Omar, D & Tartoni, N (2013). Merlin: A fast versatile readout system for Medipix3. J Instrum 8, C01038. doi:10.1088/1748-0221/8/01/C01038.
Ponchut, C, Collet, E, Hervé, C, Caer, TL, Cerrai, J, Siron, L, Dabin, Y & Ribois, JF (2015). SMARTPIX, a photon-counting pixel detector for synchrotron applications based on Medipix3RX readout chip and active edge pixel sensors. J Instrum 10, C01019C01019. doi:10.1088/1748-0221/10/01/c01019.
Rauch, EF, Portillo, J, Nicolopoulos, S, Bultreys, D, Rouvimov, S & Moeck, P (2010). Automated nanocrystal orientation and phase mapping in the transmission electron microscope on the basis of precession electron diffraction. Z Kristallogr 225, 103109. doi:10.1524/zkri.2010.1205.
Rauch, EF & Veron, M (2005). Coupled microstructural observations and local texture measurements with an automated crystallographic orientation mapping tool attached to a TEM. Materialwiss Werkst 36, 552556. doi:10.1002/mawe.200500923.
Rauch, EF & Véron, M (2014). Virtual dark-field images reconstructed from electron diffraction patterns. Eur Phys J Appl Phys 66, 10701. doi:10.1051/epjap/2014130556.
Rouvière, JL, Béché, A, Martin, Y, Denneulin, T & Cooper, D (2013). Improved strain precision with high spatial resolution using nanobeam precession electron diffraction. Appl Phys Lett 103, 241913. doi:10.1063/1.4829154.
Rouvière, JL & Sarigiannidou, E (2005). Theoretical discussions on the geometrical phase analysis. Ultramicroscopy 106, 117. doi:10.1016/j.ultramic.2005.06.001.
Savitzky, BH, Hughes, LA, Zeltmann, SE, Brown, HG, Zhao, S, Pelz, PM, Barnard, ES, Donohue, J, DaCosta, LR, Pekin, TC, Kennedy, E, Janish, MT, Schneider, MM, Herring, P, Gopal, C, Anapolsky, A, Ercius, P, Scott, M, Ciston, J, Minor, AM & Ophus, C (2020). py4DSTEM: A software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets. arXiv:2003.09523.
Savitzky, BH, Zeltmann, S, Barnard, E, lerandc, Brown, HG, Henderson, M & Ginsburg, D (2019). py4dstem/py4DSTEM: DOI release.
Schaffer, B, Grogger, W & Kothleitner, G (2004). Automated spatial drift correction for EFTEM image series. Ultramicroscopy 102, 2736. doi:10.1016/j.ultramic.2004.08.003.
Schaffer, M, Schaffer, B & Ramasse, Q (2012). Sample preparation for atomic-resolution STEM at low voltages by FIB. Ultramicroscopy 114, 6271. doi:10.1016/j.ultramic.2012.01.005.
Shibata, N, Kohno, Y, Findlay, SD, Sawada, H, Kondo, Y & Ikuhara, Y (2010). New area detector for atomic-resolution scanning transmission electron microscopy. Microscopy 59, 473479. doi:10.1093/jmicro/dfq014.
Somnath, S, Smith, CR, Laanait, N, Vasudevan, RK, Ievlev, A, Belianinov, A, Lupini, AR, Shankar, M, Kalinin, SV & Jesse, S (2019). USID and pycroscopy: Open frameworks for storing and analyzing spectroscopic and imaging data. arXiv:1903.09515.
Spence, J & Koch, C (2001). On the measurement of dislocation core periods by nanodiffraction. Philos Mag B 81, 17011711. doi:10.1080/13642810108223113.
Spence, J, Zuo, J & Lynch, J (1989). On the HOLZ contribution to STEM lattice images formed using high-angle dark-field detectors. Ultramicroscopy 31, 233239. doi:10.1016/0304-3991(89)90218-0.
Su, D & Zhu, Y (2010). Scanning moiré fringe imaging by scanning transmission electron microscopy. Ultramicroscopy 110, 229233. doi:10.1016/j.ultramic.2009.11.015.
Tate, MW, Purohit, P, Chamberlain, D, Nguyen, KX, Hovden, R, Chang, CS, Deb, P, Turgut, E, Heron, JT, Schlom, DG, Ralph, DC, Fuchs, GD, Shanks, KS, Philipp, HT, Muller, DA & Gruner, SM (2016). High dynamic range pixel array detector for scanning transmission electron microscopy. Microsc Microanal 22, 237249. doi:10.1017/S1431927615015664.
Temple, RC, Almeida, TP, Massey, JR, Fallon, K, Lamb, R, Morley, SA, Maccherozzi, F, Dhesi, SS, McGrouther, D, McVitie, S, Moore, TA & Marrows, CH (2018 a). Antiferromagnetic-ferromagnetic phase domain development in nanopatterned FeRh islands. Phys Rev Mater 2, 104406. doi:10.1103/PhysRevMaterials.2.104406.
Temple, RC, Almeida, TP, Massey, JR, Fallon, K, Lamb, R, Morley, SA, Maccherozzi, F, Dhesi, SS, McGrouther, D, McVitie, S, Moore, TA & Marrows, CH (2018 b). 4D STEM data set supporting “Antiferromagnetic-ferromagnetic phase domain development in nanopatterned FeRh islands”. University of Glasgow, Enlighten: Research Data.
The HDF Group (1997–2018). Hierarchical Data Format, version 5. Available at
Thong, JTL, Sim, KS & Phang, JCH (2001). Single-image signal-to-noise ratio estimation. Scanning 23, 328336. doi:10.1002/sca.4950230506.
Tick, T & Campbell, M (2011). TSV processing of Medipix3 wafers by CEA-LETI: A progress report. J Instrum 6, C11018C11018. doi:10.1088/1748-0221/6/11/c11018.
Tsai, C-Y, Chang, Y-C, Lobato, I, Van Dyck, D & Chen, F-R (2016). Hollow cone electron imaging for single particle 3D reconstruction of proteins. Sci Rep 6, 27701. doi:10.1038/srep27701.
Van Aert, S, Batenburg, KJ, Rossell, MD, Erni, R & Van Tendeloo, G (2011). Three-dimensional atomic imaging of crystalline nanoparticles. Nature 470, 374377. doi:10.1038/nature09741.
van der Walt, S, Schönberger, JL, Nunez-Iglesias, J, Boulogne, F, Warner, JD, Yager, N, Gouillart, E, Yu, T & the scikit-image contributors (2014). scikit-image: Image processing in Python. PeerJ 2, e453. doi:10.7717/peerj.453.
Vincent, R & Midgley, P (1994). Double conical beam-rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy 53, 271282. doi:10.1016/0304-3991(94)90039-6.
Voyles, PM & Muller, DA (2002). Fluctuation microscopy in the STEM. Ultramicroscopy 93, 147159. doi:10.1016/S0304-3991(02)00155-9.
Wang, Y, Salzberger, U, Sigle, W, Suyolcu, YE & van Aken, PA (2016). Oxygen octahedra picker: A software tool to extract quantitative information from STEM images. Ultramicroscopy 168, 4652. doi:10.1016/j.ultramic.2016.06.001.
Yakovlev, S & Libera, M (2008). Dose-limited spectroscopic imaging of soft materials by low-loss EELS in the scanning transmission electron microscope. Micron 39, 734740. doi:10.1016/j.micron.2007.10.019.
Yang, H, Jones, L, Ryll, H, Simson, M, Soltau, H, Kondo, Y, Sagawa, R, Banba, H, MacLaren, I & Nellist, PD (2015). 4D STEM: High efficiency phase contrast imaging using a fast pixelated detector. J Phys Conf Ser 644, 012032. doi:10.1088/1742-6596/644/1/012032.
Yang, Q, Sha, J, Wang, L, Wang, J & Yang, D (2006). MgO nanostructures synthesized by thermal evaporation. Mater Sci Eng C 26, 10971101. doi:10.1016/j.msec.2005.09.082.
Zeltmann, SE, Müller, A, Bustillo, KC, Savitzky, B, Hughes, L, Minor, AM & Ophus, C (2020). Patterned probes for high precision 4D-STEM bragg measurements. Ultramicroscopy 209, 112890. doi:10.1016/j.ultramic.2019.112890.
Zhu, J-G & Park, C (2006). Magnetic tunnel junctions. Mater Today 9, 3645. doi:/10.1016/S1369-7021(06)71693-5.


Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post-Acquisition Data Processing, Visualization, and Structural Characterization

  • Gary W. Paterson (a1), Robert W. H. Webster (a1), Andrew Ross (a1), Kirsty A. Paton (a1), Thomas A. Macgregor (a1), Damien McGrouther (a1), Ian MacLaren (a1) and Magnus Nord (a1) (a2)...


Altmetric attention score

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed.