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Signal Processing Tools for Electron Microscopy
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.ORCID iD: 0000-0002-6550-0087
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The detection of weak signals in noisy data is a problem which occurs across various disciplines. Here, the signal of interest is the spectral signature of the electron magnetic chiral dichroism (EMCD) effect. In principle, EMCD allows for the measurement of local magnetic structures in the electron microscope, its spatial resolution, versatility and low hardware requirements giving it an eminent position among competing measurement techniques. However, experimental shortcomings as well as intrinsically low signal to noise ratio render its measurement challenging to the present day.   

This thesis explores how posterior data processing may aid the analysis of various data from the electron microscope. Following a brief introduction to different signals arising in the microscope and a yet briefer survey of the state of the art of EMCD measurements, noise removal strategies are presented. Afterwards, gears are shifted to discuss the separation of mixed signals into their physically meaningful source components based on their assumed mathematical characteristics, so called blind source separation (BSS).    

A data processing workflow for detecting weak signals in noisy spectra is derived from these considerations, ultimately culminating in several demonstrations of the extraction of EMCD signals. While the focus of the thesis does lie on data processing strategies for EMCD detection, the approaches presented here are similarly applicable in other situations. Related topics such as the general analysis of hyperspectral images using BSS methods or the fast analysis of large data sets are also discussed.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2018. , p. 60
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1672
National Category
Physical Sciences Computer Sciences Other Mathematics
Identifiers
URN: urn:nbn:se:uu:diva-348264ISBN: 978-91-513-0345-1 (print)OAI: oai:DiVA.org:uu-348264DiVA, id: diva2:1197003
Public defence
2018-06-12, Å2001, Ångströmlaboratoriet, Lägerhyddsvägen 1, Uppsala, 09:00 (English)
Opponent
Supervisors
Available from: 2018-05-18 Created: 2018-04-11 Last updated: 2018-10-08
List of papers
1. Detecting magnetic ordering with atomic size electron probes
Open this publication in new window or tab >>Detecting magnetic ordering with atomic size electron probes
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2016 (English)In: Advanced Structural and Chemical ImagingArticle in journal (Refereed) Published
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348236 (URN)
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11
2. Magnetic measurements with atomic-plane resolution
Open this publication in new window or tab >>Magnetic measurements with atomic-plane resolution
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2016 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 12672Article in journal (Refereed) Published
Abstract [en]

Rapid development of magnetic nanotechnologies calls for experimental techniques capable of providing magnetic information with subnanometre spatial resolution. Available probes of magnetism either detect only surface properties, such as spin-polarized scanning tunnelling microscopy, magnetic force microscopy or spin-polarized low-energy electron microscopy, or they are bulk probes with limited spatial resolution or quantitativeness, such as X-ray magnetic circular dichroism or classical electron magnetic circular dichroism (EMCD). Atomic resolution EMCD methods have been proposed, although not yet experimentally realized. Here, we demonstrate an EMCD technique with an atomic size electron probe utilizing a probe-corrected scanning transmission electron microscope in its standard operation mode. The crucial element of the method is a ramp in the phase of the electron beam wavefunction, introduced by a controlled beam displacement. We detect EMCD signals with atomic-plane resolution, thereby bringing near-atomic resolution magnetic circular dichroism spectroscopy to hundreds of laboratories worldwide.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-315933 (URN)10.1038/ncomms12672 (DOI)000391876300001 ()27578421 (PubMedID)
Funder
Swedish Research CouncilGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyKnut and Alice Wallenberg Foundation, 2015.0060The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2018-04-11Bibliographically approved
3. Can we use PCA to detect small signals in noisy data?
Open this publication in new window or tab >>Can we use PCA to detect small signals in noisy data?
2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 172, p. 40-46Article in journal (Refereed) Published
Abstract [en]

Principal component analysis (PCA) is among the most commonly applied dimension reduction techniques suitable to denoise data. Focusing on its limitations to detect low variance signals in noisy data, we discuss how statistical and systematical errors occur in PCA reconstructed data as a function of the size of the data set, which extends the work of Lichtert and Verbeeck, (2013) [16]. Particular attention is directed towards the estimation of bias introduced by PCA and its influence on experiment design. Aiming at the denoising of large matrices, nullspace based denoising (NBD) is introduced.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348242 (URN)10.1016/j.ultramic.2016.10.008 (DOI)000390600200005 ()27794219 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of Technology
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-09-06Bibliographically approved
4. Analysis of electron energy loss spectroscopy data using geometric extraction methods
Open this publication in new window or tab >>Analysis of electron energy loss spectroscopy data using geometric extraction methods
2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 174, p. 14-26Article in journal (Refereed) Published
National Category
Atom and Molecular Physics and Optics Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-328271 (URN)10.1016/j.ultramic.2016.12.014 (DOI)000403342200003 ()28012371 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Göran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of Technology
Available from: 2016-12-16 Created: 2017-12-20 Last updated: 2018-04-11Bibliographically approved
5. Tensor decompositions for the analysis of atomic resolution electron energy loss spectra
Open this publication in new window or tab >>Tensor decompositions for the analysis of atomic resolution electron energy loss spectra
2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 175, p. 36-45Article in journal (Refereed) Published
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-329139 (URN)10.1016/j.ultramic.2016.12.025 (DOI)000403342500003 ()28110262 (PubMedID)
Funder
Swedish Research CouncilGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-01-11 Created: 2017-10-10 Last updated: 2018-04-11Bibliographically approved
6. Localization of magnetic circular dichroic spectra in transmission electron microscopy experiments with atomic plane resolution
Open this publication in new window or tab >>Localization of magnetic circular dichroic spectra in transmission electron microscopy experiments with atomic plane resolution
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2017 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, no 17, article id 174412Article in journal (Refereed) Published
Abstract [en]

Inelastic electron scattering is a consequence of mostly Coulomb interaction between electrons in the sample and electron beam and, as such, it is a nonlocal event. In atomic resolution experiments, it thus opens the following question: How far is the origin of the inelastic scattering signal that is observed when the electron beam is passing nearby an atomic column or plane? We analyze computationally the delocalization of the magnetic signal in electron magnetic circular dichroism (EMCD) experiments in the so-called three-beam orientation, allowing one to image individual atomic planes. We compare the classical EMCD setup using the double-difference procedure (DD-EMCD) to a recently introduced atomic plane resolution EMCD (APR-EMCD) geometry, assuming the same probe size. We observe a strong localization of the EMCD signal to the closest atomic plane, confirming the potential of EMCD to study an evolution of magnetic properties near surfaces or interfaces with atomic plane resolution. The localization of the EMCD signal is remarkably higher than the localization of the nonmagnetic component of the inelastic scattering cross section. We also analyze double-channeling effects and find them particularly strong for the DD-EMCD method, while for APR-EMCD they appear to be minor. The DD-EMCD signal, on the other hand, appears to be more robust with respect to sample thickness than that of the APR-EMCD.

Place, publisher, year, edition, pages
AMER PHYSICAL SOC, 2017
National Category
Physical Sciences Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-325336 (URN)10.1103/PhysRevB.95.174412 (DOI)000401223700004 ()
Funder
Swedish Research CouncilGöran Gustafsson Foundation for Research in Natural Sciences and Medicine
Available from: 2017-06-30 Created: 2017-06-30 Last updated: 2018-04-11Bibliographically approved
7. Towards sub-nanometer real-space observation of spin and orbital magnetism at the Fe/MgO interface
Open this publication in new window or tab >>Towards sub-nanometer real-space observation of spin and orbital magnetism at the Fe/MgO interface
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2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 44802Article in journal (Refereed) Published
Abstract [en]

While the performance of magnetic tunnel junctions based on metal/oxide interfaces is determined by hybridization, charge transfer, and magnetic properties at the interface, there are currently only limited experimental techniques with sufficient spatial resolution to directly observe these effects simultaneously in real-space. In this letter, we demonstrate an experimental method based on Electron Magnetic Circular Dichroism (EMCD) that will allow researchers to simultaneously map magnetic transitions and valency in real-space over interfacial cross-sections with sub-nanometer spatial resolution. We apply this method to an Fe/MgO bilayer system, observing a significant enhancement in the orbital to spin moment ratio that is strongly localized to the interfacial region. Through the use of first-principles calculations, multivariate statistical analysis, and Electron Energy-Loss Spectroscopy (EELS), we explore the extent to which this enhancement can be attributed to emergent magnetism due to structural confinement at the interface. We conclude that this method has the potential to directly visualize spin and orbital moments at buried interfaces in magnetic systems with unprecedented spatial resolution.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2017
National Category
Atom and Molecular Physics and Optics Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-320197 (URN)10.1038/srep44802 (DOI)000397288700001 ()28338011 (PubMedID)
Funder
Swedish Research Council, C0367901The Swedish Foundation for International Cooperation in Research and Higher Education (STINT), IG2009-2017Knut and Alice Wallenberg Foundation, 2013.0020 2012.0031eSSENCE - An eScience Collaboration
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2019-04-24Bibliographically approved
8. The usage of data compression for the background estimation of electron energy loss spectra
Open this publication in new window or tab >>The usage of data compression for the background estimation of electron energy loss spectra
2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 181, p. 117-122Article in journal (Refereed) Published
Abstract [en]

Quantitative analysis of noisy electron spectrum images requires a robust estimation of the underlying background signal. We demonstrate how modern data compression methods can be used as a tool for achieving an analysis result less affected by statistical errors or to speed up the background estimation. In particular, we demonstrate how a multilinear singular value decomposition (MLSVD) can be used to enhance elemental maps obtained from a complex sample measured with energy electron loss spectroscopy. Furthermore, the usage of vertex component analysis (VCA) for a basis vector centered estimation of the background is demonstrated. Arising computational benefits in terms of model accuracy and computational costs are studied.

Place, publisher, year, edition, pages
ELSEVIER SCIENCE BV, 2017
National Category
Physical Sciences Engineering and Technology
Identifiers
urn:nbn:se:uu:diva-336443 (URN)10.1016/j.ultramic.2017.05.017 (DOI)000411170800014 ()28549246 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Göran Gustafsson Foundation for Research in Natural Sciences and Medicine
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-04-11Bibliographically approved
9. Fully nonlocal inelastic scattering computations for spectroscopical transmission electron microscopy methods
Open this publication in new window or tab >>Fully nonlocal inelastic scattering computations for spectroscopical transmission electron microscopy methods
2017 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 96, no 24, article id 245121Article in journal (Refereed) Published
Abstract [en]

The complex interplay of elastic and inelastic scattering amenable to different levels of approximation constitutes the major challenge for the computation and hence interpretation of TEM-based spectroscopical methods. The two major approaches to calculate inelastic scattering cross sections of fast electrons on crystals—Yoshioka-equations-based forward propagation and the reciprocal wave method—are founded in two conceptually differing schemes—a numerical forward integration of each inelastically scattered wave function, yielding the exit density matrix, and a computation of inelastic scattering matrix elements using elastically scattered initial and final states (double channeling). Here, we compare both approaches and show that the latter is computationally competitive to the former by exploiting analytical integration schemes over multiple excited states. Moreover, we show how to include full nonlocality of the inelastic scattering event, neglected in the forward propagation approaches, at no additional computing costs in the reciprocal wave method. Detailed simulations show in some cases significant errors due to the z-locality approximation and hence pitfalls in the interpretation of spectroscopical TEM results.

National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-339794 (URN)10.1103/PhysRevB.96.245121 (DOI)000417831800004 ()
Funder
Swedish Research CouncilGöran Gustafsson Foundation for Research in Natural Sciences and MedicineEU, Horizon 2020, 715620
Available from: 2018-02-23 Created: 2018-02-23 Last updated: 2018-04-11Bibliographically approved
10. Unmixing hyperspectral data by using signal subspace sampling
Open this publication in new window or tab >>Unmixing hyperspectral data by using signal subspace sampling
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2017 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 182, p. 205-211Article in journal (Refereed) Published
Abstract [en]

This paper demonstrates how Signal Subspace Sampling (SSS) is an effective pre-processing step for Non-negative Matrix Factorization (NMF) or Vertex Component Analysis (VCA). The approach allows to uniquely extract non-negative source signals which are orthogonal in at least one observation channel, respectively. It is thus well suited for processing hyperspectral images from X-ray microscopy, or other emission spectroscopies, into its non-negative source components. The key idea is to resample the given data so as to satisfy better the necessity and sufficiency conditions for the subsequent NMF or VCA. Results obtained both on an artificial simulation study as well as based on experimental data from electronmicroscopy are reported. 

Place, publisher, year, edition, pages
ELSEVIER SCIENCE BV, 2017
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:uu:diva-340709 (URN)10.1016/j.ultramic.2017.07.009 (DOI)000413436500026 ()28711769 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation, 2015.0060
Available from: 2018-02-02 Created: 2018-02-02 Last updated: 2018-04-11Bibliographically approved
11. Local low rank denoising for enhanced atomic resolution imaging
Open this publication in new window or tab >>Local low rank denoising for enhanced atomic resolution imaging
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2018 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 187, p. 34-42Article in journal (Refereed) Published
Abstract [en]

Atomic resolution imaging and spectroscopy suffers from inherently low signal to noise ratios often prohibiting the interpretation of single pixels or spectra. We introduce local low rank (LLR) denoising as tool for efficient noise removal in scanning transmission electron microscopy (STEM) images and electron energy-loss (EEL) spectrum images. LLR denoising utilizes tensor decomposition techniques, in particular the multilinear singular value decomposition (MLSVD), to achieve a denoising in a general setting largely independent of the signal features and data dimension, by assuming that the signal of interest is of low rank in segments of appropriately chosen size. When applied to STEM images of graphene, LLR denoising suppresses statistical noise while retaining fine image features such as scan row-wise distortions, possibly related to rippling of the graphene sheet and consequent motion of atoms. When applied to EEL spectra, LLR denoising reveals fine structures distinguishing different lattice sites in the spinel system CoFe2O4.

Place, publisher, year, edition, pages
Elsevier, 2018
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-348246 (URN)10.1016/j.ultramic.2018.01.012 (DOI)000428131200005 ()
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-06-04Bibliographically approved
12. On the usage of ICA for the analysis of EELS and EDX data
Open this publication in new window or tab >>On the usage of ICA for the analysis of EELS and EDX data
(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348251 (URN)
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11
13. Low dose STEM imaging via inpainting of regularly undersampledimages
Open this publication in new window or tab >>Low dose STEM imaging via inpainting of regularly undersampledimages
(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348253 (URN)
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11
14. Real space mapping of magnetism at atomic resolution using APR-EMCD
Open this publication in new window or tab >>Real space mapping of magnetism at atomic resolution using APR-EMCD
(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348257 (URN)
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11
15. Blind identification of magnetic signals in electron magnetic chiral dichroism using independent component analysis
Open this publication in new window or tab >>Blind identification of magnetic signals in electron magnetic chiral dichroism using independent component analysis
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2018 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 195, p. 129-135Article in journal (Refereed) Published
Abstract [en]

Electron magnetic chiral dichroism (EMCD) is a promising technique to investigate local magnetic structures in the electron microscope. However, recognition of the EMCD signal, or also finding optimal parameter settings for given materials and sample orientations typically requires extensive simulations to aid the experiment. Here, we discuss how modern data processing techniques, in particular independent component analysis, can be used to identify magnetic signals in an unsupervised manner from energy filtered transmission electron microscopy (EFTEM) images. On the background of the recent advent of 4D scanning transmission electron microscopy, we discuss how this data processing may enable simultaneous tracking of all three spatial components of the magnetic momenta for arbitrary materials and several sample orientations without the previous need of complementary simulations.

National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348259 (URN)10.1016/j.ultramic.2018.08.021 (DOI)000450060100016 ()
Funder
Swedish Research CouncilEU, FP7, Seventh Framework Programme, 320832
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-12-19Bibliographically approved
16. Data fusion approaches for electron microscopy
Open this publication in new window or tab >>Data fusion approaches for electron microscopy
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(English)Manuscript (preprint) (Other academic)
National Category
Physical Sciences
Identifiers
urn:nbn:se:uu:diva-348262 (URN)
Available from: 2018-04-11 Created: 2018-04-11 Last updated: 2018-04-11

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