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Author |
Nord, M.; Verbeeck, J. |
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Title |
Towards Reproducible and Transparent Science of (Big) Electron Microscopy Data Using Version Control |
Type |
P1 Proceeding |
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Year |
2019 |
Publication |
Microscopy and microanalysis
T2 – Microscopy & Microanalysis 2019, 4-8 August, 2019, Portland, Oregon |
Abbreviated Journal |
Microsc Microanal |
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Volume  |
25 |
Issue |
S2 |
Pages |
232-233 |
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Keywords |
P1 Proceeding; Electron microscopy for materials research (EMAT) |
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Publication Date |
2019-08-05 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
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Approved |
Most recent IF: 1.891 |
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Call Number |
EMAT @ emat @c:irua:164058 |
Serial |
5377 |
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Author |
Nord, M.; Verbeeck, J. |
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Title |
Open Source Development Tools for Robust and Reproducible Electron Microscopy Data Analysis |
Type |
P3 |
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Year |
2019 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
25 |
Issue |
S2 |
Pages |
138-139 |
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Keywords |
P3; Electron Microscopy for Materials Science (EMAT) ; |
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Publication Date |
2019-08-05 |
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Edition |
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ISSN |
1431-9276 |
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Additional Links |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
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Approved |
Most recent IF: 1.891 |
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Call Number |
EMAT @ emat @ |
Serial |
5378 |
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Author |
Pennycook, T.J.; Martinez, G.T.; O'Leary, C.M.; Yang, H.; Nellist, P.D. |
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Title |
Efficient Phase Contrast Imaging via Electron Ptychography, a Tutorial |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
25 |
Issue |
S2 |
Pages |
2684-2685 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Publication Date |
2019-08-06 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record |
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no |
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Call Number |
EMAT @ emat @c:irua:172444 |
Serial |
6424 |
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Author |
Nord, M.; Webster, R.W.H.; Paton, K.A.; McVitie, S.; McGrouther, D.; MacLaren, I.; Paterson, G.W. |
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Title |
Fast pixelated detectors in scanning transmission electron microscopy. Part I: data acquisition, live processing, and storage |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
26 |
Issue |
4 |
Pages |
Pii S1431927620001713-666 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
The use of fast pixelated detectors and direct electron detection technology is revolutionizing many aspects of scanning transmission electron microscopy (STEM). The widespread adoption of these new technologies is impeded by the technical challenges associated with them. These include issues related to hardware control, and the acquisition, real-time processing and visualization, and storage of data from such detectors. We discuss these problems and present software solutions for them, with a view to making the benefits of new detectors in the context of STEM more accessible. Throughout, we provide examples of the application of the technologies presented, using data from a Medipix3 direct electron detector. Most of our software are available under an open source licence, permitting transparency of the implemented algorithms, and allowing the community to freely use and further improve upon them. |
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Wos |
000555537900004 |
Publication Date |
2020-07-06 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
4 |
Open Access |
OpenAccess |
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Notes |
; The performance of this work was mainly supported by the Engineering and Physical Sciences Research Council (EPSRC) of the UK via the project “Fast Pixel Detectors: a paradigm shift in STEM imaging” (grant no. EP/M009963/1). G.W.P. received additional support from the EPSRC under grant no. EP/M024423/1. M.N. received additional support for this work from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 838001. The studentship of R.W.H.W. was supported by the EPSRC Doctoral Training Partnership grant no. EP/N509668/1. S.McV. was supported by EPSRC grant no. EP/M024423/1. I.M. was supported by EPSRC grant no. EP/M009963/1. The studentship of K.A.P. was funded entirely by the UK Science and Technology Facilities Council (STFC) Industrial CASE studentship “Next2 TEM Detection” (no. ST/P002471/1) with Quantum Detectors Ltd. as the industrial partner. D.McG. was also supported by EPSRC grant no. EP/M009963/1. As an inventor of intellectual property related to the MERLIN detector hardware, he is a beneficiary of the license agreement between the University of Glasgow and Quantum Detectors Ltd. The development of the integration of TopSpin with the Merlin readout of the Medipix3 camera has been performed with the aid of financial assistance from the EPSRC under grant no. EP/R511705/1 and through direct collaboration between NanoMEGAS and Quantum Detectors Ltd. ; |
Approved |
Most recent IF: 2.8; 2020 IF: 1.891 |
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Call Number |
UA @ admin @ c:irua:171185 |
Serial |
6518 |
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Author |
Paterson, G.W.; Webster, R.W.H.; Ross, A.; Paton, K.A.; Macgregor, T.A.; McGrouther, D.; MacLaren, I.; Nord, M. |
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Title |
Fast pixelated detectors in scanning transmission electron microscopy. part II : post-acquisition data processing, visualization, and structural characterization |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
26 |
Issue |
5 |
Pages |
944-963 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
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 x 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 x 10(-4) (0.06%). |
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Wos |
000576859800011 |
Publication Date |
2020-09-04 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
3 |
Open Access |
OpenAccess |
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Notes |
; G.W.P. and M.N. were the principal authors of the fpd and pixStem libraries reported herein (details of all contributions are documented in the repositories) and have made all of these available under open source licence GPLv3 for the benefit of the community. R.W.H.W., A.R., and K.A.P. have also made contributions to the source codes in these libraries. G.W.P and M.N. have led the data acquisition and analysis, and the drafting of this manuscript. The performance of this work was mainly supported by Engineering and Physical Sciences Research Council (EPSRC) of the UK via the project “Fast Pixel Detectors: a paradigm shift in STEM imaging” (Grant No. EP/M009963/1). G.W.P. received additional support from the EPSRC under Grant No. EP/M024423/1. M.N. received additional support for this work from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 838001. R.W.H.W., A.R., K.A.P., T.A.M., D.McG., and I.M. have all contributed either through acquisition and analysis of data or through participation in the revision of the manuscript. The studentships of R.W.H.W. and T.A.M. were supported by the EPSRC Doctoral Training Partnership Grant No. EP/N509668/1. I.M. and D.McG. were supported by EPSRC Grant No. EP/M009963/1. The studentship of K.A.P. was funded entirely by the UK Science and Technology Facilities Council (STFC) Industrial CASE studentship “Next2 TEM Detection” (No. ST/ P002471/1) with Quantum Detectors Ltd. as the industrial partner. As an inventor of intellectual property related to the MERLIN detector hardware, D.McG. is a beneficiary of the license agreement between the University of Glasgow and Quantum Detectors Ltd. We thank Diamond Quantum Detectors Ltd. for Medipix3 detector support; Dr. Bruno Humbel from Okinawa Institute of Science and Technology; and Dr. Caroline Kizilyaprak from the University of Lausanne for providing the liver sample; Dr. Ingrid Hallsteinsen and Prof. Thomas Tybell from the Norwegian University of Science and Technology (NTNU) for providing the La0.7Sr0.3MnO3/LaFeO3/SrTiO3 sample shown in Figure 4; and NanoMEGAS for the loan of the DigiSTAR precession system and TopSpin acquisition software. The development of the integration of TopSpin with the Merlin readout of the Medipix3 camera has been performed with the aid of financial assistance from the EPSRC under Grant No. EP/R511705/1 and through direct collaboration between NanoMEGAS and Quantum Detectors Ltd. ; |
Approved |
Most recent IF: 2.8; 2020 IF: 1.891 |
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Call Number |
UA @ admin @ c:irua:172695 |
Serial |
6519 |
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Author |
Esteban, D.A.; Vanrompay, H.; Skorikov, A.; Béché, A.; Verbeeck, J.; Freitag, B.; Bals, S. |
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Title |
Fast electron low dose tomography for beam sensitive materials |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
27 |
Issue |
S1 |
Pages |
2116-2118 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Publication Date |
2021-07-30 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: 1.891 |
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Call Number |
EMAT @ emat @c:irua:183278 |
Serial |
6813 |
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Author |
Neelisetty, K.K.; Kumar C.N., S.; Kashiwar, A.; Scherer, T.; Chakravadhanula, V.S.K.; Kuebel, C. |
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Title |
Novel thin film lift-off process for in situ TEM tensile characterization |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Microscopy And Microanalysis |
Abbreviated Journal |
Microsc Microanal |
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Volume |
27 |
Issue |
S1 |
Pages |
216-217 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Publication Date |
2021-07-30 |
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ISSN |
1431-9276 |
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Additional Links |
UA library record |
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Impact Factor |
1.891 |
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
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Approved |
Most recent IF: 1.891 |
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Call Number |
UA @ admin @ c:irua:183617 |
Serial |
6873 |
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