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Multi-Dimensional Electron Microscopy

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Presentation on theme: "Multi-Dimensional Electron Microscopy"— Presentation transcript:

1 Multi-Dimensional Electron Microscopy
Big Data, Multimodality & Dynamic Models in Biomedical Imaging Wednesday 9th March 2016, Isaac Newton Institute, Cambridge Multi-Dimensional Electron Microscopy Rowan K. Leary Department of Materials Science and Metallurgy, University of Cambridge Junior Research Fellow, Clare College hardware advances compressed sensing machine learning image analysis spectroscopy tomography ‘computational microscopy’ diffraction big data dynamics reconstruction algorithms Chem. Phys. Lett (2015) Electron Microscopy Group

2 Burgeoning New Era A flood of multi-dimensional ‘big data’
Yet extremely limited data in many aspects Electron beam sensitivity Hardware constraints Want the salient information content J.M. Thomas, R. Leary, A.S. Eggeman, P.A. Midgley Chem. Phys. Lett (2015)

3 Tracking single atom random walks
Dynamic Imaging + Spatio-Temporal Denoising Successive frames often highly correlated Form (approx.) low rank ‘Casorati matrix’ Seek low rank to regularize noisy/incomplete sequences Tracking single atom random walks “PGURE-SVT” Raw Poisson Gaussian Unbiased Risk Estimator Singular Value Thresholding T. Furnival, R. Leary & P. Midgley (submitted)

4 Sparsity is prevalent at the nanoscale
Electron Tomography + Compressed Sensing ‘nano-container’ Sparsity is prevalent at the nanoscale Seek a sparse solution subject to data fidelity Leary et al. Ultramicroscopy 2013, 131, 70-91 Saghi et al. Nano Letters 2011, 11,

5 Multi-dimensional ‘analytical’ electron tomogram
Multi-Dimensional Tomography + Machine Learning 100 nm Multi-dimensional ‘analytical’ electron tomogram Silver nanocube localised surface plasmon resonances visualised in 3D Non-negative matrix factorisation Compressed sensing reconstruction Pertinence to plasmonic: Bio-sensing Photo-thermal cancer treatment many more… Spectroscopic (EDX+EELS) Dynamic (time-resolved) Crystallographic Vector fields Nicoletti et al. Nature 502 (2013) 80-84 Leary & Midgley MRS Bulletin (in preparation)

6 Multi-dimensional ‘analytical’ electron tomogram
Multi-Dimensional Tomography + Machine Learning Multi-dimensional ‘analytical’ electron tomogram Silver nanocube localised surface plasmon resonances visualised in 3D Non-negative matrix factorisation Compressed sensing reconstruction Pertinence to plasmonic: Bio-sensing Photo-thermal cancer treatment many more… Spectroscopic (EDX+EELS) Dynamic (time-resolved) Crystallographic Vector fields Nicoletti et al. Nature 502 (2013) 80-84 Leary & Midgley MRS Bulletin (in preparation)

7 Pixel-Wise Sub-Sampled Acquisition + Inpainting
Conventional acquisition: record signal at every pixel New thinking: sub-sample computational recovery Electron tomography: Saghi et al. Advanced Structural & Chemical Imaging 1 (2015) 7 Atomic-Resolution Imaging + Spectroscopy: (manuscripts in preparation) Quentin Ramasse, Patricia Abellan, Dorothea Mücke-Herzberg, Iain Godfrey, Michael Sarahan (SuperSTEM) Zineb Saghi, Martin Benning, Rowan Leary & Paul Midgley (University of Cambridge) Jacki Ma, Gitta Kutyniok (TU Berlin) Andrew Stevens, Nigel Browning (Duke University, PNNL)

8 Acknowledgements Tom Furnival Francisco de la Peña Tomas Ostasevicius
Duncan Johnstone Josh Einsle Sean Collins Giorgio Divitini Lech Staniewicz Jon Barnard Alex Eggeman Cate Ducati John Meurig Thomas Paul Midgley Martin Benning Carola-Bibiane Schönlieb Anders Hansen Bogdan Roman Department of Applied Mathematics and Theoretical Physics, University of Cambridge Jackie Ma Gitta Kutyniok Institute of Mathematics, Technische Universität Berlin Electron Microscopy Group, Department of Materials Science and Metallurgy University of Cambridge Daniel Holland Andy Sederman Department of Chemical Engineering and Biotechnology, University of Cambridge Quentin Ramasse Patricia Abellan Dorothea Mücke-Herzberg Iain Godfrey Michael Sarahan Clare College Cambridge Andrew Stevens Nigel Browning Duke University, Pacific Northwest National Laboratory superSTEM, STFC Daresbury Laboratories

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