ML-ED
Increased spatial resolution in electron detectors through machine learning
Abstract
Hybrid pixel detectors show great potential for use in Electron Microscopy, but poor spatial resolution - caused by large pixel size and multiple scattering in the sensor layer - are holding them back. The goal of this project is to use Machine Learning trained on simulation and measurement data to improve spatial resolution by determining the point where the electron hit the detector and assigning the signal to the correct pixel. This could enable the use of fast, radiation hard hybrid pixel detectors for diffraction experiments over a wide range of energies as well as extend the application to cryo-electron microscopy imaging of biological samples at ≤100 keV resulting as a combined diffraction/imaging detector. If successful, the models developed in this project would not be limited to the ones developed by PSI, but could be used for a wide range of hybrid pixel detectors.
People
Collaborators
Luis Barba Flores joined the SDSC in 2022 as Senior Data Scientist. He received a joined PhD in Computers Science in 2016 from the Université Libre de Bruxelles and Carleton University. He served as a postdoctoral researcher at ETH Zurich from 2016 to 2019, and then moved to EPFL Lausanne to work in the Machine Learning and Optimization Group until 2022. His research interests include distributed optimization algorithms, first-order optimization methods and their applications to Deep Learning models.
Carl holds a Ph.D in Mathematics from École des Ponts ParisTech and Université Gustave Eiffel in Paris. He has broad interests in statistics and stochastic control, and works on reinforcement learning, generative methods and time series forecasting, with applications in various domains such as energy, finance and physics. He worked with EDF R&D and Finance des Marchés de l’Energie (FiME) laboratory on applications of machine learning to risk management, including time series generation and deep hedging. He joined the SDSC in 2022 as a senior data scientist in the academic team at École Polytechnique Fédérale de Lausanne (EPFL).
Benjamín Béjar received a PhD in Electrical Engineering from Universidad Politécnica de Madrid in 2012. He served as a postdoctoral fellow at École Polytechnique Fédérale de Lausanne until 2017, and then he moved to Johns Hopkins University where he held a Research Faculty position until Dec. 2019. His research interests lie at the intersection of signal processing and machine learning methods, and he has worked on topics such as sparse signal recovery, time-series analysis, and computer vision methods with special emphasis on biomedical applications. Since 2021, Benjamin leads the SDSC office at the Paul Scherrer Institute in Villigen.
PI | Partners:
PSI, Electron Microscopy and Diffraction group:
- Dr. Elisabeth Müller
- Dr. Emiliya Poghosyan
- Dr. Erik Fröjdh
- Dr. Xie Xiangyu
description
Motivation
Hybrid pixel detectors have transformed data acquisition of synchrotrons and X-ray Free Electron Lasers and are good candidates for electron microscopy as well. However, at higher energies the incoming electron does not deposit all its energy in one pixel, but rather creates a track spanning several pixels (Figure 1) which reduces the spatial resolution.
Proposed Approach / Solution
The goal of the ML-ED project is to overcome the lack of resolution of HPDs using Machine Learning by identifying the impact points of the electrons on the sensor with pixel- or, for low energies, even sub-pixel resolution.
After hitting the silicon detector, the electrons scatter through the material, following a path that, although random, exhibits a learnable structure. To leverage this, we propose using convolutional neural networks (CNNs) to predict the electron paths from the images produced by the sensor (Figure 2). This neural network, combined with physics-based models that enforce prediction consistency, enables us to enhance the sensor’s resolution and achieve sub-pixel accuracy.
Impact
The increase in resolution benefits all currently available HPDs due to the shared nature of charge deposition and transport. There are especially applications in cryo-EM imaging of biological molecules and electron diffraction.
Presentation
Gallery
Annexe
Publications
- X. Xie, L. Barba Flores, B. Bejar Haro, A. Bergamaschi, E. Fröjdh, E. Müller, K. A. Paton, E. Poghosyan, C. Remlinger. “Enhancing spatial resolution in MÖNCH for electron microscopy via deep learning” Journal of Instrumentation, Volume 19, January 2024. Enhancing spatial resolution in MÖNCH for electron microscopy via deep learning - IOPscience
Additional resources
Bibliography
- J. P. van Schayck, E. van Genderen, E. Maddox, L. Roussel, H. Boulanger, E. Fröjdh, P. J Peters, R. B. Ravelli (2020). Sub-pixel electron detection using a convolutional neural network. Ultramicroscopy, 218, 113091. https://www.sciencedirect.com/science/article/pii/S0304399120302424
- S. Cartier, A. Bergamaschi, R. Dinapoli, D. Greiffenberg, I. Johnson, J. H. Jungmann, D. Mezza, A. Mozzanica, B. Schmitt, X. Shi. Micron resolution of MÖNCH and GOTTHARD, small pitch charge integrating detectors with single photon sensitivity, Journal of Instrumentation, Volume 9, May 2014. https://iopscience.iop.org/article/10.1088/1748-0221/9/05/C05027
- A. Bergamaschi, M. Andrä, R. Barten, C. Borca, M. Brückner, S. Chiriotti, R. Dinapoli, E. Fröjdh, D. Greiffenberg, T. Huthwelker, A. Kleibert, M. Langer, M. Lebugle, C. Lopez-Cuenca, D. Mezza, A. Mozzanica, J. Raabe, S. Redford, C. Ruder, V. Scagnoli, B. Schmitt, X. Shi, U. Staub, D. Thattil, G. Tinti, C. F. Vaz, S. Vetter, J. Vila-Comamala & J. Zhang. The MÖNCH Detector for Soft X-ray, High-Resolution, and Energy Resolved Applications, Synchrotron Radiation News, Volume 31, 2018 - Issue 6. https://www.tandfonline.com/doi/full/10.1080/08940886.2018.1528428
- S. Cartier, M. Kagias, A. Bergamaschi, Z. Wang, R. Dinapoli, A. Mozzanica, M. Ramilli, B. Schmitt, M. Brückner, E. Fröjdh, D. Greiffenberg, D. Mayilyan, D. Mezza, S. Redford, C. Ruder, L. Schädler, X. Shi, D. Thattil, G. Tinti, J. Zhang, M. Stampanoni. Micrometer-resolution imaging using MÖNCH: towards G2-less grating interferometry, Journal of Synchrotron Radiation 2016 Nov 1;23(Pt 6):1462-1473. Micrometer-resolution imaging using MÖNCH: towards G2-less grating interferometry
- L. M. Lohse, M. Vassholz, M. Töpperwien, T. Jentschke, A. Bergamaschi, S. Chiriotti, and T. Salditt. Spectral µCT with an energy resolving and interpolating pixel detector, Optics Express Vol. 28, Issue 7, pp. 9842-9859 (2020). https://opg.optica.org/oe/fulltext.cfm?uri=oe-28-7-9842
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