Data Science
Modern transmission electron microscopy methods increasingly rely on ultrafast detectors and mathematical algorithms to form images. They allow to obtain information about the specimen beyond the limits of traditional electron optics by processing tremendous amounts of data in a short period of time, on the scale of several gigabytes per second. We develop scalable high-performance processing software that can keep up with such data rates as well as tools to manage large data collections with ease.
Research topics:
- High-throughput live and offline data processing with a focus on 4D STEM
- Computational imaging with a focus on phase reconstruction / ptychography
- Metadata and FAIR data for electron microscopy: Practical interoperability with real-world software
- Reproducibility in electron microscopy
- Automation and remote control
- Research Software Engineering
points of contact
Alexander Clausen
Technical staff at ER-C-1
- er-c
- er-c-1
Room 2014
Publications
Bibliography
Bangun, A., Baumeister, P. F., Clausen, A., Weber, D., & Dunin-Borkowski, R. E. (2023, March). Wigner Distribution Deconvolution Adaptation for Live Ptychography Reconstruction. Microscopy and Microanalysis, 29, 994–1008. doi:10.1093/micmic/ozad021
Bangun, A., Melnyk, O., Marz, B., Diederichs, B., Clausen, A., Weber, D., . . . Muller-Caspary, K. (2022). Inverse Multislice Ptychography by Layer-Wise Optimisation and Sparse Matrix Decomposition. IEEE Transactions on Computational Imaging, 8, 996–1011. doi:10.1109/tci.2022.3218993
Bladt, E., Pivak, Y., Park, J., Weber, D., Jo, J., Basak, S., . . . Sun, H. (2023, July). Metal Electroplating/Stripping and 4D STEM Analysis Revealed by Liquid Phase Transmission Electron Microscopy. Microscopy and Microanalysis, 29, 1304–1305. doi:10.1093/micmic/ozad067.667
Clausen, A., Bryan, M., Pilipp, V., & Weber, D. (2021 – 2023). LiberTEM/LiberTEM-live: 0.1 – 0.2.1. LiberTEM/LiberTEM-live: 0.1 – 0.2.1. Zenodo. doi:10.5281/ZENODO.4916315
Clausen, A., Weber, D., Bryan, M., Ruzaeva, K., Migunov, V., Dagenborg, S., . . . Dunin-Borkowski, R. E. (2018 – 2024). LiberTEM/LiberTEM: 0.1 – 0.14.1. LiberTEM/LiberTEM: 0.1 – 0.14.1. Zenodo. doi:10.5281/ZENODO.1477847
Clausen, A., Weber, D., Ruzaeva, K., Bryan, M., Müller-Caspary, K., & Dunin-Borkowski, R. E. (2020 – 2024). LiberTEM/LiberTEM-blobfinder: 0.4 – 0.6.1. LiberTEM/LiberTEM-blobfinder: 0.4 – 0.6.1. Zenodo. doi:10.5281/ZENODO.3663436
Clausen, A., Weber, D., Ruzaeva, K., Migunov, V., Baburajan, A., Bahuleyan, A., . . . Dunin-Borkowski, R. (2020, June). LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy. Journal of Open Source Software, 5, 2006. doi:10.21105/joss.02006
Landers, D., Clancy, I., Dunin-Borkowski, R. E., Weber, D., & Stewart, A. (2023, August). TEMGYM Advanced: Software for electron lens aberrations and parallelised electron ray tracing. Ultramicroscopy, 250, 113738. doi:10.1016/j.ultramic.2023.113738
Landers, D., Clancy, I., Dunin-Borkowski, R. E., Weber, D., & Stewart, A. A. (2023, June). TEMGYM Advanced – NanoMi lens characterisation. Micron, 169, 103450. doi:10.1016/j.micron.2023.103450
Landers, D., Clancy, I., Weber, D., Dunin-Borkowski, R. E., & Stewart, A. (2023, July). TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation. Journal of Applied Crystallography, 56, 1267–1276. doi:10.1107/s1600576723005174
Oberaigner, M., Clausen, A., Weber, D., Kothleitner, G., Dunin-Borkowski, R. E., & Knez, D. (2023, January). Online Thickness Determination with Position Averaged Convergent Beam Electron Diffraction using Convolutional Neural Networks. Microscopy and Microanalysis, 29, 427–436. doi:10.1093/micmic/ozac050
Park, J., Dutta, S., Sun, H., Jo, J., Karanth, P., Weber, D., . . . Eichel, R.‐A. (2024, April). Toward Quantitative Electrodeposition via In Situ Liquid Phase Transmission Electron Microscopy: Studying Electroplated Zinc Using Basic Image Processing and 4D STEM. Small Methods, 8. doi:10.1002/smtd.202400081
Rosi, P., Clausen, A., Weber, D., Tavabi, A. H., Frabboni, S., Tiemeijer, P., . . . Grillo, V. (2023, January). Automatic Alignment of an Orbital Angular Momentum Sorter in a Transmission Electron Microscope Using a Convolutional Neural Network. Microscopy and Microanalysis, 29, 408–417. doi:10.1017/s143192762201248x
Strauch, A., Clausen, A., Weber, D., & Müller-Caspary, K. (2021). High-resolution 4D STEM dataset of SrTiO3 along the [1 0 0] axis at high magnification. High-resolution 4D STEM dataset of SrTiO3 along the [1 0 0] axis at high magnification. Zenodo. doi:10.5281/ZENODO.5113449
Strauch, A., Weber, D., Clausen, A., & Müller-Caspary, K. (2021). Synthetic 4D STEM dataset based on a SrTiO3 supercell with two additional artificial spatial frequencies. Synthetic 4D STEM dataset based on a SrTiO3 supercell with two additional artificial spatial frequencies. Zenodo. doi:10.5281/ZENODO.5113235
Strauch, A., Weber, D., Clausen, A., Lesnichaia, A., Bangun, A., März, B., . . . Müller-Caspary, K. (2021, August). Live Processing of Momentum-Resolved STEM Data for First Moment Imaging and Ptychography. Microscopy and Microanalysis, 27, 1078–1092. doi:10.1017/s1431927621012423
Weber, D., Clausen, A., & Dunin-Borkowski, R. E. (2020, March). Next-Generation Information Technology Systems for Fast Detectors in Electron Microscopy. In Handbook on Big Data and Machine Learning in the Physical Sciences(pp. 83–120). World Scientific. doi:10.1142/9789811204579_0005
Weber, D., Ehrig, S., Schropp, A., Clausen, A., Achilles, S., Hoffmann, N., . . . Schroer, C. G. (2024, February). Live Iterative Ptychography. Microscopy and Microanalysis, 30, 103–117. doi:10.1093/mam/ozae004
Weber, D., Landers, D., Huang, C., Liberti, E., Poghosyan, E., Bryan, M., . . . Dunin-Borkowski, R. E. (2024). Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin. Calibrating coordinate system alignment in a scanning transmission electron microscope using a digital twin. arXiv. doi:10.48550/ARXIV.2403.08538
Weber, D., Lesnichaia, A., Strauch, A., Clausen, A., Bangun, A., Melnyk, O., . . . Müller-Caspary, K. (2021). Ptychography 4.0: 0.1.0. Ptychography 4.0: 0.1.0. Zenodo. doi:10.5281/ZENODO.5055126