Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C)

Physics of Nanoscale Systems (ER-C-1)

Data Science

Modern transmission electron microscopy methods increasingly rely on ultrafast detectors and mathematical algorithms to form images. They allow scientists 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
Reseach Data Management

points of contact

Dr. Dieter Weber

Scientist at ER-C

er-c

Building 05.7 /
Room 2014

+49 2461/61-85118

E-Mail

Alexander Clausen

Technical staff at ER-C-1

er-c
er-c-1

Building 05.7 /
Room 2014

+49 2461/61-85116

E-Mail

Selected Publications

Recent 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

Last Modified: 17.09.2025