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Bibliography
I'm a PhD candidate at the Graduate School of Frontier Sciences at the University of Tokyo. I received my bachelor's degree in philosophy in 2022 and my master's degree in science in 2024, both from the University of Tokyo.
I'm interested in developing new image processing algorithms for electron microscopy imaging. Previously, I published papers about a fast noise-removal algorithm for high spatiotemporal-resolution imaging [link] and a Poisson noise-removal algorithm for pulse-count imaging [link]. I'm recently working on developing a deconvolution algorithm for 3D STEM imaging [link]. [CV]
Education
Education
Apr. 2024–Present The University of Tokyo, Graduate School of Frontier Science, PhD course
Oct. 2022–Mar. 2024 The University of Tokyo, Graduate School of Frontier Science, Master course
Apr. 2018–Sep. 2022 The University of Tokyo, Faculty of Letters
Publication
Publication
T. Shimomiya, T. Kusumi, Y. Yokoyama, M. Uesugi, A. Takeuchi, Y. Sada, H. Shouno, M. Okada, "Computed Tomography Reconstruction Algorithm Using Markov Random Field Model," under review. https://doi.org/10.48550/arXiv.2605.11637
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, "Three-dimensional deconvolution for large-angle illumination annular dark-field scanning transmission electron microscopy depth sectioning," under review.
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, T. Mullarkey, J. M. Bekkevold, J. J. P. Peters, L. Jones, N. Shibata, and M. Okada, "New Poisson denoising method for pulse-count STEM imaging," Ultramicroscopy, 264, 2024, 113996. https://doi.org/10.1016/j.ultramic.2024.113996
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, N. Shibata, and M. Okada, "Fast Reconstruction of Scanning Transmission Electron Microscopy Images Using Markov Random Field Model," Ultramicroscopy, 253, 2023, 113811. https://doi.org/10.1016/j.ultramic.2023.113811
Conference Presentations
Conference Presentations
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, "Three-dimensional deconvolution for ADF-STEM depth sectioning imaging," The 21st International Microscopy Congress 2026, Liverpool, UK, September 2026. (Poster, Abstract reviewed)
T. Kusumi, S. Sasano, R. Ishikawa, N. Shibata, and M. Okada, “Aberration correction for large-illumination angle ADF-STEM depth-sectioning imaging,” The 82nd Annual Meeting of the Japanese Society of Microscopy, Miyagi, Japan, May 2026. (Oral)
T. Futazuka, R. Ishikawa, K. Kawahara, T. Kusumi, M. Hanai, N. Shibata, “Total third-degree squared variation regularization for noise reduction of ultrafast atomic-resolution STEM images” The 82nd Annual Meeting of the Japanese Society of Microscopy, Miyagi, Japan, May 2026. (Oral, Co-author)
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, “Characterization of surface and sub-surface atomic structures by three-dimensional deconvolution for ADF-STEM depth sectioning imaging,” MRS Spring Meeting, Honolulu, Hawaii, USA, April 2025. (Oral, Abstract reviewed)
T. Shimomiya, T. Kusumi, Y. Yokoyama, M. Uesugi, A. Takeuchi, Y. Sada, H. Shouno, M. Okada, "Computed Tomography Reconstruction Algorithm Using Markov Random Field Model," The Physical Society of Japan 2026 Spring Meeting, online, March 2026. (Oral, Co-author)
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, “Three-dimensional Deconvolution Algorithm for ADF-STEM Depth Sectioning Imaging,” MRS Fall Meeting, Boston, Massachusetts, USA, December 2025. (Oral, Abstract reviewed)
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, “Three-dimensional deconvolution for large-angle illumination ADF-STEM depth sectioning,” Microscopy and Microanalysis 2025, Salt Lake City, Utah, USA, July 2025. https://doi.org/10.1093/mam/ozaf048.712 (Oral, Abstract reviewed)
J. M. Bekkevold, T. Kusumi, G. Varnavides, J. J. P. Peters, R. Ishikawa, N. Shibata, and L. Jones, “Segmented Detector Digitization and the Role of Denoising for Increasing Achievable Temporal Resolution in Phase Characterization,” Microscopy and Microanalysis 2025, Salt Lake City, Utah, USA, July 2025. https://doi.org/10.1093/mam/ozaf048.1127 (Oral, Abstract reviewed, Co-author)
T. Kusumi, H. Ueda, T. Futazuka, M. Hanai, S. Katakami, K. Kawahara, R. Ishikawa, N. Shibata, and M. Okada, "3D deconvolution for ADF-STEM depth-sectioning imaging," The 81st Annual Meeting of the Japanese Society of Microscopy, Fukuoka, Japan, June 2025. (Oral)
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, N. Shibata, and M. Okada, "Live Denoising for High Spatiotemporal-resolution STEM Imaging Using Markov Random Field Model," 13th Asia Pacific Microscopy Congress 2025, Australia, February 2025. [abstract] (Oral, Abstract reviewed)
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, N. Shibata, and M. Okada, "Real-time Denoising Algorithm for STEM Imaging Using Markov Random Field Model," The 2024 Young Researchers’ Symposium of the Japanese Society of Microscopy, Fukuoka, Japan, October 2024. (Poster)
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, N. Shibata, and M. Okada, "Real-time Denoising Algorithm for STEM Imaging Using Markov Random Field Model," Microscopy and Microanalysis 2024, Cleveland, Ohio, USA, July 2024. https://doi.org/10.1093/mam/ozae044.214 (Poster, Abstract reviewed)
T. Kusumi, S. Katakami, R. Ishikawa, K. Kawahara, N. Shibata, and M. Okada, "Real-time reconstruction of STEM images using Markov random field model," The 80th Annual Meeting of the Japanese Society of Microscopy, Chiba, Japan, June 2024. (Oral)
Awards
Awards
IFSM Young Scientist Assembly, May 2026. [link]
Dispatch for International Meetings Program, SPRING-GX, October 2025.
Dispatch for International Meetings Program, SPRING-GX, July 2025.
Dispatch for International Meetings Program, SPRING-GX, December 2024.
Best Poster Award, Young Researchers’ Symposium of the Japanese Society of Microscopy, October 2024, selected as one of the top 2 presentations out of 17. [link]
Travel Expense Grant Program for International Conferences (¥445K), Kazato Research Foundation, April 2024. [link]
Student Scholar Award ($1K + covering full registration), Microscopy and Microanalysis 2024, April 2024. [link]
Patent
Patent
Image reconstruction apparatus for electron microscopy imaging using Markov random field model
M. Okada, S. Katakami, T. Kusumi, N. Shibata, R. Ishikawa, K. Kawahara, Japanese patent application No. 2023-75963, filed on May 2, 2023, under review.
Fellowships
Fellowships
Advanced AI Talent Development to Lead the Next-Generation Intelligent Society (BOOST-NAIS), 3-year fellowship, ¥280K/month, Apr. 2024–Present.
Fostering Advanced Human Resources to Lead Green Transformation (SPRING-GX), Transitioned to BOOST-NAIS, ¥180K/month, Apr. 2024–Jun. 2024.
JSPS Research Fellowship for Young Scientists (DC2), 2025, Declined due to participation in BOOST-NAIS, acceptance rate: 14.7%.
Research Experience
Research Experience
May 2024–Present Research Assistant, The University of Tokyo, Okada Laboratory.
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